Biological complexity (Introduction)

by George Jelliss ⌂ @, Crewe, Friday, November 15, 2013, 09:34 (3787 days ago)

This may be of interest:-"Scientists solve major piece in the origin of biological complexity"-http://www.geneticarchaeology.com/research/Scientists_solve_major_piece_in_the_origin_of_biological_complexity.asp?-"In this experiment we've reordered one of the first steps in the origin of multicellularity, showing that two key evolutionary steps can occur far faster than previously anticipated."

--
GPJ

Biological complexity

by David Turell @, Friday, November 15, 2013, 14:45 (3787 days ago) @ George Jelliss

George: This may be of interest:
> 
> "Scientists solve major piece in the origin of biological complexity"
> 
> http://www.geneticarchaeology.com/research/Scientists_solve_major_piece_in_the_origin_o... 
> "In this experiment we've reordered one of the first steps in the origin of multicellularity, showing that two key evolutionary steps can occur far faster than previously anticipated."-Again, thank you for a most interesting entry. I was aware of the yeast multicellular study. As usual my analysis is that this was accomplished by human intelligence in a lab. We can only accept it as productive as it represents a possibility of the way simple multicellularity appeared. And with the standard comment: if bacteria are so successful, why bother with multicellularity?

Biological complexity: the cell, a video animation

by David Turell @, Friday, April 17, 2015, 15:54 (3269 days ago) @ David Turell

This is what evolution invented? The complexity in this video expresses just how complex life is:-http://multimedia.mcb.harvard.edu/anim_innerlife.html

Biological complexity: bacteria fight viruses

by David Turell @, Monday, April 20, 2015, 14:38 (3266 days ago) @ David Turell

A hand-like molecular structure interferes with viral RNA:-"In a recent paper in the leading journal Science, the team has shown how a surveillance complex in the bacterial immune system is able to target specific sites on RNA molecules to destroy invading viruses and other foreign genetic elements.-"The researchers, who include Otago postdoctoral fellow Dr Raymond Staals, believe this targeting mechanism could one day be adapted to engineer microbes to serve a variety of purposes, including environmental clean-up, green chemistry, and the production of safer, more effective therapeutic drugs.-"In their paper, the team have provided the first high-resolution structural images of a fully intact Type III CRISPR-Cas surveillance complex bound to its target RNA, thereby showing how the RNA-targeting mechanism in this complex works.-"Dr Staals, who is based in Otago's Department of Microbiology & Immunology, says the complex recognises and snips single-stranded RNA molecules at multiple sites allowing bacteria to destroy viral genetic material before it hijacks their cells.-"'A hand-like structure in the complex grips the RNA target, and then a thumb-like structure on the hand pushes the RNA into the right position in the catalytic site to be cleaved," he says."-
 Read more at: http://phys.org/news/2015-04-key-element-bacterial-immune.html#jCp

Biological complexity: bacteria 'see' light

by David Turell @, Wednesday, February 10, 2016, 15:25 (2970 days ago) @ David Turell

It is known that bacteria can respond to light. An understanding of that mechanism has appeared:-http://www.the-scientist.com/?articles.view/articleNo/45296/title/Sighted-Microbes/-"A cyanobacterial cell acts like an eye, refracting light onto the cell membrane in a similar way to how the lens of a human eye refracts light onto the retina, according to a study published yesterday -***-"The fact that bacteria respond to light is one of the oldest scientific observations of their behaviour,” said study coauthor Conrad Mullineaux of Queen Mary University of London in a press release. “Our observation that bacteria are optical objects is pretty obvious with hindsight, but we never thought of it until we saw it. -***-"Mullineaux and colleagues showed that a cyanobacterium, about half a billion times smaller than the human eye, refracts light onto the opposite side of the cell from the point of incidence. The focusing of light on photoreceptors in the cytoplasmic membrane then triggers the cyanobacterium to move in the opposite direction—i.e., toward the light source.-“'We noticed it accidentally,” Mullineaux told BBC News. “We suddenly saw these focused bright spots and we thought, ‘bloody hell!' Immediately, it was pretty obvious what was going on.”-"Gáspár Jékely of the Max Planck Institute for Developmental Biology in Germany told BBC News that the study offered an “elegant demonstration” of the mechanism for phototaxis in these bacteria. “Cyanobacteria are 2.7 billion years old, so it's much older than any animal eye,” he said. “Presumably, this mechanism has existed for a very long time.'”-Comment: It is as if a light-sensing structure was put in place long before evolution got to making camera eyes. Structural preparation for the future as Denton would view it. Structure first, function second. Gould also understood this, I have found in my reading.

Biological complexity: bacteria seem to learn

by David Turell @, Tuesday, March 08, 2016, 01:00 (2943 days ago) @ David Turell

In bacteria that are challenged with salt and then retested they seem to survive longer:-https://www.sciencedaily.com/releases/2016/03/160307153047.htm-Individual bacterial cells have short memories. But groups of bacteria can develop a collective memory that can increase their tolerance to stress.-***-Bacteria exposed to a moderate concentration of salt survive subsequent exposure to a higher concentration better than if there is no warning event. But in individual cells this effect is short-lived: after just 30 minutes, the survival rate no longer depends on the exposure history.-***-When an entire population is observed, rather than individual cells, the bacteria appear to develop a kind of collective memory. In populations exposed to a warning event, survival rates upon a second exposure two hours after the warning are higher than in populations not previously exposed. Using computational modelling, the scientists explained this phenomenon in terms of a combination of two factors. Firstly, salt stress causes a delay in cell division, leading to synchronization of cell cycles; secondly, survival probability depends on the individual bacterial cell's position in the cell cycle at the time of the second exposure. As a result of the cell cycle synchronization, the sensitivity of the population changes over time. Previously exposed populations may be more tolerant to future stress events, but they may sometimes even be more sensitive than populations with no previous exposure.-Comment: As the authors point out, cells are in different parts of their cycle. To me this is not a 'remembering' process. The sensitive cells seem to be culled out by their cycle position. Only a census of each cell and its cycle position will sort this out. But bacterial population size is definitely affected.

Biological complexity: bacteria use electrical signals

by David Turell @, Wednesday, March 09, 2016, 19:37 (2942 days ago) @ David Turell

Researchers have picked up electrical signals in colonies of bacteria using ion channels, a process thought only to occur in multicellular organisms:-http://www.scientificamerican.com/article/bacteria-can-convey-electrical-messages-the-same-way-neurons-do/?WT.mc_id=SA_DD_20160309-"Bacteria may be ancient organisms, but don't call them primitive. Despite being unicellular, they can behave collectively—sharing nutrients with neighbors, moving in concert with others and even committing suicide for the greater good of their colony. Molecules that travel from cell to cell enable such group behavior in a signaling process called quorum sensing. Now new evidence reveals that bacteria may have another way to “talk” to one another: communication via electrical signaling—a mechanism previously thought to occur only in multicellular organisms.-"In 2010 molecular biologist Gürol Süel, now at the University of California, San Diego, set out to understand how a soil bacterium called Bacillus subtilis could grow into massive communities of more than a million cells and still thrive. He and his colleagues found that once the colony reaches a critical size, bacteria on the periphery stop reproducing to leave core cells with a sufficient nutrient supply.-"But that observation led to the question of how the edge cells receive word to cease dividing. In a recent follow-up study, Süel discovered that the intercellular signals in this case were in fact electrical. The messages travel via ion channels, proteins on a cell's surface that control the flow of charged particles—in this case, potassium ions—into and out of a cell. The opening and closing of these channels can change the charges of neighboring cells, inducing them to release such particles and thereby relaying electrical signals from one cell to the next. “We've known that bacteria had ion channels and people have assigned them different functions, but only in the context of the single cell,” Süel says. “Now we're seeing that they're also being used to coordinate behavior over millions of cells.” The study appears in the journal Nature.-"Electrical signaling of this type is also how neurons in our brain pass along information. This and other findings are therefore prompting scientists to reevaluate their assumptions about single-celled life. “Bacteria have been thought of as limited because they are not multicellular,” says Steve Lockless, a biologist at Texas A&M University who was not involved in the study. But as unicellular organisms increasingly offer evidence of multifaceted behaviors, that may not be the case for much longer."-Comment: Bacteria are highly complex, which means the original cells were probably not very simple. Design anyone?

Biological complexity: bacteria use electrical signals

by dhw, Thursday, March 10, 2016, 17:18 (2941 days ago) @ David Turell

DAVID: Researchers have picked up electrical signals in colonies of bacteria using ion channels, a process thought only to occur in multicellular organisms:
-http://www.scientificamerican.com/article/bacteria-can-convey-electrical-messages-the-s...-QUOTE: "Electrical signaling of this type is also how neurons in our brain pass along information. This and other findings are therefore prompting scientists to reevaluate their assumptions about single-celled life. “Bacteria have been thought of as limited because they are not multicellular,” says Steve Lockless, a biologist at Texas A&M University who was not involved in the study. But as unicellular organisms increasingly offer evidence of multifaceted behaviors, that may not be the case for much longer."-David's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Design anyone?-Dhw's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Intelligent cell anyone?

Biological complexity: bacteria use electrical signals

by David Turell @, Thursday, March 10, 2016, 18:33 (2941 days ago) @ dhw


> David's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Design anyone?
> 
> Dhw's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Intelligent cell anyone?-My usual response. How did the intelligence originate? As kids we have to go to school to be taught much of what we know and use in planning.

Biological complexity: bacteria use electrical signals

by dhw, Friday, March 11, 2016, 09:00 (2940 days ago) @ David Turell

David's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Design anyone?-Dhw's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Intelligent cell anyone?-DAVID: My usual response. How did the intelligence originate? As kids we have to go to school to be taught much of what we know and use in planning.-My usual response. We don't know how the intelligence originated. Maybe God did it. The intelligent cell is a hypothesis to explain how evolution works, not how life and evolution began.

Biological complexity: bacteria use electrical signals

by David Turell @, Friday, March 11, 2016, 15:56 (2940 days ago) @ dhw


> dhw: My usual response. We don't know how the intelligence originated. Maybe God did it. The intelligent cell is a hypothesis to explain how evolution works, not how life and evolution began. - Is there an semblance of proof that cells have intelligence or instead intelligently automated responses to stimuli? Back to square one

Biological complexity: bacteria use electrical signals

by dhw, Saturday, March 12, 2016, 13:46 (2939 days ago) @ David Turell

David's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Design anyone?-Dhw's comment: Bacteria are highly complex, which means the original cells were probably not very simple. Intelligent cell anyone?-DAVID: My usual response. How did the intelligence originate? As kids we have to go to school to be taught much of what we know and use in planning.-dhw: My usual response. We don't know how the intelligence originated. Maybe God did it. The intelligent cell is a hypothesis to explain how evolution works, not how life and evolution began.-DAVID: Is there any semblance of proof that cells have intelligence or instead intelligently automated responses to stimuli? Back to square one.-You would have to ask those scientists who have spent a lifetime studying the behaviour of cells and have drawn the conclusion that they are intelligent, sentient, cognitive, decision-making beings. However, if you think such questions cannot be answered by studying behaviour (including our own), you will have to admit that one cannot prove humans are free agents and not automatons (free will versus determinism). Meanwhile, is there any semblance of proof that 3.8 billion years ago an unknown superintelligence placed a computer programme for all evolutionary innovations, lifestyles and natural wonders in the very first cells?

Biological complexity: bacteria use electrical signals

by David Turell @, Saturday, March 12, 2016, 15:41 (2939 days ago) @ dhw


> dhw: You would have to ask those scientists who have spent a lifetime studying the behaviour of cells and have drawn the conclusion that they are intelligent, sentient, cognitive, decision-making beings. However, if you think such questions cannot be answered by studying behaviour (including our own), you will have to admit that one cannot prove humans are free agents and not automatons (free will versus determinism). - I am fully convinced I have free will, philosophic debate aside. The plasticity of the brain is proof in the way it responds clearly and accurately to my use of it . - > dhw: Meanwhile, is there any semblance of proof that 3.8 billion years ago an unknown superintelligence placed a computer programme for all evolutionary innovations, lifestyles and natural wonders in the very first cells? - There is no better explanation.

Biological complexity: bacteria use electrical signals

by dhw, Sunday, March 13, 2016, 13:54 (2938 days ago) @ David Turell

dhw: You would have to ask those scientists who have spent a lifetime studying the behaviour of cells and have drawn the conclusion that they are intelligent, sentient, cognitive, decision-making beings. However, if you think such questions cannot be answered by studying behaviour (including our own), you will have to admit that one cannot prove humans are free agents and not automatons (free will versus determinism). - DAVID: I am fully convinced I have free will, philosophic debate aside. The plasticity of the brain is proof in the way it responds clearly and accurately to my use of it. - I am fully aware of your being fully convinced of your opinions! But you have no way of proving that the interaction between your “self” and your brain has not been preprogrammed by the infinite chain of cause and effect (which is the basis of your view of cellular behaviour: every action is an automatic response to a cause). However, I am not arguing against free will - I am merely pointing out that your argument that nobody can tell the difference between autonomous and preprogrammed behaviour in cells can also be applied to your own behaviour.
 
dhw: Meanwhile, is there any semblance of proof that 3.8 billion years ago an unknown superintelligence placed a computer programme for all evolutionary innovations, lifestyles and natural wonders in the very first cells?
DAVID: There is no better explanation. - You challenged my hypothesis of the intelligent cell as the driving force behind evolution and asked if there was any semblance of proof. I have returned the compliment. “There is no better explanation” is no answer. Of course there is no proof for either hypothesis, and so there is no point in your challenging mine when your own is subject to the same criticism.

Biological complexity: bacteria use electrical signals

by David Turell @, Sunday, March 13, 2016, 18:29 (2938 days ago) @ dhw


> DAVID: I am fully convinced I have free will, philosophic debate aside. The plasticity of the brain is proof in the way it responds clearly and accurately to my use of it.
> 
> I am fully aware of your being fully convinced of your opinions! But you have no way of proving that the interaction between your “self” and your brain has not been preprogrammed by the infinite chain of cause and effect ...- I am merely pointing out that your argument that nobody can tell the difference between autonomous and preprogrammed behaviour in cells can also be applied to your own behaviour.-You are ignoring the by-play back and forth between my use of the brain and its plastic responses to my use and wishes. My brain never tells me to decide to do something. Nor did it dictate this answer to you.-> dhw: You challenged my hypothesis of the intelligent cell as the driving force behind evolution and asked if there was any semblance of proof. I have returned the compliment. “There is no better explanation” is no answer. Of course there is no proof for either hypothesis, and so there is no point in your challenging mine when your own is subject to the same criticism.-Logically the complex lifestyles shown in Nature's IQ cannot have been invented by existing organisms, which can be shown to respond automatically in an algorithm of pre-programmed choices.

Biological complexity: bacteria use electrical signals

by dhw, Monday, March 14, 2016, 13:33 (2937 days ago) @ David Turell

DAVID: I am fully convinced I have free will, philosophic debate aside. The plasticity of the brain is proof in the way it responds clearly and accurately to my use of it.-Dhw: I am fully aware of your being fully convinced of your opinions! But you have no way of proving that the interaction between your “self” and your brain has not been preprogrammed by the infinite chain of cause and effect ...- I am merely pointing out that your argument that nobody can tell the difference between autonomous and preprogrammed behaviour in cells can also be applied to your own behaviour.-DAVID: You are ignoring the by-play back and forth between my use of the brain and its plastic responses to my use and wishes. My brain never tells me to decide to do something. Nor did it dictate this answer to you.-Our subject here is not free will, but the impossibility of telling the difference between free and predetermined actions. An argument against human free will is that no one can escape the chain of cause and effect, and so all actions are predetermined by factors outside personal control. That is also your argument against cellular intelligence (i.e. all cellular actions are predetermined by an automatic cause-and-effect mechanism). You say “my” as if you knew what “you” consisted of. You don't. You believe you have some form of mind that is independent of your chemicals, but others will say the chemicals dictate to “you”. The latter is the argument you use about cells. You say yourself that it is impossible from the outside to judge which version is correct, and yet somehow, using the same arguments, you seem to know that humans are autonomous and cells are not.
 
dhw: You challenged my hypothesis of the intelligent cell as the driving force behind evolution and asked if there was any semblance of proof. I have returned the compliment. “There is no better explanation” is no answer. Of course there is no proof for either hypothesis, and so there is no point in your challenging mine when your own is subject to the same criticism.
DAVID: Logically the complex lifestyles shown in Nature's IQ cannot have been invented by existing organisms, which can be shown to respond automatically in an algorithm of pre-programmed choices.-What sort of “logic” is this? As with human activities, you can pinpoint all the chemical activities that accompany decisions, but you cannot pinpoint the source of the decisions themselves. Nobody knows the origin of all these complex activities. Nobody saw the first weaverbird construct the first weaverbird nest. Even with your own theory of a 3.8-billion-year-old computer programme for weaverbird nest-building, passed down with billions of other programmes through all the different organisms and environmental changes, the first one would still have been constructed by a weaverbird! How would you have known then whether it was preprogrammed or autonomously invented (see above)? You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were.

Biological complexity: bacteria use electrical signals

by David Turell @, Monday, March 14, 2016, 15:20 (2937 days ago) @ dhw


> Our subject here is not free will, but the impossibility of telling the difference between free and predetermined actions......You believe you have some form of mind that is independent of your chemicals, but others will say the chemicals dictate to “you”. The latter is the argument you use about cells. You say yourself that it is impossible from the outside to judge which version is correct, and yet somehow, using the same arguments, you seem to know that humans are autonomous and cells are not.-I think your discussion is apples and oranges with single cells and brains light-years apart. Single cells are not multicellular organisms. Our brains are most complex organs every to appear and create phenomena that we still can't explain. My brain and I interact in the plasticity we have discovered. Since my brain and I interact beneficially , a point you ignore in your discussion, I see a cooperative brain, not a dictatorial one. Note the philosophy of no free will antedated the discovery of plasticity. 
> 
> dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were.-With good reason. Their brains are too simple to be so inventive.

Biological complexity: bacteria use electrical signals

by dhw, Tuesday, March 15, 2016, 13:59 (2936 days ago) @ David Turell

Dhw: Our subject here is not free will, but the impossibility of telling the difference between free and predetermined actions......You believe you have some form of mind that is independent of your chemicals, but others will say the chemicals dictate to “you”. The latter is the argument you use about cells. You say yourself that it is impossible from the outside to judge which version is correct, and yet somehow, using the same arguments, you seem to know that humans are autonomous and cells are not.-DAVID: I think your discussion is apples and oranges with single cells and brains light-years apart. Single cells are not multicellular organisms. Our brains are most complex organs every to appear and create phenomena that we still can't explain. My brain and I interact in the plasticity we have discovered. Since my brain and I interact beneficially, a point you ignore in your discussion, I see a cooperative brain, not a dictatorial one. Note the philosophy of no free will antedated the discovery of plasticity. -I know what you think and see, and at no time have I or any of the scientists we both refer to ever equated cellular intelligence with the human brain. Cells don't even have brains, but these particular experts believe they have the ability to think for themselves, regardless of our brain plasticity. You don't agree, and you keep telling us that what appears to be autonomous behaviour is actually automatic behaviour, and nobody can tell the difference from the outside. I am merely pointing out that determinists can use the same argument about human free will.
 
dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were.
DAVID: With good reason. Their brains are too simple to be so inventive.-Man is so sure of his dominion
That he states as fact his mere opinion.
(New Taunton proverb)

Biological complexity: bacteria use electrical signals

by David Turell @, Tuesday, March 15, 2016, 15:12 (2936 days ago) @ dhw

dhw: You don't agree, and you keep telling us that what appears to be autonomous behaviour is actually automatic behaviour, and nobody can tell the difference from the outside. I am merely pointing out that determinists can use the same argument about human free will. - Wrong analogy. Cells are material objects, free will is immaterial. In my view determinists are absolutely wrong and cannot prove their case. - 
> dhw: Man is so sure of his dominion
> That he states as fact his mere opinion.
> (New Taunton proverb) - Only when backed by facts, 
Which IM conjecture lacks.
(Texan two-gun assertion)

Biological complexity: bacteria use electrical signals

by dhw, Wednesday, March 16, 2016, 13:41 (2935 days ago) @ David Turell

dhw: You keep telling us that what appears to be autonomous behaviour is actually automatic behaviour, and nobody can tell the difference from the outside. I am merely pointing out that determinists can use the same argument about human free will.
DAVID: Wrong analogy. Cells are material objects, free will is immaterial. In my view determinists are absolutely wrong and cannot prove their case. - The analogy only seems wrong to you because (a) you think you know that cells can't think, and (b) you think you know that we have free will. Some people believe that cells can think, and some people believe we do not have free will because we are trapped by the chain of limitless causes and effects. It is because there are different opinions that the analogy is correct: nobody can tell the difference from the outside between automatic and autonomous behaviour. And neither the believers nor the sceptics can “prove their case”. - dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were. - DAVID: With good reason. Their brains are too simple to be so inventive. - dhw: Man is so sure of his dominion
That he states as fact his mere opinion.
(New Taunton proverb) - DAVID: Only when backed by facts, 
Which IM conjecture lacks.
(Texan two-gun assertion) - I ain't denyin' my IM hypothesis is simply conjecture.
So's your insistence that weavers can't think. End of lecture.
(Put your guns away)

Biological complexity: bacteria use electrical signals

by David Turell @, Wednesday, March 16, 2016, 14:25 (2935 days ago) @ dhw

dhw: The analogy only seems wrong to you because (a) you think you know that cells can't think, and (b) you think you know that we have free will. Some people believe that cells can think, and some people believe we do not have free will because we are trapped by the chain of limitless causes and effects. It is because there are different opinions that the analogy is correct: nobody can tell the difference from the outside between automatic and autonomous behaviour. And neither the believers nor the sceptics can “prove their case”.-Granted. It all becomes a matter of 'belief' on both sides .
> 
> dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were.
> 
> DAVID: With good reason. Their brains are too simple to be so inventive.
> 
> dhw: Man is so sure of his dominion
> That he states as fact his mere opinion.
> (New Taunton proverb)
> 
> DAVID: Only when backed by facts, 
> Which IM conjecture lacks.
> (Texan two-gun assertion)
> 
> I ain't denyin' my IM hypothesis is simply conjecture.
> So's your insistence that weavers can't think. End of lecture.
> (Put your guns away)-Bird brains are bird brains
Only tiny thoughts entrain
(I remain on target)

Biological complexity: bacteria use electrical signals

by dhw, Thursday, March 17, 2016, 13:28 (2934 days ago) @ David Turell

dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were. - DAVID: With good reason. Their brains are too simple to be so inventive. - dhw: Man is so sure of his dominion
That he states as fact his mere opinion.
(New Taunton proverb) - DAVID: Only when backed by facts, 
Which IM conjecture lacks.
(Texan two-gun assertion) - dhw: I ain't denyin' my IM hypothesis is simply conjecture.
So's your insistence that weavers can't think. End of lecture.
(Put your guns away) - DAVID: Bird brains are bird brains
Only tiny thoughts entrain
(I remain on target) - Bird thoughts may seem tiny
To great big thinking you,
But they're what get the birdies doing
All that birdies do.
(I think you're aiming at your foot)

Biological complexity: bacteria use electrical signals

by David Turell @, Thursday, March 17, 2016, 14:33 (2934 days ago) @ dhw

dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were.
> 
> DAVID: With good reason. Their brains are too simple to be so inventive.
> 
> dhw: Man is so sure of his dominion
> That he states as fact his mere opinion.
> (New Taunton proverb)
> 
> DAVID: Only when backed by facts, 
> Which IM conjecture lacks.
> (Texan two-gun assertion)
> 
> dhw: I ain't denyin' my IM hypothesis is simply conjecture.
> So's your insistence that weavers can't think. End of lecture.
> (Put your guns away)
> 
> DAVID: Bird brains are bird brains
> Only tiny thoughts entrain
> (I remain on target)
> 
> dhw: Bird thoughts may seem tiny
> To great big thinking you,
> But they're what get the birdies doing
> All that birdies do.
> (I think you're aiming at your foot) - Their tiny brains run simple lives
My thoughts about them still survive
Lots of patience to sit and incubate
But you think their thoughts are just first rate
Not the foot but your brain

Biological complexity: bacteria use electrical signals

by dhw, Friday, March 18, 2016, 16:31 (2933 days ago) @ David Turell

dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were. - DAVID: With good reason. Their brains are too simple to be so inventive. - dhw: Man is so sure of his dominion
That he states as fact his mere opinion.
(New Taunton proverb) - DAVID: Only when backed by facts, 
Which IM conjecture lacks.
(Texan two-gun assertion) - dhw: I ain't denyin' my IM hypothesis is simply conjecture.
So's your insistence that weavers can't think. End of lecture.
(Put your guns away) - DAVID: Bird brains are bird brains
Only tiny thoughts entrain
(I remain on target) - dhw: Bird thoughts may seem tiny
To great big thinking you,
But they're what get the birdies doing
All that birdies do.
(I think you're aiming at your foot) - DAVID: Their tiny brains run simple lives
My thoughts about them still survive
Lots of patience to sit and incubate
But you think their thoughts are just first rate
(Not the foot but your brain) - We see the nests and flights of these dear birds,
So wonderful we really can't ignore them.
I say they work these things out for themselves;
You say their God does all the thinking for them,
Because - strange logic - ever since life began,
The nests and flights were needed to make man!
(So stop waving your guns around, or you'll do yourself a mischief.)

Biological complexity: bacteria use electrical signals

by David Turell @, Friday, March 18, 2016, 18:13 (2933 days ago) @ dhw

dhw: You have admitted that your argument is based on incredulity, so please don't tell us that these complexities “cannot have been invented by existing organisms”. You simply cannot believe they were.
> 
> DAVID: With good reason. Their brains are too simple to be so inventive.
> 
> dhw: Man is so sure of his dominion
> That he states as fact his mere opinion.
> (New Taunton proverb)
> 
> DAVID: Only when backed by facts, 
> Which IM conjecture lacks.
> (Texan two-gun assertion)
> 
> dhw: I ain't denyin' my IM hypothesis is simply conjecture.
> So's your insistence that weavers can't think. End of lecture.
> (Put your guns away)
> 
> DAVID: Bird brains are bird brains
> Only tiny thoughts entrain
> (I remain on target)
> 
> dhw: Bird thoughts may seem tiny
> To great big thinking you,
> But they're what get the birdies doing
> All that birdies do.
> (I think you're aiming at your foot)
> 
> DAVID: Their tiny brains run simple lives
> My thoughts about them still survive
> Lots of patience to sit and incubate
> But you think their thoughts are just first rate
> (Not the foot but your brain)
> 
> dhw:We see the nests and flights of these dear birds,
> So wonderful we really can't ignore them.
> I say they work these things out for themselves;
> You say their God does all the thinking for them,
> Because - strange logic - ever since life began,
> The nests and flights were needed to make man!
> (So stop waving your guns around, or you'll do yourself a mischief.) -We sapiens are the pinnacle of all creation,
Here because of God's evolutionary administration;
Evolution is under His total control,
With our arrival his total destination.
He has granted us dominion over all forms,
Our required care must fit all the norms,
Our giant brains still have all the explanations.
(I'm very accurately on target)

Biological complexity: bacteria use electrical signals

by dhw, Saturday, March 19, 2016, 13:19 (2932 days ago) @ David Turell

dhw: We see the nests and flights of these dear birds,
So wonderful we really can't ignore them.
I say they work these things out for themselves;
You say their God does all the thinking for them,
Because - strange logic - ever since life began,
The nests and flights were needed to make man!
(So stop waving your guns around, or you'll do yourself a mischief.) -DAVID: We sapiens are the pinnacle of all creation,
Here because of God's evolutionary administration;
Evolution is under His total control,
With our arrival his total destination.
He has granted us dominion over all forms,
Our required care must fit all the norms,
Our giant brains still have all the explanations.
(I'm very accurately on target)-We may be the pinnacle of all creation,
But you still can't give me an explanation
Why God built the nest in the weaver's tree
When all he wanted was you and me.
(Which target?)

Biological complexity: walking along filament

by David Turell @, Friday, April 24, 2015, 18:40 (3262 days ago) @ David Turell

Protein molecules actually walk with two legs across actin filaments:-"Because cells are divided in many parts that serve different functions some cellular goodies need to be transported from one part of the cell to another for it to function smoothly. There is an entire class of proteins called 'molecular motors', such as myosin 5, that specialise in transporting cargo using chemical energy as fuel.-"Remarkably, these proteins not only function like nano-scale lorries, they also look like a two-legged creature that takes very small steps. But exactly how Myosin 5 did this was unclear.-"The motion of myosin 5 has now been recorded by a team led by Oxford University scientists using a new microscopy technique that can 'see' tiny steps of tens of nanometres captured at up to 1000 frames per second. The findings are of interest for anyone trying to understand the basis of cellular function but could also help efforts aimed at designing efficient nanomachines.-"'Until now, we believed that the sort of movements or steps these proteins made were random and free-flowing because none of the experiments suggested otherwise,' said Philipp Kukura of Oxford University's Department of Chemistry who led the research recently reported in the journal eLife. 'However, what we have shown is that the movements only appeared random; if you have the capability to watch the motion with sufficient speed and precision, a rigid walking pattern emerges.'-"One of the key problems for those trying to capture proteins on a walkabout is that not only are these molecules small - with steps much smaller than the wavelength of light and therefore the resolution of most optical microscopes - but they are also move very quickly."-
 Read more at: http://phys.org/news/2015-04-protein-harnesses-power-silly.html#jCp

Biological complexity: nucler pores

by David Turell @, Saturday, June 06, 2015, 20:28 (3219 days ago) @ David Turell

Large molecules have to go in and out of the nucleus, which has a full surrounding membrane. The pore opens and stretches dynamically. It is not rigid:-http://phys.org/news/2015-06-reveals-key-interaction-channel-cell.html-"But ongoing work in Blobel's lab indicates the central channel is anything but rigid. In previous research, a team from his lab identified a flexible ring in the middle of the central channel, the diameter of which was determined by two of the nuclear pore complex's approximately 30 nucleoporins, Nup58 and Nup54, which associate and disassociate from one another in what the researchers dubbed the ring cycle. When these two nucleoporins associate, the ring dilates to a diameter of up to 50 nanometers, a size capable of accommodating a ribosomal subunit, the largest and most complex of the cell's molecular freight. Then, when the nucleoporins separate, the single ring divides into three rings with diameters of 20 nanometers.-" This most recent research, conducted by postdoc Junseock Koh in Blobel's laboratory, examines how a transport factor known as karyopherin initiates the dilation of the ring. To accomplish this, Koh measured changes in heat during reactions between the three components, karyopherin, Nup58, and Nup54. Biophysical data like this reveals the energy dynamics during these reactions, and so provides clues to the behavior of the molecules involved. To tease apart this complex system, Koh mathematically analyzed the data collected at various conditions. His results revealed an unexpected role for a disordered region of Nup58.-"'We found that when one karyopherin molecule binds to at least two disordered regions of Nup58, it stabilizes Nup58 in such a way that the dilated conformation—in which the neighboring ordered region of Nup58 links up with Nup54—becomes more favorable. As a result, the more karyopherin molecules are present, the more the ring dilates," Koh says. "Based on these results, we were able to develop a framework for predicting the extent to which a ring will dilate given the amount of transport factors present.'"-
And just how does the Darwin theory explain this? It can't.

Biological complexity: regulating metabolism

by David Turell @, Monday, June 22, 2015, 19:40 (3203 days ago) @ David Turell

A description of some the automatic regulators in bacteria:-http://phys.org/news/2015-06-mysteries-bacterial-cell.html-"In bacteria, the cell cycle is very tightly controlled by protein-digesting enzymes called proteases that selectively destroy other proteins, called substrates, at appropriate times while the cell is undergoing growth and division. At the same time, another process called phosphorylation chemically modifies different proteins to regulate their activity in a cell-cycle-dependent way, Chien explains.-"Although the energy-dependent proteases that carry out most protein degradation can directly recognize some substrates, biological regulation often requires additional factors known as adaptors to be present to "tune" substrate selection more precisely. In the bacterium Caulobacter crescentus studied in the Chien lab, one of these adaptors, a small protein called CpdR, is specifically phosphorylated at different times in the cell cycle. Previous studies had shown that the timing of this phosphorylation correlated with the degradation of many proteins by a protease called ClpXP.-"Chien says, "Before this work, we thought most adaptors were binding to the protease and substrate at the same time, effectively leashing them together to force them to interact. Surprisingly, Joanne found that CpdR bound principally to the ClpXP protease, but didn't seem to bind the substrate well at all. Instead, CpdR binding to the ClpXP protease prepared, or primed, the protease for engaging substrates. This primed protease was now also able to recruit additional adaptors that could deliver even more protease substrates."-"He adds, "By not specifically interacting with any single substrate, this new mechanism of protease priming allows for surprisingly broad recognition of both substrates and additional regulators. This mechanism lets the cell control multiple pathways with a single regulator, which is useful when bacteria have to respond rapidly, such as during the stress they undergo when treated with antibiotics. However, this could also lead to unwanted degradation of off-target proteins. Understanding this balance of specificity and broad recognition is an outstanding question.'"

Biological complexity: vesicle membranes

by David Turell @, Friday, July 10, 2015, 16:00 (3185 days ago) @ David Turell

Vesicles transport material in cells and have a complex membrane, different in different types of vesicles:-http://phys.org/news/2015-07-cell-machinery-complex-coat.html-"Vesicles are responsible for transporting molecules between the different compartments within a cell and also for bringing material into cells from outside. There are several types of vesicle: each has a specific type of coat which is made up of different proteins and assembles onto a membrane surrounding the vesicle.-"The EMBL team has been taking a close look at a coat called COPI. This surrounds vesicles that move material around within the Golgi apparatus and to the endoplasmic reticulum (ER) - these are regions of the cell where proteins are made and modified in preparation for transport to the cell surface.-"What the images revealed was surprising: unlike other types of vesicle, where the coat is thought to be made from proteins assembled in different layers - each with a specific function - around the vesicle membrane, the EMBL team observed that the proteins in the COPI coat all intertwine together in one big layer, which is curved to fit around the membrane. More precisely, the COPI coat is made of a repetition of building blocks, called "triads", that contain all the important functional elements organised in a precise 3D structure.-"'Our images showed us how the proteins that make up the coat are arranged and it was surprising to discover how different COPI is from, for example, clathrin or COPII coated vesicles," adds Svetlana Dodonova, co-author of the paper. "Our next step will be to try to find out how this coat forms and binds to the vesicle membrane and how it arranges itself into such complex shapes.'" -My usual comment: the more complexity is shown, the less likely for a chance development of life.

Biological complexity: cell division chromosome actions

by David Turell @, Monday, July 13, 2015, 18:48 (3182 days ago) @ David Turell

The chromosomes which are divided into two complete copies and pulled apart by microtubules have an enzyme which softens the outer membrane to make way for the division into two cells:-http://www.sciencedaily.com/releases/2015/07/150713113449.htm-"It is well known that microscopic cable-like structures, called microtubules, were involved in pulling chromosomes to opposite poles of the cell during the division process. "At this time, microtubules physically separate the chromosomes via their central kinetochores while other microtubules signal to the cortex of the cell where its equator is, i.e., where division will take place," Hickson explained. Furthermore until now, it was believed that the chromosomes only played a passive role: that they were pulled by the microtubules and didn't affect cytokinesis, but this is not the case.-"Initially working with the cells of fruit flies using powerful genetic tools and sophisticated microscopy, the research team discovered that chromosomes emit signals that influence the cortex of the cell to reinforce microtubule action. One of the key signals involved that the researchers identified acts via an enzyme complex -- a phosphatase known as Sds22-PP1 -- which is found at the kinetochores.-"They also demonstrated that this signaling pathway acts in human cells. "Such evolutionary conservation from flies to humans is expected for processes as fundamental as cell division," he explained. This is what makes fruit flies such a powerful system for helping us to understand human biology. "When chromosomes are segregated, they approach the membrane at the poles of the cell, and thanks to this enzyme's actions, this contributes to the softening of the polar membrane, facilitating the elongation of the cell and the ensuing division that occurs at the equator.'"-Comment: Remember, there is unstated further complexity in that all enzymes in these processes are giant complex molecules that speed the process.

Biological complexity: metabolic gene controls

by David Turell @, Saturday, July 25, 2015, 15:46 (3170 days ago) @ David Turell

Plant research is unearthing how automatic are many of the metabolic functions which changes in gene translations. It shows it can affect development as well as metabolism.. This will be found in animal metabolism also:-http://www.sciencedaily.com/releases/2015/07/150724151844.htm-"In plants as in animals and humans, intricate molecular networks regulate key biological functions, such as development and stress responses. The system can be likened to a massive switchboard--when the wrong switches are flipped, genes can be inappropriately turned on or off, leading to the onset of diseases.-"Now, VARI scientists have unraveled how an important plant protein, known as TOPLESS, interacts with other molecules responsible for turning genes off. The findings in plants provide a general model across species for this type of gene silencing, which is linked to several vital biological functions in humans. The discovery was published today in Science Advances.-"'This is really a fundamental discovery--our structure shows the corepressor TOPLESS interacting with key repressor motifs, which constitutes a major component of gene silencing in plants," said Van Andel Research Institute's Karsten Melcher, Ph.D., one of the study's corresponding authors. "Understanding this interaction in plants gives us unique insight into similar pathways in humans that involve these proteins, which are notoriously tough to investigate."-***-"Gene expression is regulated by both activators and repressors. Although gene repression is thought to be equally important as gene activation for this regulation, relatively little is known about the mechanisms of gene repressors and co-repressors.-"TOPLESS functions as a co-repressor and interacts with repressors containing ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. EAR motifs are the most common form of transcriptional repression motifs found in plants and are thought to facilitate stable epigenetic regulation of gene expression via recruitment of chromatin modifiers.-"TOPLESS plays important roles in plant development; its name stems from the fact that mutations in TOPLESS can give rise to seedlings in which the shoot is transformed into a second root, hence "topless" seedlings.-"In humans, similar proteins also are altered in many types of tumors, and control embryonic development and the development of neurons."

Biological complexity: evolution of ion exchange pathways

by David Turell @, Monday, July 27, 2015, 15:23 (3168 days ago) @ David Turell

Cells use ions from potassium or sodium to communicate. These have changed during evolution from sponges to more complex organism:-http://phys.org/news/2015-07-illuminate-animal-evolution-protein-function.html-"Ion channels allow cells to pass electricity back and forth. Researchers looked specifically at Kir channels, which conduct potassium ions out of cells and help maintain normal cellular activity. -"For the most part, human and sponge ion channels are the same. The recent paper explores one key difference that researchers now believe developed about the time the first animals evolved. This means the changes in question occurred more recently than the appearance 2 billion years ago of complex cells, providing more evidence as to when and how the first animals evolved from single-cell organisms, or prokaryotes. -"'Evidence suggests that eukaryotic cells evolved from prokaryotic cells," Boland said. "Among eukaryotes, when sponges evolved is subject to some debate, but they seem to be positioned at a key point in animal evolution." -"All vertebrate Kir channels are activated by PIP2, a phospholipid in cell membranes that "is a master regulator of protein function," Logothetis said, and therefore triggers biochemical reactions key to intracellular function. -"The sponge Kir channel, however, does not share this high affinity with PIP2 as it lacks two amino acids necessary for the interaction. -"Researchers compared amino acids in both sponge and mammal Kir channels. They found that introducing mammalian amino acid residue into the sponge channel makes it highly sensitive to PIP2, Logothetis said. -"Properly operating Kir channels are critical for cell function. Malfunctions in these channels have been cited in several diseases, including Anderson-Tawil syndrome, which causes muscle weakness, changes in heart rhythm and developmental abnormalities. -Comment: The enormous complexity of each single cell in our bodies is slowly being elucidated. We really know just a little so far, but it is not difficult to imagine what the whole story will look like 50 years from now, an amazing biologic machinery automatically functioning, each contributing to the living whole organism in perfect coordination. This is why cells look like they 'think'.-Our multicellular selves came from single cells, as the article states. Think how self-reliant single cell organisms have to be from the start of life! Metabolize food, avoid danger and reproduce, and this can all be done automatically with the right chemical reactions if the DNA has enough initial information controls.

Biological complexity: evolution of ion exchange pathways

by dhw, Monday, July 27, 2015, 18:42 (3168 days ago) @ David Turell

DAVID: Comment: The enormous complexity of each single cell in our bodies is slowly being elucidated. We really know just a little so far, but it is not difficult to imagine what the whole story will look like 50 years from now, an amazing biologic machinery automatically functioning, each contributing to the living whole organism in perfect coordination. This is why cells look like they 'think'.-Our multicellular selves came from single cells, as the article states. Think how self-reliant single cell organisms have to be from the start of life! Metabolize food, avoid danger and reproduce, and this can all be done automatically with the right chemical reactions if the DNA has enough initial information controls.-I share your enthusiasm for the marvellous complexity of the cell, for its amazing self-reliance when it was on its own, for its astounding capacity to cooperate with other cells and form new communities that coordinate perfectly. And there can be no doubt that as these communities became more and more complex, many of them would have taken on roles which they performed automatically. But there are some problems. Why and how would they have cooperated in the first place, and why and how would they have done so to form new organs and new organisms? “Information controls” suggests they were preprogrammed to do so, which entails a set of programmes for the millions of innovations and natural wonders being passed down through thousands of millions of years and organisms etc. etc. - you know the problem. But a dear friend of mine sort of offered a glimmer of hope that there might be another solution, if we just slightly twist his wording. You see, some actions might LOOK as if they're automatic, but that doesn't mean they ARE automatic. They might also be the product of intelligence. And my friend himself agrees that both hypotheses are equally likely. We just have to pick the one we consider more convincing.

Biological complexity: evolution of ion exchange pathways

by David Turell @, Monday, July 27, 2015, 20:10 (3168 days ago) @ dhw


> dhw: I share your enthusiasm for the marvellous complexity of the cell, for its amazing self-reliance when it was on its own, for its astounding capacity to cooperate with other cells and form new communities that coordinate perfectly. .....Why and how would they have cooperated in the first place, and why and how would they have done so to form new organs and new organisms? “Information controls” suggests they were preprogrammed to do so, which entails a set of programmes for the millions of innovations and natural wonders being passed down through thousands of millions of years and organisms etc. etc. - you know the problem.-With adequate intelligent information in the DNA, cells were either shown how to innovate or had a mechanism to do so under guidelines. Either way works.-> dhw: You see, some actions might LOOK as if they're automatic, but that doesn't mean they ARE automatic. They might also be the product of intelligence. And my friend himself agrees that both hypotheses are equally likely. We just have to pick the one we consider more convincing.-Just stick to intelligent information and you've got the answer! then both are equally likely and you are allowed to choose the method you think is the best answer to the riddle.

Biological complexity: finding working proteins

by David Turell @, Thursday, July 30, 2015, 01:36 (3165 days ago) @ David Turell

To make a new animal one much find workable proteins that will function in a meaningful way in cooperation with other proteins to give life. this article shows how enormous the odds are if one starts from scratch. This is why the Cambrian is so startling if viewed from a Darwin standpoint:- http://p2c.com/students/blogs/kirk-durston/2015/07/computing-best-case-probability-prot... life requires thousands of different protein families, about 70% of which are ‘globular' proteins, each with a 3-dimensional shape that is unique to each family of proteins. An example is shown in the picture at the top of this post. This 3D shape is necessary for a particular biological function and is determined by the sequence of the different amino acids that make up that protein. In other words, it is not biology that determines the shape, but physics. Sequences that produce stable, functional 3D structures are so rare that scientists today do not attempt to find them using random sequence libraries. Instead, they use information they have obtained from reverse-engineering biological proteins to intelligently design artificial proteins.
"What are the implications of these results, obtained from actual data, for the fundamental prediction of neo-Darwinian theory mentioned above? If we assume 10^30 life forms with a fast replication rate of 30 minutes and a huge genome with a very high mutation rate over a period of 10 billion years, an extreme upper limit for the total number of mutations for all of life's history would be around 10^43. Unfortunately, a protein domain such as Ribosomal S7 would require a minimum average of 10^100 trials. In other words, the sum total of mutational events for the entire theoretical history of life falls short by at least 57 orders of magnitude from what would have a reasonable expectation of 'finding' any RS7 sequence - and this is only for one domain. Forget about ‘finding' an average sized protein, not to mention thousands.-"I downloaded 3,751 aligned sequences for the Ribosomal S7 domain, part of a universal protein essential for all life. When the data was run through the program, it revealed that the lower limit for the amount of functional information required to code for this domain is 332 Fits (Functional Bits). The extreme upper limit for the number of sequences that might be functional for this domain is around 10^92. In a single trial, the probability of obtaining a sequence that would be functional for the Ribosomal S7 domain is 1 chance in 10^100 … and this is only for a 148 amino acid structural domain, much smaller than an average protein. (my bold)-***-"As we all know from probabilities, one can get lucky once, but not thousands of times. This definitively falsifies the fundamental prediction of Darwinian theory that evolutionary processes can ‘find' functional protein families. A theory that has an essential prediction thoroughly falsified by the data should have no place in science.-"Could natural selection come to the rescue? As we know from genetic algorithms, an evolutionary ‘search' will only work for hill-climbing problems, not for ‘needle-in-a-haystack' problems. There are small proteins that require such low levels of functional information to perform simple binding tasks, that they form a nice hill-climbing problem that can be easily located in a search. This is not the case, however, for the vast majority of protein families. As real data shows, the probability of finding a functional sequence for one average protein family is so low, there is virtually zero chance of obtaining it anywhere in this universe over its entire history - never mind finding thousands of protein families."-Comment: Note the reference to the need for understanding the information required.

Biological complexity: finding working proteins

by Balance_Maintained @, U.S.A., Thursday, July 30, 2015, 07:57 (3165 days ago) @ David Turell

I'm sure they will find a way to ignore the data.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: signal pathways

by David Turell @, Thursday, July 30, 2015, 15:31 (3165 days ago) @ David Turell

Signal pathways controlled by enzymes dictate cellular functions and migration abilities. Another illustration of cell complexity and automaticity:-http://phys.org/news/2015-07-mystery-akt-cytosol-cell-membrane.html-"Using a state-of-the-art imaging tracking system, they discovered that a small protein called Ub14A can help to build "bridges," called actin branches, that bring Akt directly to the cell membrane, where it gets activated. Their findings are published in an article in the July 20 issue of the Proceedings of the National Academy of Sciences -"Akt is one of the key components in the cell-signaling network and has been a major target for therapeutic intervention, especially for anticancer drug development, for decades. To perform as a signaling molecule, Akt must move from the cytosol to the cell membrane so it can be activated by its upstream components. After it is activated, it then quickly moves back to the cytosol so that it can direct its downstream "workers" in other cellular actions, such as cell growth, proliferation, energy metabolism, and even resistance to cancer. -"'For years, scientists were puzzled as to how Akt 'moves' from the cytosol to the cell membrane," said Xiang. "There is a 'creek' flowing underneath the cell membrane, and Akt is unable to 'swim' across by itself. Using both super resolution imaging and genetic approaches, we found that Ubl4A builds 'bridges' or actin branches that bring Akt directly to the cell membrane, where it gets activated." -"Mice deficient in Ubl4A show significant impairment in Akt signaling, resulting in, for example, high neonatal birth mortality and delay in growth. Actin branches also are important for many other cellular events, such as cell migration and wound healing. "For example, white blood cells normally migrate towards bacteria during infection, but white blood cells where Ub14A is absent get so confused in the direction that they cannot effectively reach the infection site," Xiang said.-"The study therefore both fills in a missing link in the Akt signaling pathway and uncovers a novel function of actin branching."-
 Comment: All cells have actin fibers which act as pathways along which molecules travel

Biological complexity: muscle electrical grid

by David Turell @, Thursday, August 06, 2015, 00:10 (3158 days ago) @ David Turell

It is made up of mitochondria in a grid formation to provide immediate energy to muscle movement as needed.:-http://www.nih.gov/news/health/jul2015/nhlbi-30.htm-"A new study overturns longstanding scientific ideas regarding how energy is distributed within muscles for powering movement. Scientists are reporting the first clear evidence that muscle cells distribute energy primarily by the rapid conduction of electrical charges through a vast, interconnected network of mitochondria — the cell's “powerhouse” — in a way that resembles the wire grid that distributes power throughout a city. The study offers an unprecedented, detailed look at the distribution system that rapidly provides energy throughout the cell where it is needed for muscle contraction. -***-"The movement of muscles, from flexing your arms to the pumping of the heart, requires lots of energy that must be distributed throughout the cell. For example, the skeletal muscle rate of energy utilization can increase 100-fold with strenuous exercise. As a result, muscle cells contain many mitochondria, microscopic structures that are specially equipped to convert foods, including sugars and fats, into useable high-energy molecules, particularly adenosine triphosphate (ATP), for work. As part of this process, known as oxidative phosphorylation, the mitochondria, like small cellular batteries, use an electrical voltage across their membranes as an intermediate energy source in converting food into ATP. Thus, this mitochondrial membrane voltage can be considered one of the primary sources of energy in the cell.-***-"The study provides unprecedented images of how these mitochondria are arranged in muscle. “Structurally, the mitochondria are arranged in such a way that permits the flow of potential energy in the form of the mitochondrial membrane voltage throughout the cell to power ATP production and subsequent muscle contraction, or movement,” Dr. Balaban explained. Mitochondria located on the edges of the muscle cell near blood vessels and oxygen supply are optimized for generating the mitochondrial membrane voltage, while the interconnected mitochondria deep in the muscle are optimized for using the voltage to produce ATP, Balaban added.-“'These observations solve the problem of how muscle rapidly distributes energy in the cell for movement,” Dr. Balaban said. “The findings also challenge the older model that energy is distributed by the slow diffusion of high-energy molecules through the remarkably dense muscle cell.'”

Biological complexity: ATP machine produces energy

by David Turell @, Thursday, August 06, 2015, 00:21 (3158 days ago) @ David Turell

This shows how ATP in mitochondria generates energy for the body:-http://www.pnas.org/content/112/31/9626.abstract -This is an animation of how it works:-https://www.youtube.com/watch?v=XI8m6o0gXDY&feature=youtu.be

Biological complexity: ATP machine start study

by David Turell @, Thursday, August 18, 2016, 16:17 (2780 days ago) @ David Turell

ATP is the energy source of life within cells. Phosphate is an integral part of RNA. Phosphate is relatively insoluble and hard to work with. This study suggests a possible start:-http://phys.org/news/2016-08-phosphate-rna.html-"The phosphate ion is almost insoluble and is one of the most inactive of Earth's most abundant phosphate minerals. So how could phosphate have originally been incorporated into ribonucleotides, the building blocks of RNA, which are considered to be among the earliest constituents of life? American and Spanish scientists have now identified reasonable conditions to mobilize phosphate from insoluble apatite minerals for prebiotic organophosphate synthesis, including ribonucleotides. The pivotal role of urea in this process is also described in their article in the journal Angewandte Chemie.-"The energy-rich organophosphate bond is one of the basic features found in modern life. Phosphoester and phosphodiester bonds are currently formed using energy from photosynthesis and the energy in our food, and are continuously degraded and reconstructed during metabolic activity within living cells. Phosphate groups also ensure the solubility of RNA and DNA molecules. But how were the very first phosphate ester bonds formed on the prebiotic Earth? Phosphate would have been mostly locked in minerals when the first nucleobases, sugars, and amino acids started life.-***-"They were especially interested in the role of urea, a hydrolysis product of cyanamide and produced in Miller-Urey type reactions, which also has been shown to catalyze phosphate ester synthesis. The authors hypothesized that a eutectic mixture of urea, ammonium formate, and water could both serve as a milieu for direct phosphorylation and mobilize the phosphate of minerals, and thus allow phosphorylation from mineral sources. Additionally, upon heating formamide is formed, which is a cosolvent and could enhance phosphorylation from mineral sources. Therefore, the eutectic mixture would ensure "a consistent starting concentration of components regardless of their initial abundances," the authors wrote. (my bold)-"Their experiments resulted in effective phosphorylation of nucleosides when heated at moderate temperatures, provided soluble phosphate ions were available. To address the latter point, the scientists added various mixtures of ions and salts to the mixture and observed not only increased solubility of phosphate from hydroxyapatite, but also the formation of moderately soluble secondary phosphate minerals. They wrote: "These experiments suggest that an environment rich in ammonia, small organics such as urea and formate, magnesium sulfate, and phosphate could be an ideal location for prebiotic organophosphate synthesis." Every salt and ion added was very likely abundant in the environment of the prebiotic Earth. Overall, the scientists have identified realistic conditions under which early phosphorylation from insoluble sources could have taken place. So, consistent with Darwin's early thoughts: With the help of urea, phosphorylated molecules important for life can be readily formed in "warm little ponds.'" -Comment: Or in the region of hydrothermal ocean vents. I wonder where the urea came from? It is an animal waste product, and would not be natural on early Earth. Referring to the Miller- Urey experiments, (bolded above) lightning is required and the resulting proteins like urea are present in a tar-like goo, not very soluable.

Biological complexity: muscle electrical grid

by Balance_Maintained @, U.S.A., Thursday, August 06, 2015, 05:04 (3158 days ago) @ David Turell

“'These observations solve the problem of how muscle rapidly distributes energy in the cell for movement,” Dr. Balaban said. “The findings also challenge the older model that energy is distributed by the slow diffusion of high-energy molecules through the remarkably dense muscle cell.'”-They also create a problem of how such a complex network came to exist in early life.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: muscle electrical grid

by David Turell @, Thursday, August 06, 2015, 14:22 (3158 days ago) @ Balance_Maintained

“'These observations solve the problem of how muscle rapidly distributes energy in the cell for movement,” Dr. Balaban said. “The findings also challenge the older model that energy is distributed by the slow diffusion of high-energy molecules through the remarkably dense muscle cell.'”
> 
> Tony: They also create a problem of how such a complex network came to exist in early life.-Muscles appeared in the Cambrian

Biological complexity: muscle electrical grid

by Balance_Maintained @, U.S.A., Thursday, August 06, 2015, 21:17 (3158 days ago) @ David Turell

When they appeared is not the point. HOW they appeared is. This is a very intricate, efficient, multi-component system that must work cohesively and immediately. Not to mention that in addition to the complex energy network within the muscle itself, there also had to be an even more complex signalling network linking brain to muscle, plus the programming to allow them to interface.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: muscle electrical grid

by David Turell @, Thursday, August 06, 2015, 21:56 (3158 days ago) @ Balance_Maintained

Tony: When they appeared is not the point. HOW they appeared is. This is a very intricate, efficient, multi-component system that must work cohesively and immediately. Not to mention that in addition to the complex energy network within the muscle itself, there also had to be an even more complex signalling network linking brain to muscle, plus the programming to allow them to interface.-Which makes the appearance of the Cambrian organisms even more amazing and brings to the fore your description how God's computer program might work, i.e., no need for precursors.

Biological complexity: muscle electrical grid

by Balance_Maintained @, U.S.A., Saturday, August 08, 2015, 00:27 (3156 days ago) @ David Turell

Tony: When they appeared is not the point. HOW they appeared is. This is a very intricate, efficient, multi-component system that must work cohesively and immediately. Not to mention that in addition to the complex energy network within the muscle itself, there also had to be an even more complex signalling network linking brain to muscle, plus the programming to allow them to interface.
> 
>David: Which makes the appearance of the Cambrian organisms even more amazing and brings to the fore your description how God's computer program might work, i.e., no need for precursors.-Unfortunately, without assuming direct prototype creation, the assumption has to be that all possibilities were in the original source code. I'm not certain the evidence supports that. Of course, we have no access to the original source code, so...

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: muscle electrical grid

by David Turell @, Saturday, August 08, 2015, 04:16 (3156 days ago) @ Balance_Maintained


> >David: Which makes the appearance of the Cambrian organisms even more amazing and brings to the fore your description how God's computer program might work, i.e., no need for precursors.
> 
> Tony; Unfortunately, without assuming direct prototype creation, the assumption has to be that all possibilities were in the original source code. I'm not certain the evidence supports that. Of course, we have no access to the original source code, so...-It has to be one or the other.

Biological complexity: nucleus pores

by David Turell @, Friday, August 28, 2015, 14:28 (3136 days ago) @ David Turell

The nucleus is surrounded by a double membrane and has pores to allow passage of molecules in and out:-http://www.sciencedaily.com/releases/2015/08/150827215625.htm-"Building on that work, the team has now solved the architecture of the pore's inner ring, a subcomplex that is central to the NPC's ability to serve as a barrier and transport facilitator. In order to the determine that architecture, which determines how the ring's proteins interact with each other, the biochemists built up the complex in a test tube and then systematically dissected it to understand the individual interactions between components. Then they validated that this is actually how it works in vivo, in a species of fungus.-***-"Together, the inner and outer rings make up the symmetric core of the NPC, a structure that includes 21 different proteins. The symmetric core is so named because of its radial symmetry (the two remaining subcomplexes of the NPC are specific to either the side that faces the cell's cytoplasm or the side that faces the nucleus and are therefore not symmetric). Having previously solved the structure of the coat nucleoporin complex and located it in the outer rings, the researchers knew that the remaining components that are not membrane anchored must make up the inner ring.-***-"The researchers also solved a number of crystal structures from other parts of the NPC and determined how they interact with components of the inner ring. In doing so they demonstrated that one such interaction is critical for positioning the channel in the center of the inner ring. They found that exact positioning is needed for the proper export from the nucleus of mRNA and components of ribosomes, the cell's protein-making complexes, rendering it critical in the flow of genetic information from DNA to mRNA to protein."-Comment: With 21 different proteins, this mechanism is a good example of irreducible complexity

Biological complexity: nucleus pores

by David Turell @, Sunday, September 20, 2015, 14:46 (3113 days ago) @ David Turell

More information on how molecules move quickly in and out of the nucleus. It is carefully controlled:-http://www.sciencedaily.com/releases/2015/09/150918132031.htm-"'It's understood how these transport factors selectively choose and bind to their cargo," Rout says. "However, it's been unclear how such a specific process can also shepherd molecules through the nuclear pore complex so quickly."-"At the center of the NPC, the transport factors and their cargo must pass through a selectivity filter made of proteins called FG Nups. These proteins form a dense mesh that normally prevents large molecules from getting through. Using a technique known as nuclear magnetic resonance spectroscopy, the researchers collected atomic-scale information about the behavior of the FG Nups, focusing on Nsp1, the most studied representative of the FG Nups.-"Normally, proteins fold into large structures. Relative to small molecules such as water, these large protein structures move very slowly. This means their interactions are correspondingly slow.-"The researchers measured the physical state of FG repeats with and without transport factors bound to them. They found that rather than folding like proteins generally do, the FG Nups are loose and string-like, remaining highly dynamic and lacking a predictable structure.-"'Usually, binding between traditionally folded proteins is a time consuming, cumbersome process, but because the FG Nups are unfolded, they are moving very quickly, very much like small molecules. This means their interaction is very quick," explains Rout.-"The disordered structure of the FG regions is critical to the speed of transport, allowing for quick loading and unloading of cargo-carrying transport factors. At the same time, because transport factors have multiple binding sites for FG Nups, they are the only proteins that can specifically interact with them -- making transport both fast and specific.-"'We observed that there is minimal creation of a static well-ordered structure in complexes of FG Nups and transport factors," says Cowburn. "Our observations are, we propose, the first case where the 'fuzzy' property of an interaction is a key part of its actual biological function."-"The team hopes this discovery will lead to detailed characterizations of nuclear transport pathways and to more close studies of the NPC's function. Ultimately, a better understanding of how the NPC works will not only provide new insight into the basic biology of cells, but also have implications for health and disease."-Comment: Another advance in understanding the complexity of the control over movements in and out of the nucleus, the control center of the cell. Again irreducible complexity. Proteins normally function when carefully folded. In this case just the opposite. Molecules as active cogs in the machinery. Automatic or controlled by information? And if so where is the information stored? And how did the information develop?

Biological complexity: neuron pore complexity

by David Turell @, Monday, October 05, 2015, 17:02 (3098 days ago) @ David Turell

Neuron pores controlling sodium and potassium ions are highly complex and allow neurons to rest after high speed firing:-http://medicalxpress.com/news/2015-10-ion-channel-reveals-neurons.html-"Within the brain, some neurons fire off hundreds of signals per second, and after ramping up for such a barrage, they need to relax and reset. A particular type of ion channel helps bring them down, ensuring these cells don't get overstimulated—a state that potentially can lead to severe epileptic seizures, among other problems. -***
"The signals that transmit information in the nervous system are generated by electrically charged atoms moving into and out of neurons. Typically, when a neuron fires, positively charged sodium rushes into the cell, generating a pulse of electrical activity that subsides as positively charged potassium floods out.-"In certain circumstances electrical impulses in the nervous system must be transmitted at a high frequency. But too high a frequency for too long can give rise to uncontrolled electrical activity, as seen in epilepsy, and can damage cells. For this reason mechanisms have evolved to put a protective break on the process. Slo2.2 underlies one such protective mechanism.-"The Slo2.2 ion channel does this by opening in response to the very sodium that enters the cell during an electrical impulse. When it opens, Slo2.2 allows potassium to flow out of the cell, thus restoring the cell's internal electrical state. It is not the only channel through which potassium travels; however, ions flow through Slo2.2 at ten times the rate of most other potassium channels.-***-"The researchers had obtained a full structure for Slo2.2 in its closed state. They uncovered a channel with four-fold symmetry. Inside the cell, where a potassium ion's path begins, two regulator domains (from each of four subunits) form a gating ring, which must open in order for potassium to pass. This ring, in turn, creates a massive funnel; when the channel is closed, the tip of this funnel is blocked.-"With this discovery, the researchers were able to better understand how Slo2.2 conducts ions so rapidly. When they mapped out the electrical charges across the channel's surface, they found the funnel has a strongly negative charge. It attracts positively charged potassium, creating a pool of ions waiting to exit once the gating ring opens.-"Once past the ring, an ion would traverse the cell membrane through a part of the protein called a selectivity filter that allows only potassium to pass.-"'Beyond giving us new insight on the basic configuration of this channel, this new structure also explains how Slo2.2 helps to quickly reduce the internal charge of a neuron and so rapidly return it to its resting state," Hite says. "Our next step is to determine Slo2.2's structure when it's open, which would help to explain how the arrival of sodium prompts the channel to open and allow potassium out.'"-The molecule involved is enormous. Look at the diagram of its structure. Ask the question. How did any unguided evolutionary process find this or invent it?

Biological complexity: bacterial garbage systems

by David Turell @, Thursday, October 08, 2015, 18:23 (3095 days ago) @ David Turell

Bacteria use a series of molecular activities to rid themselves of used proteins:-http://phys.org/news/2015-10-protein-cleanup-factors-bacterial-growth.html-"Biochemists have long known that crucial cell processes depend on a highly regulated cleanup system known as proteolysis, where specialized proteins called proteases degrade damaged or no-longer-needed proteins. These proteases must destroy their specific targets without damaging other proteins, but how this orderly destruction works is unknown in many cases-"Lead author Kamal Joshi, a doctoral candidate in the Chien lab, conducted experiments in the model bacterium Caulobacter crescentus. In this species, the ability to grow and replicate DNA is regulated by ClpXP, a highly conserved protease that in many bacteria allows them to cope with stressful environments such as the human body. Understanding how ClpXP is controlled could open a path to antibiotics that inhibit harmful bacteria in new ways.-"Chien explains that one of the long-standing mysteries in the field is how proteolysis controls Caulobacter growth. "The odd thing is that ClpXP is always present during different growth stages, but only destroys its target proteins at a specific time," he says. This led his group to think, "There must be a missing factor that we couldn't see, because something has to come on the scene to accomplish this. There was some genetic evidence pointing to certain additional proteins, but we didn't know how they worked."-***-"His lab took a biochemical approach to the problem, purifying all available proteins and designing experiments to query how they interacted and what functions were affected in their presence or absence. In this way, "Kamal found that the ClpXP protease could not by itself destroy the target proteins," Chien says. Instead, "he found that the additional regulatory proteins we had detected were controlling different parts of the process."-"Further, Joshi found that these newly identified regulatory adaptors worked in a step-wise hierarchical way. The first adaptor was directly responsible for degrading a handful of proteins, but it could also recruit an additional adaptor that would deliver a different set of proteins and bind even more adaptors. Working with the Viollier lab from the University of Geneva, Switzerland, the researchers found scores of additional protease targets that were destroyed in this hierarchical way."
 (my bold)-Comment: Basically an automatic series of molecular actions. Remember that enzymes are enormous molecules, not likely to have developed by chance.

Biological complexity: finding working proteins

by David Turell @, Sunday, October 25, 2015, 22:36 (3078 days ago) @ David Turell

Working proteins are composed of two requirements, a special sequence of amino acids which will be several hundred acids long. Second, a required folding pattern which then produces the function of the single molecule. New research is trying to understand the mysteries of this process:-http://www.sciencedaily.com/releases/2015/10/151023121845.htm-"'We developed a model in which the amino acids that have a strong co-evolutionary relationship attracted each other, without further additional data," says Simone Marsili, researcher who has also participated in the project. "First, we simulate the folding process and then we can see how the simulations were able to predict the changes in shape of the proteins at different levels of complexity, including those required for kinases to function [these are key proteins in metabolic and cell signalling processes as well as in cell transport, amongst others]."-"This new computational method easily integrates experimental and genomic data through the use of the latest sequence analysis and 3D modelling technology. In addition, it demonstrates that genomic data can be a source of useful information to supplement the current tools used to study the structure and dynamics of proteins.-"'The ability to predict key features of proteins at this level of complexity will help to understand how the sequence of a protein determines its dynamics and, therefore, its functions," concludes Valencia." -Comment: the special sequence of amino acids will lead the the proper folding is the basic premise of this study. When first inventing life, imagine the problem of finding the right proteins for the functions needed, when it is unknown from the beginning which folds will work and which won't. This is why design has such strong support among those who look at the problem from this perspective. Since DNA makes proteins it is logical that DNA contains the information to make the correct proteins. Big question how did that initial information develop? All protein molecules are large so the odds of finding picking the right ones from scratch are tiny and each single cell is made of thousands of different molecules. No wonder Paul Davies refers to life as the "fifth miracle'. this article will show my point mathematically:-http://www.darwinismrefuted.com/molecular_biology_03.html-"For instance, an average-sized protein molecule composed of 288 amino acids, and contains twelve different types of amino acids can be arranged in 10300 different ways. (This is an astronomically huge number, consisting of 1 followed by 300 zeros.) Of all of these possible sequences, only one forms the desired protein molecule. The rest of them are amino-acid chains that are either totally useless, or else potentially harmful to living things. -"In other words, the probability of the formation of only one protein molecule is "1 in 10^300. "The probability of this "1" actually occurring is practically nil. (In practice, probabilities smaller than 1 over 10^50 are thought of as "zero probability")." (The bound for improbability is also to be 1 over 10^150)

Biological complexity: finding working proteins

by dhw, Monday, October 26, 2015, 11:57 (3077 days ago) @ David Turell

DAVID: No wonder Paul Davies refers to life as the "fifth miracle'. this article will show my point mathematically:-http://www.darwinismrefuted.com/molecular_biology_03.html-Your point is taken, and is vividly illustrated by the article. I will, however, once more draw your attention to the continued misrepresentation of Darwin's theory:-QUOTE: The theory of evolution, which claims that life emerged as a result of chance, is quite helpless in the face of this order...-Darwin's theory of evolution does not claim that life emerged as a result of chance. It does not cover the origin of life. “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated” (Difficulties on Theory). The nearest it gets to that problem is with its numerous references to the Creator, and Darwin explicitly tells us that his theory is compatible with religion, as confirmed by millions of people who believe that God was responsible for the process of evolution. However, I would agree that the unexplained complexities of life's origins must remain a problem for atheists, some of whom are equally guilty of misrepresenting Darwin by announcing that the theory of evolution claims that life emerged as a result of chance.
 
I take your point about the article, but I trust you will also take mine.

Biological complexity: finding working proteins

by David Turell @, Monday, October 26, 2015, 13:56 (3077 days ago) @ dhw


> dhw: Darwin's theory of evolution does not claim that life emerged as a result of chance. It does not cover the origin of life. “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated” (Difficulties on Theory). The nearest it gets to that problem is with its numerous references to the Creator, and Darwin explicitly tells us that his theory is compatible with religion, as confirmed by millions of people who believe that God was responsible for the process of evolution. However, I would agree that the unexplained complexities of life's origins must remain a problem for atheists, some of whom are equally guilty of misrepresenting Darwin by announcing that the theory of evolution claims that life emerged as a result of chance.
> 
> I take your point about the article, but I trust you will also take mine.-Fully accepted. Darwin's theory starts after life is established, but any study of life and evolution must be viewed as a continuum from start to now in trying to determine the underlying mechanism.

Biological complexity: finding working proteins

by dhw, Tuesday, October 27, 2015, 16:09 (3076 days ago) @ David Turell

dhw: Darwin's theory of evolution does not claim that life emerged as a result of chance. It does not cover the origin of life. “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated” (Difficulties on Theory). The nearest it gets to that problem is with its numerous references to the Creator, and Darwin explicitly tells us that his theory is compatible with religion, as confirmed by millions of people who believe that God was responsible for the process of evolution. However, I would agree that the unexplained complexities of life's origins must remain a problem for atheists, some of whom are equally guilty of misrepresenting Darwin by announcing that the theory of evolution claims that life emerged as a result of chance.
I take your point about the article, but I trust you will also take mine.-DAVID: Fully accepted. Darwin's theory starts after life is established, but any study of life and evolution must be viewed as a continuum from start to now in trying to determine the underlying mechanism.-I am very happy with this answer. Thank you. My objection is to the constant misrepresentation of Darwin's theory, which I will continue to point out as it is so common among both theists and atheists. But I agree completely that we should never lose sight of the immense problem of the source of the underlying mechanism, which is why I usually put “possibly God-given” together with my hypothetical cellular intelligence.

Biological complexity: finding working proteins

by David Turell @, Tuesday, October 27, 2015, 19:20 (3076 days ago) @ dhw


> DAVID: Darwin's theory starts after life is established, but any study of life and evolution must be viewed as a continuum from start to now in trying to determine the underlying mechanism.
> 
> dhw: I am very happy with this answer. My objection is to the constant misrepresentation of Darwin's theory, which I will continue to point out as it is so common among both theists and atheists. But I agree completely that we should never lose sight of the immense problem of the source of the underlying mechanism, which is why I usually put “possibly God-given” together with my hypothetical cellular intelligence.-Agreed. Stay on your fence.

Biological complexity: finding working proteins

by David Turell @, Wednesday, October 28, 2015, 23:14 (3074 days ago) @ David Turell

Another article on the rarity of functional proteins:-http://www.evolutionnews.org/2015/10/proteins_by_acc100411.html-"In fact, the vast majority of possible protein chains are like strands of beads -- lacking any fixed shape. Life, however, makes critical use of a very special subset of the possibilities. These special proteins are coaxed into forming precise shapes by the sequence of amino acids along their chains. The process triggered by this coaxing, where a floppy protein chain rapidly acquires a well-formed structure, is known as folding.-"To give you an idea of how special these folding sequences are, the Journal of Molecular Biology paper referred to in the video estimates the proportion of chains that fold to be in the range of one in 10^50 to one in 10^74, depending on the complexity of the fold.-"Even for simple folds, this means fewer than one in a trillion trillion trillion trillion amino acid sequences forms any well-defined shape at all. So the idea that every protein sequence has a shape is not at all accurate.-"Secondly, the related idea that mutations merely change the shapes of proteins is equally inaccurate. The highly cooperative nature of protein folding means that it tends to be all-or-nothing. A particular protein sequence either forms structure A or it doesn't, and likewise for structure B. So for a series of mutations to convert a protein from forming structure A to forming structure B, they would first have to undo the A structure (producing a chain with no well-defined structure) and then stabilize the B structure.-"In other words, changing the structure of a protein isn't nearly as easy as changing the shape of a lump of clay. The clay always has a shape, and with a little imagination we can even say the shape always represents something (which is all we ask of a lump of clay).-"Proteins are different. Only highly exceptional proteins even have a shape, and these shapes are therefore fragile. Mutations are tolerated to a modest extent, after which all shape is lost.-Comment: If mutations are the result of blind searching, based on the odds above, how does evolution find the right proteins for a new adaptation for innovation? There must be DNA guidelines on board or there is not enough time for evolution to fit the timelines we know. Thus the two approaches we discuss: on board guidance or external guidance. There can be nothing else.

Biological complexity: finding working proteins

by dhw, Thursday, October 29, 2015, 11:51 (3074 days ago) @ David Turell

DAVID: Another article on the rarity of functional proteins:http://www.evolutionnews.org/2015/10/proteins_by_acc100411.html-David's comment: If mutations are the result of blind searching, based on the odds above, how does evolution find the right proteins for a new adaptation for innovation? There must be DNA guidelines on board or there is not enough time for evolution to fit the timelines we know. Thus the two approaches we discuss: on board guidance or external guidance. There can be nothing else.-External guidance means God dabbling to create every innovation, lifestyle and natural wonder. On board “guidance” means a 3.8-billion-year-computer programme passed down by the very first cells, or a collection of autonomous “minds” capable of cooperating to making all the necessary changes. The latter would account for the astonishing range of life forms extinct and extant, and since we have no precedent to tell us how long it should take intelligent minds to make such changes, time is not a factor. 
 
xxxxxxxxxxxxxxxxxxxxxx-Your posts on microglia and coral reef fish (I really enjoyed that one!) contain the following:-David's comment: Show me a computer that cannibalizes itself? Again high complexity beyond the abilities of random evolution.-Agreed, but not beyond the abilities of intelligent cells monitoring themselves and cooperating to create an efficient structure and system.
 
QUOTE: "'It all goes to show that coral reef fish have evolved quite a range of clever strategies for survival which are deployed when a threatening situation demands.'"-David's comment: A very common strategy with animals and also plants.-But every strategy for survival has to be individually adapted to the environment and the particular nature of the organism and the threatening situations with which it is confronted. I like the word “clever” in the quote, and can't help wondering if the vast range of such clever survival strategies might not be the product of cellular intelligence - in plants as well as in animals - rather than a 3.8-billion-year computer programme passed down by the very first cells for each individual strategy.

Biological complexity: finding working proteins

by David Turell @, Thursday, October 29, 2015, 21:06 (3074 days ago) @ dhw


> David's comment: If mutations are the result of blind searching, based on the odds above, how does evolution find the right proteins for a new adaptation for innovation? There must be DNA guidelines on board or there is not enough time for evolution to fit the timelines we know. Thus the two approaches we discuss: on board guidance or external guidance. There can be nothing else.
> 
> dhw: External guidance means God dabbling to create every innovation, lifestyle and natural wonder. On board “guidance” means a 3.8-billion-year-computer programme passed down by the very first cells, or a collection of autonomous “minds” capable of cooperating to making all the necessary changes. The latter would account for the astonishing range of life forms extinct and extant, and since we have no precedent to tell us how long it should take intelligent minds to make such changes, time is not a factor.-So would the former. How do cellular minds understand the complexity of forming a new species de novo? We do not see intermediate forms. 
> 
> xxxxxxxxxxxxxxxxxxxxxx
> 
> Your posts on microglia and coral reef fish (I really enjoyed that one!) contain the following:
> 
> David's comment: Show me a computer that cannibalizes itself? Again high complexity beyond the abilities of random evolution.
> 
> dhw: Agreed, but not beyond the abilities of intelligent cells monitoring themselves and cooperating to create an efficient structure and system.-They would have to understand design for the future organism to work at first try. No intermediate forms means no chance for trial and error. got to be right the first time.
> 
> QUOTE: "'It all goes to show that coral reef fish have evolved quite a range of clever strategies for survival which are deployed when a threatening situation demands.'"
> 
> David's comment: A very common strategy with animals and also plants.
> 
> dhw: But every strategy for survival has to be individually adapted to the environment and the particular nature of the organism and the threatening situations with which it is confronted. I like the word “clever” in the quote, and can't help wondering if the vast range of such clever survival strategies might not be the product of cellular intelligence - in plants as well as in animals - rather than a 3.8-billion-year computer programme passed down by the very first cells for each individual strategy.-Same answer. The new strategy has to work the first time or no survival.

Biological complexity: molecular transport in cells

by David Turell @, Thursday, November 05, 2015, 15:52 (3067 days ago) @ David Turell

Kinesin walks across microtubules carrying the molecule:-http://phys.org/news/2015-11-ministry-silly-cells.html-"Intracellular transport takes place along the fibres of the cytoskeleton, a structure developed by eukaryotic cells (possessing a cell nucleus). The fibres forming the network - microtubules - are made of polymers of the protein tubulin twisted spirally into long tubes. Since each 'brick' of the polymer, i.e., each monomer, consists of a pair of alpha-tubulin and beta-tubulin. Along the microtubule, the alpha and beta domains are arranged alternately, like the black-and-white squares along the length of a chessboard if it were rolled up into a tube.-"The microtubules are the roads along which the intracellular tractors, the kinesin molecules, move. One part of kinesin is equipped with fragments that bind to molecules in order to transport them, while the driving part consists of a flexible connector, the so-called linker, fastening together the two 'legs', i.e. the movable domains that step along the 'chess fields' of the microtubules. In addition, the legs are so large that kinesin can only step on every second monomer (that is, fields of the same colour).-"'Kinesin walks along the microtubules. But how? In order to understand the problem, one needs only to realize that kinesin does not wander along the microtubules like a man does along the pavement. Its movements are more reminiscent of what a mountain climber does when scaling a vertical wall without any safeguards: one mistake, and he falls off," says Prof. Robert Holyst (IPC PAS). "How does kinesin know it can free one leg without risking detachment from the microtubules? It isn't an animal equipped with eyes and a brain, it's just a simple molecule. Where does it get the energy to take the step?'"-Comment: Play the video to really understand what this process looks like. Of course chance invention cannot create this.

Biological complexity: molecular transport in nuclei

by David Turell @, Saturday, November 07, 2015, 20:21 (3065 days ago) @ David Turell

The wall of the nucleus has controls in its pores to manage the molecules that go in and out. I've described this before:-http://www.sciencedaily.com/releases/2015/11/151106144521.htm-"Scientists from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have uncovered new clues to how a molecular machine inside the cell acts as a gatekeeper, allowing some molecules to enter and exit the nucleus while keeping other molecules out.-
"The scientists studied the nuclear pore complex, which crosses the membrane that separates the nucleus from the rest of the cell. Amazingly, this nanomachine can handle the selective transport of more than one thousand molecules per second. The complex is critical to maintaining an organism's health, including ours. It transports RNA and ribosomal proteins out of the nucleus, and allows only important molecules to enter. (my bold)-***-"Despite decades of research, however, scientists don't know what makes the nuclear pore complex both high throughput and highly selective. It's well known the nanopore uses a family of proteins called FG Nups to transport molecules. These proteins are inside the pore and have floppy regions that briefly interact with molecules, allowing passage to some and blocking others. But it's unclear how these proteins perform this job.-"Now, as reported November 6 in the journal Scientific Reports, Berkeley Lab scientists found that the proteins' cargo-transporting ability is likely due to specific features encoded in their sequences. Protein sequences are primarily composed of amino acids, and in FG Nups proteins, the scientists found different types of amino acids arranged just so within their sequences. This arrangement of amino acids appears to form a network inside the nuclear pore complex that is optimized for one purpose only: the extremely efficient transport of molecular cargo into and out of the nucleus.-"'Our results suggest a striking cooperation among the different types of amino acids that are meticulously positioned within the sequences of FG Nups," says Mohammad Mofrad, a faculty scientist in Berkeley Lab's Molecular Biophysics.-***-"Specifically, the scientists identified polar amino acids, and a newly discovered sequence of charged amino acids, which they named "Like Charge Region," as the likely players in forming FG Nups networks in nuclear protein complexes. They also found that positively charged "Like Charge Regions" prepare the pore for negatively charged cargos and regulate the size of the FG Nups network, while polar amino acids facilitate the formation of FG Nups-rich regions in the pore."-Comment: Ever more complex than we knew. Not by chance. Complex information has to be at the controls of forming such a nanomachine.

Biological complexity: vision complexity

by David Turell @, Monday, November 16, 2015, 17:53 (3056 days ago) @ David Turell

Rhodopsin at molecular levels makes changes in 200 millions of a billion of a second:-http://phys.org/news/2015-11-molecular-breakdance.html-"The retinal chromophore in rhodopsin, also called vitamin A aldehyde, derives its light sensitivity from a repeating chain of single- and double-bonded carbon atoms. The absorption of a photon by retinal causes an extremely short transient weakening of a specific double bond resulting in rotation about that bond. Pinpointing how fast this so-called chemical isomerization reaction occurs has been difficult, however, and has largely tracked the technological advances in pulsed laser sources. With femtosecond lasers it was shown that the isomerization takes place within 200 femtoseconds (that is 200 millionths of a billionth of a second), and is likely a vibrationally-coherent chemical reaction, meaning the vibrational motions of the retinal chromophore itself help directing the isomerization reaction.-"Using a highly sensitive technique from the field of ultrafast spectroscopy called heterodyne-detected transient grating spectroscopy, scientists in the laboratories of Professors R. J. Dwayne Miller (University of Toronto and Max Planck Institute for the Structure and Dynamics of Matter) and Oliver P. Ernst (University of Toronto) revisited the isomerization reaction of bovine rhodopsin with unprecedented sensitivity and temporal resolution. Such an approach revealed that the isomerization takes place on a timescale of 30 femtoseconds. "It turns out that the primary step of vision is nearly ten times faster than anyone thought," says Professor Miller, "and the atomic motions are all perfectly choreographed by the protein." -"Temporal analysis of the experimental data revealed these choreographed vibrational dynamics, which are comprised of localized stretching, out-of-plane wagging, and torsional motions. "Such a fast timescale sets distinct limitations on the vibrationally-coherent reaction coordinate," says Dr. Philip Johnson, lead author of the study, "and this work indicates that it is local to the specific isomerizing double bond." "Moreover," he adds, "the isomerization reaction proceeds within a single period of the relevant torsional vibrational motion."-Comment: this is all automatic molecular action in the retina. No intelilgence involved, and a great design.

Biological complexity: plant responses to shade

by David Turell @, Thursday, December 24, 2015, 22:47 (3018 days ago) @ David Turell

Plants can recognize being shaded, and they have direct responses to solve the problem:-http://phys.org/news/2015-12-sun-cellular-sensor.html-"To escape this deadly shade, plants have light sensors that can set off an internal alarm when threatened by the shade of other plants. Their sensors can detect depletion of red and blue light (wavelengths absorbed by vegetation) to distinguish between an aggressive nearby plant from a passing cloud.-"Scientists at the Salk Institute have discovered a way by which plants assess the quality of shade to outgrow menacing neighbors, a finding that could be used to improve the productivity of crops. The new work, published Dec. 24, 2015 in Cell, shows how the depletion of blue light detected by molecular sensors in plants triggers accelerated growth to overcome a competing plant.-***-"The focus of the team's research efforts was cryptochromes, blue light-sensitive sensors that are responsible for telling a plant when to grow and when to flower. Cryptochromes were first identified in plants and later found in animals, and in both organisms they are associated with circadian rhythm (the body's biological clock). The protein's role in sensing depletion of blue light had been known, but this study is the first to show how cryptochromes promote growth in a shaded environment.-"The team placed normal and mutant Arabidopsis plants in a light-controlled room where blue light was limited. The mutant plants lacked either cryptochromes or a PIF transcription factor, a type of protein that binds to DNA to control when genes are switched on or off. PIFs typically make direct contact with red light sensors, called phytochromes, to initiate shade avoidance growth. The researchers compared the responses of the mutant and normal plants in the varying blue light conditions by monitoring the growth rate of the stems and looking at contacts between cryptochromes, PIFs and chromosomes.-"'We found that cryptochromes contact these transcription factors on DNA, activating genes completely different than what other photoreceptors activate," says Ullas Pedmale, first author of the work and a Salk research associate. "This is also a very short pathway so plants can rapidly respond to their light environment.'"-Comment: Another example of my concept that direct molecular reactions can be automatically interpreted with DNA interaction to achieve the best response to a stimulus. No cellular consciousness involved, just instructions in the information available to the plant.

Biological complexity: ion channels

by David Turell @, Monday, January 18, 2016, 22:07 (2993 days ago) @ David Turell
edited by David Turell, Monday, January 18, 2016, 22:13

The very complex structure is now shown:-http://www.sciencedaily.com/releases/2016/01/160118134434.htm--"Many cells have microscopic gates, called ion channels, which open to allow the flow of ions across the cell membrane. Thanks to these gates, cells can detect stimuli such as heat, pain, pressure and even spicy food.-***-"Lander and his colleagues focused on an ion channel called the transient receptor potential vanilloid-2 (TRPV2), which resides within the membranes of cells throughout the body. Previous research had suggested TRPV2 was involved in sensing physical stresses, such as changes in pressure and temperature, as well as in detecting immune challenges and activating the immune system's T cells.-"In the new study, the researchers used an imaging technique called cryo-electron microscopy, in which a sample is pelted with high-energy electrons. Through the use of new sample preparation techniques, computer programs and a new generation of cameras, researchers at TSRI have improved the potential resolution of cryo-electron microscopy images to the point that TRPV2 could be imaged with near-atomic precision.-***-"When the researchers compared the structure of TRPV2 with TRPV1, a genetically similar ion channel found only in the nervous system, they noticed some significant differences. TRPV2's architectural components near the central gate and the peripheral domains were in a previously unobserved configuration. Together, this led the authors to propose that this configuration represents a 'desensitized' state, providing a new molecular snapshot of these ion channels at work.-"'The TRVP2 ion channel is likely a global internal sensor--playing an important role in our immune response," said Lander."-Second source: http://phys.org/news/2016-01-scientists-blueprint-body-sensor.html-
&a... a hot stove, and your fingers will recoil in pain because your skin carries tiny temperature sensors that detect heat and send a message to your brain saying, "Ouch! That's hot! Let go!"
 
"The pain is real and it serves a purpose, otherwise we'd suffer greater injury. But for many people with chronic pain, that signal keeps getting sent for months or years, even when there is no clear cause.-"Now, researchers have discovered the structure of a protein linked to pain and heat perception. It is an ion channel in the cell surface membrane called TRPV2. This port-like structure plays a role in a number of disparate biological processes, such as maintaining a healthy heart, helping dispose of pathogens and inducing cell death in certain cancers."-Comment: Look at the model. How does chance evolution create this stuff?

Biological complexity: cell molecular communication

by David Turell @, Wednesday, January 27, 2016, 18:29 (2984 days ago) @ David Turell

Cells respond to molecular signals they are programmed to interpret:-http://www.sciencedaily.com/releases/2016/01/160121121825.htm-"To decide whether and where to move in the body, cells must read chemical signals in their environment. Individual cells do not act alone during this process, two new studies on mouse mammary tissue show. Instead, the cells make decisions collectively after exchanging information about the chemical messages they are receiving.
"Cells talk to nearby cells and compare notes before they make a move," says Ilya Nemenman, a theoretical biophysicist at Emory University and a co-author of both studies, published by the Proceedings of the National Academy of Sciences (PNAS). The co-authors also include scientists from Johns Hopkins, Yale and Purdue.-"The researchers discovered that the cell communication process works similarly to a message relay in the telephone game. "Each cell only talks to its neighbor," Nemenman explains. "A cell in position one only talks to a cell in position two. So position one needs to communicate with position two in order to get information from the cell in position three."-"And like the telephone game -- where a line of people whisper a message to the person next to them -- the original message starts to become distorted as it travels down the line.-"The researchers found that, for the cells in their experiments, the message begins to get garbled after passing through about four cells, by a factor of about three.-***-"Since at least the 1970s, and pivotal work by Howard Berg and Ed Purcell, scientists have been trying to understand in detail how cells decide to take an action based on chemical cues.-"Every cell in a body has the same genome but they can do different things and go in different directions because they measure different chemical signals in their environment. Those chemical signals are made up of molecules that randomly move around.-"'Cells can sense not just the precise concentration of a chemical signal, but concentration differences," Nemenman says. "That's very important because in order to know which direction to move, a cell has to know in which direction the concentration of the chemical signal is higher. Cells sense this gradient and it gives them a reference for the direction in which to move and grow."-***-"The clumps of cells, working collectively, could detect insanely small differences in concentration gradients -- such as 498 molecules of EGF versus 502 molecules -- on different sides of one cell," Nemenman says. "That accuracy is way better than the best possible margin of error determined by Berg and Purcell of about plus or minus 20. Even at these small concentration gradients, the organoids start reshaping and moving toward the higher concentration. These cells are not just optimal gradient detectors. They seem super optimal, defying the laws of nature."-***-"Together, the two papers offer a detailed model for collective cellular gradient sensing, verified by experiments in mouse mammary organoids. The collective model expands the classic Berg-Purcell results for the best accuracy of an individual cell, which stood for almost forty years. The new formula quantifies the additional advantages and limitations on the accuracy coming from the cells working collectively."-Comment: Note that the cells identify the type of signal and the strength of the signal. This study implies automaticity. Bacteria studied by Shapiro are on their own and must be more independent so I believe they are also automatic but have a greater variety of programmed esponses.

Biological complexity: cell molecular communication

by dhw, Thursday, January 28, 2016, 18:15 (2983 days ago) @ David Turell

DAVID: Cells respond to molecular signals they are programmed to interpret:-A misleading introduction! The article does not say the cells are programmed to do anything!-http://www.sciencedaily.com/releases/2016/01/160121121825.htm-QUOTE: "To decide whether and where to move in the body, cells must read chemical signals in their environment. Individual cells do not act alone during this process, two new studies on mouse mammary tissue show. Instead, the cells make decisions collectively after exchanging information about the chemical messages they are receiving.
"Cells talk to nearby cells and compare notes before they make a move," says Ilya Nemenman....-If cells were programmed, they would not have to exchange information or “talk” to nearby cells or “compare notes” or, above all, make decisions. The decisions would already have been made for them.
 
QUOTE: "A cell in position one only talks to a cell in position two. So position one needs to communicate with position two in order to get information from the cell in position three."
"And like the telephone game -- where a line of people whisper a message to the person next to them -- the original message starts to become distorted as it travels down the line. "The researchers found that, for the cells in their experiments, the message begins to get garbled after passing through about four cells, by a factor of about three.-Why are garbled messages a sign of automaticity? The image used here could hardly be clearer: that there is a degree of subjectivity within each individual cell, and it can affect the way in which cooperation works.
 
David's comment: Note that the cells identify the type of signal and the strength of the signal. This study implies automaticity. Bacteria studied by Shapiro are on their own and must be more independent so I believe they are also automatic but have a greater variety of programmed responses.-Identifying the type and strength of signals is the equivalent of our perception. The next stage is processing the information received, communicating it to others, and taking a collective decision. All these are hallmarks of intelligence, and not automaticity. Shapiro (like McClintock, Margulis, Buehler etc.) is quite specific in attributing independent intelligence to cells in general and not just bacteria, and this study explicitly describes cooperative, decision-making procedures, as opposed to automatic responses! Thank you for drawing it to our attention.

Biological complexity: cell molecular communication

by David Turell @, Thursday, January 28, 2016, 19:08 (2983 days ago) @ dhw

dhw: Identifying the type and strength of signals is the equivalent of our perception. The next stage is processing the information received, communicating it to others, and taking a collective decision. All these are hallmarks of intelligence, and not automaticity. Shapiro (like McClintock, Margulis, Buehler etc.) is quite specific in attributing independent intelligence to cells in general and not just bacteria, and this study explicitly describes cooperative, decision-making procedures, as opposed to automatic responses! Thank you for drawing it to our attention.-As usual we are having the same battle. If the cells respond as the article states that can be by automatic programmed responses just as well as by your interpretation. Shapiro works with single-celled organisms responsible only to themselves. These are not the same as cells in a multicellular organism where the cells must work with each other in a coordinated fashion which is programmed and controlled. Different cells have different DNA controls.

Biological complexity: cell molecular communication

by dhw, Friday, January 29, 2016, 13:44 (2982 days ago) @ David Turell

dhw: Identifying the type and strength of signals is the equivalent of our perception. The next stage is processing the information received, communicating it to others, and taking a collective decision. All these are hallmarks of intelligence, and not automaticity. Shapiro (like McClintock, Margulis, Buehler etc.) is quite specific in attributing independent intelligence to cells in general and not just bacteria, and this study explicitly describes cooperative, decision-making procedures, as opposed to automatic responses! Thank you for drawing it to our attention.
DAVID: As usual we are having the same battle. If the cells respond as the article states that can be by automatic programmed responses just as well as by your interpretation.-It is not quite the same battle. You claim that the researchers are on your side, and I am claiming them as my allies. The section that requires comment is as follows:
 
QUOTE: "To decide whether and where to move in the body, cells must read chemical signals in their environment. Individual cells do not act alone during this process, two new studies on mouse mammary tissue show. Instead, the cells make decisions collectively after exchanging information about the chemical messages they are receiving.
"Cells talk to nearby cells and compare notes before they make a move," says Ilya Nemenman....-Dhw: If cells were programmed, they would not have to exchange information or “talk” to nearby cells or “compare notes” or, above all, make decisions. The decisions would already have been made for them. -I know you still insist that cells are automatons. My point is that these researchers disagree with you, so please explain how the above MEANS that cells are programmed and therefore do not take their own decisions.-DAVID: Shapiro works with single-celled organisms responsible only to themselves. These are not the same as cells in a multicellular organism where the cells must work with each other in a coordinated fashion which is programmed and controlled. Different cells have different DNA controls.-You also claim that bacteria are automatons. Of course cells in multicellular organisms must work together, but that does not make them automatons. Anyway, we needn't argue about the relevance of Shapiro's research. He has already stated his opinion about the intelligence of cells in the interview I quoted earlier, as have increasing numbers of experts in the field (Bruce Lipton was the latest in the line, see my post of 22 December 2015). We are now arguing about whose side these particular researchers are on. Unless you can explain how processing and exchanging information before making a decision constitutes preprogramming, I would suggest they are on the side of the “intelligent cell” brigade.

Biological complexity: cell molecular communication

by David Turell @, Friday, January 29, 2016, 18:30 (2982 days ago) @ dhw


> Dhw: If cells were programmed, they would not have to exchange information or “talk” to nearby cells or “compare notes” or, above all, make decisions. The decisions would already have been made for them. 
> 
> I know you still insist that cells are automatons. My point is that these researchers disagree with you, so please explain how the above MEANS that cells are programmed and therefore do not take their own decisions.-It is still the same battle. These cells communicate with molecular reactions as their 'talk'. The responses can be automated decisions as I've told you over and over.-> dhw: Unless you can explain how processing and exchanging information before making a decision constitutes preprogramming, I would suggest they are on the side of the “intelligent cell” brigade.-Very simple: cell A sends a series of molecules B,C,D. Cell E receives them and this sets off an automatic response of molecules F,G, and H back to A. We were taught several series of these reactions in biochemistry in Med school. This is how cells 'talk'.

Biological complexity: cell molecular communication

by dhw, Saturday, January 30, 2016, 13:36 (2981 days ago) @ David Turell

Dhw: If cells were programmed, they would not have to exchange information or “talk” to nearby cells or “compare notes” or, above all, make decisions. The decisions would already have been made for them. -I know you still insist that cells are automatons. My point is that these researchers disagree with you, so please explain how the above MEANS that cells are programmed and therefore do not take their own decisions.-DAVID: It is still the same battle. These cells communicate with molecular reactions as their 'talk'. The responses can be automated decisions as I've told you over and over.-I'm afraid this is another case of failed communication between us. I was only repeating what the researchers said and asking why you think their findings support your opinion.-dhw: Unless you can explain how processing and exchanging information before making a decision constitutes preprogramming, I would suggest they are on the side of the “intelligent cell” brigade.-DAVID: Very simple: cell A sends a series of molecules B,C,D. Cell E receives them and this sets off an automatic response of molecules F,G, and H back to A. We were taught several series of these reactions in biochemistry in Med school. This is how cells 'talk'.-Once again, I know you believe what you were taught at medical school. I am only pointing out that these researchers do not say cellular communication is automatic, but on the contrary emphasize the active, individual link between information processing, communication, cooperation and, above all, decision-making, which are hallmarks of intelligence. I am not asking you to change your belief. I am simply asking you to accept that these researchers disagree with you.

Biological complexity: cell molecular communication

by David Turell @, Saturday, January 30, 2016, 14:22 (2981 days ago) @ dhw

DAVID: It is still the same battle. These cells communicate with molecular reactions as their 'talk'. The responses can be automated decisions as I've told you over and over.
> 
> dhw: I'm afraid this is another case of failed communication between us. I was only repeating what the researchers said and asking why you think their findings support your opinion.-To repeat: I have the right to read their papers and reach a different conclusion from their findings.-> dhw: I am not asking you to change your belief. I am simply asking you to accept that these researchers disagree with you.-Of course they disagree or we would not be in discussion about it. But there are others who agree with me. So? You have picked sides and found folks whose opinions you like. I come from a background of a trained viewpoint.

Biological complexity: cell molecular communication

by dhw, Sunday, January 31, 2016, 13:12 (2980 days ago) @ David Turell

dhw: I am not asking you to change your belief. I am simply asking you to accept that these researchers disagree with you.-DAVID: Of course they disagree or we would not be in discussion about it. But there are others who agree with me. So? You have picked sides and found folks whose opinions you like. I come from a background of a trained viewpoint.-Again you have misunderstood. I did not find these folk. You presented us with this research yourself and made the following comments (my bold):
DAVID: Cells respond to molecular signals they are programmed to interpret:
DAVID: Note that the cells identify the type of signal and the strength of the signal. This study implies automaticity.-My posts are a response to these comments and are an attempt to show why this study does NOT imply automaticity but in fact argues the very opposite. You have now agreed. Thank you. The fact that these researchers disagree with you does not, of course, invalidate your belief in automaticity, any more than your medical background invalidates their conclusions.

Biological complexity: cell molecular communication

by David Turell @, Sunday, January 31, 2016, 15:30 (2980 days ago) @ dhw

DAVID: Note that the cells identify the type of signal and the strength of the signal. This study implies automaticity.
> 
> dhw: My posts are a response to these comments and are an attempt to show why this study does NOT imply automaticity but in fact argues the very opposite. You have now agreed. Thank you. The fact that these researchers disagree with you does not, of course, invalidate your belief in automaticity, any more than your medical background invalidates their conclusions.-With my training, it is easy to understand that I would disagree with their conclusions. I saw the human body automatically solving problems all the time.

Biological complexity: how heart mucle works

by David Turell @, Tuesday, February 09, 2016, 00:35 (2971 days ago) @ David Turell

Driven by a giant protein molecule, larger than any other one in life:-http://medicalxpress.com/news/2016-02-molecular-mechanism-heart-blood.html-"A healthy heart regulates itself so that with each beat, it pumps out as much blood as it receives. When blood enters the heart, it stretches the wall of the pumping chamber, triggering muscle to contract and pump blood out. This regulatory-control mechanism is known as the Frank-Starling law, named after physiologists Otto Frank and Ernest Starling.-"In heart failure patients, the Frank-Starling law breaks down. Heart muscle becomes too weak to pump out of the heart the same amount of blood that flows into the heart. To compensate, the heart enlarges, develops more muscle mass and beats faster. But eventually these compensatory measures fall short. The heart cannot pump enough blood to meet the body's needs for blood and oxygen, leading to shortness of breath, fatigue, weakness, swelling in legs, fluid retention, and other symptoms.-"The study by de Tombe and colleagues found that the titin protein is key to understanding the Frank-Starling mechanism and therefore how much blood the heart is able to pump out with each beat. Titin is an essential component of muscle. It's the largest protein in the body, weighing about 15 times as much as an average protein. In the heart, it acts like a spring, affecting the heart's ability to contract and relax. Normally when people age, the titin protein gets shorter. But in heart failure patients, the protein grows longer and becomes less effective."-Comment: And how did a blind process like the Darwin theory find this giant molecule. Not hunt and peck.

Biological complexity: building celllular microtubules

by David Turell @, Thursday, February 11, 2016, 20:40 (2969 days ago) @ David Turell

Led by an enzyme:-http://www.sciencedaily.com/releases/2016/02/160211085202.htm-"Professor Rob Cross, Professor of Mechanochemical Cell Biology at Warwick Medical School, said: "Every cell in our bodies contains a railway network, a system of tiny tracks called microtubules that run between important destinations inside the cell and allow cargo to be carried from one place to another. The tracks of this cellular railway are almost unimaginably small -- just 25 nanometers across (a nanometer is a millionth of a millimeter). The railway is just as crucial to a well-run cell as a full-size railway is to a well-run country."-"The microtubule tracks are vital for functions such as cell division and are a key target for key cancer drugs. The Cross lab is researching how these microtubule tracks are assembled.-"Professor Cross said: "It has been known for some time that a team of proteins called TOGs sits on the tip of the growing microtubule track and works like a team of tiny railway workers to rapidly lay the new microtubule track. But exactly how this team works so effectively has been mysterious."-"In their new work the Cross lab shows that TOGs are held in place at microtubule tips by other proteins called TACCs, and that the TOG-TACC machinery then stabilises the growing microtubule track as well as speeding up the assembly of the new track.-"The tip-tracking TOG-TACC machinery acts as a catalyst of microtubule assembly, and it turns out, based on the new results, that TOG-TACC is a very unusual type of catalyst that stabilises its product (the microtubule railway) as well as speeding up its growth."-Comment: Enzymes are giant molecules that run processes. How did chance evolution find this one?

Biological complexity: more cell pore complexity

by David Turell @, Wednesday, February 24, 2016, 21:53 (2956 days ago) @ David Turell

Materials must move and out of the nucleus and the cell at high speed. Very lage and complex molecular structures control this process:-http://phys.org/news/2016-02-nuclear-pore-complex-billion-years.html-"The interactome is exactly what it sounds like: any exhaustive set of molecules that can be connected with thin black lines in a figure in a research paper. Practically speaking, this meant starting with a few fluorescently-tagged versions of known core nuclear pore component proteins (called nucleoporins or Nups), and 'walking out' from there using affinity capture and mass spectrometry to identify other proteins that stick.-"While there are plenty of contenders for the title of world's greatest protein complex—the ribosome, proteosome, ATPase, and centromere for example—the NPC may be the mightiest of all. At an undisputed 50 MEGADaltons (124 for the mammalian), the NPC contains about 500 subunits comprised of some 30 different Nups. Rather than splashed together like a respiratory complex, the NPC is carefully assembled into an 8-fold symmetric structure that rivets the double nuclear membrane together. To give some idea of the budget that cells are on, the nucleus might have 2000 NPCs (more if mitosis is coming), each ferrying consumables at a rate of 1000 translocations per second.-"What exactly is a translocation you might ask, and who gets to go in or out? That depends on a lot of things, like that minimum pore size we mentioned above. Although there is no hard and fast size limit to what can pass through by unaided diffusion, things slow down considerably for proteins at around 60kDa. Above that, translocation doesn't become energy dependent per say, but ultimately the ferryman needs to get paid with the hydrolysis of two GTP each time the turnstyle turns. The way it works is neatly described by something known as the Ran-GTP cycle. Many folks are familiar with the idea of gradients across membranes (usually electrical, proton, sodium or other ion), which are harnessed to power auxiliary movements. -"The Ran cycle is said to run on a Ran protein gradient where the concentration of the GTP bound form is high inside. and GDP bound form is low outside the nucleus. The tricky part is biasing the pore to get things moving in the right direction. Ribosomes and mRNAs made in the nucleus need to get out, while nuclear proteins translated in the cytoplasm need to get in. These affairs are all neatly enforced by an expansive array of adapters which recognize and bind canonical nucleic acid cytoplasmic localization sequences on the former, and amino acid nuclear localization sequences on the later.-***-"Among the critical conserved components that the researchers in all eukaryote NUPs were the major protein folds on the core scaffold Nups lining the main pore. The Nups form the two inner rings which are in turn sandwiched between two outer rings. They contain folds known as ?-solenoids and ?-barrels or propellers. The importance of these folds is increasingly appreciated as they continue be found at the heart of many newly determined protein crystal structures. The mitochondrial Tom and Sam translocases have them, as do various vesicle coat proteins, including clathrin/adaptin, COPI, and COPII proteins. The authors note that these proteins share architectural characteristics with outer ring Nups, and hint at a common ancestry between the endomembrane trafficking system and the NPC. This so-called 'proto-coatomer hypothesis' further suggests that key components of the cell's secretory system took origin by virtue of their ability to bend membranes, a key first step in the assembly of the pore."-Comment: A highly complex set of structures for pores in the nucleus, the mitochondria and the cell wall. How did evolution find this when it was needed to be invented? Obviously requires planning to get it right. Only mentation can do this. Look at the diagram.

Biological complexity: photosynthesis

by David Turell @, Saturday, February 27, 2016, 15:32 (2953 days ago) @ David Turell

This is a highly complex mechanism which protects itself from the oxygen produced:-https://www.sciencedaily.com/releases/2016/02/160226143945.htm-"Photosynthesis takes place in stages. In the 'first stage' light is absorbed and used to produce energy molecules, with oxygen as a byproduct. These energy molecules are then used to power the 'second stage' of photosynthesis, in which carbon dioxide from the air is fixed into carbon-based sugars, such as glucose and sucrose.-***-"The team was able to figure out that at least one aspect of CGL71's job is to protect the photosynthetic apparatus from oxygen during its assembly. Yes, that's right, from oxygen. You see, photosynthesis first evolved in bacteria about 3 billion years ago, a time when the Earth's atmosphere had very little oxygen. Of course, as photosynthetic bacteria became more and more populous on ancient Earth, the atmosphere changed, eventually creating the oxygen-rich air that we breathe today.-"Oxygen is a very reactive molecule that can disrupt the iron-and-sulfur-containing clusters of proteins that are crucial to photosynthesis. Like CGL71, these clusters are critical for the first stage of photosynthesis, where they move electrons in order to create the energy molecules. Just as oxygen can rust iron that makes up a horseshoe or frying pan, it can damage the iron-and-sulfur proteins of the photosynthetic apparatus.-"So as oxygen accumulated in the Earth's atmosphere, the photosynthetic mechanism needed protection from its own byproduct, and CGL71 is one component that evolved to keep the photosynthetic apparatus stable under these new conditions."-Comment; Any aspect of life's chemistries is complex. Photosynthesis also has ben shown to have quantum mechanics as part of the reaction. (Friday, June 21, 2013, 15:06)

Biological complexity: smell nerve plasticity

by David Turell @, Thursday, March 03, 2016, 14:35 (2948 days ago) @ David Turell

We are born knowing how to interpret smells and odors. This must be learned and develops into adulthood. The exact mechanism of how the neurons In the olfactory bulb learn to do this is not exactly known, but specific neurons develop and axons attach, resulting in smell discrimination that can pick up differences of two atoms in molecules!:-http://www.evolutionnews.org/2016/03/more_news_on_th102651.html-"Last time we focused on the olfactory epithelium, the tissue that receives the odor molecules. We saw how it is organized into a hierarchical pattern that provides the best possible reception for different kinds of odorants. Each nostril's epithelium contains half a million olfactory sensory neurons (OSNs), long cells with cilia at one end and an axon at the other end. The cilia are where the odor molecules make contact with olfactory receptors (ORs). When a molecule "fits" just right, the receptor responds, triggering a cascade of activity. -***-"A team from Italy, publishing in Scientific Reports, found evidence for discrimination between molecules with identical shapes but different vibrations. Four pairs of odorant molecules were carefully designed to be identical except that some hydrogen atoms were replaced with deuterium (heavy hydrogen, containing an extra neutron). The slight mass difference in these "isotopomers" ("same topology") alters the vibration frequency of the molecule. These same-shaped odorants were wafted into the noses of honeybees while the scientists monitored their brains in real time.-"Sure enough, the bees appeared able to discriminate them, showing very different responses to the same-shaped pairs.-***-"The debate [as to how it works] will continue, undoubtedly, but more to our interest, it illustrates the complexity of the olfactory sense and its extreme precision that has baffled scientists for decades. Imagine a honeybee, fruit fly, or salmon being able to discriminate twin molecules that differ only by one or two atomic mass units. Design doesn't get better than that.-***-"Meanwhile, a recent paper in Nature Communications takes us down the other end of the olfactory neuron to the tip of the axon. As shown in the Illustra animation, the nerve endings of a million OSNs converge on a remarkable organ, the olfactory bulb (OB), which is studded with connection points called glomeruli. In an amazing example of preprogrammed networking, these axons "know" during development somehow which glomerulus to attach to, depending on the type of odorant receptor they express (and there are hundreds of those). Axons for one receptor might grow toward a glomerulus on top of the bulb; axons for another to the backside. Between top-bottom, front-back, and left-right, the OB has three axes by which to discriminate connections coming from different classes of receptors. This is the first stage of sorting and classifying odorant types. -***-"We've discussed "plasticity" before as a challenge to Darwinism. Why would a blind evolutionary process create "plasticity potential" that can be "harnessed when needed" in case of an altered experience? Darwinian evolution has no foresight. Plasticity makes perfect sense, though, from a design-based perspective on biology. There's no better example than right there in a salmon's nose, where the olfactory system will be encountering numerous new environments over a period of years. The scientists' expectations of roles for synaptic plasticity were confirmed in their conclusions.-Comment: That last paragraph is the nub of the issue.

Biological complexity: mitochondria on circadian timers

by David Turell @, Saturday, March 19, 2016, 23:50 (2931 days ago) @ David Turell

Mitochondria have peaks of activity for sugar and four hours into the day and fats in the evening:-https://www.sciencedaily.com/releases/2016/03/160316113353.htm-"Dr. Gad Asher of the Weizmann Institute's Biomolecular Sciences Department, who led the study, explains that circadian clocks, which are found in living things from bacteria to flies and humans, control our rhythms of sleep, activity, eating and metabolism. "In a sense," he says, "it's like a daily calendar, telling the body what to expect, so it can prepare for the future and operate optimally."-***-"Among the essential proteins the researchers uncovered was a key enzyme that determines the rate of sugar use for energy production. This protein reaches its maximal amount four hours into daylight, suggesting that the mitochondria's capacity for burning sugar peaks around this time, as well. To check, the researchers provided mitochondria with sugar and found that at around hour four, respiration and glucose utilization were indeed at their highest. They also found that the protein responsible for the entry of fatty acids into the mitochondria only peaks at the eighteenth hour and, again, tests showed fat processing was optimal at the same time.-***-"In mice with a genetic mutation that interferes with their overall biological clocks, the amounts of these proteins did not change over the course of the day, and the decomposition activity of fats and sugars was steady throughout."-Comment: Circadian clocks are set by the 24 hour day where the person lives. An automatic activity. I wonder how Darwinian evolution developed this. Not by hunt and peck.

Biological complexity: wired bacteria

by David Turell @, Thursday, March 24, 2016, 22:32 (2927 days ago) @ David Turell

They produce tiny protein polypeptide wires that carry electrons at high speed:-https://www.sciencedaily.com/releases/2016/03/160324104809.htm-"The discovery, featured in the current issue of Scientific Reports, describes the high-speed protein fiber produced by uranium-reducing Geobacter bacteria. The fibers are hair-like protein filaments called "pili" that have the unique property of transporting charges at speeds of 1 billion electrons per second.-"'This microbial nanowire is made of but a single peptide subunit," said Gemma Reguera, lead author and MSU microbiologist. "Being made of protein, these organic nanowires are biodegradable and biocompatible.-***-"How the nanowires function in nature is comparable to breathing. Bacterial cells, like humans, have to breathe. The process of respiration involves moving electrons out of an organism. Geobacter bacteria use the protein nanowires to bind and breathe metal-containing minerals such as iron oxides and soluble toxic metals such as uranium. The toxins are mineralized on the nanowires' surface, preventing the metals from permeating the cell.-***-"They are like power lines at the nanoscale," Reguera said. "This also is the first study to show the ability of electrons to travel such long distances -- more than a 1,000 times what's been previously proven -- along proteins."-"The researchers also identified metal traps on the surface of the protein nanowires that bind uranium with great affinity and could potentially trap other metals."-Comment: These bacteria need the wires to breathe. Did the bacteria appear with the wires when they evolved? I would think so. Once again, completeness without tiny steps of adaptation. Not Darwin.

Biological complexity: fish filters for eating

by David Turell @, Friday, April 01, 2016, 00:33 (2919 days ago) @ David Turell

Some fish have a complex filtering system for eating tiny organisms, a better filtering system than we humans use for many applications: - http://www.nature.com/ncomms/2016/160329/ncomms11092/full/ncomms11092.html - "Suspension-feeding fishes such as goldfish and whale sharks retain prey without clogging their oral filters, whereas clogging is a major expense in industrial crossflow filtration of beer, dairy foods and biotechnology products. Fishes' abilities to retain particles that are smaller than the pore size of the gill-raker filter, including extraction of particles despite large holes in the filter, also remain unexplained. Here we show that unexplored combinations of engineering structures (backward-facing steps forming d-type ribs on the porous surface of a cone) cause fluid dynamic phenomena distinct from current biological and industrial filter operations. This vortical cross-step filtration model prevents clogging and explains the transport of tiny concentrated particles to the oesophagus using a hydrodynamic tongue. Mass transfer caused by vortices along d-type ribs in crossflow is applicable to filter-feeding duck beak lamellae and whale baleen plates, as well as the fluid mechanics of ventilation at fish gill filaments. - *** - "Our cross-step filtration model based on paddlefish and basking shark morphology takes advantage of vortical flow in porous slots to reduce clogging by concentrating particles along the slot margins. Furthermore, by varying model parameters, we show that modified configurations can generate vortices that suspend and transport concentrated particles. - *** - "As more than 30,000 fish species possess branchial arches that may form d-type ribs, potential vortex formation in the slots between branchial arches has substantial implications for the fluid dynamics of fish feeding and ventilation throughout ontogeny and evolution. Vortical cross-step filtration could be applicable to feeding in a diversity of fish species. In addition, many filtration structures involved in vertebrate suspension feeding are composed of d-type ribs in crossflow, including fish gill rakers, tadpole gill filters, bird beak lamellae and whale baleen plates, suggesting that principles of vortical cross-step filtration could have widespread application." - Comment: A very complex engineering article which basically says directed vortices of water flow keep the filters clean, a system better than current human inventions for filtering. How is a natural process of evolution able to invent such complex solutions better than thinking humans seem able to do? Possibly a better mind behind it all.

Biological complexity: kidney circadian clock

by David Turell @, Friday, April 08, 2016, 16:15 (2912 days ago) @ David Turell

the kidney, along with the liver, is the master controller of many chemical levels in the body:-https://www.sciencedaily.com/releases/2016/04/160407221703.htm-"Many of the body's processes follow a natural daily rhythm or circadian clock that is based on regular light-dark cycles as Earth rotates. Dmitri Firsov, PhD, Natsuko Tokonami, PhD (University of Lausanne, in Switzerland) and their colleagues have now demonstrated that the kidney possesses such an intrinsic circadian clock that regulates and coordinates a variety of the organ's functions. "Since urine formation and excretion by the kidney is one of the most easily detectable rhythmic processes (we are forming and excreting much more urine during the day), we hypothesized that at least a part of this rhythmicity is dependent on the circadian clock mechanism," said Dr. Tokonami.-"By blocking kidney cells' expression of a gene that is critically involved in the circadian clock system, the team found that the clock is responsible for the temporal adaptation of kidney function to the light and dark phases of the day that correspond to activity and rest. Such adaptations have an important effect on the levels of various amino acids, lipids, and other components of blood in the body. Furthermore, in individuals who take medications, the kidney's circadian clock controls the process of drug elimination from the body and therefore can influence the duration of a drug's action and the effectiveness of the therapy.-"'We've shown that the circadian clock in the kidney plays an important role in different metabolic and homeostatic processes at both the intra-renal and systemic levels and is involved in drug disposition," said Dr. Firsov."-Comment: All of the chemicals controlled by the kidney, both salts and protein compounds are held in tight ranges of concentrations. Water volume in the body is also tightly controlled. In the Cambrian the kidney appears with no precursor. How? Not committees of thinking cells. I prefer saltation.

Biological complexity: kidney circadian clock

by dhw, Saturday, April 09, 2016, 12:52 (2911 days ago) @ David Turell

DAVID: the kidney, along with the liver, is the master controller of many chemical levels in the body:-https://www.sciencedaily.com/releases/2016/04/160407221703.htm-David's comment: All of the chemicals controlled by the kidney, both salts and protein compounds are held in tight ranges of concentrations. Water volume in the body is also tightly controlled. In the Cambrian the kidney appears with no precursor. How? Not committees of thinking cells. I prefer saltation.-“Committees of thinking cells” are an explanation of saltation, not an alternative.

Biological complexity: kidney circadian clock

by David Turell @, Saturday, April 09, 2016, 16:33 (2911 days ago) @ dhw

David's comment: All of the chemicals controlled by the kidney, both salts and protein compounds are held in tight ranges of concentrations. Water volume in the body is also tightly controlled. In the Cambrian the kidney appears with no precursor. How? Not committees of thinking cells. I prefer saltation.
> 
> dhw: “Committees of thinking cells” are an explanation of saltation, not an alternative.-True.

Biological complexity: how plants wither old parts

by David Turell @, Thursday, April 14, 2016, 15:25 (2906 days ago) @ David Turell

It is a very complex molecular mechanism with a giant molecule at the center of the reactions:-https://www.sciencedaily.com/releases/2016/04/160414081845.htm-"During their life, plants constantly renew themselves. They sprout new leaves in the spring and shed them in the fall. No longer needed, damaged or dead organs such as blossoms and leaves are also cast off by a process known as abscission-***-"It was already known that the membrane receptor protein HAESA and a small peptide -a short chain of amino acids -- hormone called IDA are involved in the same signaling pathway and, together, control the shedding of floral organs. So far, however, the mechanism underlying their interaction was poorly understood," explaind Michael Hothorn, professor at the Department of Botany and Plant Biology of the Faculty of Science of UNIGE. By solving the crystal structure of HAESA (from the Greek 'to shed') in complex with IDA, Hothorn and his team found out that the receptor directly senses the peptide hormone. They observed that HAESA contains a small cleft into which IDA fits perfectly. However, it only binds halfway to the receptor. To fully initiate the abscission process, another player is needed: the helper protein SERK1. IDA then works like a double-sided Scotch tape that tethers the entire complex together. The binding of SERK1 to HAESA and IDA triggers the molecular switch that instructs the cell to shed the organ.-"'The fascinating thing about SERK1 is that it not only plays a role in the shedding mechanism of plant organs, but also acts together with other membrane receptors that regulate totally different aspects of plant development," says Julia Santiago, first author of the study. Indeed, SERK1 is a versatile helper protein shared between different signaling pathways. When bound to another protein receptor, it can also for example signal the plant to grow."-Comment: The process is partially understood. Look at the model. ISA is not a 'short' chain', just smaller than its two giant partners. These are giant specialized molecules. How did Darwin-style evolution find them from the available supply of possibilities? The lock and key model is a standard pattern in the biochemistry of life.

Biological complexity: how cells maintain phosphate levels

by David Turell @, Thursday, April 14, 2016, 21:41 (2906 days ago) @ David Turell

As usual it is a complex mechanism which is important because phosphate is a major ingredient in all the ATP mechanism, the energy source of the cell:-http://phys.org/news/2016-04-cellular-sensor-phosphate.html-"Researchers from the University of Geneva (UNIGE) and the University of Lausanne (UNIL), Switzerland, report that a region of specific proteins, the so-called SPX domain, signals the phosphate status to fungal, plant and human cells. This domain provides a binding surface for small molecules that regulate the uptake of the nutrient into the cell.-***-"Michael Hothorn, Professor at the Department of Botany and Plant Biology of the Faculty of Science of UNIGE, and his research group revealed the crystal structure of a novel protein domain called SPX, which is involved in many phosphate signaling pathways. They discovered that SPX provides a binding surface for small compounds called inositol pyrophosphate signaling molecules (InsP), which can interact with other proteins only when they are bound to the SPX domain. As SPX domains can be attached to different proteins, such as enzymes, transporters or signaling proteins, the biologists hypothesized that InsP regulate various cell processes involved in phosphate homeostasis, from yeast to human cells.-***-"'We found out that the concentration of InsP changes in response to phosphate availability. InsP levels are high in cells that have sufficient phosphate, and drop when phosphate becomes scarce," explains Ruta Gerasimaite from UNIL, one of the first co-authors of the study. "In phosphate-starved plants, specific transcription factors turn on the expression of phosphate transporter genes. Once the plant is satiated, SPX domains filled with InsP will bind and inactivate these transcription factors, and no more phosphate will be absorbed from the soil into the cell," says Rebekka Wild from UNIGE, another of the first co-authors.-***-"The role of InsP was initially elucidated in yeast cells: "We came across InsP while studying the mechanism of phosphate polymerization - its assembly into long chains - for the storage of this compound, and our data show that the SPX domain is a receptor for InsP," states Andreas Mayer, Professor at the Department of Biochemistry of UNIL. Once the SPX domain is filled, it activates the enzyme involved in phosphate storage.-Comment: this is a typical closed-loop feedback system to control levels. One wonders how such a complex system develops all of its parts at once. Consider the cells must have a steady level of phosphate as a fuel. It suggests the entire system appeared all at once.

Biological complexity: Molecule transporter to brain

by David Turell @, Friday, April 22, 2016, 20:17 (2898 days ago) @ David Turell

It structure has just been discovered. The blood/brain barrier is very strong and so it is difficult to administer drugs to the brain. Look at the diagram to see how complex the molecules of life have to be; - http://phys.org/news/2016-04-scientists-harness-nature-brain.html

Biological complexity: Feedback loop importance

by David Turell @, Saturday, April 23, 2016, 22:06 (2897 days ago) @ David Turell

Without feedback loops in cells function and even embryonic formation of organs would not take place. DNA makes proteins, but the controls for the uses of those proteins lie in feedback loops present in cells. This is where the 'intelligent' reaction of cells is managed. This is a long essay, which should be fully read, because it shows how DNA is just a starting pint for life to form itself and work at living:- https://aeon.co/essays/the-feedback-loop-is-a-better-symbol-of-life-than-the-helix?utm_... "DNA on its own is just a chemical polymer, after all, essential for life but not itself alive. Yet it holds out the promise that we can explain living processes purely in terms of the interactions between simple molecules.-***-" The concept of ‘the gene for feature x' is giving way to a much more complicated story. Think something like: ‘the gene for protein a, that interacts with proteins b, c and d to allow a cell to undertake process p, that allows that cell to co?ordinate with other cells to make body feature x'. The very length of the above phrase, and the weakness of the blueprint metaphor, emphasises a conceptual distance that is opening up between the molecular-scale, mechanical function of genes and the interesting large-scale features of bodies.-***-"When cells first meet, in normal development or in a culture dish, neither can ‘know' in advance precisely where contact will first be made. The internal cytoskeletons of the cells cannot, therefore, be built to an advanced plan; they must develop adaptively to suit the precise conditions at the time.-***-"Thus the cytoskeleton's anatomy organises itself according to its environment and adapts continuously to changing mechanical loads.-This is just a very small-scale example of adaptive self-organisation. But the same principles work at larger scales, too. Organs consist of vast numbers of cells of different types, intricately assembled to perform whatever the organ's function might be. -***-"In some cases, we are starting to understand how this self-organisation happens, and how it relies on cell-to-cell communication. The growth of blood capillaries provides a good illustration. Tissues need blood capillaries to bring them oxygen and nutrients and to take away waste products, but a cell that is too far from the nearest blood capillary will find itself short of oxygen. At this point, a protein called HIF1A, which is normally destroyed by an oxygen-dependent process almost as soon as it is made, starts to accumulate. HIF1A puts a temporary brake on further cell proliferation and also causes the cell to secrete a protein called VEGF, which spreads out through the surrounding tissue. The cells that make blood capillary walls are sensitive to VEGF: if they detect it, they begin to proliferate and extend new capillary branches towards its source, and so the tissue cells that were short of oxygen will receive a supply from the new blood vessels. When capillary growth is adequate, there will be enough oxygen to make HIF1A unstable again, so the brake on tissue proliferation is released, VEGF production will cease and so will capillary growth. In a growing organ, this sort of thing happens again and again to make sure that growth doesn't outstrip blood supply. (Comment: perfect feedback loop)-***-"In the case of the blood capillaries, the extent to which present growth has been adequate to bring enough oxygen into the tissues is fed back, via VEGF, to control whether the capillaries continue to grow or remain as they are. -***-"Genes are therefore essential to self-organisation at all the scales of life - just not in a deterministic way. Rather, the genes are needed to make the machines that mediate feedback-driven self-organisation: the self-organisation is a high-level property that emerges from the underlying network, not a feature of any of the individual components.-***-"The DNA helix is important, of course...Unlike the helix, loops also operate at scales far above the molecular, covering a range of sizes from bacterial colonies to the vast ecosystems of the rainforest - perhaps to the ecosystem of the entire Earth."-Comment: Why Shapiro is wrong.

Biological complexity: Feedback loop importance

by dhw, Sunday, April 24, 2016, 13:13 (2896 days ago) @ David Turell

DAVID: Without feedback loops in cells function and even embryonic formation of organs would not take place. DNA makes proteins, but the controls for the uses of those proteins lie in feedback loops present in cells. This is where the 'intelligent' reaction of cells is managed. This is a long essay, which should be fully read, because it shows how DNA is just a starting pint for life to form itself and work at living:-https://aeon.co/essays/the-feedback-loop-is-a-better-symbol-of-life-than-the-helix?utm_...-I read the essay and made my own list of quotes, which I then found was more or less the same as yours. There is no need to repeat them. The gist of the whole article (correct me if necessary) is that cell communities throughout Nature organize themselves to cope with the demands of the environment. The feedback loop simply tells us how they interact. Strikingly, the essay only talks about adaptation, and never about innovation, which is the great mystery underlying evolution, but in both processes there obviously has to be a physical mechanism whereby cells can make changes to themselves. Over and over again, we see the expression “self-organize” which takes place through communication between the cells. Advance planning is not possible, because organisms cannot predict environmental change. And that is as far as the essay can take us. It does not tell us that “Shapiro is wrong”, or that your theory concerning God's “guidance” is wrong. It only tells us that cell communities “self-organize” (without advance planning) to enable themselves to function, and makes no attempt to explain what directs the mechanisms that do the organizing.

Biological complexity: Feedback loop importance

by David Turell @, Sunday, April 24, 2016, 15:29 (2896 days ago) @ dhw

https://aeon.co/essays/the-feedback-loop-is-a-better-symbol-of-life-than-the-helix?utm_... 
> dhw: read the essay and made my own list of quotes, which I then found was more or less the same as yours. There is no need to repeat them. The gist of the whole article (correct me if necessary) is that cell communities throughout Nature organize themselves to cope with the demands of the environment. The feedback loop simply tells us how they interact. Strikingly, the essay only talks about adaptation, and never about innovation, which is the great mystery underlying evolution, but in both processes there obviously has to be a physical mechanism whereby cells can make changes to themselves. Over and over again, we see the expression “self-organize” which takes place through communication between the cells. Advance planning is not possible, because organisms cannot predict environmental change. And that is as far as the essay can take us. It does not tell us that “Shapiro is wrong”, or that your theory concerning God's “guidance” is wrong. It only tells us that cell communities “self-organize” (without advance planning) to enable themselves to function, and makes no attempt to explain what directs the mechanisms that do the organizing.-I appreciate your reading it.The article is not meant to supply what you seem to hope for. It simply shows how complex the art/act of living happens to be. How well-organized cells are for cooperation in their functions and HOW automatic it all is. Those feedback loops are simply series of organic molecular reactions which lead to a chemical conclusion that the level of this or that is correct, or to produce this or that product. As an example look at this diagram of the Krebs cycle which produced energy everywhere in aerobic organisms:-https://en.wikipedia.org/wiki/Citric_acid_cycle-Click on the diagram to enlarge and see the complexity. -This article illustrates the required automaticity of cell function for life to persist, while the cells are constantly replacing parts of the cells. 'Beehive of constant activity' falls short as a description of the comparison. Shapiro's bacteria are no different. I'm looking backward from the multicellular result of evolution.

Biological complexity: Feedback loop importance

by dhw, Monday, April 25, 2016, 12:25 (2895 days ago) @ David Turell

dhw: I read the essay and made my own list of quotes, which I then found was more or less the same as yours. There is no need to repeat them. The gist of the whole article (correct me if necessary) is that cell communities throughout Nature organize themselves to cope with the demands of the environment. The feedback loop simply tells us how they interact. Strikingly, the essay only talks about adaptation, and never about innovation, which is the great mystery underlying evolution, but in both processes there obviously has to be a physical mechanism whereby cells can make changes to themselves. Over and over again, we see the expression “self-organize” which takes place through communication between the cells. Advance planning is not possible, because organisms cannot predict environmental change. And that is as far as the essay can take us. It does not tell us that “Shapiro is wrong”, or that your theory concerning God's “guidance” is wrong. It only tells us that cell communities “self-organize” (without advance planning) to enable themselves to function, and makes no attempt to explain what directs the mechanisms that do the organizing. - DAVID: I appreciate your reading it. The article is not meant to supply what you seem to hope for. It simply shows how complex the art/act of living happens to be. - First of all, I cannot repeat too often how much I appreciate the trouble you take in presenting us with all this material. However, your conclusion was that the essay showed Shapiro was wrong - i.e. that cells are not intelligent. And so I'm sorry to say the article “is not meant to supply what you seem to hope for”. It has nothing to do with intelligence versus automaticity and “makes no attempt to explain what directs the mechanisms that do the organizing”. Let me assure you that I have always been acutely aware of the complexity of living organisms, and this complexity has always been a major factor in my own arguments against atheism. I have also accepted that much of the activity of cells HAS to be automatic for organisms to work (as exemplified by our bodily functions, or by bacterial acquisition of information). My hypothesis is that it ceases to be automatic when problems arise (the need for adaptation), or when innovations take place (exploitation of changed conditions). That is when we have processes of problem-solving and decision-making that demand intelligence. You continue to have faith that these have all been preprogrammed or personally “guided” by your God and that your God (theistic version of my hypothesis) did not give cells/cell communities the autonomy to make their own decisions. The rest of your post once again shifts attention from the problem of what directs cellular behaviour to the behaviour itself.

Biological complexity: Feedback loop importance

by David Turell @, Monday, April 25, 2016, 15:14 (2895 days ago) @ dhw


> dhw: First of all, I cannot repeat too often how much I appreciate the trouble you take in presenting us with all this material...... My hypothesis is that it ceases to be automatic when problems arise (the need for adaptation), or when innovations take place (exploitation of changed conditions). That is when we have processes of problem-solving and decision-making that demand intelligence. You continue to have faith that these have all been preprogrammed or personally “guided” by your God and that your God (theistic version of my hypothesis) did not give cells/cell communities the autonomy to make their own decisions. The rest of your post once again shifts attention from the problem of what directs cellular behaviour to the behaviour itself.-
Thank you, and we are back at it. The cells do have the 'autonomy to make their own decisions'. It is a series of built-in chemical reactions using feed-back loops that work automatically. We agree to that point. Where we disagree is you want the cell to self-apply some decision making point which implies a sense of mental decision making that sets their response in motion. I think it is all automatically triggered chemical responses. Shapiro is exactly correct. The cells make decisions. His more important point is cells, with seeming initiative, make epigenetic changes, but we know that does not seem to lead to speciation.

Biological complexity: teaching bacteria new tricks

by David Turell @, Monday, April 25, 2016, 18:31 (2895 days ago) @ David Turell

In the discussion of how bacteria respond, the fact that the bacterial genome can be manipulated to make bacteria have new behaviors plays a strong role in my contention that it is all automatic:-https://www.sciencedaily.com/releases/2016/04/160425095345.htm-"Johanna Roßmanith and her doctoral supervisor Prof Dr Franz Narberhaus from the Chair of Microbial Biology carried out a successful study where they controlled the type of proteins a bacterium would manufacture and its behaviour. This is how they have made a bacterium swim that hadn't previously had the ability to move. The researchers made that possible by combining various modules from the bacterium's RNA in a new way.-"In the study, which was published in the journal Nucleic Acids Research, the biologists utilised so-called riboswitches, also called RNA switches, and RNA thermometers. Riboswitches detect if there is a surplus of a certain metabolic product in the cell, and they regulate the biosynthesis or intake of that substance, if necessary.-"RNA thermometers control a number of temperature-sensitive processes. For example, a bacterium that finds its ways from contaminated water into the human body notices the difference in temperature. As a result, it produces certain factors that lead to an infection of the host.-***-"Following an alternative strategy, she integrated the thermometer structure in the riboswitch. Both methods resulted in the creation of novel functional elements that respond to a combination of one chemical and one physical signal, in this instance temperature.-***-"In order to make the above-mentioned bacteria swim, the researchers placed a gene responsible for bacterial locomotion under the control of the newly combined RNA regulators. The correct signal combination was crucial for the experiment to succeed. The riboswitch required, for example, a certain chemical substance in combination with a certain temperature.-"'RNA switches are not quite as modular as bricks in a model kit," admits Franz Narberhaus. "Ms Roßmanith had to test and optimise many combinations before she achieved functional blocks. Nevertheless, our results show that RNA modules have great potential in biotechnology for controlling processes in bacterial cells in a targeted manner."-Comment: A human acting like a god. Demonstrates it can all be automatic! Thank God for roboswitches (pun intended).

Biological complexity: enzyme complexity

by David Turell @, Tuesday, April 26, 2016, 19:25 (2894 days ago) @ David Turell

Enzymes Are huge molecules which have specialized areas that lock in reactive areas. Without this lock and key arrangement necessary reactions could take hundreds of years to happen instead of the instantaneous time table of life:-https://www.sciencedaily.com/releases/2016/04/160425112511.htm-"The team, working under Professor John Schwabe from the University of Leicester's Department of Molecular and Cell Biology, focuses on understanding the structure and function of large protein complexes in the body that are involved in the regulation of gene expression called co-repressor complexes.-"These complexes contain histone deacetylase (HDAC) enzymes, which alter how DNA is packaged within cells.-***-"Professor Schwabe explained: "Previously our team had discovered that the activity of the enzymes in co-repressor complexes is regulated by a small molecule called inositol phosphate.-"'We wished to further understand the mechanism of enzyme activation by inositol phosphates and how substrate is recognised.-"'This work provides fundamental basic insights into the HDAC enzymes and may provide the basis for the development of drugs that are more specific and efficient. Ultimately, a greater understanding of how these enzymes work and how substrate interacts may lead to the development of better drugs."-"Working with collaborators from the University of Leicester's Department of Chemistry (Dr Andrew Jamieson's research group) and researchers at the University of Bath (Professor Barry Potter's research group), the team synthesised a number of unique tool compounds which allowed them to investigate how inositol phosphates and substrate bind to co-repressor complexes.-" They were then able to work out the specific features of inositol phosphates and how they bind to activate the HDAC enzyme. They then solved the crystal structure of a novel peptide inhibitor, which is based upon the enzymes' substrate, in complex with HDAC1: co-repressor. This not only gave insights into how substrate interacts with the enzyme but could also help to improve drug treatments for a variety of health issues. Taken together these results have shed light on the mechanism of activation by inositol phosphates."-Comment: Be sure to use the link and look at the diagram and the specialized binding pocket. How did chance evolution ever find this monster molecule?

Biological complexity: gene product controls

by David Turell @, Tuesday, April 26, 2016, 19:34 (2894 days ago) @ David Turell

It is important to control the amount of product a gene manufactures in cells. The mechanism has been found and is highly complex:-https://www.sciencedaily.com/releases/2016/04/160426110657.htm-"A team of researchers led by the University of Leicester has shed new light on how the regulation machinery that controls gene expression works by characterising a complex known as the NuRD complex.-
"The study, led by John Schwabe, Professor of Structural Biology and Head of Department of Molecular and Cell Biology at the University of Leicester and published in the journal eLIFE, focuses on three protein components which make up the core of the NuRD complex: MTA1, RBBP4 and HDAC1.-"The function of the NuRD complex is to control the amount of protein made by the cell -- a process called gene regulation. Unregulated protein expression disrupts the equilibrium within a healthy cell and can lead to abnormal cell division and tumour growth.-***-"By examining the relationship between the three proteins, the team was able to show unprecedented detail about the 3D structure of the NuRD complex as well as to characterise the molecular nature of the 'extensive interface' between MTA1 and RBBP4.-***-"The findings paint a clearer picture about how the complex is assembled and the way in which it interacts with the proteins that package the human genome in the cell. A deeper knowledge of how these complexes are recruited to genes will help to design treatments to combat aberrant gene activity."-Comment: Again, look at the link to see the complexity of these proteins. This is another example of a feed back loop

Biological complexity: enzyme complexity

by David Turell @, Tuesday, December 17, 2019, 19:05 (1564 days ago) @ David Turell

More on how enzymes work:

https://phys.org/news/2019-12-reveal-enzyme-motions-catalyze-reactions.html

"In a time-resolved X-ray experiment, researchers uncovered, at atomic resolution and in real time, the previously unknown way that a microbial enzyme breaks down organic compounds.

"The team, led by Mark Wilson at the University of Nebraska Lincoln (UNL) and Henry van den Bedem at the Department of Energy's SLAC National Accelerator Laboratory (now at Atomwise Inc.), published their findings last week in the Proceedings of the National Academy of Sciences. What they learned about this enzyme, whose structure is similar to one that is implicated in neurodegenerative diseases such as Parkinson's, could lead to a better understanding of how antibiotics are broken down by microbes and to the development of more effective drugs.

"Previously, the researchers used SLAC's Stanford Synchrotron Radiation Lightsource (SSRL) to obtain the structure of the enzyme at very low temperatures using X-ray crystallography. In this study, Medhanjali Dasgupta, a UNL graduate student who was the study's first author, used the Linac Coherent Light Source (LCLS), SLAC's X-ray laser, to watch the enzyme and its substrate within the crystal move and change as it went through a full catalytic cycle at room temperature.

"The scientists used special software, designed by van den Bedem, that is highly sensitive to identifying protein movement from X-ray crystallography data to interpret the results, revealing never-before-seen motions that play a key role in catalyzing complex reactions, such as breaking down antibiotics. Next, the researchers hope to use LCLS to obtain room temperature structures of other enzymes to get a better look at how the motions occurring within them help move along reactions."

Comment: See the diagrams to learn how the enzyme changes chemical bonds to achieve the new reaction. Without enzymes there would be no biochemical activity and life would not exist. Enzyme molecular complexity requires design. From the journal itself:

"Significance
Protein structures fluctuate owing to thermal motion and in response to functional changes such as ligand binding. As a consequence, it is challenging to determine which protein motions are functionally most important at equilibrium. Enzymes that are transiently covalently modified during catalysis offer a way to identify functional motions, as the modification can trigger catalytically important conformational changes. The covalent modification of the active-site cysteine in isocyanide hydratase weakens a critical hydrogen bond required for reactivity. Hydrogen bond disruption triggers a cascade of conformational changes whose modulation by mutation is detrimental to enzyme turnover. Most enzymes that form catalytic intermediates will experience similar transient changes in active-site electrostatics, suggesting that modification-gated conformational dynamics is common in enzymes."

Biological complexity: How ATP supplies needed energy

by David Turell @, Thursday, December 19, 2019, 00:05 (1562 days ago) @ David Turell

A carefully described process with great graphics:

https://evolutionnews.org/2019/12/the-ultimate-recycler/

"We already know from a previous post (“The Mystery of Energy Metabolism”) that the cell has an energy budget that is out of balance based solely on biosynthesis and use of ATP. It is in a predicament. It has an extreme shortfall in ATP in its balance sheet, needing six ATP just to make one. ATP is a high energy molecule. All that energy has to be loaded into the molecule during its synthesis by using up other ATP molecules.

***

"The cell needs to have ATP before it can make ATP, and it has to have more ATP than it can make. Can the cell rescue its metabolic state by bringing in ATP from outside? Sure, indirectly — if it eats biological material other cells have made, it can get ATP by breaking down glucose into pyruvate, and then pyruvate into citrate, and then ultimately, the energy is harvested and a net gain in ATP is produced. The glucose-to-pyruvate digestion happens in the cytoplasm, but the citrate-to-final-energy harvest all occurs in marvelous, mysterious voyagers in our cells called mitochondria.

***

"Mitochondria are the microscopic power plants of the cell whose purpose is to take citrate and convert it to ATP, the cell’s energy currency. Resembling miniature blimps with corrugated double membranes, they carry out an interlocking series of chemical reactions that squeeze out every last possible ATP from the breakdown of glucose. It’s a highly efficient, environmentally friendly process. Everything is recycled — one part of the process is called the citric acid cycle because it regenerates itself with each new round. In fact, everything cycles.

"Most cells have many mitochondria, whose characteristic wrinkled stroma serve to increase the interior membrane surface area. Think of a bag with a much bigger bag neatly tucked in folds inside. Embedded in that folded inner membrane are all machinery of energy production that makes life possible. And that machinery is considerable. An ensemble of multiple proteins comes together to make 5 protein complexes, shown in the picture below. In complexes 1-4, energy in the form of electrons is received by them and cycled through, using some of that energy to pump protons across the membrane. As citrate is gradually broken down, compounds like NADH or succinate are produced, and shunted off to the electron transport chain, and they also contribute to the process.

"Even the last high-energy electrons from the breakdown process are not wasted: a chain of proteins in the inner membrane passes these electrons like little hot potatoes from one to another, using the energy of each transfer to pump hydrogen ions across the membrane, so that a molecular machine called ATP synthase can take advantage of the hydrogen gradient to create even more ATP.

***

"The fifth complex is ATP synthase. This is where the miracle happens that makes life possible. ATP synthase harvests the energy of the proton gradient to recycle ADP to ATP. Like a turbine in a hydroelectric plant, ATP synthase lets the hydrogen ions flow back across the membrane through itself, rotating as the ions pass through. As it rotates it adds a phosphate to ADP at each crank, thus restoring ATP to use.

"The engine ATP synthase is 98 percent efficient at what it does! Human machines can’t approach that. But this is what permits life. We burn through our body weight in ATP every day. Just breathing burns ATP.

"Right now, within your bodies this little engine is cranking away. Without this machine, oxygen-dependent life could not exist. Strong statement, but I stand by it."

Comment: The diagrams will help follow the text. As usual one sees the use of circular mechanisms where one very complex molecule feeds another complex molecule around the loop just like feedback loops work. The design work is magnificent and achieves efficiencies that humans can never achieve, meaning our mental power is a fraction of God's. In understanding the complexity, please appreciate not just the way loops work, but that each molecule is exquisitely complex to begin with and designed to fit into its cog-like position. Chance formation is inconceivable.

Biological complexity: teaching bacteria new tricks

by dhw, Tuesday, April 26, 2016, 20:56 (2894 days ago) @ David Turell

DAVID: In the discussion of how bacteria respond, the fact that the bacterial genome can be manipulated to make bacteria have new behaviors plays a strong role in my contention that it is all automatic:-https://www.sciencedaily.com/releases/2016/04/160425095345.htm-QUOTE: "Johanna Roßmanith and her doctoral supervisor Prof Dr Franz Narberhaus from the Chair of Microbial Biology carried out a successful study where they controlled the type of proteins a bacterium would manufacture and its behaviour. This is how they have made a bacterium swim that hadn't previously had the ability to move. The researchers made that possible by combining various modules from the bacterium's RNA in a new way.”-It has been observed that narcotics, medication, alcohol, diseases and other interventions can have such an influence on the human body that they change a person's behaviour. That plays a strong role in some people's contention that human behaviour is all automatic. Other people contend that without such interference, human behaviour is controlled by autonomous mental processes. For the latter group of thinkers, the fact that interference can change the behaviour of non-human organisms can therefore hardly be taken as evidence that those organisms are incapable of autonomous mental processes, even if those are of a different and less complex nature.

Biological complexity: teaching bacteria new tricks

by David Turell @, Wednesday, April 27, 2016, 01:01 (2893 days ago) @ dhw


> dhw: It has been observed that narcotics, medication, alcohol, diseases and other interventions can have such an influence on the human body that they change a person's behaviour. That plays a strong role in some people's contention that human behaviour is all automatic. Other people contend that without such interference, human behaviour is controlled by autonomous mental processes. For the latter group of thinkers, the fact that interference can change the behaviour of non-human organisms can therefore hardly be taken as evidence that those organisms are incapable of autonomous mental processes, even if those are of a different and less complex nature.-Apples and oranges! You are comparing chemical effects on functioning organisms, not the question of when the controlling genome is manipulated directly to force change in function. Swimming is an athletic activity, not a 'behavior' in the sense you are using it.

Biological complexity: teaching bacteria new tricks

by dhw, Wednesday, April 27, 2016, 12:45 (2893 days ago) @ David Turell

dhw: It has been observed that narcotics, medication, alcohol, diseases and other interventions can have such an influence on the human body that they change a person's behaviour. That plays a strong role in some people's contention that human behaviour is all automatic. Other people contend that without such interference, human behaviour is controlled by autonomous mental processes. For the latter group of thinkers, the fact that interference can change the behaviour of non-human organisms can therefore hardly be taken as evidence that those organisms are incapable of autonomous mental processes, even if those are of a different and less complex nature.-DAVID: Apples and oranges! You are comparing chemical effects on functioning organisms, not the question of when the controlling genome is manipulated directly to force change in function. Swimming is an athletic activity, not a 'behavior' in the sense you are using it.-It was you and the researchers who introduced the term “behaviour”:-DAVID: In the discussion of how bacteria respond, the fact that the bacterial genome can be manipulated to make bacteria have new behaviors plays a strong role in my contention that it is all automatic…(my bold)-QUOTE: "Johanna Roßmanith and her doctoral supervisor Prof Dr Franz Narberhaus from the Chair of Microbial Biology carried out a successful study where they controlled the type of proteins a bacterium would manufacture and its behaviour. This is how they have made a bacterium swim that hadn't previously had the ability to move. The researchers made that possible by combining various modules from the bacterium's RNA in a new way.” (my bold)-Regardless of the meaning of “behaviour”, perhaps you could briefly explain how manipulating the genome to enable a bacterium to swim (an athletic activity) strongly supports your contention that ALL bacterial behaviour is automatic (i.e. bacteria are incapable of any autonomous mental activity, such as decision-making or problem-solving).

Biological complexity: teaching bacteria new tricks

by David Turell @, Wednesday, April 27, 2016, 15:00 (2893 days ago) @ dhw


> dhw: Regardless of the meaning of “behaviour”, perhaps you could briefly explain how manipulating the genome to enable a bacterium to swim (an athletic activity) strongly supports your contention that ALL bacterial behaviour is automatic (i.e. bacteria are incapable of any autonomous mental activity, such as decision-making or problem-solving). - Changing a sessile bacteria to a motile bacteria for that bacteria is a monster change in function, which automatically occurs when the genome is manipulated. This is direct proof that the genome can automatically dictate a movement response. It is no stretch to understand that a bacteria senses a chemical which implies a food source and automatically moves toward it, all mediated by automated chemical reactions. Humans smell a delicious aroma and automatically feel hungry without intervening thought. As you like to point out there are similarities from bottom to top of evolution.

Biological complexity: teaching bacteria new tricks

by dhw, Thursday, April 28, 2016, 11:39 (2892 days ago) @ David Turell

dhw: Regardless of the meaning of “behaviour”, perhaps you could briefly explain how manipulating the genome to enable a bacterium to swim (an athletic activity) strongly supports your contention that ALL bacterial behaviour is automatic (i.e. bacteria are incapable of any autonomous mental activity, such as decision-making or problem-solving). - DAVID: Changing a sessile bacteria to a motile bacteria for that bacteria is a monster change in function, which automatically occurs when the genome is manipulated. This is direct proof that the genome can automatically dictate a movement response. It is no stretch to understand that a bacteria senses a chemical which implies a food source and automatically moves toward it, all mediated by automated chemical reactions. Humans smell a delicious aroma and automatically feel hungry without intervening thought. As you like to point out there are similarities from bottom to top of evolution. - Smelling an aroma and feeling hungry are automatic actions. If there is a barrier between me and my chocolate, however, I'll need to work out how to overcome it, and that is when we have “intervening thought”. But according to you, bacteria do not work out how to overcome barriers. God "guides" them over each and every one.
 
The beginning of your post describes an innovation: scientists deliberately tinkered with the genome to produce a new function (the bacterium was able to swim). This was a deliberate intervention, and of course if you deliberately engineer a change from a known function A to a known function B you will automatically get function B. However, this takes us back to the whole evolutionary process. If a sessile bacterium is suddenly able to swim by way of a change in its genome, and if there is no scientist around to manipulate the genome, how might such an innovation take place? Your answer: God is the scientist, preprogramming or personally intervening in order to manipulate the genome. Darwinian answer: chance mutation. My hypothesis: conditions changed, and some intelligent bacteria - with their intelligence possibly God-given - worked out the internal engineering for themselves (perhaps horizontal gene transfer plays a role here?). These hypotheses must apply to all innovations throughout the history of evolution. They produce the same results, though there is no evidence for any of them, and nobody knows how any of them would actually work. - Finally, your response still doesn't explain how the researcher's manipulation of the genome, enabling bacteria to swim, supports your contention that bacteria can't think for themselves (take their own decisions, work out their own solutions to problems). If your God intervened and changed my legs into flippers, would that mean I couldn't think for myself? I see no connection between the two processes.

Biological complexity: teaching bacteria new tricks

by David Turell @, Friday, April 29, 2016, 01:47 (2891 days ago) @ dhw


> dhw: My hypothesis: conditions changed, and some intelligent bacteria - with their intelligence possibly God-given - worked out the internal engineering for themselves (perhaps horizontal gene transfer plays a role here?). These hypotheses must apply to all innovations throughout the history of evolution. They produce the same results, though there is no evidence for any of them, and nobody knows how any of them would actually work. -I just don't see how your hypothesis would work, since proper results require planning, unless God given guidelines are present. 
> 
> dhw: Finally, your response still doesn't explain how the researcher's manipulation of the genome, enabling bacteria to swim, supports your contention that bacteria can't think for themselves (take their own decisions, work out their own solutions to problems). If your God intervened and changed my legs into flippers, would that mean I couldn't think for myself? I see no connection between the two processes.-For me it is simple. Put in proper genes and automatically swimming begins, without lessons or thought!.

Biological complexity: teaching bacteria new tricks

by dhw, Friday, April 29, 2016, 16:20 (2891 days ago) @ David Turell

dhw: My hypothesis: conditions changed, and some intelligent bacteria - with their intelligence possibly God-given - worked out the internal engineering for themselves (perhaps horizontal gene transfer plays a role here?). These hypotheses must apply to all innovations throughout the history of evolution. They produce the same results, though there is no evidence for any of them, and nobody knows how any of them would actually work. -DAVID: I just don't see how your hypothesis would work, since proper results require planning, unless God given guidelines are present.-Since nobody knows how any of the hypotheses would work, or how innovations could be “planned” (especially if changing environmental conditions were not “planned”), it is hardly surprising that you don't see how mine would work. Our only clue is that some organisms survive by adapting swiftly to seemingly unpredictable changes in conditions, so maybe some can also innovate. I myself have difficulty trying to work out how your God could have preprogrammed every single innovation, lifestyle and natural wonder in evolutionary history to be passed down by the first few cells, or how he could have personally dabbled with the genome of every individual organism that ever produced an innovation, not to mention giving personal tuition to every organism that produced a new lifestyle or natural wonder.
 
dhw: Finally, your response still doesn't explain how the researcher's manipulation of the genome, enabling bacteria to swim, supports your contention that bacteria can't think for themselves (take their own decisions, work out their own solutions to problems). If your God intervened and changed my legs into flippers, would that mean I couldn't think for myself? I see no connection between the two processes.-DAVID: For me it is simple. Put in proper genes and automatically swimming begins, without lessons or thought!-But putting in the proper genes for swimming does not prove that the bacterium is incapable of thought!

Biological complexity; bacteria sense touch

by David Turell @, Monday, August 14, 2017, 21:24 (2419 days ago) @ dhw

Touching bacteria releases calcium ions much as our cells use ion transport for sensing touch:

https://phys.org/news/2017-08-bacteria.html

"For humans, our sense of touch is relayed to the brain via small electrical pulses. Now, University of Colorado Boulder scientists have found that individual bacteria, too, can feel their external environment in a similar way.

"In a new study, CU Boulder researchers have demonstrated that E. coli bacteria cells get excited when poked, sending out voltage induced calcium ion signals—the same way a vertebrate's sensory nervous system works. The results are believed to be the first documented observation of electrical excitability in individual bacteria cells.

***

"What we think could be happening is that they're using these electrical signals to modify their lifestyle," said Joel Kralj, the senior author of the study and an assistant professor in MCDB and the BioFrontiers Institute.

"To study how bacteria feel their surroundings, the team inserted special genes into E. coli bacteria that glow when calcium ions or electricity pulse through them. The cells were placed in a sticky substrate under a microscope. Left alone, the cells remained dim. But when the scientists pushed a pad against them, the bacteria lit up. The sparks of light indicated that proteins, ions and electricity were moving around in the bacteria.

"The results indicate that bacteria and other creatures share a common tool for sensing their environment—an electrical pathway with the same functionality as human sensory neurons. From an evolutionary perspective, this signaling trait could be billions of years old and used by some of the oldest organisms on Earth."

Comment: In my view the starting point for future evolution was present in first life. As God started life he placed early starting points for future developments such as the appearance of neurons in multicellular organisms. I think there was pre-planning.

Biological complexity; bacteria sense touch

by dhw, Tuesday, August 15, 2017, 11:49 (2418 days ago) @ David Turell

DAVID: Touching bacteria releases calcium ions much as our cells use ion transport for sensing touch:
https://phys.org/news/2017-08-bacteria.html

QUOTE: "For humans, our sense of touch is relayed to the brain via small electrical pulses. Now, University of Colorado Boulder scientists have found that individual bacteria, too, can feel their external environment in a similar way.
"In a new study, CU Boulder researchers have demonstrated that E. coli bacteria cells get excited when poked, sending out voltage induced calcium ion signals—the same way a vertebrate's sensory nervous system works
.”

A very important breakthrough for those of us who believe it is possible for brainless organisms to be intelligent, although it is quite surprising to find a dualist who believes that intelligence can survive the death of the brain and yet refuses to believe that intelligence can exist in organisms that have no brain. All the signs are that bacteria are sentient, cognitive, decision-making, intelligent beings, and if they have some kind of equivalent to the nervous system, it may well be that they have some kind of equivalent to the brain itself.

Biological complexity; bacteria sense touch

by David Turell @, Tuesday, August 15, 2017, 14:35 (2418 days ago) @ dhw

DAVID: Touching bacteria releases calcium ions much as our cells use ion transport for sensing touch:
https://phys.org/news/2017-08-bacteria.html

QUOTE: "For humans, our sense of touch is relayed to the brain via small electrical pulses. Now, University of Colorado Boulder scientists have found that individual bacteria, too, can feel their external environment in a similar way.
"In a new study, CU Boulder researchers have demonstrated that E. coli bacteria cells get excited when poked, sending out voltage induced calcium ion signals—the same way a vertebrate's sensory nervous system works
.”

dhw: A very important breakthrough for those of us who believe it is possible for brainless organisms to be intelligent, although it is quite surprising to find a dualist who believes that intelligence can survive the death of the brain and yet refuses to believe that intelligence can exist in organisms that have no brain. All the signs are that bacteria are sentient, cognitive, decision-making, intelligent beings, and if they have some kind of equivalent to the nervous system, it may well be that they have some kind of equivalent to the brain itself.

All we see is an automatic calcium ion reaction, just as ions are automatically produced to send signals on our nerves. Intelligently designed automaticity in an early form of life.

Biological complexity; bacteria sense touch

by dhw, Wednesday, August 16, 2017, 08:51 (2417 days ago) @ David Turell

dhw: A very important breakthrough for those of us who believe it is possible for brainless organisms to be intelligent, although it is quite surprising to find a dualist who believes that intelligence can survive the death of the brain and yet refuses to believe that intelligence can exist in organisms that have no brain. All the signs are that bacteria are sentient, cognitive, decision-making, intelligent beings, and if they have some kind of equivalent to the nervous system, it may well be that they have some kind of equivalent to the brain itself.

DAVID: All we see is an automatic calcium ion reaction, just as ions are automatically produced to send signals on our nerves. Intelligently designed automaticity in an early form of life.

It is not possible to see intelligence. As a dualist you believe that intelligence is the immaterial power that gives instructions to the material body. We can only see the material body’s manifestations of intelligence - in humans and in all other organisms.

Biological complexity; bacteria sense touch

by David Turell @, Wednesday, August 16, 2017, 15:29 (2417 days ago) @ dhw

dhw: A very important breakthrough for those of us who believe it is possible for brainless organisms to be intelligent, although it is quite surprising to find a dualist who believes that intelligence can survive the death of the brain and yet refuses to believe that intelligence can exist in organisms that have no brain. All the signs are that bacteria are sentient, cognitive, decision-making, intelligent beings, and if they have some kind of equivalent to the nervous system, it may well be that they have some kind of equivalent to the brain itself.

DAVID: All we see is an automatic calcium ion reaction, just as ions are automatically produced to send signals on our nerves. Intelligently designed automaticity in an early form of life.

dhw: It is not possible to see intelligence. As a dualist you believe that intelligence is the immaterial power that gives instructions to the material body. We can only see the material body’s manifestations of intelligence - in humans and in all other organisms.

What we see are the manifestations of intelligent planning and instructions.

Biological complexity; bacteria sense touch

by dhw, Thursday, August 17, 2017, 13:25 (2416 days ago) @ David Turell

dhw: It is not possible to see intelligence. As a dualist you believe that intelligence is the immaterial power that gives instructions to the material body. We can only see the material body’s manifestations of intelligence - in humans and in all other organisms.

DAVID: What we see are the manifestations of intelligent planning and instructions.

Not altogether happy with "planning" but otherwise agreed. What we do not see is the source of the intelligent responses and instructions. You say it’s God. I say it may be the intelligence (possibly God-given) of the organisms themselves, including bacteria.

Biological complexity; bacteria sense touch

by David Turell @, Thursday, August 17, 2017, 14:55 (2416 days ago) @ dhw

dhw: It is not possible to see intelligence. As a dualist you believe that intelligence is the immaterial power that gives instructions to the material body. We can only see the material body’s manifestations of intelligence - in humans and in all other organisms.

DAVID: What we see are the manifestations of intelligent planning and instructions.

dhw: Not altogether happy with "planning" but otherwise agreed. What we do not see is the source of the intelligent responses and instructions. You say it’s God. I say it may be the intelligence (possibly God-given) of the organisms themselves, including bacteria.

We are at the same endpoint.

Biological complexity: Feedback loop importance

by dhw, Tuesday, April 26, 2016, 20:53 (2894 days ago) @ David Turell

DAVID: The cells do have the 'autonomy to make their own decisions'. It is a series of built-in chemical reactions using feed-back loops that work automatically. We agree to that point. Where we disagree is you want the cell to self-apply some decision making point which implies a sense of mental decision making that sets their response in motion. I think it is all automatically triggered chemical responses. Shapiro is exactly correct. The cells make decisions. His more important point is cells, with seeming initiative, make epigenetic changes, but we know that does not seem to lead to speciation.-Speciation, or innovation, is the phenomenon nobody can explain. We have a totally different concept of autonomy, so let's forget about speciation for the moment, and focus solely on the behaviour of cells and precisely what we mean by “autonomous decision-making”. Shapiro and others maintain that cells are intelligent, sentient, cooperative, decision-making beings, and not automatons obeying in-built instructions. If they are “exactly correct”, the decisions are not the result of automatically triggered chemical responses. The chemical “reactions and feedback loops” are the gathering of information and the physical implementations of the decisions, but NOT the decisions themselves, as you acknowledge to be the case with humans and other large organisms. Once again: my hypothesis (not stated as a belief or fact) is that, although most cellular behaviour is automatic, autonomous intelligence comes into play when there are problems to be solved (adaptation) or opportunities to be exploited (innovation). Autonomous does not mean automatic or preprogrammed.

Biological complexity: Feedback loop importance

by David Turell @, Wednesday, April 27, 2016, 00:57 (2893 days ago) @ dhw

dhw: Once again: my hypothesis (not stated as a belief or fact) is that, although most cellular behaviour is automatic, autonomous intelligence comes into play when there are problems to be solved (adaptation) or opportunities to be exploited (innovation). Autonomous does not mean automatic or preprogrammed. - I agree that the organisms can adapt through epigenetic mechanisms, and I still believe those adaptive abilities are programmed. We remain apart.

Biological complexity: neuron receptors

by David Turell @, Monday, May 02, 2016, 19:26 (2888 days ago) @ David Turell

Note the complexity of this neuron receptor just described:-http://phys.org/news/2016-05-views-nmda-receptor-action-aid.html-"NMDA receptors are embedded in the membrane of many nerve cells in the brain and are involved in the signaling between cells that is essential to basic brain functions, including learning and memory formation. Structurally, the NMDA receptor is made up of various protein segments, called domains, which together resemble a hot air balloon. The upper, balloon-like portion is comprised of the amino terminal domain (ATD); protruding from the outer surface of the cell is the ligand binding domain (LBD); and the lower, basket-like portion of the receptor, called the transmembrane domain (TMD), drops down inside the cell.-"Activation of the NMDA receptor requires binding of brain chemicals called neurotransmitters at specific sites on the LBD. This binding together with structural rearrangement of the ATD triggers the opening of the channel formed by the TMD. This molecular event causes charged atoms called ions flow into the cell. When this occurs in many channels at once, an electrical current is generated that rapidly propagates through the neuron and triggers the release of neurotransmitters. These chemical signals, in turn, bind to receptors on neighboring cells-***-"In addition to describing the NMDA receptor's balloon-like structure, Furukawa and the team of CSHL structural biologists have previously revealed many important features of NMDA receptors, including the distinctive ways in which a number of drug compounds attach to the receptor at its various binding sites. "The NMDA receptor architecture itself is quite complicated," says Furukawa, "but most recently we've been really fascinated by how each of its domains moves in a sophisticated but organized manner.'"-Comment: Be sure to look at the complex diagram. The brain is more than an electric machine. Various molecules are at work to modulated the connections and responses

Biological complexity: smell nerve memory creation

by David Turell @, Tuesday, December 26, 2017, 15:53 (2285 days ago) @ David Turell

How odor memory is controlled in the brain is shown:

https://www.sciencedaily.com/releases/2017/12/171222092552.htm

"Some odours can trigger memories of experiences from years back. The current study shows that the piriform cortex, a part of the olfactory brain, is involved in the process of saving those memories; the mechanism, however, only works in interaction with other brain areas.

***

"It is known that the piriform cortex is able to temporarily store olfactory memories. We wanted to know, if that applies to long-term memories as well," says Christina Strauch.

"Synaptic plasticity is responsible for the storing of memories in the memory structures of the brain: During that process the communication between neurons is altered by means of a process called synaptic plasticity, so that a memory is created. Strauch and Manahan-Vaughan examined if the piriform cortex of rats is capable of expressing synaptic plasticity and if this change lasts for more than four hours; indicating that long-term memory may have been established.

"The scientists used electrical impulses in the brain to emulate processes that trigger the encoding of an olfactory sensation as a memory. They used different stimulation protocols which varied in the frequency and intensity of the pulses. It is known that these protocols can induce long-term effects in another brain area that is responsible for long term memories: the hippocampus. Strikingly, the same protocols did not induce long-term information storage in the form of synaptic plasticity in the piriform cortex.

"The scientists wondered whether the piriform cortex needs to be instructed to create a long-term memory. They then stimulated a higher brain area called the orbitofrontal cortex, which is responsible for the discrimination of sensory experiences. This time the stimulation of the brain area generated the desired change in the piriform cortex. "Our study shows that the piriform cortex is indeed able to serve as an archive for long-term memories. But it needs instruction from the orbitofrontal cortex -- a higher brain area -- indicating that an event is to be stored as a long-term memory," says Strauch."

Comment: It should be remembered we still don't know exactly how odors, chemicals in air become nerve impulses understood by the brain with specificity. There is no question odors trigger memories. All of our senses are really electrical representations of reality.

Biological complexity: more cell pore complexity

by David Turell @, Tuesday, May 03, 2016, 15:28 (2887 days ago) @ David Turell

The nuclear pore can now be visualized, as this paper shows, controlling the flow of molecules in and out of the nuclear membrane:- http://www.the-scientist.com/?articles.view/articleNo/46003/title/Observing-the-Nuclear... ultra fast-scanning atomic force microscopy (AFM), scientists have filmed nuclear pore complexes in action for the first time. The work reveals how these structures selectively bar some substances from entering the nucleus, researchers at the University of Basel, Switzerland, reported today (May 2) in Nature Nanotechnology.-“'With the high-speed AFM we could, for the first time, peer inside native nuclear pore complexes only forty nanometers in size,” study coauthor Roderick Lim of the University of Basel said in a statement. “This method is a real game changer.”-"Nuclear pores consist of a central transport channel surrounded by intrinsically disordered proteins called nucleoporins. Lim and his colleagues used high-speed AFM to visualize the behavior of phenylalanine-glycine nucleoporins (FG Nups) inside the nuclei of African clawed frog (Xenopus laevis) cells at a resolution of about 100 milliseconds. To access the nuclear pore at such high resolution, the researchers had to grow ultra-sharp carbon nanofibers on the AFM probes.-"AFM imaging revealed how the FG Nups rapidly expand and contract, like tentacles, to form a kind of mesh across the nuclear opening. Large molecules move more slowly than these pore proteins and are blocked from entering the nucleus, whereas small molecules move more quickly and have a much better chance of getting in, the researchers explained in their paper."-Comment: Look at the high speed image, kind of grainy but you can see the movement of the parts. In previous entries I've shown the complexity of the molecules that make up the pore. Not invented by chance or by cell communities, since each cell has a nucleus which must work at the start. Remember unicellular organisms have no nucleus, so multicellularity involves inventing it. We now must consider unicellular organisms in an invention committee communicating their proposed plans for the nucleus, which then arrives full-blown; communicating how? I see a hypothesis sinking.

Biological complexity: more cell pore complexity

by David Turell @, Tuesday, May 03, 2016, 23:49 (2887 days ago) @ David Turell

I hope dhw will comment

Biological complexity: more cell pore complexity

by dhw, Wednesday, May 04, 2016, 12:24 (2886 days ago) @ David Turell

DAVID: The nuclear pore can now be visualized, as this paper shows, controlling the flow of molecules in and out of the nuclear membrane:
http://www.the-scientist.com/?articles.view/articleNo/46003/title/Observing-the-Nuclear...
David's comment: Look at the high speed image, kind of grainy but you can see the movement of the parts. In previous entries I've shown the complexity of the molecules that make up the pore. Not invented by chance or by cell communities, since each cell has a nucleus which must work at the start. Remember unicellular organisms have no nucleus… -First of all, you know as well as I do that although bacteria do not have a nucleus, there are single-celled eukaryotes that do.
 
DAVID: …so multicellularity involves inventing it. We now must consider unicellular organisms in an invention committee communicating their proposed plans for the nucleus, which then arrives full-blown; communicating how? I see a hypothesis sinking.-Secondly, again you know perfectly well that single cells do communicate and do cooperate, and you have posted many articles explaining how they do it (thank you again). Of course, it is part of the game to exploit poor old dhw's inability to solve puzzles such as the origin of life, multicellularity, the mechanism for innovation, consciousness etc. which nobody else including yourself can solve, but in this particular case, the puzzle involves the evolution of prokaryotes into eukaryotes, and someone else came up donkey's years ago with a now widely accepted theory:-	From prokaryotes to eukaryotes - Understanding Evolution
evolution.berkeley.edu/evolibrary/article/_0/endosymbiosis_03
(Sorry, but once again I can't establish the link.)-QUOTE: “The complex eukaryotic cell ushered in a whole new era for life on Earth, because these cells evolved into multicellular organisms. But how did the eukaryotic cell itself evolve? How did a humble bacterium make this evolutionary leap from a simple prokaryotic cell to a more complex eukaryotic cell? The answer seems to be symbiosis — in other words, teamwork. 
Evidence supports the idea that eukaryotic cells are actually the descendents of separate prokaryotic cells that joined together in a symbiotic union. In fact, the mitochondrion itself seems to be the "great-great-great-great-great-great-great-great-great granddaughter" of a free-living bacterium that was engulfed by another cell, perhaps as a meal, and ended up staying as a sort of permanent houseguest. The host cell profited from the chemical energy the mitochondrion produced, and the mitochondrion benefited from the protected, nutrient-rich environment surrounding it. This kind of "internal" symbiosis — one organism taking up permanent residence inside another and eventually evolving into a single lineage — is called endosymbiosis.”-This was Lynn Margulis's theory, and Lynn Margulis was a champion of cellular intelligence. You may not believe the theory (which would appear to involve an initial degree of chance followed by intelligent cooperation), but you can argue about it with the ghost of Margulis or with all the other specialists who agree with her. -Finally, the hypothesis over which we disagree concerns how evolution works, not how the mechanism for evolution came into existence. Once more, I cannot see how the long acknowledged complexity of the cell provides any more support for your divine preprogramming or direct guidance of all innovations, lifestyles and natural wonders than it does for the possibly divine design of an autonomous, inventively intelligent mechanism to produce the same innovations etc. The hypothesis remains afloat.

Biological complexity: more cell pore complexity

by David Turell @, Wednesday, May 04, 2016, 16:23 (2886 days ago) @ dhw


> dhw: First of all, you know as well as I do that although bacteria do not have a nucleus, there are single-celled eukaryotes that do.-You are correct. I had forgotten about them. But that makes the point I'm trying to present in this series on pores in membranes. How did single cells create such a complex mechanisms as pores in a nuclear membrane? We don't know but the complexity begs for advanced planning. Those pores allow two direction traffic controls keeping required levels of concentration of molecules in tight ranges. That is just how a cell lives and works.-> dhw:(Sorry, but once again I can't establish the link.)-Here it is and it begs my question:-http://evolution.berkeley.edu/evolibrary/article/_0/endosymbiosis_03->> 
> This was Lynn Margulis's theory, and Lynn Margulis was a champion of cellular intelligence. You may not believe the theory (which would appear to involve an initial degree of chance followed by intelligent cooperation), but you can argue about it with the ghost of Margulis or with all the other specialists who agree with her. -How does it beg? It dos not explain the formation of the nucleus, only why there are mitochondria, which also have membranes, pre-formed when swallowed. I grant that single cells have their outer membrane, but that membrane allows in food sources and spits out waste, but the nucleus membrane is much more complex with all the processes of life being managed.
> 
> dhw: Finally, the hypothesis over which we disagree concerns how evolution works, not how the mechanism for evolution came into existence. Once more, I cannot see how the long acknowledged complexity of the cell provides any more support for your divine preprogramming or direct guidance of all innovations, lifestyles and natural wonders than it does for the possibly divine design of an autonomous, inventively intelligent mechanism to produce the same innovations etc. The hypothesis remains afloat.-I feel the complexity demands guidance. the cell nuclear pore is just one of hundreds of examples, perhaps thousands.

Biological complexity: more cell pore complexity

by dhw, Thursday, May 05, 2016, 12:19 (2885 days ago) @ David Turell

dhw: First of all, you know as well as I do that although bacteria do not have a nucleus, there are single-celled eukaryotes that do.
DAVID: You are correct. I had forgotten about them. But that makes the point I'm trying to present in this series on pores in membranes. How did single cells create such a complex mechanisms as pores in a nuclear membrane? We don't know but the complexity begs for advanced planning. Those pores allow two direction traffic controls keeping required levels of concentration of molecules in tight ranges. That is just how a cell lives and works.-You are now shifting from the evolution of a membrane to the evolution of a more complex membrane, and your question applies to every post-bacterial complexity you can think of (see below).
 
DAVID: [Margulis's theory of endosymbiosis] does not explain the formation of the nucleus, only why there are mitochondria, which also have membranes, pre-formed when swallowed. I grant that single cells have their outer membrane, but that membrane allows in food sources and spits out waste, but the nucleus membrane is much more complex with all the processes of life being managed.-Again, you are challenging me to explain how the comparatively simple membrane develops into a more complex membrane. And again, nobody knows. Just as nobody knows the extent to which further improvements might be made by intelligent organisms cooperating with one another, as explained by Margulis's endosymbiosis. I wonder how many biologists would agree with the hypothesis that God preprogrammed the first cells or personally dabbled to provide the pores. (See below)
 
dhw: Finally, the hypothesis over which we disagree concerns how evolution works, not how the mechanism for evolution came into existence. Once more, I cannot see how the long acknowledged complexity of the cell provides any more support for your divine preprogramming or direct guidance of all innovations, lifestyles and natural wonders than it does for the possibly divine design of an autonomous, inventively intelligent mechanism to produce the same innovations etc. The hypothesis remains afloat.-DAVID: I feel the complexity demands guidance. the cell nuclear pore is just one of hundreds of examples, perhaps thousands.-Yes, thousands, perhaps millions. According to you, EVERY innovation, plus EVERY lifestyle, plus EVERY natural wonder demands advanced planning and “guidance” (preprogramming or personal dabbling) by your God, because they are ALL too complex for organisms to work out for themselves. When I ask how God did all this, you complain that I am demanding exactitudes which you cannot provide. I cannot provide exactitudes either, which is why the autonomous, inventive mechanism (intelligence - possibly designed by your God) remains a hypothesis. But the hypothesis is not going to be sunk by your feeling that all evolutionary complexities demand your God's “guidance”!

Biological complexity: more cell pore complexity

by David Turell @, Thursday, May 05, 2016, 15:43 (2885 days ago) @ dhw


> DAVID: I feel the complexity demands guidance. the cell nuclear pore is just one of hundreds of examples, perhaps thousands.
> 
> dhw: Yes, thousands, perhaps millions. According to you, EVERY innovation, plus EVERY lifestyle, plus EVERY natural wonder demands advanced planning and “guidance” (preprogramming or personal dabbling) by your God, because they are ALL too complex for organisms to work out for themselves. When I ask how God did all this, you complain that I am demanding exactitudes which you cannot provide.-Our gulf in thought is shown in this statement of yours. I am incredulous at the complexity and recognize how difficult it is to plan for. You recognize the complexity (sort of) and hunt for any other possible explanation except God. I don't now how God did it, but you have no idea how the complexity might have happened. You don't accept chance, and then hope cells are smart enough on their own to figure it out, while offering the sop that perhaps God helped. Hard to balance on that fence.

Biological complexity: more cell pore complexity

by dhw, Friday, May 06, 2016, 13:07 (2884 days ago) @ David Turell

dhw: Finally, the hypothesis over which we disagree concerns how evolution works, not how the mechanism for evolution came into existence…
DAVID: I feel the complexity demands guidance. the cell nuclear pore is just one of hundreds of examples, perhaps thousands.
dhw: Yes, thousands, perhaps millions. According to you, EVERY innovation, plus EVERY lifestyle, plus EVERY natural wonder demands advanced planning and “guidance” (preprogramming or personal dabbling) by your God, because they are ALL too complex for organisms to work out for themselves. When I ask how God did all this, you complain that I am demanding exactitudes which you cannot provide. I cannot provide exactitudes either, which is why the autonomous, inventive mechanism (intelligence - possibly designed by your God) remains a hypothesis. But the hypothesis is not going to be sunk by your feeling that all evolutionary complexities demand your God's “guidance”!-DAVID: Our gulf in thought is shown in this statement of yours. I am incredulous at the complexity and recognize how difficult it is to plan for. You recognize the complexity (sort of) and hunt for any other possible explanation except God. I don't know how God did it, but you have no idea how the complexity might have happened. You don't accept chance, and then hope cells are smart enough on their own to figure it out, while offering the sop that perhaps God helped. Hard to balance on that fence.-I'm afraid the gulf extends to your interpretation of my thought. I do not “sort of” recognize the complexity. I am as incredulous as you. It is a major factor in my rejecting atheism, and as an agnostic I do not “hunt for any other possible explanation except God”. I hunt for an explanation of evolution that will exclude random mutations as the driving force of innovation (which I find so unconvincing). But it must also account for what I see as the higgledy-piggledy history of countless species coming and going without any apparent overall linking purpose - in stark contrast to the “planning” that seems to be your starting-point. I therefore find your anthropocentric theory of divine preprogramming and/or dabbling for every innovation, lifestyle and natural wonder every bit as unconvincing as random mutations. The discovery that so many scientists believe in cellular intelligence seems to me to offer a possible explanation for the higgledy-piggledy course of evolution, but I have emphasized from the very beginning that it does not exclude your God, who for me remains a 50/50 possible source of the (hypothetical) intelligent and inventive cell. My hypothesis is neither “hope” nor “sop” nor ”help”. It is an alternative to chance, to your divine “guidance” of every step, and to your anthropocentric reading of your God's mind. I suspect the latter is the main reason for your hostility, but an alternative reading of your God's mind and of evolutionary history is not hunting “for any other possible explanation except God”.

Biological complexity: more cell pore complexity

by David Turell @, Friday, May 06, 2016, 15:53 (2884 days ago) @ dhw


> dhw: I'm afraid the gulf extends to your interpretation of my thought. I do not “sort of” recognize the complexity. I am as incredulous as you. It is a major factor in my rejecting atheism, and as an agnostic I do not “hunt for any other possible explanation except God”. I hunt for an explanation of evolution that will exclude random mutations as the driving force of innovation (which I find so unconvincing).-I'm with you here.-> dhw: But it must also account for what I see as the higgledy-piggledy history of countless species coming and going without any apparent overall linking purpose - in stark contrast to the “planning” that seems to be your starting-point.-I view your problem here as an over analysis. Why not just accept the notion that the process of life includes enormous inventiveness, once multicellularity appears. God can plan for humans while the forms of life explode in all directions around the main thrust of His purpose. All analysis must include a look at possible purpose. that cannot be excluded.-> dhw: The discovery that so many scientists believe in cellular intelligence seems to me to offer a possible explanation for the higgledy-piggledy course of evolution,-'So many' is really how many? Just a few are always listed. And that cell intelligence can simply be automaticity seen from outside the cell. When 'inside' the processes are always simple molecular processes and often feedback loops. -> dhw: but I have emphasized from the very beginning that it does not exclude your God, who for me remains a 50/50 possible source of the (hypothetical) intelligent and inventive cell. -Accepted-> dhw: My hypothesis is neither “hope” nor “sop” nor ”help”. It is an alternative to chance, to your divine “guidance” of every step, and to your anthropocentric reading of your God's mind. I suspect the latter is the main reason for your hostility, but an alternative reading of your God's mind and of evolutionary history is not hunting “for any other possible explanation except God”.-I am certainly not hostile, but I can see you continuing to seek an alternative to chance or design, while I see no alternative, and frankly I have not seen you present an alternative that is reasonable to me. From my viewpoint I see your conjectures as tortured. We are a gulf apart.

Biological complexity: more cell pore complexity

by dhw, Saturday, May 07, 2016, 11:39 (2883 days ago) @ David Turell

DAVID: Why not just accept the notion that the process of life includes enormous inventiveness, once multicellularity appears. God can plan for humans while the forms of life explode in all directions around the main thrust of His purpose. All analysis must include a look at possible purpose. that cannot be excluded. -We agree on the enormous inventiveness, but not on how and why it might have come about. There is a huge gulf between planning evolution for the sake of humans and individually designing an explosion of organisms, lifestyles and natural wonders that have no conceivable connection with humans - to the extent that approx. 99% have now disappeared. The need for the weaverbird's nest to “balance nature” for humans is what I'd call a “tortured conjecture” (see below). As regards an overall divine purpose, you have told us yours (to create humans), but when I suggest an alternative (experiment, entertainment, curiosity, relief of boredom), you tell me not to try and read God's mind. How do you gauge purpose without reading the mind? As regards a purpose behind the drive for complexity, you have again rejected my alternative, which is the drive for survival and improvement.-dhw: The discovery that so many scientists believe in cellular intelligence seems to me to offer a possible explanation for the higgledy-piggledy course of evolution.

DAVID: 'So many' is really how many? Just a few are always listed. And that cell intelligence can simply be automaticity seen from outside the cell. When 'inside' the processes are always simple molecular processes and often feedback loops.-I am in no position to conduct a census, but after McClintock and Margulis, we keep coming across others like Bühler, Shapiro and Lipton, and there's a whole raft of entries on Google under “bacterial/microbial intelligence” if you really want to follow it up. I may as well ask you how many scientists believe in divine preprogramming or personal intervention for every innovation, lifestyle and natural wonder in evolutionary history.
 
DAVID: […} I can see you continuing to seek an alternative to chance or design, while I see no alternative, and frankly I have not seen you present an alternative that is reasonable to me. From my viewpoint I see your conjectures as tortured. We are a gulf apart.-On the subject of evolution, there is indeed a gulf: once again, my explanation is NOT an alternative to design (or to your God). It is an alternative to your personal interpretation of evolution and your God's purpose. But in terms of God's existence, I accept all your arguments relating to complexity, and your posts - as well as your books - on this and other related subjects have been an ongoing education for me, for which I shall always be grateful. So there are still plenty of bridges, even if they only take me halfway across the theist-atheist gulf!

Biological complexity: more cell pore complexity

by David Turell @, Saturday, May 07, 2016, 15:11 (2883 days ago) @ dhw

dhw: How do you gauge purpose without reading the mind? As regards a purpose behind the drive for complexity, you have again rejected my alternative, which is the drive for survival and improvement.-I think a result gives purpose: humans here against all odds =s purposeful result. Deciding a mind must be behind it, a secondary conclusion. A drive to complexity =s survival and improvement, no Darwin involved which is the basis of your thought.-
> dhw: I may as well ask you how many scientists believe in divine preprogramming or personal intervention for every innovation, lifestyle and natural wonder in evolutionary history.-There are many hundreds of doctors in an organization called "physicians against Darwin", to which I once sold books (about 2002).-> dhw: I accept all your arguments relating to complexity, and your posts - as well as your books - on this and other related subjects have been an ongoing education for me, for which I shall always be grateful. So there are still plenty of bridges, even if they only take me halfway across the theist-atheist gulf!-My job when invited to comment on this website was to extend the bridge. I'll keep engineering.

Biological complexity: more cell pore complexity

by dhw, Sunday, May 08, 2016, 13:01 (2882 days ago) @ David Turell

dhw: How do you gauge purpose without reading the mind? As regards a purpose behind the drive for complexity, you have again rejected my alternative, which is the drive for survival and improvement.
DAVID: I think a result gives purpose: humans here against all odds =s purposeful result. Deciding a mind must be behind it, a secondary conclusion. A drive to complexity =s survival and improvement, no Darwin involved which is the basis of your thought.-Yes, humans are here, as are millions of other organisms, and 99% of all organisms have disappeared, every one having been against the odds. I think it is very reasonable to attribute the complexity of life to a mind. (My arguments against the existence of God approach the subject from a different direction.) But is it reasonable to conclude that the mind specially created all those organisms extant and extinct in order to produce/feed humans? Is it not just as reasonable to conjecture that the mind wanted to see what would happen if it created an autonomous mechanism to do all the inventing? (But perhaps allowed itself the occasional dabble?)
I don't understand what you mean by “no Darwin involved”. Darwin's common descent (but not random mutations) is basic to my thinking. Did you mean “no God involved”? A God who invents a self-directing toy is just as “involved” as a God who invents a toy that only he can direct.
 
dhw: I may as well ask you how many scientists believe in divine preprogramming or personal intervention for every innovation, lifestyle and natural wonder in evolutionary history.
DAVID: There are many hundreds of doctors in an organization called "physicians against Darwin", to which I once sold books (about 2002).-What does “against Darwin” mean? Are they against common descent or only against random mutations? Are they all Creationists? How many of them specifically argue that God preprogrammed or “guided” every step in evolution?-dhw: I accept all your arguments relating to complexity, and your posts - as well as your books - on this and other related subjects have been an ongoing education for me, for which I shall always be grateful. So there are still plenty of bridges, even if they only take me halfway across the theist-atheist gulf!
DAVID: My job when invited to comment on this website was to extend the bridge. I'll keep engineering.-My aim when setting up the website was to get help in delving as deep as possible into all the unsolved mysteries of our existence. No one has been more instrumental than you in fulfilling this aim. No solutions, of course, but the view from my picket fence has been hugely extended!

Biological complexity: more cell pore complexity

by David Turell @, Sunday, May 08, 2016, 15:26 (2882 days ago) @ dhw

dhw: But is it reasonable to conclude that the mind specially created all those organisms extant and extinct in order to produce/feed humans? Is it not just as reasonable to conjecture that the mind wanted to see what would happen if it created an autonomous mechanism to do all the inventing? -If the 'mind' was an ordinary human, yes. What did develop, for me, is so extraordinary it strongly supports the contention purpose is involved.-> dhw: I don't understand what you mean by “no Darwin involved”. Darwin's common descent (but not random mutations) is basic to my thinking.-Darwin's basic point is based on survivability. I've come to the conclusion that survival is not the only driver of evolution, just one aspect. A drive to complexity seems built in and more to the point than natural selection. Denton has this viewpoint. I find it very persuasive. Bacteria have not modified much to survive forever. Is there a reason for multicellularity? It just IS.
> 
> dhw: What does “against Darwin” mean? Are they against common descent or only against random mutations? Are they all Creationists? How many of them specifically argue that God preprogrammed or “guided” every step in evolution?-They liked my first book, and believed God's guidance necessary. 40% of physicians believe in God. -> 
> dhw: My aim when setting up the website was to get help in delving as deep as possible into all the unsolved mysteries of our existence. No one has been more instrumental than you in fulfilling this aim. No solutions, of course, but the view from my picket fence has been hugely extended!-In length or width?

Biological complexity: more cell pore complexity

by dhw, Monday, May 09, 2016, 13:13 (2881 days ago) @ David Turell

dhw: But is it reasonable to conclude that the mind specially created all those organisms extant and extinct in order to produce/feed humans? Is it not just as reasonable to conjecture that the mind wanted to see what would happen if it created an autonomous mechanism to do all the inventing? 
DAVID: If the 'mind' was an ordinary human, yes. What did develop, for me, is so extraordinary it strongly supports the contention purpose is involved.-But the only purpose you offer us is the creation of humans. When pressed, you dare to conjecture that the purpose of creating humans might have been for your God to have some sort of relationship with them - which I pointed out is not much of a relationship if he insists on remaining hidden. Meanwhile, the human-related purpose of the weaverbird's nest plus the other billions of organisms, lifestyles and natural wonders extant and extinct is apparently not to be questioned, but is somehow connected with the “balance of nature”. Under “Crocodile vision” (for which many thanks) you commented:-DAVID: An amazing adaptation, but all animals have them. Life's development in evolution has the property to create necessary helpful complexities. Planned?-Yes, all animals have them, because the history of evolution is one of organisms finding ways to improve as well as survive. Why would God specially plan a particular kind of vision for the crocodile in order to produce and/or feed humans?-dhw: I don't understand what you mean by “no Darwin involved”. Darwin's common descent (but not random mutations) is basic to my thinking.
David: Darwin's basic point is based on survivability. I've come to the conclusion that survival is not the only driver of evolution, just one aspect. A drive to complexity seems built in and more to the point than natural selection. Denton has this viewpoint. I find it very persuasive. Bacteria have not modified much to survive forever. Is there a reason for multicellularity? It just IS.-The other driver of evolution, I keep suggesting, is improvement. Even if your theistic interpretation of evolution was correct, the pattern would still be the same, from bacteria to humans. You think all the improvements were “guided”, and I suggest he may have given organisms the intelligence to work out their own. Why, then, do you not find improvement “very persuasive” as the other driving force of evolution?-dhw: What does “against Darwin” mean? Are they against common descent or only against random mutations? Are they all Creationists? How many of them specifically argue that God preprogrammed or “guided” every step in evolution?
DAVID: They liked my first book, and believed God's guidance necessary. 40% of physicians believe in God. -I liked your first book AND your second book, but I wonder if your opinion poll among your fans actually specified their liking for the Turell God-guided-it-all-just-for-humans Theory of Evolution. And 60% of physicians not believing in God is no endorsement either.

Biological complexity: more cell pore complexity

by David Turell @, Monday, May 09, 2016, 19:12 (2881 days ago) @ dhw


> dhw: But the only purpose you offer us is the creation of humans. When pressed, you dare to conjecture that the purpose of creating humans might have been for your God to have some sort of relationship with them - which I pointed out is not much of a relationship if he insists on remaining hidden.-Have you offered a 'purpose' for reality: yes, just start things up and have fun watching what happens. Light-hearted, but not a serious approach. -> dhw: Meanwhile, the human-related purpose of the weaverbird's nest plus the other billions of organisms, lifestyles and natural wonders extant and extinct is apparently not to be questioned, but is somehow connected with the “balance of nature”. -Yes, 'balanced' is my reasonable answer. Everyone has to eat.-> 
> dhw: Yes, all animals have them, because the history of evolution is one of organisms finding ways to improve as well as survive. Why would God specially plan a particular kind of vision for the crocodile in order to produce and/or feed humans?-Bacteria have not bothered to improve. And all improvement led to humans! Hard to get around that fact. I've covered balance of nature above.
> 
> dhw: The other driver of evolution, I keep suggesting, is improvement. Even if your theistic interpretation of evolution was correct, the pattern would still be the same, from bacteria to humans. You think all the improvements were “guided”, and I suggest he may have given organisms the intelligence to work out their own. Why, then, do you not find improvement “very persuasive” as the other driving force of evolution?-Improvement is another way of saying increased complexity, which may not necessarily be an improvement. Dinosaurs didn't last but bacteria have. Note, not improvement, just complexity. Whales are an increase in complexity to survive as sea creatures. Not much of an improvement with very complex anatomical changes. This is why I identified a 'drive to complexity' in my first book. You are still following Darwin and his thoughts about survival by improvement. Structuralism is the other early thought, development by an increase in structural complexity. Which is what our brain happens to be!

Biological complexity: more cell pore complexity

by dhw, Tuesday, May 10, 2016, 16:45 (2880 days ago) @ David Turell

DAVID: Have you offered a 'purpose' for reality: yes, just start things up and have fun watching what happens. Light-hearted, but not a serious approach.-It's simply a variation on Deism, the essence of which is that God started life off and then allowed it to pursue its own course. Why would he would start it off but not intervene? Relief from eternal boredom is a possible answer, that's all. The fact that you don't like it does not mean it is not to be taken seriously. On the other hand, I find your own proposed ‘purpose' - a relationship in which one partner says and does nothing but chooses to remain hidden - difficult to take seriously. -dhw: Meanwhile, the human-related purpose of the weaverbird's nest plus the other billions of organisms, lifestyles and natural wonders extant and extinct is apparently not to be questioned, but is somehow connected with the “balance of nature”. 
DAVID: Yes, 'balanced' is my reasonable answer. Everyone has to eat.-Of course they do, and some survive and some don't. It is your anthropocentric interpretation of the history of evolution that I am questioning, not the need for organisms to eat. You play the same game in the post on “Carnivorous plant robbed” (thank you), in which bugs and plants form a symbiotic relationship:-QUOTE: "For example, the capsid bug feeds on the insects caught by the pitcher plant, and the plant absorbs the capsids' faeces to derive nutrition in return."
Your comment: Life is as inventive as ever. Again note this is an example of the balance of nature, which is everywhere.-Yes, the balance of nature is everywhere, and it keeps changing as conditions change, some species flourish and others disappear. Nature takes its own course. But according to you, God has had to “guide” all these coming-and-going natural wonders - since the organisms are incapable of organizing themselves - so that humans could appear and eat. THAT is the disconnection I keep pointing out.
 
dhw: The other driver of evolution, I keep suggesting, is improvement…
DAVID: Improvement is another way of saying increased complexity, which may not necessarily be an improvement. Dinosaurs didn't last but bacteria have. Note, not improvement, just complexity. […] You are still following Darwin and his thoughts about survival by improvement. Structuralism is the other early thought, development by an increase in structural complexity. Which is what our brain happens to be!-We should distinguish between improvement, innovation, variation and complexity. Every surviving innovation will be an improvement and will entail an increase in complexity, but increased complexity does not necessarily mean innovation; variations may increase complexity; I don't know where exactly one draws the line between innovative improvements and variations, but I would regard the human brain as a variation of increased complexity, and an improvement, but not an innovation. As regards bacteria and dinosaurs, firstly every improvement and every innovation must take place in INDIVIDUAL organisms. When Billy Bacterium swallowed a what's-it and they became the first eukaryote, it didn't mean that every bacterium should then have changed into a eukaryote! BOTH forms survived and eukaryotes cooperated to create more and more innovative improvements while bacteria remained the same, though with variations. As the environment changed, new cell communities formed and many old ones died, but the improvements with their variations did not die: dinosaurs had sexual reproduction, vision, hearing, brains, kidneys, which were all innovative improvements once, and you and I and all our existing fellow animals have them now. This has nothing to do with Darwin's random mutations, but it does have everything to do with his theory of common descent, which you say you accept, and with his natural selection, which decides what will survive. And so if you also accept that brains, wings, the senses, limbs etc. represent some sort of improvement over bacterial life, I really don't see how you can deny that evolution has proceeded through a drive for improvement. I would also suggest that from the beginnings of multicellularity, increased complexity has been the result of the drive for improvement rather than a drive for complexity resulting in improvement.

Biological complexity: more cell pore complexity

by David Turell @, Tuesday, May 10, 2016, 18:26 (2880 days ago) @ dhw


> dhw: Yes, the balance of nature is everywhere, and it keeps changing as conditions change, some species flourish and others disappear. Nature takes its own course. But according to you, God has had to “guide” all these coming-and-going natural wonders - since the organisms are incapable of organizing themselves - so that humans could appear and eat. THAT is the disconnection I keep pointing out. - Evolution had to continue, so all who survived had to eat. It is still happening. Note your chocolate! Without balance, no chocolate, imagine. - > 
> dhw: We should distinguish between improvement, innovation, variation and complexity. Every surviving innovation will be an improvement and will entail an increase in complexity, but increased complexity does not necessarily mean innovation; variations may increase complexity; I don't know where exactly one draws the line between innovative improvements and variations, but I would regard the human brain as a variation of increased complexity, and an improvement, but not an innovation. - I disagree. you have a good discussion going and then denigrate the huge advance of consciousness in human brains! - >dhw: When Billy Bacterium swallowed a what's-it and they became the first eukaryote, it didn't mean that every bacterium should then have changed into a eukaryote! - The emergence of a nuclear membrane was a major event not done by swallowing. That is the mitochondria theory. From Carl Woese: - "Next comes the evolution of the eucaryotic cell itself. While biologist have traditionally seen it as a step (saltation) beyond the stage of bacterial cells, I do not. The idea that eukaryotic cell structure is the product of a symbioses among bacteria, and so represents a higher stage than that of the bacterial cell, goes back a good century and a half, but there has been no effort to seriously rethink the matter in the light of modern biological knowledge. Nowhere in thinking about a symbiotic origin of the eukaryotic cell has consideration been given to the fact that the process as envisioned would involve radical change of the designs of the cells involved. You can?t just tear cell designs apart and willy-nilly construct a new type of design from the parts. The cells we know are not just loosely coupled arrangements of quasi-independent modules. They are highly, intricately, and precisely integrated networks of entities and interactions. Any dismantling of a cell design would not reverse the evolution that brought it into existence; that is not possible. To think that a new cell design can be created more or less haphazardly from chunks of other modern cell design is just another fallacy born of a mechanistic, reductionist view of the organism.” - A New Biology for a New Century (2004)" - http://www.uncommondescent.com/origin-of-life/comet-craters-were-melting-pots-for-life-... - > dhw: I really don't see how you can deny that evolution has proceeded through a drive for improvement. I would also suggest that from the beginnings of multicellularity, increased complexity has been the result of the drive for improvement rather than a drive for complexity resulting in improvement. - Complexity is not necessarily improvement: Whales!

Biological complexity: more cell pore complexity

by dhw, Wednesday, May 11, 2016, 13:02 (2879 days ago) @ David Turell

dhw: Yes, the balance of nature is everywhere, and it keeps changing as conditions change, some species flourish and others disappear. Nature takes its own course. But according to you, God has had to “guide” all these coming-and-going natural wonders - since the organisms are incapable of organizing themselves - so that humans could appear and eat. THAT is the disconnection I keep pointing out.-DAVID: Evolution had to continue, so all who survived had to eat. It is still happening. Note your chocolate! Without balance, no chocolate, imagine.-Yes, organisms have to eat to survive, but that doesn't mean they only survive in order to produce or feed humans. I do not believe for one minute that your God taught the weaverbird to build its nest so that I could have my chocolate. And I'm happy to say I firmly believe that if there were no more weaverbirds around, I would still have my chocolate. Ditto the bugs in the flowers, the wasp larvae on the spider, and the cuttlefish with its camouflage. And if a terrible disease wiped out all the cacao trees in the world, I would tell you through my tears: “It's all part of the higgledy-piggledy, unplanned history of evolution.” And you would reply, “No, God is balancing Nature, because his plan has always been for you to eat soya beans.”-dhw: We should distinguish between improvement, innovation, variation and complexity. Every surviving innovation will be an improvement and will entail an increase in complexity, but increased complexity does not necessarily mean innovation; variations may increase complexity; I don't know where exactly one draws the line between innovative improvements and variations, but I would regard the human brain as a variation of increased complexity, and an improvement, but not an innovation.
DAVID: I disagree. you have a good discussion going and then denigrate the huge advance of consciousness in human brains!-No denigration. All our fellow animals have brains. The human brain is not an innovation, and there are many similarities between it and other brains. That does not mean human consciousness is not a huge advance on chimp consciousness. Of course it is. I only gave this as an example of variations on existing physical organs. The same applies to the eagle's eyes, the dog's nose and any other organ you can think of: my point is that all these organs were innovations at one time, and were improvements that increased complexity; variations may also increase complexity, but we would not necessarily regard them as improvements: how do you measure whether the crocodile's eyes are an “improvement” over a sparrow's eyes? They are simply different, and suit the organism concerned. That is how evolution seems to me to work: each organism finding (or not finding) its own means of survival and/or improvement.-dhw: When Billy Bacterium swallowed a what's-it and they became the first eukaryote, it didn't mean that every bacterium should then have changed into a eukaryote! 
DAVID: The emergence of a nuclear membrane was a major event not done by swallowing. That is the mitochondria theory. From Carl Woese:
"Next comes the evolution of the eucaryotic cell itself. While biologist have traditionally seen it as a step (saltation) beyond the stage of bacterial cells, I do not.” [...]-So Woese disagrees with Margulis. I'll leave that discussion to the experts. Ours concerned the fact that bacteria are still bacteria, and my point was that when innovations take place, that doesn't mean every individual organism will switch to being the new organism. Bacteria have stayed bacteria, whereas eukaryotes - no matter how they came into being - gave rise to the multicellularity which produced evolutionary innovation. You can't use unchanging bacteria as evidence that humans didn't have to happen and therefore God geared evolution to the production of humans. As I keep saying, NO other life form had to happen.
 
dhw: I really don't see how you can deny that evolution has proceeded through a drive for improvement. I would also suggest that from the beginnings of multicellularity, increased complexity has been the result of the drive for improvement rather than a drive for complexity resulting in improvement.
DAVID: Complexity is not necessarily improvement: Whales!-I didn't say it was. I said innovation meant increased complexity. See above. You have said that it is the divinely guided “drive to complexity” that propels evolution. My point is that evolution is propelled by the (possibly God-given) drive for improvement, which gives rise to complexity. And I still don't understand why you object, since it fits into your scenario (always improving till God finally produces humans) just as snugly as it fits into mine (all innovations stem from individual organisms looking to improve), whereas you quite rightly point out that the ‘drive to complexity' in itself would NOT necessarily mean improvement.

Biological complexity: more cell pore complexity

by David Turell @, Wednesday, May 11, 2016, 15:33 (2879 days ago) @ dhw


> dhw: Yes, organisms have to eat to survive, but that doesn't mean they only survive in order to produce or feed humans. I do not believe for one minute that your God taught the weaverbird to build its nest so that I could have my chocolate. And I'm happy to say I firmly believe that if there were no more weaverbirds around, I would still have my chocolate.-An analogy: did you pick the cocoa beans yourself? Of course not. The interlocking interdependent relationships of human society produced your chocolate. The balance of nature is exactly the same. Evolution could not have continued without it, although the weaver's nest is not critical to the scheme, just an example of the widespread net of interdependence. Balance kept everyone who survived eating and n now we are here.
 
>> DAVID: I disagree. you have a good discussion going and then denigrate the huge advance of consciousness in human brains!
> 
> No denigration. All our fellow animals have brains. The human brain is not an innovation, and there are many similarities between it and other brains.-We are back to 'degree or kind'. Sure the toad brain has early aspects of ours.-> dhw: That does not mean human consciousness is not a huge advance on chimp consciousness. Of course it is. -Thank you for that admission. -> dhw: I only gave this as an example of variations on existing physical organs. ... how do you measure whether the crocodile's eyes are an “improvement” over a sparrow's eyes? They are simply different, and suit the organism concerned. That is how evolution seems to me to work: each organism finding (or not finding) its own means of survival and/or improvement.-Each species has its own set of improvements, I agree, but if we agree that chance variation is not the mechanism, what must be present is an underlying 'drive to complexity and possible improvement sorted out in time but not necessarily competition between animals as much as competition with changing environment; Raup's book on extinctions and bad luck.
> 
> dhw: So Woese disagrees with Margulis. I'll leave that discussion to the experts.-Woese doesn't disagree. Mitochondria were ingested. You are missing the point that bacteria have free floating DNA. To get to true multicellularity a nuclear membrane and other organelles had to be added to the complexity of the cell. Woese wonders how. It is neat how you stick to 'your' small group of experts! -> dhw: Ours concerned the fact that bacteria are still bacteria, ....You can't use unchanging bacteria as evidence that humans didn't have to happen and therefore God geared evolution to the production of humans. As I keep saying, NO other life form had to happen.-Exactly my point. WHY did life advance beyond bacteria? Humans did not have to happen, but they did. You cannot avoid the significance of that juxtaposition of events. Not HOW we appeared, but WHY?->> DAVID: Complexity is not necessarily improvement: Whales!
> 
> dhw: I didn't say it was. I said innovation meant increased complexity. See above. You have said that it is the divinely guided “drive to complexity” that propels evolution. My point is that evolution is propelled by the (possibly God-given) drive for improvement, which gives rise to complexity. And I still don't understand why you object, since it fits into your scenario (always improving till God finally produces humans) just as snugly as it fits into mine (all innovations stem from individual organisms looking to improve), whereas you quite rightly point out that the ‘drive to complexity' in itself would NOT necessarily mean improvement.-Just how do individual 'organisms look to improve'? Sound very anthropomorphic to me. I still think the underlying built-in drive is for complexity which then may bring improvement.

Biological complexity: very important enzyme found

by David Turell @, Wednesday, May 11, 2016, 19:39 (2879 days ago) @ David Turell

In a bacterium at the bottom of the ocean. this is the natural form which synthesizes an antibody. Note its complexity in the second website::-https://www.sciencedaily.com/releases/2016/05/160511105356.htm-http://pubs.acs.org/doi/abs/10.1021/jacs.6b00232-"The Diels-Alder reaction, discovered by Nobel Prize-wining chemists Otto Diels and Kurt Alder, is one of the most powerful chemical reactions known, and is used extensively by synthetic chemists to produce many important molecules, including antibiotics, anti-cancer drugs and agrochemicals.-"However, there has been much debate and controversy about whether nature uses the reaction to produce its own useful molecules. If it does, the identity of the biological catalysts (enzymes) responsible for performing this reaction have remained a mystery until now.-"Some candidate natural 'Diels-Alderases' have been identified, but these have either been shown not to perform the reaction, or the evidence that they catalyse a Diels-Alder reaction is ambiguous.-"Now, researchers at BrisSynBio, a BBSRC/EPSRC Synthetic Biology Research Centre at the University of Bristol and the School of Biology at Newcastle University have conclusively shown that a true 'Diels-Alderase' (Diels-Alder enzyme) exists. They have also established in atomic detail how it catalyses the reaction.-"Dr Paul Race, from BrisSynBio, said: "We found the enzyme, called AbyU, in a bacterium called Verrucosispora maris (V. maris), which lives on the Pacific seabed. V. maris uses the AbyU enzyme to biosynthesise a molecule called abyssomicin C, which has potent antibiotic properties."-"To establish the details of how the AbyU enzyme catalyses the Diels-Alder reaction, the team first had to solve the atomic structure of AbyU, and then simulate the enzyme reaction using quantum mechanics methods.-"Dr Race said: "Once we had figured out how AbyU was able to make natural antibiotic, we were able to show that it could also perform the Diels-Alder reaction on other molecules that are difficult to transform using synthetic chemistry."-***-"Dr Jem Stach, from Newcastle University, was also a co-author of the paper. He said: "Nature, not only in the compounds it produces, but also the means by which it does so, is the best chemist. This has never been clearer to me than it was during this collaboration between biologists and chemists. Starting with genome gazing, and ending with new chemistry, on a journey that took in structural biology, synthetic chemistry and computational chemistry, was utterly rewarding, educational and fascinating.'"-Comment: And all by chance! 'Nature' is sure smart all by itself; NEVER

Biological complexity: more cell pore complexity

by dhw, Thursday, May 12, 2016, 17:46 (2878 days ago) @ David Turell

dhw: I'm happy to say I firmly believe that if there were no more weaverbirds around, I would still have my chocolate.
DAVID: An analogy: did you pick the cocoa beans yourself? Of course not. The interlocking interdependent relationships of human society produced your chocolate. The balance of nature is exactly the same. Evolution could not have continued without it, although the weaver's nest is not critical to the scheme, just an example of the widespread net of interdependence. Balance kept everyone who survived eating and now we are here.-Yes, evolution is a history of cooperating cell communities, and all organisms are dependent on some others for their survival. But what you call the balance has never stopped changing, and apparently 99% of those organisms are now extinct! All survivors, including ourselves, are “here” and dependent, but even now the balance keeps changing as species go extinct. Somehow, you seem to think the fact that we humans are here means that nothing else mattered to your God, and yet he took the trouble to “guide” the rest including those NOT “critical to the scheme”. It's the untold numbers of the latter that make your scenario so creaky.
 
dhw: The human brain is not an innovation, and there are many similarities between it and other brains. That does not mean human consciousness is not a huge advance on chimp consciousness. Of course it is. 
DAVID: Thank you for that admission.-I have never questioned the huge advance in consciousness. My point is that the human brain was not an innovation. 
 
dhw: They are simply different, and suit the organism concerned. That is how evolution seems to me to work: each organism finding (or not finding) its own means of survival and/or improvement.
DAVID: Each species has its own set of improvements, I agree, but if we agree that chance variation is not the mechanism, what must be present is an underlying 'drive to complexity and possible improvement sorted out in time but not necessarily competition between animals as much as competition with changing environment; Raup's book on extinctions and bad luck.-Why have you suddenly brought Darwinian competition into the discussion? It's obvious that all innovations and variations must somehow be linked to coping with the environment. Competition may be a reason for seeking improvement, or organisms may simply be motivated by new opportunities offered by changes in the environment. But complexity for its own sake to me seems utterly pointless. I don't see why even in your scenario God would try to complexify organisms just for the sake of it.
 
dhw: So Woese disagrees with Margulis. I'll leave that discussion to the experts.

DAVID: Woese doesn't disagree. Mitochondria were ingested. You are missing the point that bacteria have free floating DNA. To get to true multicellularity a nuclear membrane and other organelles had to be added to the complexity of the cell. Woese wonders how. It is neat how you stick to 'your' small group of experts!-Once again, you are switching the argument to how eukaryotes came into being. I am not sticking to “my” experts. I did not know there was controversy over the completeness of the endosymbiosis theory, but that has nothing to do with my point, which was: 
dhw: You can't use unchanging bacteria as evidence that humans didn't have to happen and therefore God geared evolution to the production of humans. As I keep saying, NO other life form had to happen.
DAVID: Exactly my point. WHY did life advance beyond bacteria? Humans did not have to happen, but they did. You cannot avoid the significance of that juxtaposition of events. Not HOW we appeared, but WHY?-And you continue to ignore the fact that it's not just we who appeared! NO other life form HAD to appear. And I keep suggesting that WHY is because there was a built-in drive not only for survival but also for improvement. And I do not think for one minute that every organism was saying to itself: “I wanner be human”, or that your God “guided” every extinct and extant organism, lifestyle and natural wonder in order to produce/feed humans.-DAVID: Complexity is not necessarily improvement: Whales!
dhw: My point is that evolution is propelled by the (possibly God-given) drive for improvement, which gives rise to complexity. […] whereas you quite rightly point out that the ‘drive to complexity' in itself would NOT necessarily mean improvement.

DAVID: Just how do individual 'organisms look to improve'? Sound very anthropomorphic to me. I still think the underlying built-in drive is for complexity which then may bring improvement.-How do organisms look to survive? (And in your scheme of things, how do they look to complexify?) Do you think God even has to instruct them to want to go on living? It makes more sense to me that an organism would say to itself in its own particular way: “I wanner survive/improve” rather than “I wanner complexify.” But in your view, they don't say anything to themselves. God “guides” them to complexify for the sake of becoming more complex - and apparently this sometimes leads to improvement, though apparently it's all been carefully planned to produce humans. Your scenario is getting fuzzier and fuzzier.

Biological complexity: more cell pore complexity

by David Turell @, Friday, May 13, 2016, 00:12 (2877 days ago) @ dhw

David: Balance kept everyone who survived eating and now we are here.[/i]
> 
> dhw: Yes, evolution is a history of cooperating cell communities, and all organisms are dependent on some others for their survival. But what you call the balance has never stopped changing, and apparently 99% of those organisms are now extinct! -So what. As long as nature keeps its balance throughout evolution, everyone eats.-
> dhw: Somehow, you seem to think the fact that we humans are here means that nothing else mattered to your God, and yet he took the trouble to “guide” the rest including those NOT “critical to the scheme”. It's the untold numbers of the latter that make your scenario so creaky.-You've forgotten that I think the process of life is very inventive (we don't know how), but the weird species are everywhere. Again, so what! I still no odds that dictate humans should be here. I am sure the odds against chance humans are enormously enormous.-> 
> dhw: I have never questioned the huge advance in consciousness. My point is that the human brain was not an innovation. -But human consciousness, coming out of the structure of the human brain is an innovation.
> 
> dhw: Why have you suddenly brought Darwinian competition into the discussion? It's obvious that all innovations and variations must somehow be linked to coping with the environment. -That is not true. One can make the argument that a drive to complexification is primary and improvement a secondary result mediated by the selection process on the variation presented.-> dhw;Competition may be a reason for seeking improvement, or organisms may simply be motivated by new opportunities offered by changes in the environment. But complexity for its own sake to me seems utterly pointless. I don't see why even in your scenario God would try to complexify organisms just for the sake of it.-In order to drive evolution to the most complex of all, humans-> 
> dhw: So Woese disagrees with Margulis. I'll leave that discussion to the experts.
> 
> DAVID: Woese doesn't disagree. Mitochondria were ingested. You are missing the point that bacteria have free floating DNA. To get to true multicellularity a nuclear membrane and other organelles had to be added to the complexity of the cell. Woese wonders how. It is neat how you stick to 'your' small group of experts!
> 
> dhw: Once again, you are switching the argument to how eukaryotes came into being. I am not sticking to “my” experts. I did not know there was controversy over the completeness of the endosymbiosis theory.-There is not just one way of thinking about evolution. I know you knew that.-> 
> dhw: And you continue to ignore the fact that it's not just we who appeared! NO other life form HAD to appear. And I keep suggesting that WHY is because there was a built-in drive not only for survival but also for improvement.-And I'm suggesting that a complexity drive is all that is needed for evolution to work. All living organisms try to survive with the attributes they have. -> 
> dhw: How do organisms look to survive? (And in your scheme of things, how do they look to complexify?) Do you think God even has to instruct them to want to go on living? -No. It is built in.-> dhw: But in your view, they don't say anything to themselves. God “guides” them to complexify for the sake of becoming more complex - and apparently this sometimes leads to improvement, though apparently it's all been carefully planned to produce humans. Your scenario is getting fuzzier and fuzzier.-From my comments above you will not see fuzziness, just a process managed by increasing complexity.

Biological complexity: more cell pore complexity

by dhw, Friday, May 13, 2016, 12:32 (2877 days ago) @ David Turell

David: Balance kept everyone who survived eating and now we are here.
dhw: Yes, evolution is a history of cooperating cell communities, and all organisms are dependent on some others for their survival. But what you call the balance has never stopped changing, and apparently 99% of those organisms are now extinct!
DAVID: So what. As long as nature keeps its balance throughout evolution, everyone eats.-No they don't. 99% of species have disappeared. Your concept of balance seems to be that if humans are here and able to eat, nature is and always has been balanced.-dhw: Somehow, you seem to think the fact that we humans are here means that nothing else mattered to your God, and yet he took the trouble to “guide” the rest including those NOT “critical to the scheme”. It's the untold numbers of the latter that make your scenario so creaky.
DAVID: You've forgotten that I think the process of life is very inventive (we don't know how), but the weird species are everywhere. Again, so what! I still no odds that dictate humans should be here. I am sure the odds against chance humans are enormously enormous.-The odds against chance producing life in ALL its different forms are enormously enormous. What is this “process of life”? It sounds as if you are now suggesting that the process of life works independently of your God's plans and instructions. But according to you, the organisms that produce the innovations, lifestyles and natural wonders are all “guided” to do so! So God “guided” all the weird species etc., extant and extinct, for the sake of humans, even though they have nothing to do with humans. Fuzz!-dhw: I have never questioned the huge advance in consciousness. My point is that the human brain was not an innovation.
DAVID: But human consciousness, coming out of the structure of the human brain is an innovation.-We are talking about the course of evolution, not the unsolved problem of consciousness. The human brain is a physical entity which has clear links with the brains of our animal ancestors, and as such is a variation, not an innovation.-dhw: Why have you suddenly brought Darwinian competition into the discussion? It's obvious that all innovations and variations must somehow be linked to coping with the environment.
DAVID: That is not true. One can make the argument that a drive to complexification is primary and improvement a secondary result mediated by the selection process on the variation presented.-What is not true? No innovation or variation would have survived if it had not somehow helped the organism to cope with its environment. Yes, you are making the argument that complexification takes place for its own sake and improvement is secondary, and I am asking why an organism or your God would create a new complexity just for the sake of complexity. If it didn't help the organism to survive or to improve its mode of existence, it would be pointless.-dhw; I don't see why even in your scenario God would try to complexify organisms just for the sake of it.
DAVID: In order to drive evolution to the most complex of all, humans.-Then it's not for the sake of complexity - it's for the sake of improvement, unless you believe your God produced humans because he wanted a creature with lots more twiddly bits than a bacterium and not a creature with lots more useful attributes.
The remaining exchanges all deal with the same point, so I shan't repeat them.

Biological complexity: more cell pore complexity

by David Turell @, Friday, May 13, 2016, 16:01 (2877 days ago) @ dhw

DAVID: So what. As long as nature keeps its balance throughout evolution, everyone eats.
> 
> dhw: No they don't. 99% of species have disappeared. Your concept of balance seems to be that if humans are here and able to eat, nature is and always has been balanced.-Of course it always has been balanced until we humans have started upsetting it. Things arrive, things disappear, always balanced, always my concept of balance, from the beginning of life, a vital system.-> 
> dhw: The odds against chance producing life in ALL its different forms are enormously enormous. What is this “process of life”? It sounds as if you are now suggesting that the process of life works independently of your God's plans and instructions.-Correct. Any branch of the bush of life has high odds, if one proposes it must arrive. In my view complexity is the main drive with God dabbling to guide it.- -> 
> dhw: We are talking about the course of evolution, not the unsolved problem of consciousness. The human brain is a physical entity which has clear links with the brains of our animal ancestors, and as such is a variation, not an innovation.-You cannot separate consideration of our brain without including the development of its consciousness, even if we don't know how consciousness develops from it. It is the same as your argument trying to separate origin from evolution. You can't. 'I want to think about this but not about that' is discontinuous reasoning.-> 
> dhw: No innovation or variation would have survived if it had not somehow helped the organism to cope with its environment. Yes, you are making the argument that complexification takes place for its own sake and improvement is secondary, and I am asking why an organism or your God would create a new complexity just for the sake of complexity.-Perhaps by driving complexity it allows evolution to advance through survivability as an automatic mechanism, with God stepping in the dabble as necessary. Complexity explains the weird branches of the bush.
> 
> dhw: Then it's not for the sake of complexity - it's for the sake of improvement, unless you believe your God produced humans because he wanted a creature with lots more twiddly bits than a bacterium and not a creature with lots more useful attributes. - I don't believe the crazy sentence about God you proposed above. Of course with complex improvement survivability will guarantee that useful attributes for that organism are present. Complexify and see what variations are better and survive. Makes God's work easier.

Biological complexity: protozoa sans mitochondria

by David Turell @, Friday, May 13, 2016, 14:30 (2877 days ago) @ David Turell

A startling new find. A protozoa, which means a eukaryote, without mitochondria. Of course the authors insist, per Darwin, that they must have had them and modified to lose them, per common descent, but did they?:-http://www.the-scientist.com/?articles.view/articleNo/46077/title/Mysterious-Eukaryote-Missing-Mitochondria/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=29555469&_hsenc=p2ANqtz--CKLrHgo8ZgM3kquTKL8rNpjpGLfmL1zHFrThZ0J1T7op9N6vsWmnOdHxnL8yBBiGZZV7B2w2ssEsFKAn_KpBnitrOew&_hsmi=29555469/-"Scientists have long thought that mitochondria—organelles responsible for energy generation—are an essential and defining feature of a eukaryotic cell. Now, researchers from Charles University in Prague and their colleagues are challenging this notion with their discovery of a eukaryotic organism, Monocercomonoides species PA203, which lacks mitochondria. The team's phylogenetic analysis, published today (May 12) in Current Biology, suggests that Monocercomonoides—which belong to the Oxymonadida group of protozoa and live in low-oxygen environments—did have mitochondria at one point, but eventually lost the organelles.-***-"This study shows that mitochondria are not so central for all lineages of living eukaryotes,” Toni Gabaldon of the Center for Genomic Regulation in Barcelona, Spain, who also was not involved in the work, wrote in an email to The Scientist. “Yet, this mitochondrial-devoid, single-cell eukaryote is as complex as other eukaryotic cells in almost any other aspect of cellular complexity.”-***-"Hampl decided to sequence the genome of Monocercomonoides, a little-studied protist that lives in the digestive tracts of vertebrates. The 75-megabase genome—the first of an oxymonad—did not contain any conserved genes found on mitochondrial genomes of other eukaryotes, the researchers found. It also did not contain any nuclear genes associated with mitochondrial functions.-***-"Some anaerobic protists, for example, have only pared down versions of mitochondria, such as hydrogenosomes and mitosomes, which lack a mitochondrial genome. But these mitochondrion-like organelles perform essential functions of the iron-sulfur cluster assembly pathway, which is known to be conserved in virtually all eukaryotic organisms studied to date.-"Yet, in their analysis, the researchers found no evidence of the presence of any components of this mitochondrial pathway.-"To form the essential iron-sulfur clusters, the team discovered that Monocercomonoides use a sulfur mobilization system found in the cytosol, and that an ancestor of the organism acquired this system by lateral gene transfer from bacteria. This cytosolic, compensating system allowed Monocercomonoides to lose the otherwise essential iron-sulfur cluster-forming pathway in the mitochondrion, the team proposed.-“'This work shows the great evolutionary plasticity of the eukaryotic cell,” said Karnkowska, who participated in the study while she was a postdoc at Charles University. Karnkowska, who is now a visiting researcher at the University of British Columbia in Canada, added: “This is a striking example of how far the evolution of a eukaryotic cell can go that was beyond our expectations.”-“'The results highlight how many surprises may await us in the poorly studied eukaryotic phyla that live in under-explored environments,” Gabaldon said.-"Ettema agreed. “Now that we've found one, we need to look at the bigger picture and see if there are other examples of eukaryotes that have lost their mitochondria, to understand how adaptable eukaryotes are.'”-Comment: I like the phrase 'evolutionary plasticity' It fits my contention that a 'drive to complexity' is all that is needed to advance evolution and explain to dhw all the weird parts of the bush of life. Invent novelty, however complex, and what survives becomes the evolutionary advance (per Darwin). Perhaps learning to live on sulfur, not oxygen, negated the need for mitochondria which are generally the oxygen-burning organelles.

Biological complexity: protozoa sans mitochondria

by dhw, Saturday, May 14, 2016, 10:27 (2876 days ago) @ David Turell

DAVID: A startling new find. A protozoa, which means a eukaryote, without mitochondria. Of course the authors insist, per Darwin, that they must have had them and modified to lose them, per common descent, but did they?:-http://www.the-scientist.com/?articles.view/articleNo/46077/title/Mysterious-Eukaryote-... -QUOTE: Now that we've found one, we need to look at the bigger picture and see if there are other examples of eukaryotes that have lost their mitochondria, to understand how adaptable eukaryotes are.”-David's comment: I like the phrase 'evolutionary plasticity' It fits my contention that a 'drive to complexity' is all that is needed to advance evolution and explain to dhw all the weird parts of the bush of life. Invent novelty, however complex, and what survives becomes the evolutionary advance (per Darwin). Perhaps learning to live on sulfur, not oxygen, negated the need for mitochondria which are generally the oxygen-burning organelles.-I would suggest “evolutionary plasticity” means the organism adapts itself to its needs in relation to the environment, precisely as you have suggested (“learning to live in sulphur”). Adapting to the environment or innovating in order to exploit new opportunities clearly explains all the weird parts of the bush of life, whereas God specifically guiding all the weirdnesses of evolution in order to produce and feed humans, though they have nothing to do with humans, is confusing. But see the post under “algae” for a wider ranging discussion.

Biological complexity: protozoa sans mitochondria

by David Turell @, Saturday, May 14, 2016, 14:03 (2876 days ago) @ dhw

dhw: Adapting to the environment or innovating in order to exploit new opportunities clearly explains all the weird parts of the bush of life, whereas God specifically guiding all the weirdnesses of evolution in order to produce and feed humans, though they have nothing to do with humans, is confusing.-If one takes as a proposition that God created a complexification process, or better, a drive to complexity that is free-ranging, and allowing for Darwin-style survival testing, then all God would have to do is tweak here or there until the most complex, humans, arrived. No need for poor automatic organisms trying to improve, as they automatically become more complex, and perhaps more survivable. A somewhat deist approach which also uses an extension of Denton's structuralism as the basis for evolution, by viewing evolution as basic structures driven to further complexity. It certainly fits the whale puzzle.

Biological complexity: protozoa sans mitochondria

by dhw, Sunday, May 15, 2016, 17:46 (2875 days ago) @ David Turell

dhw: Adapting to the environment or innovating in order to exploit new opportunities clearly explains all the weird parts of the bush of life, whereas God specifically guiding all the weirdnesses of evolution in order to produce and feed humans, though they have nothing to do with humans, is confusing. - DAVID: If one takes as a proposition that God created a complexification process, or better, a drive to complexity that is free-ranging, and allowing for Darwin-style survival testing, then all God would have to do is tweak here or there until the most complex, humans, arrived. - “Free-ranging” is precisely the type of mechanism I have been proposing: i.e. your God does not “guide” organisms to innovate or pursue a particular lifestyle or create a natural wonder (or complexify), but they do it themselves. In my theistic version, I also allow for an occasional dabble. I will refer back to this in the discussion under “algae”.

Biological complexity: protozoa sans mitochondria

by David Turell @, Sunday, May 15, 2016, 20:02 (2875 days ago) @ dhw


> dhw: “Free-ranging” is precisely the type of mechanism I have been proposing: i.e. your God does not “guide” organisms to innovate or pursue a particular lifestyle or create a natural wonder (or complexify), but they do it themselves. In my theistic version, I also allow for an occasional dabble. I will refer back to this in the discussion under “algae”. - In tis possible scheme of things,where we differ is I am referring to complexity as working in the arena of body type and abilities of that body. The weaver nest, migration, etc., I consider lifestyle, where God probably does more.

Biological complexity: protozoa sans mitochondria

by dhw, Monday, May 16, 2016, 15:58 (2874 days ago) @ David Turell

dhw: “Free-ranging” is precisely the type of mechanism I have been proposing: i.e. your God does not “guide” organisms to innovate or pursue a particular lifestyle or create a natural wonder (or complexify), but they do it themselves. In my theistic version, I also allow for an occasional dabble. I will refer back to this in the discussion under “algae”. - DAVID: In this possible scheme of things, where we differ is I am referring to complexity as working in the arena of body type and abilities of that body. The weaver nest, migration, etc., I consider lifestyle, where God probably does more.
 - The “arena of body type and abilities of that body” is what I call innovation, which is the key to evolution. The weaver nest is what I refer to as a natural wonder, and migration as a lifestyle. According to you in every discussion we have had up to now, ALL of them are too complex for the organisms to work out by themselves, and so they ALL have to be “guided”. According to my hypothesis (theistic version), your God endowed cell communities with the intelligence to work these complexities out for themselves. More under “algae”.

Biological complexity: protozoa sans mitochondria

by David Turell @, Monday, May 16, 2016, 17:39 (2874 days ago) @ dhw


> dhw: The “arena of body type and abilities of that body” is what I call innovation, which is the key to evolution. The weaver nest is what I refer to as a natural wonder, and migration as a lifestyle. According to you in every discussion we have had up to now, ALL of them are too complex for the organisms to work out by themselves, and so they ALL have to be “guided”. According to my hypothesis (theistic version), your God endowed cell communities with the intelligence to work these complexities out for themselves. -We disagree to some degree on terms, but at least we are separating the component parts of the evolutionary process. I see no difference in the manufacture of a complex nest and the migration of monarchs though eight metamorphoses as well as the geographic movement as all being part of how the animals conduct their lives (lifestyle), and at the same time the same events are covered equally well by the term natures' wonders. Why differentiate?

Biological complexity: protozoa sans mitochondria

by dhw, Tuesday, May 17, 2016, 11:50 (2873 days ago) @ David Turell

dhw: The “arena of body type and abilities of that body” is what I call innovation, which is the key to evolution. The weaver nest is what I refer to as a natural wonder, and migration as a lifestyle. According to you in every discussion we have had up to now, ALL of them are too complex for the organisms to work out by themselves, and so they ALL have to be “guided”. According to my hypothesis (theistic version), your God endowed cell communities with the intelligence to work these complexities out for themselves. -DAVID: We disagree to some degree on terms, but at least we are separating the component parts of the evolutionary process. I see no difference in the manufacture of a complex nest and the migration of monarchs though eight metamorphoses as well as the geographic movement as all being part of how the animals conduct their lives (lifestyle), and at the same time the same events are covered equally well by the term natures' wonders. Why differentiate?-It's a very minor distinction, of no significance whatsoever in our discussion. I have made it since we started this discussion several years ago, probably when you introduced our much loved weaver nest, which I do not regard as a lifestyle but as a construction. Let's call them all nature's wonders from now on. The important point, of course, is the fact that until now you have always considered organisms incapable of organizing any of them. More under “algae”.

Biological complexity: protozoa sans mitochondria

by David Turell @, Tuesday, May 17, 2016, 22:03 (2873 days ago) @ dhw

David: at the same time the same events are covered equally well by the term natures' wonders. Why differentiate?[/i]
> 
> dhw; It's a very minor distinction, of no significance whatsoever in our discussion. I have made it since we started this discussion several years ago, probably when you introduced our much loved weaver nest, which I do not regard as a lifestyle but as a construction. Let's call them all nature's wonders from now on. The important point, of course, is the fact that until now you have always considered organisms incapable of organizing any of them.-Haven't changed my mind.

Biological complexity: protozoa sans mitochondria

by dhw, Wednesday, May 18, 2016, 11:45 (2872 days ago) @ David Turell

David: ...at the same time the same events are covered equally well by the term natures' wonders. Why differentiate?-dhw; It's a very minor distinction, of no significance whatsoever in our discussion. I have made it since we started this discussion several years ago, probably when you introduced our much loved weaver nest, which I do not regard as a lifestyle but as a construction. Let's call them all nature's wonders from now on. The important point, of course, is the fact that until now you have always considered organisms incapable of organizing any of them.-DAVID: Haven't changed my mind.-And yet the free-ranging “phenotype complexifier mechanism” is capable of inventing “increasingly complex structural changes”, which “in some cases will lead to strange lifestyles as a secondary effect”. So organisms are capable of creating the changes to their bodies, but not of creating the lifestyles that result from them? Does that make sense?

Biological complexity: how viurses attack bacteria

by David Turell @, Wednesday, May 18, 2016, 18:47 (2872 days ago) @ dhw

Bacteriophages are viruses who attack bacteria. Here is how they inject your DNA control mechanisms:-http://phys.org/news/2016-05-viruses-infect-bacteria-tale-tail.html-"To infect bacteria, most bacteriophages employ a 'tail' that stabs and pierces the bacterium's membrane to allow the virus's genetic material to pass through. The most sophisticated tails consist of a contractile sheath surrounding a tube akin to a stretched coil spring at the nanoscale. When the virus attaches to the bacterial surface, the sheath contracts and drives the tube through it. All this is controlled by a million-atom baseplate structure at the end of the tail. EPFL scientists have now shown, in atomic detail, how the baseplate coordinates the virus's attachment to a bacterium with the contraction of the tail's sheath. -***-"The laboratory of Petr Leiman at EPFL has now created a detailed, atom-level model of the transformation of a phage's baseplate, an important structure that controls the phage's ability to find its target bacterium and attach to it, contract its tail, and inject its DNA. The entire baseplate-tail-tube complex consists of one million atoms, making up 145 chains of 15 different proteins, most of which had to be modeled from scratch. To do this, Leiman's lab used the state-of-the-art equipment of the Center for Cellular Imaging and NanoAnalytics (C-CINA) at the University of Basel and the computing resources of EPFL's High Performance Computing department.-"The scientists were also able to identify a minimal set of molecular components in the baseplate that work together like miniature gears to control the activity of the virus's tail. These components, and the underlying functional mechanism, are the same across many viruses and even bacteria that use similar tail-like structures to inject toxins into neighboring cells.-The laboratory of Petr Leiman at EPFL has now created a detailed, atom-level model of the transformation of a phage's baseplate, an important structure that controls the phage's ability to find its target bacterium and attach to it, contract its tail, and inject its DNA. The entire baseplate-tail-tube complex consists of one million atoms, making up 145 chains of 15 different proteins, most of which had to be modeled from scratch. To do this, Leiman's lab used the state-of-the-art equipment of the Center for Cellular Imaging and NanoAnalytics (C-CINA) at the University of Basel and the computing resources of EPFL's High Performance Computing department.-"The scientists were also able to identify a minimal set of molecular components in the baseplate that work together like miniature gears to control the activity of the virus's tail. These components, and the underlying functional mechanism, are the same across many viruses and even bacteria that use similar tail-like structures to inject toxins into neighboring cells."-Comment: How did viruses develop this level of complexity? All of biology shows this, not by chance!

Biological complexity: protozoa sans mitochondria

by David Turell @, Wednesday, May 18, 2016, 20:22 (2872 days ago) @ dhw


> dhw: And yet the free-ranging “phenotype complexifier mechanism” is capable of inventing “increasingly complex structural changes”, which “in some cases will lead to strange lifestyles as a secondary effect”. So organisms are capable of creating the changes to their bodies, but not of creating the lifestyles that result from them? Does that make sense?-Quoting me does not demonstrate that you fully understand my concept: IF organisms are given a 'complexifier mechanism' it will be under God's guidance controls. I've never changed from that position. Therefore they have it, but they don't really control it. As for lifestyles, I've given you examples of Giraffes with giant necks who graze and ignore trees. The necks allow acacia grazing, but it is not a required lifestyle as a result of the development, but it does allow an optional adaptation. It doesn't take much thought to: see tree, eat from tree, but it does require a detoxification process of the poisons. How did that develop, if the first attempts at nibbling induce death? My line of reasoning makes perfect sense if viewed from my propositions.

Biological complexity: protozoa sans mitochondria

by dhw, Thursday, May 19, 2016, 12:42 (2871 days ago) @ David Turell

dhw: And yet the free-ranging “phenotype complexifier mechanism” is capable of inventing “increasingly complex structural changes”, which “in some cases will lead to strange lifestyles as a secondary effect”. So organisms are capable of creating the changes to their bodies, but not of creating the lifestyles that result from them? Does that make sense?
DAVID: Quoting me does not demonstrate that you fully understand my concept: IF organisms are given a 'complexifier mechanism' it will be under God's guidance controls. I've never changed from that position. Therefore they have it, but they don't really control it. -I asked you (under “algae”) to make a choice: did God guide all the complexifications or did organisms work them out autonomously apart from when he occasionally dabbled. Here is your reply: “I've agreed that God might have implanted a phenotype complexifier mechanism which operated on its own but under his watchful eye.” What does “on its own” mean, if not autonomously? And watching is not guiding. You knew what I was asking, but now you do NOT agree that such a mechanism acts on its own, and God does not merely watch, he guides and controls every innovation and natural wonder. Ugh,and there was me thinking we'd saved him all that work! Ugh,ugh, if I can't quote you on your views, who can I quote? Ugh, ugh, ugh, we are back to square one!-DAVID: As for lifestyles, I've given you examples of Giraffes with giant necks who graze and ignore trees. The necks allow acacia grazing, but it is not a required lifestyle as a result of the development, but it does allow an optional adaptation. It doesn't take much thought to: see tree, eat from tree, but it does require a detoxification process of the poisons. How did that develop, if the first attempts at nibbling induce death? My line of reasoning makes perfect sense if viewed from my propositions.-Re giraffes and whales, see “Weird animal forms”. I don't know why you have switched to detoxification, but once again if an innovation is to work, the whole organism must fit in with the novelty, i.e. all the cell communities must cooperate. No advantage from noshing the top of the tree if you end up lying dead at the bottom. But now once more we have your God controlling not only the long neck but also the detoxification process. I note that you also still have God preprogramming every solution to every problem faced by bacteria for the last 3.8 billion years (my post of 17 May at 12.03 under “algae”).

Biological complexity: protozoa sans mitochondria

by David Turell @, Thursday, May 19, 2016, 22:54 (2871 days ago) @ dhw

DAVID: Quoting me does not demonstrate that you fully understand my concept: IF organisms are given a 'complexifier mechanism' it will be under God's guidance controls. -> dhw: I asked you (under “algae”) to make a choice: did God guide all the complexifications or did organisms work them out autonomously apart from when he occasionally dabbled. Here is your reply: “I've agreed that God might have implanted a phenotype complexifier mechanism which operated on its own but under his watchful eye.” What does “on its own” mean, if not autonomously? And watching is not guiding. -I assume you know my thinking. I can envision an automatic mechanism that starts a complexity, but if God doesn't approve, he watches and then corrects the course. It is what I have always meant by 'semi-automatic'. I forget you are the English Professor and I am sometimes sloppy in my descriptions.-> 
> dhw: Re giraffes and whales, see “Weird animal forms”. I don't know why you have switched to detoxification, but once again if an innovation is to work, the whole organism must fit in with the novelty, i.e. all the cell communities must cooperate.-Why? Remember, detox of acacia was a requirement for the giraffes' development, simultaneous with the neck elongation. Shows how the so-called improvement is overly complex.

Biological complexity: protozoa sans mitochondria

by dhw, Friday, May 20, 2016, 13:17 (2870 days ago) @ David Turell

DAVID: Quoting me does not demonstrate that you fully understand my concept: IF organisms are given a 'complexifier mechanism' it will be under God's guidance controls. 
dhw: I asked you (under “algae”) to make a choice: did God guide all the complexifications or did organisms work them out autonomously apart from when he occasionally dabbled. Here is your reply: “I've agreed that God might have implanted a phenotype complexifier mechanism which operated on its own but under his watchful eye.” What does “on its own” mean, if not autonomously? And watching is not guiding. 

DAVID: I assume you know my thinking. I can envision an automatic mechanism that starts a complexity, but if God doesn't approve, he watches and then corrects the course. It is what I have always meant by 'semi-automatic'. I forget you are the English Professor and I am sometimes sloppy in my descriptions.-I hope, hope, hope that you are being sloppy here too and accidentally misreading the above. There is a polar distance between automatic and autonomous. You have always used the word ‘semi-autonomous', and if that is what you mean, we are in business together. If, however, you really mean automatic (i.e. robot-like, following implanted instructions), I shall have to ask which half of the mechanism is NOT automatic and what the non-automatic half actually does, and especially why God might disapprove of a complexity he was responsible for starting.
 
I will now try to formulate the implications of ‘semi-autonomous', if that's what you meant. You would then accept that organisms are possessed of an inventive mechanism (aka phenotype complexification mechanism), which ‘on its own' (autonomously) begins and implements every evolutionary innovation. So when the pre-giraffe starts lengthening its neck and the pre-whale starts adapting itself to the water, God approves and watches them carry on doing their own thing. He may possibly have to step in (this is the non-autonomous bit) if the male protogiraffes kill each other with one bash of the two skulls, or the protowhales drown, i.e. they are making a mess of their ‘complexities', but it is also possible that their autonomous IM makes the adjustments itself. So God allows the autonomous IM to take evolution in whatever direction it pleases, and we can only assume that he approves of the millions of species and variations that come and go (including what you have mysteriously described as “aberrant” and “side channel”), though perhaps he occasionally steps in, e.g. to throw down an asteroid to get rid of the dinosaurs, or to make adjustments to certain apes so that they become human. Otherwise the balance of nature is also left to the organisms themselves, with God watching. We don't know to what extent the all-important environmental changes are left to chance or are also the result of dabbles, but in any case, it is still the autonomous IM that dictates what happens next.-If this summary is accurate, it has major implications for the rest of our discussion, so I'd better stop here to see if I've got it right. I shan't reply to your post on “Weird animal forms”, as that too will depend on the accuracy of the above.

Biological complexity: protozoa sans mitochondria

by David Turell @, Friday, May 20, 2016, 20:26 (2870 days ago) @ dhw
edited by David Turell, Friday, May 20, 2016, 20:39

dhw: I hope, hope, hope that you are being sloppy here too and accidentally misreading the above. There is a polar distance between automatic and autonomous. You have always used the word ‘semi-autonomous', and if that is what you mean, we are in business together. If, however, you really mean automatic (i.e. robot-like, following implanted instructions), I shall have to ask which half of the mechanism is NOT automatic and what the non-automatic half actually does, and especially why God might disapprove of a complexity he was responsible for starting.-You don't view God as I do, even when you put on your theistic hat. First point is that He always uses an evolutionary process for the universe and for life. Secondly, He controls. He may well control the environmental changes as well as the evolutionary processes. You are right, I am sloppy in the way I write about it. I can imagine an IM which is somewhat pre-programmed, starts complexification automatically. It may or may not be a response to stress, or simply a timed drive to complexity. God dabbles if He doesn't like how things are going. All of this is because we do not know how speciation is accomplished. Again it is the dilemma of pre-programming or dabbling or both. -> dhw: If this summary is accurate, it has major implications for the rest of our discussion, so I'd better stop here to see if I've got it right. -I skipped your summary since the above statement of mine clarifies, I hope.

Biological complexity: finding Nucleolus functions

by David Turell @, Friday, May 20, 2016, 22:21 (2870 days ago) @ David Turell

This little dark spot in all nuclei has definite functions in the handling of RNA's, while being composed of liquid layers:-http://phys.org/news/2016-05-liquid-fluid-self-organizes-cell-growth.html-"Although known since the 1830s as a round, dark spot in a cell's nucleus, only recently has the nucleolus gotten its full due. Scientists have learned that besides building a cell's protein factories, this specialized subunit, or organelle, serves more broadly as a control center for cellular growth and health. - ***-"somehow, this biological droplet maintains a complex, compartmentalized internal structure. Brangwynne, an assistant professor of chemical and biological engineering, and other researchers have puzzled over how such a liquid-like object could develop stably compartmentalized layers, rather than just fusing into a homogenous glob.-***-"the constituent proteins and RNA of nucleoli spontaneously assemble themselves into three distinct, liquid layers, thanks to their differing properties such as surface tension and viscosity. Rather like how oil and water can coexist yet remain separate, the nucleolus develops liquid subcompartments, which enable its critical functions. -***-"the protein-based lab work, led by Vaidya, found that droplets of the two main nucleolar proteins, dubbed FIB1 and NPM1, would not blend into each other as a homogenous fluid. Instead, because FIB1's surface tension was higher than NPM1, the former became engulfed by the latter, precisely mimicking the nucleolar structure seen in living cells. As a demonstration of this phenomenon, the researchers also created similar multi-phase drops —liquids embedded within other liquids—using vegetable oil and silicone oil in water.- ***-"For the nucleolus, this layered form follows function. Newly made RNA molecules proceed from the organelle's core into the middle, then outer components, receiving modifications as they do so, as if on an assembly line. Like a factory, nucleoli churn out these RNA bits, which after leaving the nucleolus ultimately enter into the cell's cytoplasm and link up to form structures called ribosomes. Factories in their own right, these ribosomes manufacture a cell's many thousands of proteins.-"Beyond making ribosomes, the nucleolus has lately emerged as a hub for coordinating cellular growth, helping to regulate cell division and even setting the timing of a cell's self-destruction in reaction to stress or damage."-Comment: How much complexity has to be shown in the cell before it is realized that this structure as well as the rest of the cell must have been planned from the beginning? All of this apparatus runs at high speed second by second, and is monitored for mistakes by feedback loops. How did evolution in a blind search find these two cooperative liquids with differing surface tensions? Check out my entry: Friday, May 20, 2016, 15:04 to see Kaufmann's thoughts.

Biological complexity: How to make methane

by David Turell @, Friday, May 20, 2016, 22:38 (2870 days ago) @ David Turell

There are organisms, called methanogens, which make methane naturally by a complex process involving an enzyme with a nickel atom:-http://phys.org/news/2016-05-chemists-longstanding-debate-methane-biologically.html-"More than 90 percent of methane is (and has been) generated by microbes known as methanogens, which are related to bacteria. To make the gas, methanogens use a particular protein known as an enzyme. Enzymes aid chemical reactions in the biological realm like synthetic catalysts do in industrial chemical conversions. Also, the enzyme can run the reaction in reverse to break down methane for energy consumption.-"Scientists know a lot about this microbial enzyme. It creates the burnable gas by slapping a hydrogen atom onto a molecule called a methyl group. A methyl group contains three hydrogens bound to a carbon atom, just one hydrogen shy of full-grown methane.-"To generate methane, the enzyme pulls the methyl group from a helper molecule called methyl-coenzyme M. Coenzyme M's job is to nestle the methyl group into the right spot on the enzyme. What makes the spot just right is a perfectly positioned nickel atom, which is largely responsible for transferring the last hydrogen.- ***-"They also performed another biochemical test and showed that the structure of the major intermediate was the nickel stuck to coenzyme M, the expected result if the reactions took the methyl radical path.- ***-"To further substantiate their results, the team modeled the reaction computationally. They zoomed in on the action within the enzyme, known as methyl-coenzyme M reductase.-"'We found that the methyl radical required the least amount of energy to produce, making that mechanism the frontrunner yet again," said Bojana Ginovska, a computational scientist part of the PNNL team.-"In fact, one of the other intermediates required three times as much energy to make, compared to the methyl radical, clearly putting it out of the running.-"Modeling the reaction computationally also allowed the team to look inside the reductase. Experiments showed that the reaction happens faster at higher temperatures and why: Parts of the protein that helped move the reaction along would move the nickel closer to the methyl-coenzyme M. Shorter distances allowed things to happen faster.-***-"'Nature has designed a protein scaffold that works very precisely, efficiently and rapidly, taking a simple methyl group and a seemingly innocent hydrogen atom and turning it into methane as well as running that reaction in both directions," Ragsdale said. "Now how can chemists design a scaffold to achieve similar results?"-"Raugei said that it would be a major breakthrough if they were able to devise a biomimetic strategy to activate methane, which means to turn it into more useful fuels.-""If nature figured out how to do it in mild conditions, then perhaps we can devise an inexpensive way to design catalysts to convert methane into liquid fuels like we use in our vehicles and jets," he said."-Comment: Again enormous complexity. Enzymes are huge molecules and how did cell communities know to use a nickel atom? Note my bold. Maybe someday we'll be as smart as nature (or God).

Biological complexity: protozoa sans mitochondria

by dhw, Saturday, May 21, 2016, 11:09 (2869 days ago) @ David Turell

dhw: I hope, hope, hope that you are being sloppy here too and accidentally misreading the above. There is a polar distance between automatic and autonomous. You have always used the word ‘semi-autonomous', and if that is what you mean, we are in business together. If, however, you really mean automatic (i.e. robot-like, following implanted instructions), I shall have to ask which half of the mechanism is NOT automatic and what the non-automatic half actually does, and especially why God might disapprove of a complexity he was responsible for starting.-DAVID: You don't view God as I do, even when you put on your theistic hat. First point is that He always uses an evolutionary process for the universe and for life. Secondly, He controls. He may well control the environmental changes as well as the evolutionary processes. You are right, I am sloppy in the way I write about it. I can imagine an IM which is somewhat pre-programmed, starts complexification automatically. It may or may not be a response to stress, or simply a timed drive to complexity. God dabbles if He doesn't like how things are going. All of this is because we do not know how speciation is accomplished. Again it is the dilemma of pre-programming or dabbling or both.-Ah well, square one it is. You have often commented on my vivid imagination, but it lags far behind yours. I simply cannot imagine your God supplying the first cells with programmes to pass on through billions of years and organisms for every single “complexification” in the history of evolution (= preprogramming). Or even constantly dabbling to add twiddly bits (complexities) just for the sake of adding twiddly bits. Nor can I imagine each of these countless “complexities” being timed (long neck on 21 May Year X) or ready for triggering in response to stress - you have discounted a shortage of food for the long neck, so I wonder what alternative “stress” you can think of. Anyway, why stress? Why not in response to an environmental change that allows for new “complexities”? Nor can I imagine God setting up a programme only to find that he doesn't like how it's working out, so he has to dabble to put right his own blunders. What sort of planning is that? -I note you have qualified pre-programmed with “somewhat”, and re-introduced “semi” (now automatic, but previously autonomous). But if God starts each “complexification” automatically according to his own pre-set programme (or dabbles some of them), and organisms do not have an autonomous inventive mechanism to produce their own “complexities”, I can't imagine any kind of “somewhat” or “semi” that will enable organisms to complexify in a way he doesn't like. Please tell us more.

Biological complexity: protozoa sans mitochondria

by David Turell @, Saturday, May 21, 2016, 15:35 (2869 days ago) @ dhw

David: All of this is because we do not know how speciation is accomplished. Again it is the dilemma of pre-programming or dabbling or both.[/i]
> 
> dhw: Ah well, square one it is. I simply cannot imagine your God supplying the first cells with programmes to pass on through billions of years and organisms for every single “complexification” in the history of evolution (= preprogramming). Or even constantly dabbling to add twiddly bits (complexities) just for the sake of adding twiddly bits.-Fair enough: You have given me the task of explaining my vision of God's actions, when all we can see is results. Evolution produces very extreme complexity developed beyond what simple adaptation to stress or competition would imply. This is seen in body forms (neck), mammals birthing in water (Whales), extensive migrations (birds, insects), when the simple thought is 'why bother?' This is where purpose comes into play. Unless you realize this needs planning you won't use purpose as explanations, and you rely on 'imagining' without the underpinning of 'purpose'. My presumed purpose is to produce humans. If that is accepted, all falls into place as a overall concept. We have a beginning (bacteria) and an endpoint (us) but your 'how' questions are what bother you about this. I would like to understand the 'how' but from a different viewpoint; I'm interested, you are critical. Would you be less critical if you understood fully how evolution works? Well, we have to work with what we have.-> dhw: Anyway, why stress? Why not in response to an environmental change that allows for new “complexities”? -The adaptations of epigenetics are small, not very complex, and so far no explanation for speciation.-> dhw:Nor can I imagine God setting up a programme only to find that he doesn't like how it's working out, so he has to dabble to put right his own blunders. What sort of planning is that?-You are describing my problem in trying to explain evolution guided by God: it is still pre-planning codes or dabbles along the way. One or both can be correct, but we have no clue. 
> 
> dhw: But if God starts each “complexification” automatically according to his own pre-set programme (or dabbles some of them), and organisms do not have an autonomous inventive mechanism to produce their own “complexities”, I can't imagine any kind of “somewhat” or “semi” that will enable organisms to complexify in a way he doesn't like. Please tell us more.-What you are asking is when God sets a process in motion, how much leeway is allowed, if any. Tony, I think would say none. But from my non-religious approach, I admit I have no way of knowing when looking at the results evolution produced. It is your suggestion, not mine, that God sets evolution in motion and sits back to watch the fun, making God sound human. He isn't.

Biological complexity: protozoa sans mitochondria

by dhw, Sunday, May 22, 2016, 17:54 (2868 days ago) @ David Turell

dhw: I simply cannot imagine your God supplying the first cells with programmes to pass on through billions of years and organisms for every single “complexification” in the history of evolution (= preprogramming). Or even constantly dabbling to add twiddly bits (complexities) just for the sake of adding twiddly bits.
DAVID: Fair enough: You have given me the task of explaining my vision of God's actions, when all we can see is results. Evolution produces very extreme complexity developed beyond what simple adaptation to stress or competition would imply. This is seen in body forms (neck), mammals birthing in water (Whales), extensive migrations (birds, insects), when the simple thought is 'why bother?' This is where purpose comes into play. Unless you realize this needs planning you won't use purpose as explanations, and you rely on 'imagining' without the underpinning of 'purpose'. My presumed purpose is to produce humans. If that is accepted, all falls into place as a overall concept.-On the contrary, I see purpose as an explanation for every single “complexification” - and the purpose is not complexification for its own sake, or for the production of humans. If an almighty God just wanted to create humans, I can see no reason why he would have specially equipped the first cells to pass on millions of other weird and wonderful “complexifications”, 99% of which have disappeared. What I can imagine is a God who creates an autonomous, inventive mechanism the purpose of which is to seek its own means of survival and improvement. THAT would explain the bush and the extinctions and every other characteristic of evolutionary history.
 
DAVID: We have a beginning (bacteria) and an endpoint (us) but your 'how' questions are what bother you about this. I would like to understand the 'how' but from a different viewpoint; I'm interested, you are critical. Would you be less critical if you understood fully how evolution works? Well, we have to work with what we have.-I don't know how you can be so sure that we are the endpoint. Evolution presumably still has a few more billion years to go. But I am not disputing the extraordinary success of our species: wearing my theist hat, I even consider it feasible that your God might have dabbled to get us. It is the gearing of all forms of life to humanity that I criticize for the reason given above, and because I am interested, I look for an alternative ‘how'. Working with what we have, I have offered you one, but you are so fixed on your God controlling every step that you in turn cannot imagine him deliberately setting up a mechanism that can act without his control. And yet, conversely, you insist that he did precisely that with humans by giving them free will.-dhw: Anyway, why stress? Why not in response to an environmental change that allows for new “complexities”? 
DAVID: The adaptations of epigenetics are small, not very complex, and so far no explanation for speciation.-I am not talking about adaptation. It is innovation that drives evolution, and a change in the environment (e.g. an increase in oxygen) might allow organisms to develop new forms.
 
dhw: Nor can I imagine God setting up a programme only to find that he doesn't like how it's working out, so he has to dabble to put right his own blunders. What sort of planning is that?-DAVID: You are describing my problem in trying to explain evolution guided by God: it is still pre-planning codes or dabbles along the way. One or both can be correct, but we have no clue.-You do indeed have a huge problem, but it would disappear if you acknowledged the possibility that God created a mechanism that would come up with its own inventions. Then it would make sense for him to dabble if he did not like the results, because they would not have been his design.-dhw: But if God starts each “complexification” automatically according to his own pre-set programme (or dabbles some of them), and organisms do not have an autonomous inventive mechanism to produce their own “complexities”, I can't imagine any kind of “somewhat” or “semi” that will enable organisms to complexify in a way he doesn't like. Please tell us more.
DAVID: What you are asking is when God sets a process in motion, how much leeway is allowed, if any. Tony, I think would say none. But from my non-religious approach, I admit I have no way of knowing when looking at the results evolution produced. It is your suggestion, not mine, that God sets evolution in motion and sits back to watch the fun, making God sound human. He isn't.-Since you insist that the inventive mechanism is either programmed or dabbled with, you leave no room for ANY leeway in the creation of new “complexities”. God controls everything. Yes, it is my suggestion that he might have set the mechanism up to relieve boredom, though reserving the right to dabble. But you yourself have frequently referred to God making man in his own image, so it must be possible that he and we have certain attributes in common. After all, you also suggested that he wanted a relationship with us. He could hardly do that if he and we were 100% “different in kind”.

Biological complexity: protozoa sans mitochondria

by David Turell @, Sunday, May 22, 2016, 21:48 (2868 days ago) @ dhw

dhw: What I can imagine is a God who creates an autonomous, inventive mechanism the purpose of which is to seek its own means of survival and improvement. THAT would explain the bush and the extinctions and every other characteristic of evolutionary history.-No it does not explain the weird animals in the bush. Both the whale and the giraffe require enormous physiologic changes to adapt to those body forms. I don't view them as improvements, but complexifications. There is a wide difference in the two words.
> 
> DAVID: We have a beginning (bacteria) and an endpoint (us) but your 'how' questions are what bother you about this. I would like to understand the 'how' but from a different viewpoint; I'm interested, you are critical. Would you be less critical if you understood fully how evolution works? Well, we have to work with what we have.
> 
> dhw: It is the gearing of all forms of life to humanity that I criticize for the reason given above, and because I am interested, I look for an alternative ‘how'. Working with what we have, I have offered you one, but you are so fixed on your God controlling every step that you in turn cannot imagine him deliberately setting up a mechanism that can act without his control. And yet, conversely, you insist that he did precisely that with humans by giving them free will.-The mechanism of evolution with God's control is not the same as giving us consciousness with free will. We then have to deal with the moral concepts of right and wrong. No other animal has to worry about that, and can on on eating each other at will.->> dhw: But you yourself have frequently referred to God making man in his own image, so it must be possible that he and we have certain attributes in common. After all, you also suggested that he wanted a relationship with us. He could hardly do that if he and we were 100% “different in kind”.-Our image relationship is He is consciousness or mind and we also have both, but not to His magnitude. Difference in degree.

Biological complexity: protozoa sans mitochondria

by dhw, Monday, May 23, 2016, 12:53 (2867 days ago) @ David Turell

dhw: What I can imagine is a God who creates an autonomous, inventive mechanism the purpose of which is to seek its own means of survival and improvement. THAT would explain the bush and the extinctions and every other characteristic of evolutionary history.
DAVID: No it does not explain the weird animals in the bush. Both the whale and the giraffe require enormous physiologic changes to adapt to those body forms. I don't view them as improvements, but complexifications. There is a wide difference in the two words.-We don't know why the pre-whale took to water or the pre-giraffe to neck-stretching, but that makes no difference to how it was done. Whether they/God said: “Yippee, this will improve things” or “Yippee, this will complexify things”, your organisms were preprogrammed or dabbled with, and mine were given the means to make their own improvements/complexifications. As regards purpose, your God also said, somewhat cryptically: “I'm complexifying the pre-whale and the pre-giraffe, because my aim is to produce humans.” Mine said, "Just do what you wanner do." Which of those is more likely to lead to the higgledy-piggledy bush?
 
dhw: …you are so fixed on your God controlling every step that you in turn cannot imagine him deliberately setting up a mechanism that can act without his control. And yet, conversely, you insist that he did precisely that with humans by giving them free will.
DAVID: The mechanism of evolution with God's control is not the same as giving us consciousness with free will. We then have to deal with the moral concepts of right and wrong. No other animal has to worry about that, and can on on eating each other at will.-I am not comparing an evolutionary free-for-all to moral choice! My point is that your God was willing to set up “a mechanism that can act without his control”. If he gave humans a freedom of choice between right and wrong, he could also have given other organisms the freedom to work out their own ”complexifications”. -dhw: But you yourself have frequently referred to God making man in his own image, so it must be possible that he and we have certain attributes in common. After all, you also suggested that he wanted a relationship with us. He could hardly do that if he and we were 100% “different in kind”.
DAVID: Our image relationship is He is consciousness or mind and we also have both, but not to His magnitude. Difference in degree.-You are playing with words. Having a relationship with someone does not mean comparing levels of consciousness. If your God's purpose was to create humans, he must have had a reason. You suggested a relationship with us. You also clearly believe that he is aware of right and wrong: otherwise how could he give us the choice? Once you open the door to human attributes, you can hardly close it if I suggest one (boredom) you don't like. God's boredom, stuck there in eternity with nothing but himself to be conscious of, would certainly be of a magnitude far exceeding ours.

Biological complexity: protozoa sans mitochondria

by David Turell @, Monday, May 23, 2016, 15:32 (2867 days ago) @ dhw

DAVID: No it does not explain the weird animals in the bush. Both the whale and the giraffe require enormous physiologic changes to adapt to those body forms. I don't view them as improvements, but complexifications. There is a wide difference in the two words.
> 
> dhw: We don't know why the pre-whale took to water or the pre-giraffe to neck-stretching, but that makes no difference to how it was done. .... As regards purpose, your God also said, somewhat cryptically: “I'm complexifying the pre-whale and the pre-giraffe, because my aim is to produce humans.” Mine said, "Just do what you wanner do." Which of those is more likely to lead to the higgledy-piggledy bush?-I wish we had a reasonable story for whales, giraffes and all the other oddball items in the h-p bush. You are certainly correct that complexifying is present. And since the human brain is the most complex thing evolution has produced, it must be the pinnacle and end point, currently, of that process. And you are correct that God might have let the process do 'just do what you wanner do', and then, I assume, dropped in from time to time to help with problems that developed as complexity went too far. No complexification mechanism is in sight in current research. Unless it is found, and epigenetics is a weak possibility, external intervention is a reasonable conclusion.
> 
> dhw: My point is that your God was willing to set up “a mechanism that can act without his control”. If he gave humans a freedom of choice between right and wrong, he could also have given other organisms the freedom to work out their own ”complexifications”. -Not the same. Our ability of introspection and moralizing is due to consciousness, a result of complexification. Free will/ free choice comes with that. Increasing complexity is built into evolution, so organisms may have a way of increasing it but only humans ended up with a consciousness mimicking God's.
> 
> dhw: Having a relationship with someone does not mean comparing levels of consciousness. If your God's purpose was to create humans, he must have had a reason. You suggested a relationship with us. You also clearly believe that he is aware of right and wrong: otherwise how could he give us the choice? Once you open the door to human attributes, you can hardly close it if I suggest one (boredom) you don't like. God's boredom, stuck there in eternity with nothing but himself to be conscious of, would certainly be of a magnitude far exceeding ours.-Religions give us reasons for God's activities and relationship to us. I simply say I don't know. Adler said God was responsive to our prayers on a 50/50 level of probability. You try to assign human attributes, i.e., boredom, as a way of exploring your concept of God. Don't try. There is no way of knowing. This is not an area of knowledge that has any degree of exactitude, when we have to work backward from what we see. All religion is guesswork.

Biological complexity: red cell enzyme activity

by David Turell @, Monday, May 23, 2016, 15:48 (2867 days ago) @ David Turell

Red cells have no nucleus but have the task of carrying oxygen to the tissues of the body as fuel, and then hauling out CO2 as waste product. The transfer of the gases must be instantaneous, and of course, there is the appropriate enzyme in place:- http://phys.org/news/2016-05-captures-ultrafast-motion-proteins.html-"A new study by an international team of researchers, affiliated with Ulsan National Institute of Science and Technology (UNIST) has announced that they have succeeded for the first time in observing the structural changes in carbonic anhydrase.-*** -"Carbonic anhydrase, which is found within red blood cells, is a crucial enzyme that stabilizes carbon dioxide (CO2 ) concentrations. This enzyme catalyzes a reaction converting CO2 and water into carbonic acid, which associates into protons and bicarbonate ions.-"Moreover, it is also known that carbonic anhydrase is able to catalyze at a rate of 106 reactions per second. In the absence of this catalyst, the conversion from CO2 to bicarbonate, and vice versa, would be extremely slow and difficult.-"One of the important functions of the enzyme in humans is to adjust the acidity of the chemical environment to prevent damage to the body, as well as to help transport carbon dioxide out from tissue cells to the lungs. -***-"Prof. Kim, the lead researcher of the study states, "The reaction rate of carbonic anhydrase is one of the fastest of all enzymes." He continues, "Due to the rapid movement of proteins, direct observation for such movement has been extremely difficult to obtain, protein scientists say.'"-Comment: a movie diagram at the link gives a sense of the speed of the reaction. Usual question: enzymes are huge molecules. How did evolution search for it and get it just right?

Biological complexity: a protein molecule counts

by David Turell @, Monday, May 23, 2016, 17:47 (2867 days ago) @ David Turell

In sorting through DNA, counting for exact stretches is done by a molecule:-https://www.sciencedaily.com/releases/2016/05/160523083825.htm-"A protein of the ISWI family (Imitation Switch, or nucleosome remodelling motors) is endowed with a special property: despite having no organ of sense it is nonetheless able to assess the length of DNA strands. A study just published in the Journal of Statistical Mechanics: Theory and Experiment and carried out by SISSA, the MAX Planck Institute and the NIH has discovered how it works.-"Picture a chromosome as a string of beads. The beads are in fact called nucleosomes and are formed by the DNA strand that makes up the chromosome itself, tightly wrapped around proteins, called histones, which act a bit like spools. Nucleosomes are joined to one other by a segment, of varying length, of the same strand of DNA. The "beads" can be moved along the strand, grouped close together or moved apart, by the action of special proteins called "remodelling motors." One type of these motors arranges the nucleosomes equidistantly on the "string of beads." To know where to move the nucleosomes, the motors need to assess the length of the segments joining them. And this is where the question arises: how can a single molecule "sense" how long a piece of DNA is? (my bold)-***- "'It is indeed a 'sensory' issue, but let's not forget we are dealing with protein complexes, which don't have organs of sense," explains Florescu. (my bold)-***-"What we observed in our calculations is that the longer the DNA segment between one nucleosome and the next the shorter the time it takes the motor to bind to it." In fact the strands immersed in fluid tend to fluctuate randomly and the magnitude and speed of their movement depend on the length of the segment. In practice, the shorter the segment, the faster it oscillates: "in this case, the molecule has more trouble capturing the segment, and it cannot carry out its action until it binds to it." The time it takes the motor to bind to the segment is therefore an indicator of the length of the segment itself.-"The ultimate function of DNA is protein synthesis, a process that starts with the first crucial step of gene transcription: pieces of code contained in the genes are copied to be used as a matrix to build new proteins. For this to happen, the nitrogen bases that make up the DNA strand need to be accessible. When they are tightly packed around the histones, they are unusable. Their rearrangement by the remodelling motors is crucial for freeing them.-"'DNA is tightly packaged because otherwise it wouldn't fit inside the cell nucleus, as we're talking about over two metres of strand in total if we consider the complete human genome. This, though, has the disadvantage of having to unpack it each time it's needed, a task carried out by the remodelling motors that make the chromatin strand accessible so that the transcription process can take place" explains Florescu."-Comment: Obviously, to tightly pack DNA in the nucleus, it is tightly wrapped, and therefore, there must be an unwrapping agent on site. Takes lots of planning. Chance can't do it. It probably works by molecular signals between DNA and the operating molecule, at high speed based on my previous entry about speed of reactions. Note my bolded statements.

Biological complexity: protozoa sans mitochondria

by dhw, Tuesday, May 24, 2016, 13:40 (2866 days ago) @ David Turell

dhw: As regards purpose, your God also said, somewhat cryptically: “I'm complexifying the pre-whale and the pre-giraffe, because my aim is to produce humans.” Mine said, "Just do what you wanner do." Which of those is more likely to lead to the higgledy-piggledy bush?
DAVID: I wish we had a reasonable story for whales, giraffes and all the other oddball items in the h-p bush. You are certainly correct that complexifying is present. And since the human brain is the most complex thing evolution has produced, it must be the pinnacle and end point, currently, of that process. And you are correct that God might have let the process do 'just do what you wanner do', and then, I assume, dropped in from time to time to help with problems that developed as complexity went too far. No complexification mechanism is in sight in current research. Unless it is found, and epigenetics is a weak possibility, external intervention is a reasonable conclusion.-Thank you for this conciliatory post. We all wish we had a reasonable story, not only for whales etc. but for life itself! I agree that humans are the most complex species in terms of what we have created through our extraordinary degree of consciousness, and I am delighted at your acknowledging the possibility that God may have given organisms the means to conduct their own evolution. But with my theistic hat still on, I'm a little surprised at your reason for God dropping in. I can think of at least three different reasons: 1) to get rid of organisms because he's had enough of them; 2) to allow organisms a wider range of inventiveness by changing the environment, e.g. increasing the amount of oxygen; 3) to experiment. The latter would, for instance, allow for special attention to pre-humans, as he worked on them to produce a being “in his own image”. (I too can be conciliatory!) You are of course quite right that no autonomous inventive mechanism - complexification is your term, not mine - has been found, just as no evidence for divine intervention has been found (your explanation that God hides himself does not help the case), but the very fact that some scientists believe cells/cell communities to be intelligent does at least give us a possible starting point.-dhw: My point is that your God was willing to set up “a mechanism that can act without his control”. If he gave humans a freedom of choice between right and wrong, he could also have given other organisms the freedom to work out their own ”complexifications”. 
DAVID: Not the same. Our ability of introspection and moralizing is due to consciousness, a result of complexification. Free will/ free choice comes with that. Increasing complexity is built into evolution, so organisms may have a way of increasing it but only humans ended up with a consciousness mimicking God's.-You left out the fact that I said it was not the same! (“I am not comparing an evolutionary free-for-all to moral choice!”) My only point was to show that your God was willing to give up control.-dhw: Having a relationship with someone does not mean comparing levels of consciousness. If your God's purpose was to create humans, he must have had a reason. You suggested a relationship with us. You also clearly believe that he is aware of right and wrong: otherwise how could he give us the choice? Once you open the door to human attributes, you can hardly close it if I suggest one (boredom) you don't like… 
DAVID: Religions give us reasons for God's activities and relationship to us. I simply say I don't know. Adler said God was responsive to our prayers on a 50/50 level of probability. You try to assign human attributes, i.e., boredom, as a way of exploring your concept of God. Don't try. There is no way of knowing. This is not an area of knowledge that has any degree of exactitude, when we have to work backward from what we see. All religion is guesswork.-Of course it is. And currently all the theories relating to the origin of life and to the mechanism that drives evolution are also guesswork, but that doesn't and shouldn't stop us from trying to find answers to these unsolved mysteries. You yourself have tried to explain how and why God started the process of evolution, and I am doing the same but offering a different view. Both of us are looking for a pattern to explain “what we see”, and there is no reason at all why we should not apply our pattern-forming reason to your God's actions just as we do to every other aspect of our existence. The fact that there cannot be any definitive answers did not stop you writing two excellent books exploring an area of knowledge that has no degree of exactitude, working backward from what you think you see, and coming up with a conclusion that can only be guesswork: “Science is finding God”.

Biological complexity: protozoa sans mitochondria

by David Turell @, Tuesday, May 24, 2016, 20:16 (2866 days ago) @ dhw

dhw: But with my theistic hat still on, I'm a little surprised at your reason for God dropping in. I can think of at least three different reasons: 1) to get rid of organisms because he's had enough of them; 2) to allow organisms a wider range of inventiveness by changing the environment, e.g. increasing the amount of oxygen; 3) to experiment. - God steps in (in my view) to make sure that evolution stays on course to produce humans. The bush is allowed to spread as it wishes. - > dhw;the very fact that some scientists believe cells/cell communities to be intelligent does at least give us a possible starting point.
> 
> dhw: My point is that your God was willing to set up “a mechanism that can act without his control”. If he gave humans a freedom of choice between right and wrong, he could also have given other organisms the freedom to work out their own ”complexifications”. - You still keep touting a small group of scientists to support your hypothesis. So be it. Their chance of being correct is no more than 50/50 and in my view much less. - > 
> dhw: You left out the fact that I said it was not the same! (“I am not comparing an evolutionary free-for-all to moral choice!”) My only point was to show that your God was willing to give up control. - And my point is God knew that having an organism with consciousness would automatically give it free will. His intent was humans with consciousness, so that choice forced Him to accept humans with free will. He was required to allow it or have a limited consciousness. - > David: All religion is guesswork[/i].
> 
> Of course it is.... The fact that there cannot be any definitive answers did not stop you writing two excellent books exploring an area of knowledge that has no degree of exactitude, working backward from what you think you see, and coming up with a conclusion that can only be guesswork: “Science is finding God”. - Thank you.

Biological complexity: protozoa sans mitochondria

by dhw, Wednesday, May 25, 2016, 12:56 (2865 days ago) @ David Turell

dhw: But with my theistic hat still on, I'm a little surprised at your reason for God dropping in. I can think of at least three different reasons: 1) to get rid of organisms because he's had enough of them; 2) to allow organisms a wider range of inventiveness by changing the environment, e.g. increasing the amount of oxygen; 3) to experiment.
DAVID: God steps in (in my view) to make sure that evolution stays on course to produce humans. The bush is allowed to spread as it wishes. - With my theistic hat on, I was surprised at your assumption that God stepped in to “help with problems that developed as complexity went too far”. However, my next sentence concerning experimentation was: “The latter would, for instance, allow for special attention to pre-humans, as he worked on them to produce a being “in his own image””. With God allowing the bush to spread as it wishes (which can only mean organisms having autonomy) - apart from when he dabbles - it seems we are rapidly reaching agreement on our theistic interpretation of evolution. Under “Our reality keeps evolving”, however, you wrote: - “You keep wondering about the bushiness of the bush. This is what complexity for the sake of complexity brings. It also brings the most complex of all, humans, in phenotype and in consciousness. If we could find the mechanism for complexification, perhaps then we would know how much freedom God gave it. Now it is guesswork.” - It makes far more sense to me that organisms and/or your God should look for different means of survival/improvement, rather than complexity just for the sake of complexity. It is perfectly feasible that the giraffe and the whale developed as they did because at the time these changes gave them a better chance of acquiring food. I find it difficult to believe that they (autonomously) or your God (dabbling) would have decided on a longer neck or a life on the ocean wave just for the sake of their becoming more complex. The quest for survival/improvement (whether pursued autonomously or by God's dabbling) would also result in pre-humans eventually becoming more conscious, more intelligent, more flexible, more inventive than all other species. But I agree totally with your final remark: the extent of autonomy, the extent of God's interventions, and the existence of the mechanism and indeed of God himself are all matters of guesswork. What we have are hypotheses, but in terms of how evolution works, an autonomous inventive mechanism provides a convincing explanation for the higgledy-piggledy bush of evolution.
 
dhw: the very fact that some scientists believe cells/cell communities to be intelligent does at least give us a possible starting point.
dhw: My point is that your God was willing to set up “a mechanism that can act without his control”. If he gave humans a freedom of choice between right and wrong, he could also have given other organisms the freedom to work out their own ”complexifications”. 
DAVID: You still keep touting a small group of scientists to support your hypothesis. So be it. Their chance of being correct is no more than 50/50 and in my view much less. - If your God allowed the bush to spread of its own accord, apart from when he dabbled, there has to be an autonomous mechanism. That is why the “intelligent cell” (possibly designed by God) may well be the key to our understanding of evolutionary innovation. But of course it's still only a hypothesis.

Biological complexity: protozoa sans mitochondria

by David Turell @, Thursday, May 26, 2016, 01:40 (2864 days ago) @ dhw


> dhw: It makes far more sense to me that organisms and/or your God should look for different means of survival/improvement, rather than complexity just for the sake of complexity. It is perfectly feasible that the giraffe and the whale developed as they did because at the time these changes gave them a better chance of acquiring food. -I think a drive to complexity is quite apparent, for that is what we see, ending in humans. Your explanation for giraffes and whales as it pertains to food is a real stretch. Some giraffe types graze and don't bother with trees. But the maasai giraffes chose poisonous leaves; what? In desperation because there was nothing else around? And whale precursors jumped into the water because the fish looked so delicious. Sorry, both evolutions require vast physiologic and anatomic phenotypical changes. Complexity!!!-> dhw: But I agree totally with your final remark: the extent of autonomy, the extent of God's interventions, and the existence of the mechanism and indeed of God himself are all matters of guesswork. What we have are hypotheses, but in terms of how evolution works, an autonomous inventive mechanism provides a convincing explanation for the higgledy-piggledy bush of evolution.-You autonomous inventive mechanism (aim) is really equivalent to my drive to complexity mechanism (dcm). In both cases new forms and lifestyles are created, the bush grows, but in my approach God is always guiding, perhaps after seeing what has developed. This is one way dabbling can happen. I'm also still open to full guidance by God. 
> 
> dhw: the very fact that some scientists believe cells/cell communities to be intelligent does at least give us a possible starting point.
> 
> dhw: If your God allowed the bush to spread of its own accord, apart from when he dabbled, there has to be an autonomous mechanism. That is why the “intelligent cell” (possibly designed by God) may well be the key to our understanding of evolutionary innovation. But of course it's still only a hypothesis.-You are correct and I'm toying with my dcm idea which closely approaches yours.

Biological complexity: how we smell odors

by David Turell @, Thursday, May 26, 2016, 15:53 (2864 days ago) @ David Turell

It is a highly complex arrangement where neurons are on the body's surface and are specialized:-http://inference-review.com/article/smells-spanners-and-switches-"Primary olfactory neurons are, under normal circumstances, the only part of our central nervous system that is exposed to the outside air. Each neuron carries on its surface one of a large number of different protein receptors. An even larger number of volatile drugs called odorants are capable of turning on these receptors. The result is the sensation of smell. Two things are peculiar about smell. First, the sensation unerringly discriminates among odorants. As far as we know, no two odorants in the pure state smell the same to us. Second, it has turned out to be impossible to predict the smell of a molecule from its molecular structure.-***-"The most commonly accepted theory is that odor is not written into the molecule, but arises because the odorant happens to fit the shape of its many receptors. If you could by some means change the specificity of each receptor, the perceived odor would be completely different. This makes sense. Lock and key molecular recognition is everywhere in biology; antibodies and enzymes would not work without it.-***
"If both assumptions are correct, then even if receptors have only two positions, N receptors will be able to distinguish 2N smells. For fruit flies, this would mean 2^63, or approximately 10^19 smells. (my bold)
***-"There are sixty-three receptors in fruit flies, approximately four hundred in human beings, and close to a thousand in mice.-***-"To most biochemists, the notion that a vast number of olfactory receptors results in an effectively infinite range of sensations therefore poses no conceptual problem at all. It is small wonder that we cannot predict odor from molecular structure. The task would be difficult enough if there were one receptor involved, as is the case when designing drugs. When there are dozens of receptors, the problem is simply intractable. Whatever the steps from molecular structure to odor, they cannot be followed in reverse. If this is correct, all we can do is retreat and declare victory, which is what mainstream thinking in the field appears to be doing.-***-"The Database of Odorant Responses compiled at the University of Konstanz lists identified receptors in the fruit fly and the molecules known to turn them on (or off) What is striking is the vast range of odorants to which each receptor responds. If a particular odorant generates a significant receptor response, it would be tempting to call the excited receptor the receptor for that odorant. But that would be foolish, since another as yet untried odorant might always give a still larger response.3 Conversely, some odorants inhibit the receptor. This pattern is true of all fruit fly receptors, and there are strong indications of something similar occurring in vertebrate receptors.***-***-"Most odorants activate most receptors to some extent, and if there is a pattern, it must lie in the relative degree of excitation. It is very hard to estimate the discriminatory ability of such a system. Exciting many receptors promiscuously, certain odors may reduce a system's discrimination, while a system's ability to make use of different degrees of excitation may increase it. The balance between the two determines how many odorants can be discriminated. Given our current state of knowledge, we cannot estimate, even approximately, this balance. -***-"No matter its structure, if a molecule contains an -SH group, a rotten egg character is superimposed upon the molecule's other smells. If the molecule smells of pine needles, the total will smell of eggy pine needles, such as in the case of pinanethiol, a grapefruit odorant.-***-"But the situation is more tangled than that. Our ability to detect the presence of distinctive groups of atoms—called functional groups because in large part they determine the chemistry of the molecule—extends far beyond -SH. -***-"No receptor could unerringly detect these functional groups, whatever the molecular context, by conventional molecular recognition. They are too small to have a distinctive shape, and they only interact through one, or perhaps two, hydrogen bonds. Are our noses somehow reading the atomic composition of the molecule?"-Comment: I've presented the beginning of the article, the problem. The author is looking for a solution. We can smell too much for lock and key. (Note my bolded sentence) He proposes looking at electron currents in his future research.

Biological complexity: how we smell odors

by David Turell @, Thursday, May 26, 2016, 18:36 (2864 days ago) @ David Turell

David's Comment: I've presented the beginning of the article, the problem. The author is looking for a solution. We can smell too much for lock and key. (Note my bolded sentence) He proposes looking at electron currents in his future research.-Being afraid of space limitations, I kept comments short. My point in presenting this is the amazing system that is being uncovered, which is thought to involve electron tunneling in a biologic system, a quantum process seen in photosynthesis, which illustrates that quantum mechanics is probably everywhere in biologic evolution. Not surprising, since QM is the basis of everything.-What is surprising is how did evolution see a future need for smelling all these odors, many of which are not predator smell, obviously a necessary one? Although the author dies not state it, I'm sure, like color, the capacity to differentiate is learned. Once again I view this as a drive for complexification, not for survival: men love perfume on women, but that is a late arrival in society, and we were breeding for many years before its arrival. This is one area where humans have a lesser ability than other animals, but we don't need it. We train dogs to follow criminal trails, to spot drugs, etc. We have our 'smarts' to close the gap.

Biological complexity: how plants bind nitrogen

by David Turell @, Thursday, May 26, 2016, 22:04 (2864 days ago) @ David Turell

Legumes are plants that work symbiotically with bacteria to fix atmospheric nitrogen into the soil through their roots. A protein that manages this has been found:-http://phys.org/news/2016-05-scientists-link-nitrogen-fixation.html-
"Scientists at the John Innes Centre have discovered an important component in the process of nitrogen fixation in plants. They have identified a key protein that facilitates the movement of calcium in plant cells. This movement of calcium signals to the plant that nitrogen-fixing bacteria are close by and triggers the development of nodules on its roots to house these bacteria.-"Nitrogen is the most abundant gas in the atmosphere and legumes are able to take nitrogen out of the air and incorporate it into their cells. This is possible because legumes have developed a symbiotic relationship with a particular type of soil bacteria that are housed within their roots. These bacteria take up (or 'fix') the nitrogen and pass it to the plant in exchange for sugars and other nutrients. This function enables legumes to grow with less nitrogen fertiliser.-***-"It has long been known that the interaction between plants and bacteria depends on movement of calcium in plant root cells. This movement of calcium takes place in the central nucleus of plant cells. New research from the John Innes Centre lead by Dr Myriam Charpentier and Professor Giles Oldroyd discovered a set of critically important proteins, called cyclic nucleotide gated channel 15s (CNGC15s), which are essential for the movement of calcium into the nucleus. They found that the CNGC15s facilitate the calcium movement into the nucleus allowing the plant to transfer the information that the nitrogen-fixing soil bacteria are nearby. This enables the plant to initiate the cellular and developmental processes that facilitate bacterial accommodation, allowing establishment of the nitrogen-fixing symbiosis and thus nitrogen fixation.-***-"Professor Oldroyd said: "This discovery demonstrates that there is a CNGC protein located at the edge of the nucleus in plant cells which controls the movement of calcium into the nucleus. This is an important step towards understanding nitrogen fixation in legumes and this understanding will help us to develop more efficient crops."-"Dr Charpentier said: "Although the presence of nuclear calcium signals in plants was demonstrated more than a decade ago, the exact identity of the nuclear calcium channel has remained a mystery. This research identifies the first nuclear calcium channel in plants. Calcium signalling is not only important for symbioses but also for many other processes happening in the plant during development and in response to the environment. Knowing the identity of the nuclear calcium channel will now enable us to better understand how plants use nuclear calcium signals to grow and respond to their environments.'" -Comment: As shown in 'natures wonders', symbiosis is a major part of life's processes. In symbiosis everyone wins, and it can be imagined that this particular case developed stepwise.

Biological complexity: how plants bind nitrogen

by David Turell @, Wednesday, January 29, 2020, 21:05 (1521 days ago) @ David Turell

Another way using bacteria and altered flavonoids:

https://phys.org/news/2020-01-scientists-soil-environment-cheap-steady.html

"Researchers in Rice University's Systems, Synthetic and Physical Biology program detailed how plants have evolved to call for nutrients, using convenient bacteria as a delivery service.

"Their open-access report in Science Advances looks at how plants read the local environment and, when necessary, make and release molecules called flavonoids. These molecules attract microbes that infect the plants and form nitrogen nodules—where food is generated—at their roots.

"When nitrogen is present and available, plants don't need to order in. Their ability to sense the presence of a nearby slow-release nitrogen source, organic carbon, is the key.


"'It's a gorgeous example of evolution: Plants change a couple of (oxygen/hydrogen) groups here and there in the flavonoid, and this allows them to use soil conditions to control which microbes they talk to," said Rice biogeochemist Caroline Masiello, a co-author of the study.

***

"Plants use flavonoids as a defense mechanism against root pathogens and could manipulate the organic carbon they produce to interfere with signaling between microbes and other plants that compete for the same nutrients.

"Overall, they showed that higher organic carbon levels in soil repressed flavonoid signals by up to 98%. In one set of experiments, interrupting the signals between legume plants and microbes sharply cut the formation of nitrogen nodules.

***

"They found the most dramatic effects when dissolved carbons derived from plant matter or compost were present. Plants employ naringenin, a variant of the flavonoid that gives grapefruit its bitter taste, and luteolin, expressed by leaves and many vegetables, to call for microbial nitrogen fixation. These were most curtailed in their ability to find microbes. Quercetin, also found in foods like kale and red onions and used for defense against pests, did not suffer the same fate.

"Masiello noted there's a cost for plants to connect with microbes in the soil.
"These relationships with symbionts are metabolically costly," she said. "Plants have to pay the microbes in photosynthesized sugar, and in exchange the microbes mine the soil for nutrients. Microbial symbionts can be really expensive subcontractors, sometimes taking a significant fraction of a plant's photosynthate.

"'What Ilenne and Tara have shown is one mechanism through which plants can control whether they invest in expensive symbionts," she said. "Among a wide class of signaling compounds used by plants for many purposes, one specific signal related to nutrients is shut off by high soil organic matter, which is a slow-release source of nutrients. The plant signal that says 'come live with us' doesn't get through.

"'This is good for plants because it means they don't waste photosynthate supporting microbial help they don't need. Ilenne and Tara have also shown that signals used for other purposes are slightly chemically modified so their transmission is not affected at the same rate.'"


Comment: this three-way arrangement depends upon carbon availability, plant responses and soil bacteria. So complex I wounder if it possibly evolve by chance, Since it involves figuratively juggling three balls in the air, I would think it was designed.

Biological complexity: how plants roots find potassium

by David Turell @, Tuesday, March 23, 2021, 19:38 (1102 days ago) @ David Turell

Special cell reactions do it:

https://www.sciencedaily.com/releases/2021/03/210323131227.htm

"Even when there was no potassium deficiency, the research team made a very surprising discovery: the concentration of this nutrient in the cytoplasm of the cells increased with each cell layer within the root, from the outside to the inside.

***

"The team of researchers subsequently examined how roots react to potassium deficiency. In doing so, they demonstrated for the first time that if plants are subjected to potassium deficiency, the concentration of potassium is reduced only within certain cells in the root tip. These "postmeristematic cells" directly above the viable stem cells in the root tip react extremely rapidly to potassium deficiency; the concentration of potassium inside the cell (in the cytoplasm) decreases within seconds. It had not previously been known that a certain group of cells located centrally inside the root tip reacts to a potassium deficiency in its surroundings. The researchers named this group of cells "potassium-sensitive niche."

***

"Simultaneously with the decrease in the potassium concentration in the potassium-sensitive niche, calcium signals occur in these cells and spread out in the root. As a messenger substance, calcium controls many processes in living organisms -- just as it does here: the calcium signals start off a complex molecular signalling cascade. This chain of signals, which the researchers were the first to define in detail, ultimately causes not only an increased formation of potassium transport proteins, but also brings about changes in tissue differentiation in the root. This facilitates a more efficient absorption of potassium ions and maintains its distribution in the plant. "For the first time," says Kudla, "using imaging methods, we have visualized the path of potassium in a living organism.'"

Comment: Again we see a complex mechanism that protects the plants ability to find a necessary nutrient. More design evidence.

Biological complexity: how we smell odors

by dhw, Friday, May 27, 2016, 12:57 (2863 days ago) @ David Turell

DAVID: What is surprising is how did evolution see a future need for smelling all these odors, many of which are not predator smell, obviously a necessary one? Although the author dies not state it, I'm sure, like color, the capacity to differentiate is learned. Once again I view this as a drive for complexification, not for survival: men love perfume on women, but that is a late arrival in society, and we were breeding for many years before its arrival. This is one area where humans have a lesser ability than other animals, but we don't need it. We train dogs to follow criminal trails, to spot drugs, etc. We have our 'smarts' to close the gap.
-I have never thought of smell as quite such a mystery, so this article is a real eye-opener (or nose-opener). Unfortunately, it is a bit too technical for me to follow, so perhaps you could just explain what the author regards as the SOURCE of smell, if it's not the molecular structure. I have always assumed that all forms of matter had their own smell, and that dogs, for instance, were able to distinguish the finest nuances - or whatever is the right term for scents. -What I think is beyond question, though, is that in many organisms the sense of smell performs a much wider range of functions than awareness of a predator: alertness to danger, communication, identification, marking out territory, sexual attraction, the hunt for food etc., all of which are essential to survival. I really can't see how the development of any of the senses can be regarded as complexification for its own sake when each of them is so useful in its own right. We know of course that organisms can survive without them, but does anyone seriously believe that having them is not an improvement over not having them?

Biological complexity: how we smell odors

by David Turell @, Friday, May 27, 2016, 15:13 (2863 days ago) @ dhw


> dhw: What I think is beyond question, though, is that in many organisms the sense of smell performs a much wider range of functions than awareness of a predator: alertness to danger, communication, identification, marking out territory, sexual attraction, the hunt for food etc., all of which are essential to survival. I really can't see how the development of any of the senses can be regarded as complexification for its own sake when each of them is so useful in its own right. We know of course that organisms can survive without them, but does anyone seriously believe that having them is not an improvement over not having them?-My interpretation is quite different. Of course, a complex result which is successful will be an improvement. The basic drive is to create complexity to achieve that result. I view 'drive to complexity' as a shotgun approach, and then, per Darwin, what works stays. Your 'seeking improvement' approach sounds more theistically teleological than an agnostic should sound. -As to your question of how it all works, the 'smell buds' are neurons at the surface which then appreciate the chemicals by structure, somehow, yet to be worked out, through theories listed by the author. He doesn't know just yet, but fascinating.

Biological complexity: how we smell odors

by dhw, Saturday, May 28, 2016, 11:35 (2862 days ago) @ David Turell

dhw: What I think is beyond question, though, is that in many organisms the sense of smell performs a much wider range of functions than awareness of a predator: alertness to danger, communication, identification, marking out territory, sexual attraction, the hunt for food etc., all of which are essential to survival. I really can't see how the development of any of the senses can be regarded as complexification for its own sake when each of them is so useful in its own right. We know of course that organisms can survive without them, but does anyone seriously believe that having them is not an improvement over not having them?-DAVID: My interpretation is quite different. Of course, a complex result which is successful will be an improvement. The basic drive is to create complexity to achieve that result. I view 'drive to complexity' as a shotgun approach, and then, per Darwin, what works stays. Your 'seeking improvement' approach sounds more theistically teleological than an agnostic should sound. -A remarkable twist. From having your God maintaining control and carefully planning every innovation and natural wonder, either preprogramming or organizing them all personally, you have suddenly switched to him allowing organisms to do their own thing (yippee for autonomy!) and leaving it to chance whether their purposeless complexifications will actually work (other than when he dabbles). “God guides everything” becomes “Go forth and complexify, and let us hope for the best - except when I dabble.” I love it.-Theistic teleology? If your God designed the autonomous mechanism, I'd suggest he wanted to see what it would come up with (apart from when he dabbled - which leaves scope for special favourites like us humans). Then the only difference between our versions is that your God made organisms seek to complexify for the sake of complexifying, whereas mine made them seek to survive and/or improve. Your mechanism luckily comes up with readymade (saltational) eyes, livers, kidneys, wings by shotgun complexifications, much like Darwin's random mutations without his gradualism, and mine works out how to construct them. If God did not design the mechanism - atheistic version - we still have the same autonomous mechanism producing the same results, yours still by Darwinian luck, mine still by cellular intelligence (See “protozoa” for further discussion.)

Biological complexity: how we smell odors

by David Turell @, Saturday, May 28, 2016, 21:42 (2862 days ago) @ dhw


> dhw: A remarkable twist. From having your God maintaining control and carefully planning every innovation and natural wonder, either preprogramming or organizing them all personally, you have suddenly switched to him allowing organisms to do their own thing (yippee for autonomy!) and leaving it to chance whether their purposeless complexifications will actually work (other than when he dabbles).-I'm just testing out an extension of my original concept from my first book, a drive to complexity. Direct programming or dabbling still remains an issue, which of course, cannot be resolved. But a free complexity mechanism sure explains the weird bush of adaptations.-> 
> Theistic teleology? If your God designed the autonomous mechanism, I'd suggest he wanted to see what it would come up with (apart from when he dabbled - which leaves scope for special favourites like us humans). Then the only difference between our versions is that your God made organisms seek to complexify for the sake of complexifying, whereas mine made them seek to survive and/or improve. ..... we still have the same autonomous mechanism producing the same results, yours still by Darwinian luck, mine still by cellular intelligence -As I have previously explained what appears to be cellular intelligence are purposeful-acting molecular reactions appearing as a neural network look-alike, supported by my recent entry. (Friday, May 27, 2016, 19:12)

Biological complexity: how we smell odors

by dhw, Sunday, May 29, 2016, 13:28 (2861 days ago) @ David Turell

dhw: A remarkable twist. From having your God maintaining control and carefully planning every innovation and natural wonder, either preprogramming or organizing them all personally, you have suddenly switched to him allowing organisms to do their own thing (yippee for autonomy!) and leaving it to chance whether their purposeless complexifications will actually work (other than when he dabbles).-DAVID: I'm just testing out an extension of my original concept from my first book, a drive to complexity. Direct programming or dabbling still remains an issue, which of course, cannot be resolved. But a free complexity mechanism sure explains the weird bush of adaptations.-I am happy that you are now testing out an alternative to your God's preprogramming or dabbling for every innovation and natural wonder in evolutionary history. An autonomous inventive mechanism based on intelligence sure explains the weird bush of functioning adaptations and innovations, not to mention such natural wonders as the weaverbird's nest.-dhw: Theistic teleology? If your God designed the autonomous mechanism, I'd suggest he wanted to see what it would come up with (apart from when he dabbled - which leaves scope for special favourites like us humans). Then the only difference between our versions is that your God made organisms seek to complexify for the sake of complexifying, whereas mine made them seek to survive and/or improve. ..... we still have the same autonomous mechanism producing the same results, yours still by Darwinian luck, mine still by cellular intelligence. 
DAVID: As I have previously explained what appears to be cellular intelligence are purposeful-acting molecular reactions appearing as a neural network look-alike, supported by my recent entry. (Friday, May 27, 2016, 19:12)-A neural network look-alike does not preclude intelligence, any more than a neural network precludes intelligence. I very much doubt that the researchers who confronted the bacteria with “previously un-encountered environmental conditions” concluded that your God had either preprogrammed the bacterial response 3.8 billion years ago or had popped into the laboratory to give the bacteria instructions. The experiment neither supports nor contradicts your belief that bacteria cannot think.

Biological complexity: how we smell odors

by David Turell @, Sunday, May 29, 2016, 15:11 (2861 days ago) @ dhw


> dhw: I am happy that you are now testing out an alternative to your God's preprogramming or dabbling for every innovation and natural wonder in evolutionary history. An autonomous inventive mechanism based on intelligence sure explains the weird bush of functioning adaptations and innovations, not to mention such natural wonders as the weaverbird's nest.-Intelligence was in short supply on the hot barren Earth when life appeared 3.8 billion years ago. Intelligence implies planning, requires thought. That did not appear naturally. Information codes run life's processes. thus the conclusion, that it can only be supplied by God.
> 
> dhw: A neural network look-alike does not preclude intelligence, any more than a neural network precludes intelligence. I very much doubt that the researchers who confronted the bacteria with “previously un-encountered environmental conditions” concluded that your God had either preprogrammed the bacterial response 3.8 billion years ago or had popped into the laboratory to give the bacteria instructions. The experiment neither supports nor contradicts your belief that bacteria cannot think.-A set of molecular reactions that accomplish a purposeful response are a neural network look-alike. Intelligence plans it. Your use of the word 'intelligence' is ethereal. What creates it; where does it come from? Sourceless.

Biological complexity: how we smell odors

by dhw, Monday, May 30, 2016, 09:10 (2860 days ago) @ David Turell

dhw: I am happy that you are now testing out an alternative to your God's preprogramming or dabbling for every innovation and natural wonder in evolutionary history. An autonomous inventive mechanism based on intelligence sure explains the weird bush of functioning adaptations and innovations, not to mention such natural wonders as the weaverbird's nest.-DAVID: Intelligence was in short supply on the hot barren Earth when life appeared 3.8 billion years ago. Intelligence implies planning, requires thought. That did not appear naturally. Information codes run life's processes. thus the conclusion, that it can only be supplied by God.-There are two questions here: 1) are bacteria intelligent? 2) If so, where did their intelligence come from? Since some scientists inform us that bacteria are sentient, cognitive, cooperative, communicative, decision-making beings, we should recognize the possibility that they are intelligent, as all of these are hallmarks of intelligence. If they are intelligent, we should also recognize the possibility that their intelligence may have been given to them by the creative power you call God. As an agnostic, I have never denied this possibility. -dhw: A neural network look-alike does not preclude intelligence, any more than a neural network precludes intelligence. I very much doubt that the researchers who confronted the bacteria with “previously un-encountered environmental conditions” concluded that your God had either preprogrammed the bacterial response 3.8 billion years ago or had popped into the laboratory to give the bacteria instructions. The experiment neither supports nor contradicts your belief that bacteria cannot think.

DAVID: A set of molecular reactions that accomplish a purposeful response are a neural network look-alike. Intelligence plans it. Your use of the word 'intelligence' is ethereal. What creates it; where does it come from? Sourceless.-Yes indeed, a purposeful response is a sign of intelligence. As for the source, see above. However, I must point out that your use of “God” or a “Universal Intelligence” is ethereal. What created it? Where did it come from? Sourceless. And please don't mention First Cause, which explains absolutely nothing.

Biological complexity: how we smell odors

by David Turell @, Monday, May 30, 2016, 14:43 (2860 days ago) @ dhw


> dhw: There are two questions here: 1) are bacteria intelligent? 2) If so, where did their intelligence come from? Since some scientists inform us that bacteria are sentient, cognitive, cooperative, communicative, decision-making beings, we should recognize the possibility that they are intelligent, as all of these are hallmarks of intelligence. If they are intelligent, we should also recognize the possibility that their intelligence may have been given to them by the creative power you call God. As an agnostic, I have never denied this possibility.-I know that. What I cannot accept is in innate ' bacterial intelligence' as a concept, when I can see a logical series of chemical reactions making the proper responses occur.- 
> DAVID: A set of molecular reactions that accomplish a purposeful response are a neural network look-alike. Intelligence plans it. Your use of the word 'intelligence' is ethereal. What creates it; where does it come from? Sourceless.
> 
> dhw: Yes indeed, a purposeful response is a sign of intelligence. As for the source, see above. However, I must point out that your use of “God” or a “Universal Intelligence” is ethereal. What created it? Where did it come from? Sourceless. And please don't mention First Cause, which explains absolutely nothing.-If one believes, as I do in cause and effect, there must be a first cause.

Biological complexity: how we smell odors

by dhw, Tuesday, May 31, 2016, 13:16 (2859 days ago) @ David Turell

DAVID: What I cannot accept is in innate ' bacterial intelligence' as a concept, when I can see a logical series of chemical reactions making the proper responses occur.-I don't have a problem when you agree - as you frequently do - that there is a 50/50 chance that you are wrong. Under “Denton” you have acknowledged that “lesser” organisms are able to recognize beneficial relationships, and again you agree that nobody knows the extent to which individual cells (bacteria) can think. But all too often you state your negative view as fact, and this has major ramifications for the concept of an autonomous, intelligent, inventive, “complexification” mechanism. For further discussion, please see under “protozoa”. -DAVID: A set of molecular reactions that accomplish a purposeful response are a neural network look-alike. Intelligence plans it. Your use of the word 'intelligence' is ethereal. What creates it; where does it come from? Sourceless.-dhw: Yes indeed, a purposeful response is a sign of intelligence. As for the source, see above. However, I must point out that your use of “God” or a “Universal Intelligence” is ethereal. What created it? Where did it come from? Sourceless. And please don't mention First Cause, which explains absolutely nothing.-DAVID: If one believes, as I do in cause and effect, there must be a first cause.
-Once more, I also believe in cause and effect, but that does not mean the first cause has to be a conscious mind. I can ask how “pure energy” could always have been conscious (and what was there for it to be conscious of), and you can ask how an unconscious first cause acquired consciousness. Impossible to answer. The term is a philosophical dead end.

Biological complexity: how we smell odors

by David Turell @, Wednesday, June 01, 2016, 01:39 (2858 days ago) @ dhw


> dhw: I don't have a problem when you agree - as you frequently do - that there is a 50/50 chance that you are wrong. Under “Denton” you have acknowledged that “lesser” organisms are able to recognize beneficial relationships, and again you agree that nobody knows the extent to which individual cells (bacteria) can think.-The implication of the way you have stated my position is wrong. No one knows if cells think. But that is a concept I totally reject. They cannot think, but are programmed to look as if they can. Thru God's agency.-> DAVID: If one believes, as I do in cause and effect, there must be a first cause.
> -> 
> dhw: Once more, I also believe in cause and effect, but that does not mean the first cause has to be a conscious mind. I can ask how “pure energy” could always have been conscious (and what was there for it to be conscious of)-Itself-> dhw:and you can ask how an unconscious first cause acquired consciousness. Impossible to answer. The term is a philosophical dead end.- You can have your first cause and I can have mine. At least my thinking type can explain the complexity of reality.

Biological complexity: how we smell odors

by dhw, Wednesday, June 01, 2016, 12:48 (2858 days ago) @ David Turell

dhw: I don't have a problem when you agree - as you frequently do - that there is a 50/50 chance that you are wrong. Under “Denton” you have acknowledged that “lesser” organisms are able to recognize beneficial relationships, and again you agree that nobody knows the extent to which individual cells (bacteria) can think.
DAVID: The implication of the way you have stated my position is wrong. No one knows if cells think. But that is a concept I totally reject. They cannot think, but are programmed to look as if they can. Thru God's agency.-As I said in the rest of the passage you have quoted: “...all too often you state your negative view as fact.” This dogmatic approach colours all your thinking, even though the concept of the intelligent cell is in no way a threat to your theism. Of course, you are perfectly entitled to your opinion, and as nobody knows the truth, you may be right, but this forum is a quest for possible truths (we are never going to establish absolute, objective truths), so I hope you will forgive me if I continue to probe, as with your comment under “intercellular signalling”: 
 
DAVID: It is all molecular, purposeful transmembrane reactions:-http://www.the-scientist.com/?articles.view/articleNo/45904/title/Kissing-Cousins/&...-All communication (other than what we term “psychic”) depends on molecular reactions of one sort or another. The mystery is not the technique of communicating but the source of the messages to be communicated.-David's comment: this exact mechanism is not the important point. It is a good illustration of how cells communicate in organisms, and these various communication techniques are still being found. This may look like the cells are intelligent in signaling, but the opposite view is this is an aspect of intelligent planning in the information that is at the basis of life's processes.-If the cells don't do their own “planning”, either your God preprogrammed all the messages when life began, or he personally provided and provides them ad hoc (dabbled/dabbles) when each new situation arises. This seems to me somewhat less likely than cells doing their own processing and taking their own decisions on what to communicate to one another. It is perfectly possible that what looks like intelligence actually is intelligence, and of course they may have acquired their intelligence “thru God's agency”.-DAVID: If one believes, as I do in cause and effect, there must be a first cause.

dhw: Once more, I also believe in cause and effect, but that does not mean the first cause has to be a conscious mind. 
DAVID: You can have your first cause and I can have mine. At least my thinking type can explain the complexity of reality.-Fair comment. Unfortunately, an atheist could say that an infinite and eternal process of self-transforming energy and matter would eventually and inevitably produce the same complexity of our reality.

Biological complexity: how we smell odors

by David Turell @, Wednesday, June 01, 2016, 21:29 (2858 days ago) @ dhw


> dhw: Of course, you are perfectly entitled to your opinion, and as nobody knows the truth, you may be right, but this forum is a quest for possible truths (we are never going to establish absolute, objective truths), so I hope you will forgive me if I continue to probe,-I want you to probe. It helps clarify my thoughts. -> 
> dhw: All communication (other than what we term “psychic”) depends on molecular reactions of one sort or another. The mystery is not the technique of communicating but the source of the messages to be communicated.-In cells it is the molecular reactions that act purposively and are programmed that way. The source is not chance but design.-
> 
> David's comment: this exact mechanism is not the important point. It is a good illustration of how cells communicate in organisms, and these various communication techniques are still being found. This may look like the cells are intelligent in signaling, but the opposite view is this is an aspect of intelligent planning in the information that is at the basis of life's processes.
> 
> dhw: If the cells don't do their own “planning”, either your God preprogrammed all the messages when life began, or he personally provided and provides them ad hoc (dabbled/dabbles) when each new situation arises. This seems to me somewhat less likely than cells doing their own processing and taking their own decisions on what to communicate to one another. It is perfectly possible that what looks like intelligence actually is intelligence, and of course they may have acquired their intelligence “thru God's agency”.-Nice balancing act on your fence.
> 
> dhw: Fair comment. Unfortunately, an atheist could say that an infinite and eternal process of self-transforming energy and matter would eventually and inevitably produce the same complexity of our reality.-The atheist has to propose that energy can be self-transforming, something no one has ever observed.

Biological complexity: how we smell odors

by dhw, Thursday, June 02, 2016, 12:40 (2857 days ago) @ David Turell

dhw: Of course, you are perfectly entitled to your opinion, and as nobody knows the truth, you may be right, but this forum is a quest for possible truths (we are never going to establish absolute, objective truths), so I hope you will forgive me if I continue to probe.
DAVID: I want you to probe. It helps clarify my thoughts. - Thank you. The discussions and articles on the latest research are immensely helpful to me too. - dhw: All communication (other than what we term “psychic”) depends on molecular reactions of one sort or another. The mystery is not the technique of communicating but the source of the messages to be communicated.
DAVID: In cells it is the molecular reactions that act purposively and are programmed that way. The source is not chance but design. - It is clear that after your brief flirtation with a “free” complexity mechanism you are now reverting to preprogramming and dabbling. But we should be careful to distinguish between stages. I am also claiming that the source of the messages is “design” in the sense that cellular intelligence (possibly designed by your God) processes and communicates the information and takes the decisions based on that information. Chance is not an option. - dhw: If the cells don't do their own “planning”, either your God preprogrammed all the messages when life began, or he personally provided and provides them ad hoc (dabbled/dabbles) when each new situation arises. This seems to me somewhat less likely than cells doing their own processing and taking their own decisions on what to communicate to one another. It is perfectly possible that what looks like intelligence actually is intelligence, and of course they may have acquired their intelligence “thru God's agency”.
DAVID: Nice balancing act on your fence. - Not quite. “Somewhat less likely” is a gently understated way of tilting the balance! Your “free complexity mechanism” which allows the bush to “spread as it wishes”, while God “only steps in to dabble” seems to me vastly more likely than your dramatic reversion to your God putting in “programs to organize what complexifications are created”. - dhw: … an atheist could say that an infinite and eternal process of self-transforming energy and matter would eventually and inevitably produce the same complexity of our reality.
DAVID: The atheist has to propose that energy can be self-transforming, something no one has ever observed. - But that is YOUR proposal: that “pure energy” transformed itself into a universe! My atheistic proposal is based on the fact that energy and matter are forever transforming themselves, and we see it all the time in the physical world around us and even within us!

Biological complexity: how we smell odors

by David Turell @, Friday, June 03, 2016, 01:55 (2856 days ago) @ dhw


> dhw: It is clear that after your brief flirtation with a “free” complexity mechanism you are now reverting to preprogramming and dabbling. But we should be careful to distinguish between stages. I am also claiming that the source of the messages is “design” in the sense that cellular intelligence (possibly designed by your God) processes and communicates the information and takes the decisions based on that information. Chance is not an option.-I'm still working on the complexification theory. Note previous comments today.->> Not quite. “Somewhat less likely” is a gently understated way of tilting the balance! Your “free complexity mechanism” which allows the bush to “spread as it wishes”, while God “only steps in to dabble” seems to me vastly more likely than your dramatic reversion to your God putting in “programs to organize what complexifications are created”.-I am inclined to agree with your assessment.-> DAVID: The atheist has to propose that energy can be self-transforming, something no one has ever observed.
> 
> dhw; But that is YOUR proposal: that “pure energy” transformed itself into a universe! My atheistic proposal is based on the fact that energy and matter are forever transforming themselves, and we see it all the time in the physical world around us and even within us!-But my original cause is a mind! From the beginning, no conversions. And of course energy/matter transformations are under the control of the mechanisms that mind set up.

Biological complexity: chromosome and how we smell odors

by David Turell @, Saturday, January 19, 2019, 00:43 (1896 days ago) @ David Turell

Chromosomes change neurons as part of the process; one odor per neuron:

https://www.nature.com/articles/d41586-019-00010-6

"Mammals can discriminate between a vast number of volatile compounds — perhaps more than a trillion. This extraordinary capacity is encoded by a repertoire of hundreds of olfactory-receptor genes, distributed in small groups that are present on almost all chromosomes2. To ensure that the response to individual odours is specific, each olfactory sensory neuron (OSN) expresses a single, randomly selected olfactory-receptor gene. Writing in Nature, Monahan et al.3 show that, in the nuclei of mouse OSNs, certain regions of multiple chromosomes assemble in a structure that controls the expression of the full repertoire of olfactory-receptor genes in the nose, while making sure that each cell expresses only one type of receptor. These exciting findings show that interchromosomal interactions can have a determinant role in regulating gene expression.

"The expression of vertebrate genes is regulated by activating genomic elements called enhancers. Enhancers can be located far from the genes themselves4, but they are typically present on the same chromosome as the gene they regulate (cis interactions). These regulatory interactions are mediated by transcription factors, assisted by other proteins, and require the participating proteins and DNA elements to be closely connected in the nucleus.

"Molecular techniques, such as Hi-C5, that capture the 3D folding of chromatin (DNA and associated proteins) have revealed that the interactions between genes and their enhancers occur in compact structures called topologically associating domains (TADs) that organize chromosomes into distinct cis neighbourhoods6. Hi-C analyses have also uncovered specific interactions between genes and genomic elements located much farther away from each other, in different TADs and even on different chromosomes (these are called trans interactions)

***

"why would olfactory-receptor genes require such a large number of elements to regulate their expression, whereas most other genes need only a few? One possibility is that the transition of olfactory-receptor genes from a repressed, heterochromatic state to an active state requires many LHX2 binding sites to ensure that enough chromatin-remodelling proteins, which are necessary for this transition, are recruited. Alternatively, the use of ‘weak’ enhancers that only function as activators collectively might limit the possibility that more than one olfactory-receptor gene is expressed in a cell, and also avoid favouring the expression of olfactory-receptor genes close to ‘strong’ enhancers. The principle underlying this mechanism would be similar to the use of transcription-factor binding sites that have low or modest affinity at enhancers to achieve specificity of gene expression.

***

"It remains unclear whether interchromosomal interactions similar to those displayed by olfactory-receptor genes in OSNs occur frequently between other genomic regions in other cell types, although trans interactions have been reported in a few other cases of stochastic regulation of gene expression15,16. Interchromosomal interactions might therefore be primarily a mechanism for generating diversity in a population of otherwise indistinguishable cells. Because their characteristic signatures are masked by cell-population averages, these cases are difficult to identify. The development and improvement of techniques for analysing gene expression and chromatin conformation in single cells might, in the near future, reveal new examples of 3D genomic structures and functional trans-regulatory interactions."

Comment: The obvious reason for the complexity is our ability to distinguish each odor as learned by memory with every new encounter and keep the recognitions separate and pure. What is the real question is how did this evolve? Were the variety of odors minimal in early mammalian life so the mechanism could develop bit by bit? Or perhaps, more reasonably, was this all designed from the beginning?

Biological complexity: how we smell odors

by David Turell @, Tuesday, August 13, 2019, 21:10 (1690 days ago) @ David Turell

A new review:

https://www.scientificamerican.com/article/how-we-are-wired-for-smell/?utm_source=newsl...

"Olfactory neurons in your nose have evolved some 400 odor receptors, and each neuron contains only one. Receptors are tuned to detect a few basic odors apiece: some detect geranium petals or pine needles, while others detect the by-products of putrefaction. To organize all this information, your olfactory neurons wire into an “olfactory map” on your brain’s olfactory bulb. Olfactory neurons are one of the few types of neurons that are born throughout your life, and each of the roughly 10,000 such neurons born each day in your nose subsequently wires into the olfactory map in your brain.

"Incredibly, all the neurons containing a given odor receptor wire to the same spot on the map, such that each half of your olfactory bulb has 400 distinct regions. The combination of regions turned on by a given odor is what makes it seem unique. This fact may be why odors are so evocative: that glass of wine reminds you of a freshly opened can of tennis balls because whatever was in the can is also in the wine.

***

"Working in mice—which have more than 1,000 odor receptors—the study’s authors showed that each receptor, in the absence of an odor, produces a specific type of electrical noise. This might mean firing in short bursts between long pauses; it could also mean firing on specific intervals. These noise events then exquisitely control the set of genes directing an olfactory neuron’s growth as it wires to the olfactory map. Because two neurons with the same odor receptor will experience very similar noise, they will end up wiring to the same place. And because all 400 of your receptors are different—if only slightly—the noise they produce is different, too, causing them to wire to distinct locations. The end result is a 400-location map that functions like the perfumer’s organ equivalent of the “The Library of Babel.”

"These discoveries open up a number of avenues for further work. For example, we do not understand how noisy electrical activity could so precisely control the activity of genes involved in neuronal wiring.

Comment: Amazing setup. One neuron, one odor. It is obvious that these are special focused neurons Which had to designed to work from the beginning of noses starting to operate 'smelling' odor identification, which is learned from each new experience.

Biological complexity: how we smell odors

by David Turell @, Wednesday, September 04, 2019, 22:55 (1668 days ago) @ David Turell

Much more complex than thought:

https://medicalxpress.com/news/2019-07-quantifying-brain.html

"Scientists haven't quite decoded how animals smell, but researchers at Cold Spring Harbor Laboratory (CSHL) found that it's different from previously thought.

***

"Their results, published in the journal Nature Neuroscience, differ from other published studies that found predictable relations between molecular properties of odors and activity in the early stages of the olfactory system. The new research found that while there were some correlations between some molecular properties of odors and corresponding neuron activity response, they "held little predictive power when new odor pairs or shuffled properties were tested."

"When it comes to smell, "we don't really know what the brain is looking for, and we don't know what physical or chemical features, if any, the brain extracts," Albeanu said.

Generally, scientists know that odor particles first enter through the nasal cavity, where odorant receptors expressed by olfactory receptor neurons in the sensory tissue bind to them. The olfactory bulb, a structure located in the forebrain of mammals, then processes information sent up from the receptors. Afterwards, the bulb sends out this information to several higher processing brain areas, including the cerebral cortex. There, the olfactory output messages are further analyzed and broadcast across the brain before they're conveyed back to the bulb in a feedback loop.

"'Rich feedback makes the olfactory system somewhat different from the visual system," Koulakov said. "Olfactory experience is very subjective, perception of smells actually depends on the context, and on an individual's prior experience."

"Factoring these in, Albeanu and Koulakov said it's probable that the entry-level of olfactory inputs and the further processed bulb outputs care about different aspects of smell.

"The "rather unexpected" results of the new research, Koulakov said, are an exciting opportunity to build a more comprehensive and testable computational model for the odor space that captures the differences in informational relevance for scent features across the various levels of olfactory processing."

Comment: It was known that individual neurons picked up individual scents, but how the brain processed them is more complex than thought. It is obvious that prior experience is a great teacher. But the mechanism of smell is a very sophisticated design:

From the article itself:

https://evolutionnews.org/2019/08/sense-of-smell-requires-optimized-scalable-network-ci...

"Specifically, identification of individual odors is linked to the strength and combination of firing neurons in the circuit that can be likened to music from a piano, whose notes spring from the depression of multiple keys to create chords, or the arrangement of letters that form the words on this page.

“The discrimination of odors is based on the firing rate, the electric pulse that travels down the neuron’s axon,” says Srinivasan. “One odor, say for coffee, may elicit a slow response in a neuron while the same neuron may respond to chocolate at a faster rate.'”

Biological complexity: how we smell odors; very well

by David Turell @, Monday, March 30, 2020, 21:03 (1460 days ago) @ David Turell

As a highly advanced species we have not lost our sense of smell, and it is not fooled like our vision can be:

https://aeon.co/essays/why-might-it-be-easier-to-fool-your-eyes-than-your-nose

Your nose is the best biosensor on the face of the Earth. This claim must sound counterintuitive since the sense of smell has acquired a rather poor reputation over the past centuries.

***

"Recent scientific advances have debunked several myths about smell. First, human olfactory physiology is not in evolutionary decline. In 2017, a review in Science finally set the record straight by analysing contemporary research in olfaction. Although smaller in proportion to overall body mass, the olfactory bulb (the first cortical structure of the olfactory pathway) in humans has just as many neurons as in rodents. Further, the bulb is one of the most densely populated neuronal areas of the brain. It thus depends on how you measure size and define proportions. (my bold)

"Second, the sense of smell continues to be important to human cognition and to culture. Cross-cultural studies about language use have shown that other societies, such as the Jahai and Maniq in Southeast Asia, have extensive odour vocabularies and rites. Likewise, in the Western hemisphere, the fragrance industry has been successively expanding.

***

"How good is your sense of smell, really? The human nose has been measured to detect minuscule amounts of molecules in complex chemical mixtures. Humans can sense the presence of particular odorants (smelly molecules) in dilutions of less than one part in several billion parts of air. Take the case of corked wine, which is primarily caused by the compound 2,4,6-trichloroanisole, in short: TCA. Although sensitivity to this compound varies between individuals, the threshold for its detection lies in the 10 to single-digit parts per trillion.

***

"Why did the nose evolve to be so sensitive? Most of the molecules you smell could kill you in high enough concentrations, in addition to your chemical environment changing constantly. Humans, in particular, move habitats a lot. Their sense of smell thus needs to be fairly sensitive and flexible to measure the largely unpredictable chemical constituents of changing environments. So it’s good to have such a fine-tuned instrument monitoring the fluctuating chemical concentrations in your surroundings. It’s just not helpful to be aware of its workings all the time. Sitting in the backseat of conscious awareness, we simply don’t pay much attention to what the nose knows. Olfaction further does not fit well in traditionally visuocentric understandings of the nature of perception.

***

"Varying sensitivities to odorants, including androstenone, have notably been linked to genetic differences in the olfactory receptor repertoire of people (most prominently in a recent series of studies). To be sure, diversity of olfactory receptor genetics is not the only causal factor explaining the variations in sensitivities to odorants. Other factors include a person’s familiarity with an odour, as well as age and sensitivity training.

***

"Illusions provide us with examples of how our visual system can be fooled based on its distinct causal set-up.

"By comparison, it is much harder to trick your nose. Certainly, olfaction is much more variable in its perceptual expression than vision. But this variation doesn’t mean that the nose has been misled. Olfaction simply does not work analogously to the visual system. Crucially, feature coding in smell is not viewpoint-invariant. On the contrary, the causal principles of the olfactory system facilitate a cue-dependent interpretation in the computational integration of its neural signals.

***

"Received philosophical analysis approaching the objectivity of the senses as ‘one percept matching one stimulus’ proved an ill-defined artifact of a prescientific intellectual tradition. It obscures our understanding of smell. It bypasses a lot of other sensory sensations, including the hidden senses of proprioception and interoception. And it even obscures genuine understanding of vision. In effect, it is their causal principles and mechanisms – not some naive input-output pairing that treats the sensory system as a black box – that determines how our senses grant us access to reality. To understand perception across all senses, including perceptual constancy as well as variation, requires a much more detailed look at the actual processes that connect the world with our mind. Only that way might we get to understand both."

Comment: Our nose really knows, as a very specialized part of our brain. Note my bold above.

Biological complexity: how we smell odors; very well

by David Turell @, Sunday, April 12, 2020, 21:27 (1447 days ago) @ David Turell

More studies on odor identification:

https://www.sciencedaily.com/releases/2020/04/200409141541.htm

"The cells in the nose that detect smells each have one of a wide range of different sensors, or receptors; humans, for example have up to 400 different types of these receptors. For a pure, single odor, only the cells whose receptors are sensitive to that odor will become active, sending a code to the brain that it can identify as that odor. But for more complex mixtures of odors, this code would become increasingly complex to interpret.

"The researchers expected to see that the cells activated by mixtures of odors would be equivalent to adding together responses to individual odors. In fact, they found that in some cases an odor can actually turn off a cell's response to another odor in a mixture; in other cases, a first odor could amplify a cell's response to a second odor.

***

"The team's data challenged the traditional view that the brain makes sense of a mixture of scents by figuring out all of the individual components. It confirmed what perfumers have long known: combining different scents can create a certain experience on its own, essentially becoming an entirely new scent that can provide a completely different experience.

"'We were excited to find that these changes in the code happened in the nose, before signals even get to the brain," said Lu Xu, a doctoral candidate in the Firestein lab and the co-first author of today's study. "We think that these effects could help us to detect and identify a much larger range of odors and mixtures than a simple additive code could convey."

"'Our results showed that scent molecules can both activate and deactivate receptors, masking other scents not by overpowering them, but by changing the way cells respond to them," said Dr. Hillman, who is professor of biomedical engineering at Columbia School of Engineering and Applied Science. "These findings could actually be very useful, for example to make better air fresheners that actually block out any unwanted smells."

"'These results are also exciting because we didn't expect that this kind of receptor could be enhanced or suppressed in this way," added Dr. Firestein. "Being able to change the way a receptor responds to one substance is very important for drug development. Our studies in the nose actually shed new light on possible ways to modulate the response of other cell types that might be involved in disease.'"

Comment: A very complex system which does a lot of sorting in the olfactory bulb before sending signals to the brain. This is one area where the specialization of humans changed nothing.

Biological complexity: how we smell odors; very well

by David Turell @, Wednesday, August 04, 2021, 22:55 (968 days ago) @ David Turell

New research on how receptors work to sort out odors:

https://phys.org/news/2021-08-reveals-receptors.html

"'The olfactory system has to recognize a vast number of molecules with only a few hundred odor receptors or even less," says Rockefeller neuroscientist Vanessa Ruta. "It's clear that it had to evolve a different kind of logic than other sensory systems."

***

"The findings, published in Nature, reveal that olfactory receptors indeed follow a logic rarely seen in other receptors of the nervous system. While most receptors are precisely shaped to pair with only a few select molecules in a lock-and-key fashion, most olfactory receptors each bind to a large number of different molecules. Their promiscuity in pairing with a variety of odors allows each receptor to respond to many chemical components. From there, the brain can figure out the odor by considering the activation pattern of combinations of receptors.

***

"The team turned to the jumping bristletail, a ground-dwelling insect whose genome has been recently sequenced and has only five kinds of olfactory receptors. Although the jumping bristletail's olfactory system is simple, its receptors belong to a large family of receptors with tens of millions of variants thought to exist in the hundreds of thousands of different insect species. Despite their diversity, these receptors function the same way: They form an ion channel—a pore through which charged particles flow—that opens only when the receptor encounters its target odorant, ultimately activating the sensory cells that initiate the sense of smell.

"The researchers chose OR5, a receptor from the jumping bristletail with broad recognition ability, responding to 60 percent of small molecules they tested.

***

"It turned out that both DEET and eugenol bind at the same location and fit entirely inside a simple pocket within the receptor. And surprisingly, the amino acids lining the pocket didn't form strong, selective chemical bonds with the odorants, but only weak bonds. Whereas in most other systems, receptors and their target molecules are good chemical matches, here they seemed more like friendly acquaintances. "These kinds of nonspecific chemical interactions allow different odorants to be recognized," Ruta says. "In this way, the receptor is not selective to a specific chemical feature. Rather, it's recognizing the more general chemical nature of the odorant," Ruta says.

"And as computational modeling revealed, the same pocket could accommodate many other odor molecules in just the same way.

"But the receptor's promiscuity doesn't mean it has no specificity, Ruta says. Although each receptor responds to a large number of molecules, it is insensitive to others. Moreover, a simple mutation in the amino acids of the binding site would broadly reconfigure the receptor, changing the molecules with which it prefers to bind. This latter finding also helps to explain how insects have been able to evolve many millions of odor receptor varieties suited for the wide range of lifestyles and habitats they encounter."

Comment: this gives us a general idea of how the receptors attach to odorant chemicals, bu t not how the brain sorts out the complex messages it must be getting.

Biological complexity: protozoa sans mitochondria

by dhw, Thursday, May 26, 2016, 17:17 (2864 days ago) @ David Turell

DAVID: I think a drive to complexity is quite apparent, for that is what we see, ending in humans. Your explanation for giraffes and whales as it pertains to food is a real stretch. Some giraffe types graze and don't bother with trees. But the maasai giraffes chose poisonous leaves; what? In desperation because there was nothing else around? And whale precursors jumped into the water because the fish looked so delicious. Sorry, both evolutions require vast physiologic and anatomic phenotypical changes. Complexity!!!-Yes of course there is complexity, but we are talking about WHY pre-giraffes first grew long necks and pre-whales first entered the water, i.e. why the new complexity may have been necessary in the first place. You suggest that either the pre-giraffes/whales or God said: “Let there be complexity for the sake of complexity.” I suggest: “Not much food here. Better try higher up/the sea.” Once the new species was established, conditions may have changed, or it may subsequently have moved to different environments, but if it has been successful, it will survive. No need to shorten the neck again, or go back to living on land! In other words, the new complexities resulted from the drive for survival/improvement and were not an end in themselves.-dhw: …in terms of how evolution works, an autonomous inventive mechanism provides a convincing explanation for the higgledy-piggledy bush of evolution.
DAVID: You autonomous inventive mechanism (aim) is really equivalent to my drive to complexity mechanism (dcm). In both cases new forms and lifestyles are created, the bush grows, but in my approach God is always guiding, perhaps after seeing what has developed. This is one way dabbling can happen. I'm also still open to full guidance by God.-“Always guiding” is misleading. If “the bush is allowed to spread as it wishes” (which can only mean autonomy) and then God sees what has developed, guidance will only begin AFTER the autonomous inventive mechanism has done its work. If he approves, there is nothing for him to guide, so he can't be “always” guiding. The mechanism is autonomous until he dabbles. Of course you have every right to remain open to your own hypothesis of “full guidance”, which I take to mean a 3.8-billion-year computer programme for every innovation and natural wonder in the history of evolution, along with personal dabbling. My plea has always been that you should consider my alternative as feasible.-dhw: If your God allowed the bush to spread of its own accord, apart from when he dabbled, there has to be an autonomous mechanism. That is why the “intelligent cell” (possibly designed by God) may well be the key to our understanding of evolutionary innovation. But of course it's still only a hypothesis.
DAVID: You are correct and I'm toying with my dcm idea which closely approaches yours.-Thank you. If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.

Biological complexity: protozoa sans mitochondria

by David Turell @, Thursday, May 26, 2016, 22:25 (2864 days ago) @ dhw

dhw: Once the new species was established, conditions may have changed, or it may subsequently have moved to different environments, but if it has been successful, it will survive. No need to shorten the neck again, or go back to living on land! In other words, the new complexities resulted from the drive for survival/improvement and were not an end in themselves.-I agree success is present if a new form survives. but I am not convinced that your Darwinian approach of seeking improvement for survival is correct. Since (as Denton shows) there are basic patterns from which everything develops, and everything certainly becomes more complex even unto unreasonable forms, I still hold to the view that making organisms more complex is the driving mechanism in evolution. Darwin looked at breeders using variability of animals to create slightly different forms. We don't see that, as you know, in evolution. We see punctuated jumps in fossils, fully formed and functioning new animals, not Darwin's tiny steps. This can only occur if giant steps in complexity occur. Then the issue of superiority in survival takes over.-
> 
> dhw: If “the bush is allowed to spread as it wishes” (which can only mean autonomy) and then God sees what has developed, guidance will only begin AFTER the autonomous inventive mechanism has done its work. If he approves, there is nothing for him to guide, so he can't be “always” guiding. The mechanism is autonomous until he dabbles. Of course you have every right to remain open to your own hypothesis of “full guidance”,.... My plea has always been that you should consider my alternative as feasible.-I am open to a complexity drive, and if your concept is in play, God keeps on eye on everything, and steps in if he doesn't like an outcome. This means He gets his desired end results. It is a reasonable alternative/
> 
> dhw:Thank you. If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.-'Wanting' is very anthropomorphic, isn't it? Complexity, if it works, is always improvement. Of course, what we see in the fossil record are the improved forms. We don't see the failures, only the comings and goings of successful species through the ages due to extinctions, which it has been shown are usually just bad luck with the environment.

Biological complexity: protozoa sans mitochondria

by dhw, Friday, May 27, 2016, 13:04 (2863 days ago) @ David Turell

dhw: Once the new species was established, conditions may have changed, or it may subsequently have moved to different environments, but if it has been successful, it will survive. …In other words, the new complexities resulted from the drive for survival/improvement and were not an end in themselves.
DAVID: I agree success is present if a new form survives. but I am not convinced that your Darwinian approach of seeking improvement for survival is correct. Since (as Denton shows) there are basic patterns from which everything develops, and everything certainly becomes more complex even unto unreasonable forms, I still hold to the view that making organisms more complex is the driving mechanism in evolution. […] We see punctuated jumps in fossils, fully formed and functioning new animals, not Darwin's tiny steps. This can only occur if giant steps in complexity occur. Then the issue of superiority in survival takes over.-We have long since agreed that gradualism (tiny steps) is out. My approach is not “seeking improvement for survival”. Survival may be one spur for innovation (the giraffe and the whale), but I keep stressing that changes in the environment may not be a threat - they may also allow for new opportunities/improvements. An increase in oxygen, waters receding, climate change…Of course this means saltation and not tiny steps, and of course the development of new structures means greater complexity. -DAVID: I am open to a complexity drive, and if your concept is in play, God keeps on eye on everything, and steps in if he doesn't like an outcome. This means He gets his desired end results. It is a reasonable alternative.-Thank you. That gets rid of “always guiding” and grants autonomy to the inventive mechanism, which you prefer to call a complexification mechanism. -dhw: If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.
DAVID: 'Wanting' is very anthropomorphic, isn't it? Complexity, if it works, is always improvement. Of course, what we see in the fossil record are the improved forms. We don't see the failures, only the comings and goings of successful species through the ages due to extinctions, which it has been shown are usually just bad luck with the environment.-Why is ‘wanting' anthropomorphic? Other organisms don't speak English, but that doesn't mean they don't understand the experience of survival, danger, hunger, pain - or even improvement. I would reverse your next statement: improvement is (almost) always complexity. As for failures, either organisms cannot adapt to new environments (bad luck) or they fail in their quest for improvement (a fish explores the land, and goes too far from the water). But you would say they fail in their attempts to become more complex for no reason other than to become more complex.

Biological complexity: protozoa sans mitochondria

by David Turell @, Friday, May 27, 2016, 18:52 (2863 days ago) @ dhw


> dhw: We have long since agreed that gradualism (tiny steps) is out. My approach is not “seeking improvement for survival”. Survival may be one spur for innovation (the giraffe and the whale), but I keep stressing that changes in the environment may not be a threat - they may also allow for new opportunities/improvements.-You are quite correct, but partially. Of course environment can become friendly and allow for advances, such as more oxygen, but it also can wipe out 90% of all species as in the Permian extinction with volcanic activity and more:-https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0ahUKEwiNxv7E5frMAhUD72MKHaI8CTAQFggsMAI&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FPermian%25E2%2580%2593Triassic_extinction_event&usg=AFQjCNGxphhHZs2s8fZw6HFEOvb-XvCk-A&bvm=bv.122676328,d.cGc-Please explain how 'survival' is a spur for innovation. How do animals turn on their genome for invent survival mechanisms? There is no known mechanism, only epigenetic adaptations have been found, and phenotypical changes are saltational through an unknown process and are giant leaps in functionality.
> 
> dhw: If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.-Anthropomorphic 'wanting', a mental illusion, doesn't work in my view. A built-in drive to complexity doesn't require any mental wanting. And it explains the weird branches of the bush. If unimpeded it can create all sorts of strange variations. See the further discussion below: -> DAVID: 'Wanting' is very anthropomorphic, isn't it? Complexity, if it works, is always improvement. Of course, what we see in the fossil record are the improved forms. We don't see the failures, only the comings and goings of successful species through the ages due to extinctions, which it has been shown are usually just bad luck with the environment.
> 
> dhw: Why is ‘wanting' anthropomorphic? Other organisms don't speak English, but that doesn't mean they don't understand the experience of survival, danger, hunger, pain - or even improvement.-Come on, talk with an ape and ask him what improvement is. Of course they know fear, etc., and try to actively survive. All animals cling to life. But they don't 'want'.-> dhw: I would reverse your next statement: improvement is (almost) always complexity. As for failures, either organisms cannot adapt to new environments (bad luck) or they fail in their quest for improvement (a fish explores the land, and goes too far from the water). But you would say they fail in their attempts to become more complex for no reason other than to become more complex.-Yes, but I've covered this. Complexity explains the bush better than any other approach I know.

Biological complexity: protozoa sans mitochondria

by dhw, Saturday, May 28, 2016, 11:43 (2862 days ago) @ David Turell

dhw: We have long since agreed that gradualism (tiny steps) is out. My approach is not “seeking improvement for survival”. Survival may be one spur for innovation (the giraffe and the whale), but I keep stressing that changes in the environment may not be a threat - they may also allow for new opportunities/improvements.-DAVID: You are quite correct, but partially. Of course environment can become friendly and allow for advances, such as more oxygen, but it also can wipe out 90% of all species as in the Permian extinction with volcanic activity and more:-Please believe me when I say I know that environmental change can also be a threat, and I know there have been extinctions. My point was that environmental changes can also be a spur for improvement!-DAVID: Please explain how 'survival' is a spur for innovation. How do animals turn on their genome for invent survival mechanisms? There is no known mechanism, only epigenetic adaptations have been found, and phenotypical changes are saltational through an unknown process and are giant leaps in functionality-‘Survival' could be a spur for innovation if, for example, the pre-whale finds food is scarce on land, and decides to hunt in the water. That is when the mechanism might set to work making the necessary changes - in contrast to your shotgun complexifications through which the pre-whale suddenly by sheer chance finds itself able to live in the sea or God steps in to do a dabble, and then a few more dabbles to take the pre-whale through its different phases (as if he couldn't have done it all in one go) - presumably in order to balance Nature so that humans can be produced and have food. How does the mechanism work? Nobody knows. That's why we have all these hypotheses, like your divine 3.8-billion-year programme for every single innovation and natural wonder. Has anyone found the programme yet? Has anyone seen God dabble?
 
dhw: If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.
DAVID: 'Wanting' is very anthropomorphic, isn't it? 
dhw: Why is ‘wanting' anthropomorphic? Other organisms don't speak English, but that doesn't mean they don't understand the experience of survival, danger, hunger, pain - or even improvement.
DAVID: Come on, talk with an ape and ask him what improvement is. Of course they know fear, etc., and try to actively survive. All animals cling to life. But they don't 'want'.-They know fear, try to survive, cling to life, but they don't want to live? This is simply quibbling over language. Mickey Monkey wants Minnie Monkey's banana, so tries to grab it. Find me another word for ‘want' to describe Mickey's motivation. -DAVID: Complexity explains the bush better than any other approach I know.-Well, I must say I prefer it to your 3.8-billion-year plan plus occasional dabbling. An autonomous inventive mechanism explains the bush better than any other approach I know, but if you prefer to call it an autonomous complexification mechanism, that's fine with me. We'll just stick to our different views on the methods of and motivation for the autonomous mechanism.

Biological complexity: protozoa sans mitochondria

by David Turell @, Saturday, May 28, 2016, 21:48 (2862 days ago) @ dhw


> dhw: If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.
> DAVID: 'Wanting' is very anthropomorphic, isn't it? 
> dhw: Why is ‘wanting' anthropomorphic? Other organisms don't speak English, but that doesn't mean they don't understand the experience of survival, danger, hunger, pain - or even improvement.
> DAVID: Come on, talk with an ape and ask him what improvement is. Of course they know fear, etc., and try to actively survive. All animals cling to life. But they don't 'want'.
> 
> dhw: They know fear, try to survive, cling to life, but they don't want to live? This is simply quibbling over language. Mickey Monkey wants Minnie Monkey's banana, so tries to grab it. Find me another word for ‘want' to describe Mickey's motivation.-You know darn well I was referring to conceptual wanting, not immediate objecvtive wanting a banana. 
> 
> DAVID: Complexity explains the bush better than any other approach I know.
> 
> dhw; Well, I must say I prefer it to your 3.8-billion-year plan plus occasional dabbling. An autonomous inventive mechanism explains the bush better than any other approach I know, but if you prefer to call it an autonomous complexification mechanism, that's fine with me. We'll just stick to our different views on the methods of and motivation for the autonomous mechanism.-Well, I've said I am looking at expanding my concept of complexification, and your point is helping. Complexification just for the sake of it does explain the weird bush of life.

Biological complexity: protozoa sans mitochondria

by dhw, Sunday, May 29, 2016, 13:34 (2861 days ago) @ David Turell

dhw: If your dcm is autonomous, it is exactly the same as mine, except that you give it a different motivation: it wants to be more complex for the sake of complexity, whereas mine becomes more complex because it wants to survive and/or improve.
DAVID: 'Wanting' is very anthropomorphic, isn't it? 
dhw: Why is ‘wanting' anthropomorphic? Other organisms don't speak English, but that doesn't mean they don't understand the experience of survival, danger, hunger, pain - or even improvement.
DAVID: Come on, talk with an ape and ask him what improvement is. Of course they know fear, etc., and try to actively survive. All animals cling to life. But they don't 'want'.
dhw: They know fear, try to survive, cling to life, but they don't want to live? This is simply quibbling over language. Mickey Monkey wants Minnie Monkey's banana, so tries to grab it. Find me another word for ‘want' to describe Mickey's motivation.
-DAVID: You know darn well I was referring to conceptual wanting, not immediate objective wanting a banana.
 
I would suggest that apes, like other organisms, want to live, to eat, to avoid pain, just as Mickey wants the banana, but I would go further and suggest that nest-building, use of tools, development of strategies are all evidence of conceptual thinking arising from the desire for (= “wanting”) improvement. This may extend to exploring the potential of new environmental conditions.-DAVID: Complexity explains the bush better than any other approach I know.dhw; Well, I must say I prefer it to your 3.8-billion-year plan plus occasional dabbling. An autonomous inventive mechanism explains the bush better than any other approach I know, but if you prefer to call it an autonomous complexification mechanism, that's fine with me. We'll just stick to our different views on the methods of and motivation for the autonomous mechanism.
DAVID: Well, I've said I am looking at expanding my concept of complexification, and your point is helping. Complexification just for the sake of it does explain the weird bush of life.-So does targeted complexification. But my emphasis all along has been on the autonomy of the mechanism, and “complexification” versus “survival/improvement” is peripheral. You cannot have a “free complexity mechanism” that allows the bush to “spread as it wishes” without the organisms themselves being able to invent. If their complexifications result in new functioning organs, I'd have thought you would be the last person to say “what a stroke of luck!” since complexity has always been your main argument against Darwin's randomness. The inventiveness of the mechanism requires intelligence. And so, if you are expanding your concept of complexification, perhaps you could expand it to the point at which your God has endowed organisms with the intelligence to do their own inventing.

Biological complexity: protozoa sans mitochondria

by David Turell @, Sunday, May 29, 2016, 15:17 (2861 days ago) @ dhw


> dhw: I would suggest that apes, like other organisms, want to live, to eat, to avoid pain, just as Mickey wants the banana, but I would go further and suggest that nest-building, use of tools, development of strategies are all evidence of conceptual thinking arising from the desire for (= “wanting”) improvement. This may extend to exploring the potential of new environmental conditions.-IMHO you attribute far too much conceptual thought to animals. But that is your prerogative. -> DAVID: Well, I've said I am looking at expanding my concept of complexification, and your point is helping. Complexification just for the sake of it does explain the weird bush of life.
> 
> dhw: So does targeted complexification. But my emphasis all along has been on the autonomy of the mechanism, and “complexification” versus “survival/improvement” is peripheral. ...The inventiveness of the mechanism requires intelligence. And so, if you are expanding your concept of complexification, perhaps you could expand it to the point at which your God has endowed organisms with the intelligence to do their own inventing.-It is just that possibility I'm exploring, keeping in mind God is guiding

Biological complexity: protozoa sans mitochondria

by dhw, Monday, May 30, 2016, 09:14 (2860 days ago) @ David Turell

dhw: I would suggest that apes, like other organisms, want to live, to eat, to avoid pain, just as Mickey wants the banana, but I would go further and suggest that nest-building, use of tools, development of strategies are all evidence of conceptual thinking arising from the desire for (= “wanting”) improvement. This may extend to exploring the potential of new environmental conditions.-DAVID: IMHO you attribute far too much conceptual thought to animals. But that is your prerogative. -Thank you. We shall have to agree to disagree.-DAVID: Well, I've said I am looking at expanding my concept of complexification, and your point is helping. Complexification just for the sake of it does explain the weird bush of life.-dhw: So does targeted complexification. But my emphasis all along has been on the autonomy of the mechanism, and “complexification” versus “survival/improvement” is peripheral. ...The inventiveness of the mechanism requires intelligence. And so, if you are expanding your concept of complexification, perhaps you could expand it to the point at which your God has endowed organisms with the intelligence to do their own inventing.-DAVID: It is just that possibility I'm exploring, keeping in mind God is guiding.
-I am happy that you are exploring it. But I would hate to see you lose your balance on a bit of slippery language. A “free complexity mechanism” that allows the bush “to spread as it wishes” cannot be “guided”. Your God may approve or disapprove of the products of the mechanism, and he may dabble, but it has to be autonomous. Otherwise, you are stuck with your 3.8-billion-year computer programme plus dabbling, with God responsible for every innovation and natural wonder, planning every branch of the weird bush.

Biological complexity: protozoa sans mitochondria

by David Turell @, Monday, May 30, 2016, 14:50 (2860 days ago) @ dhw


> DAVID: It is just that possibility I'm exploring, keeping in mind God is guiding.
> 
> 
> dhw: I am happy that you are exploring it. But I would hate to see you lose your balance on a bit of slippery language. A “free complexity mechanism” that allows the bush “to spread as it wishes” cannot be “guided”. Your God may approve or disapprove of the products of the mechanism, and he may dabble, but it has to be autonomous. Otherwise, you are stuck with your 3.8-billion-year computer programme plus dabbling, with God responsible for every innovation and natural wonder, planning every branch of the weird bush.-Your point is exactly correct. If complexification is a free property anything can happen. And God only steps in to dabble, which means modify a form or possibly change course. Go forth and multiply becomes go forth and complexify. A reasonable alternative

Biological complexity: protozoa sans mitochondria

by dhw, Tuesday, May 31, 2016, 13:23 (2859 days ago) @ David Turell

DAVID: It is just that possibility I'm exploring, keeping in mind God is guiding.

dhw: I am happy that you are exploring it. But I would hate to see you lose your balance on a bit of slippery language. A “free complexity mechanism” that allows the bush “to spread as it wishes” cannot be “guided”. Your God may approve or disapprove of the products of the mechanism, and he may dabble, but it has to be autonomous. Otherwise, you are stuck with your 3.8-billion-year computer programme plus dabbling, with God responsible for every innovation and natural wonder, planning every branch of the weird bush.-DAVID: Your point is exactly correct. If complexification is a free property anything can happen. And God only steps in to dabble, which means modify a form or possibly change course. Go forth and multiply becomes go forth and complexify. A reasonable alternative.-I am delighted that you acknowledge its reasonableness. We now have a mechanism that is capable of producing new functioning complexities (innovations) without “guidance”. You have always, in my view quite rightly, rejected chance as the agent that can process the necessary information and assemble the new structure. So if your God has not programmed the innovation and does not produce it by dabbling, and you do not believe it can assemble itself by chance, it seems to me you are left with only one possible explanation: namely, that the mechanism itself has the intelligence to invent the innovation. And so we now have an autonomous intelligent, inventive mechanism. If you believe in common descent, then every single evolutionary innovation (not to mention every natural wonder) that is not the product of a separate creative act by God can only have been created by this mechanism possessed by individual organisms, and these are communities of cells. Whether you think the cell communities are motivated to change by a higgledy-piggledy quest for complexification for its own sake, or by a specifically targeted quest for their own survival or improvement, makes not the slightest difference to the nature of the mechanism itself: it is autonomous and it works out its own complexities or improvements or strategies for survival. This does not mean that every cell is inventive, but it does mean that there are cells which do the inventive thinking and coordinate with other cells to ensure that the whole community implements the new system. In any community, there are members that perform different roles. There is therefore no escaping the concept of cellular intelligence. You can of course claim that the all-important switch from unicellularity to multicellularity was the result of a dabble, but sooner or later autonomous cellular intelligence has to take over. Sooner of course = bacterial intelligence.

Biological complexity: intercellular signalling

by David Turell @, Tuesday, May 31, 2016, 15:05 (2859 days ago) @ dhw

It is all molecular, purposeful transmembrane reactions:-http://www.the-scientist.com/?articles.view/articleNo/45904/title/Kissing-Cousins/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=30090040&_hsenc=p2ANqtz-8EZAy2t5EQjdis9kKx3hS-bn0lEAJgoSterbxt4piM3G0mU1qvg3kUvCCJRIBiZ-mrNQictDo6MmUmFim4W6Bob9wdNA&_hsmi=30090040/-"Kirsten Hattermann knows a thing or two about chemokines. A researcher working with Janka Held-Feindt's lab at the University of Kiel in Germany, Hattermann has spent the last decade studying these little proteins, which bind—either as transmembrane (tm) proteins or as soluble (s) equivalents that are shed from the membrane or secreted by the cell—to complementary receptors on target cells. Binding of the s-chemokines can elicit several responses in target cells, including cell migration and proliferation, but scientists are still working out the consequences of tm-chemokine binding.-"Recently, while investigating chemokine signaling in tumor cells from a variety of human cancers, Hattermann and her colleagues found something they couldn't explain. When they exposed glioma and carcinoma cells lacking known chemokine receptors to the soluble form of the chemokines CXCL16 and fractalkine, the researchers assumed there would be no binding and, hence, no signal transduction. But to their surprise, Hattermann says, “we observed intracellular signaling.”-***-"Using immuno-electron microscopy, the researchers showed that s-CXCL16 and s-fractalkine directly bind to their transmembrane equivalents, implicating tm-chemokines as the elusive signal transducers. “If it's correct, it's paradigm-shifting in terms of the way we understand how some of these molecules work,” says Gerry Graham, a professor of molecular and structural immunology at the University of Glasgow. “Binding of a soluble [chemokine] to a membrane-anchored one to transduce a signal is completely new.”-"Transfecting the melanoma cells with tm-CXCL16 and tm-fractalkine partly activated s-chemokine signal transduction, the researchers found, while silencing the tm-chemokines in otherwise responsive, receptor-negative tumor cells abolished the effect. This novel mode of communication, which the team has termed “inverse signaling,” may fine-tune classical signaling mechanisms, Hattermann suggests."-Comment: this exact mechanism is not the important point. It is a good illustration of how cells communicate in organisms, and these various communication techniques are still being found. This may look like the cells are intelligent in signaling, but the opposite view is this is an aspect of intelligent planning in the information that is at the basis of life's processes.

Biological complexity: protozoa sans mitochondria

by David Turell @, Wednesday, June 01, 2016, 01:54 (2858 days ago) @ dhw
edited by David Turell, Wednesday, June 01, 2016, 02:04


> dhw: I am delighted that you acknowledge its reasonableness. We now have a mechanism that is capable of producing new functioning complexities (innovations) without “guidance”. You have always, in my view quite rightly, rejected chance as the agent that can process the necessary information and assemble the new structure. So if your God has not programmed the innovation and does not produce it by dabbling, and you do not believe it can assemble itself by chance, it seems to me you are left with only one possible explanation: namely, that the mechanism itself has the intelligence to invent the innovation.-Twisting my concepts once again. A complexity mechanism is programmed to try new combinations of living form and processes. The intelligence is God's as the designer of the complexifier.-> dhw: Whether you think the cell communities are motivated to change by a higgledy-piggledy quest for complexification for its own sake, or by a specifically targeted quest for their own survival or improvement, makes not the slightest difference to the nature of the mechanism itself: it is autonomous and it works out its own complexities or improvements or strategies for survival.-This is your concept, not mine.-> dhw: This does not mean that every cell is inventive, but it does mean that there are cells which do the inventive thinking and coordinate with other cells to ensure that the whole community implements the new system.-Yipes, no. Give you an inch, you take miles.-> dhw: In any community, there are members that perform different roles. There is therefore no escaping the concept of cellular intelligence. You can of course claim that the all-important switch from unicellularity to multicellularity was the result of a dabble, but sooner or later autonomous cellular intelligence has to take over. Sooner of course = bacterial intelligence.-You are having fun.-Shapiro quote: " Genome change is not the result of accidents. If you have accidents and they're not fixed, the cells die. It's in the course of fixing damage or responding to damage or responding to other inputs—in the case I studied, it was starvation—that cells turn on the systems they have for restructuring their genomes. So what we have is something different from accidents and mistakes as a source of genetic change. We have what I call “natural genetic engineering.” Cells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change.-"This is consistent with what Barbara McClintock first discovered in the 30s when she was studyng chromosome repair an then later in the 40s when her experiments uncovered transposable elements. All of these natural genetic engineering systems are regulated or sensitive to biological inputs. That sensitivity is what we've learned about cell regulation in general. As I say, cells don't act blindly, and they don't act blindly when they change their genomes." (my bold)-Comment: I know you will interpret Shapiro to fit the theory you desire, but my bolded segment can be interpreted by emphasizing the words 'regulated or sensitive' as indicating automatic molecular reactions in series or in feedback loops.

Biological complexity: protozoa sans mitochondria

by dhw, Wednesday, June 01, 2016, 13:04 (2858 days ago) @ David Turell

dhw: …if your God has not programmed the innovation and does not produce it by dabbling, and you do not believe it can assemble itself by chance, it seems to me you are left with only one possible explanation: namely, that the mechanism itself has the intelligence to invent the innovation.
DAVID: Twisting my concepts once again. A complexity mechanism is programmed to try new combinations of living form and processes. The intelligence is God's as the designer of the complexifier.-You have agreed to the possibility that what you call a “free complexity mechanism” allows the bush “to spread as it wishes”, and “God only steps in to dabble”. If so, the mechanism has to be autonomous, which means it has to come up with its own combinations! But yes, theistic version: God is the designer of the autonomous mechanism.
 
dhw: Whether you think the cell communities are motivated to change by a higgledy-piggledy quest for complexification for its own sake, or by a specifically targeted quest for their own survival or improvement, makes not the slightest difference to the nature of the mechanism itself: it is autonomous and it works out its own complexities or improvements or strategies for survival. This does not mean that every cell is inventive, but it does mean that there are cells which do the inventive thinking and coordinate with other cells to ensure that the whole community implements the new system.
DAVID: Yipes, no. Give you an inch, you take miles.-Organisms are cell communities. Once more: If they contain what you call a “free complexity mechanism”, the bush can “spread as it wishes”, and God “only steps in to dabble, which means modify a form or possibly change course”, please explain how the cell communities can cooperate to create the forms although their "free complexity mechanism" does NOT enable them to work these complexities out for themselves.
 
dhw: In any community, there are members that perform different roles. There is therefore no escaping the concept of cellular intelligence. You can of course claim that the all-important switch from unicellularity to multicellularity was the result of a dabble, but sooner or later autonomous cellular intelligence has to take over. Sooner of course = bacterial intelligence.
DAVID: You are having fun.-Why is this argument not to be taken seriously?-DAVID, quoting Shapiro: " Genome change is not the result of accidents. If you have accidents and they're not fixed, the cells die. It's in the course of fixing damage or responding to damage or responding to other inputs—in the case I studied, it was starvation—that cells turn on the systems they have for restructuring their genomes. (dhw's bold) So what we have is something different from accidents and mistakes as a source of genetic change. We have what I call “natural genetic engineering.” Cells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change. (dhw's bold)
"This is consistent with what Barbara McClintock first discovered in the 30s when she was studying chromosome repair and then later in the 40s when her experiments uncovered transposable elements. All of these natural genetic engineering systems are regulated or sensitive to biological inputs. That sensitivity is what we've learned about cell regulation in general. (David's bold) As I say, cells don't act blindly, and they don't act blindly when they change their genomes." (dhw's bold)-David's comment: I know you will interpret Shapiro to fit the theory you desire, but my bolded segment can be interpreted by emphasizing the words 'regulated or sensitive' as indicating automatic molecular reactions in series or in feedback loops.-Of course these systems respond to biological inputs and involve automatic molecular reactions and feedback loops. Our own intelligence works in the same way. Once we have absorbed and weighed the information and made our decision (non-automatic, unless you believe humans are also automatons), every action we take entails the same processes to implement those decisions. Since you know as well as I do that Shapiro believes in cellular intelligence, as did McClintock, you can hardly claim that three words removed from their context support your hypothesis. But perhaps you are "having fun"!

Biological complexity: protozoa sans mitochondria

by David Turell @, Wednesday, June 01, 2016, 21:22 (2858 days ago) @ dhw


> dhw: You have agreed to the possibility that what you call a “free complexity mechanism” allows the bush “to spread as it wishes”, and “God only steps in to dabble”. If so, the mechanism has to be autonomous, which means it has to come up with its own combinations! But yes, theistic version: God is the designer of the autonomous mechanism.-And God, therefore, has put in programs to organize what complexifications are created, probably allowing for outlandish results like whales.
> 
> dhw; Organisms are cell communities. Once more: If they contain what you call a “free complexity mechanism”, the bush can “spread as it wishes”, and God “only steps in to dabble, which means modify a form or possibly change course”, please explain how the cell communities can cooperate to create the forms although their "free complexity mechanism" does NOT enable them to work these complexities out for themselves.-As stated God programs for complexity.
> 
> dhw: In any community, there are members that perform different roles. There is therefore no escaping the concept of cellular intelligence. You can of course claim that the all-important switch from unicellularity to multicellularity was the result of a dabble, but sooner or later autonomous cellular intelligence has to take over. Sooner of course = bacterial intelligence.
> DAVID: You are having fun.
> 
> dhw: Why is this argument not to be taken seriously?-Because cell intelligent responses can be intelligently planned fixed molecular reactions.
> 
> dhw: Of course these systems respond to biological inputs and involve automatic molecular reactions and feedback loops. Our own intelligence works in the same way. Once we have absorbed and weighed the information and made our decision (non-automatic, unless you believe humans are also automatons), every action we take entails the same processes to implement those decisions. Since you know as well as I do that Shapiro believes in cellular intelligence, as did McClintock, you can hardly claim that three words removed from their context support your hypothesis. But perhaps you are "having fun"!-Yes, fun. I have my point of view developed from my teachings in medical school. Cells are automatic, as are organs such as livers (a cell community). I'd love to interview Shapiro. I think we actually believe the same things.

Biological complexity: protozoa sans mitochondria

by dhw, Thursday, June 02, 2016, 12:27 (2857 days ago) @ David Turell

dhw: You have agreed to the possibility that what you call a “free complexity mechanism” allows the bush “to spread as it wishes”, and “God only steps in to dabble”. If so, the mechanism has to be autonomous, which means it has to come up with its own combinations! But yes, theistic version: God is the designer of the autonomous mechanism.
DAVID: And God, therefore, has put in programs to organize what complexifications are created, probably allowing for outlandish results like whales.-Where does your “therefore” come from? If God put in programmes for every complexification, the complexity mechanism is NOT free, the bush spreads as God wishes and not as “it” wishes, and God does not “only step in to dabble”, he has organized everything!-DAVID: As stated God programs for complexity.-There is a world of difference between God programming for complexity by creating a mechanism which freely (autonomously) creates its own complexities and God putting in programmes for the creation of every complexity!-dhw: In any community, there are members that perform different roles. There is therefore no escaping the concept of cellular intelligence […]
DAVID: You are having fun.
dhw: Why is this argument not to be taken seriously?
DAVID: Because cell intelligent responses can be intelligently planned fixed molecular reactions.-“Can be” fixed reactions, but “can” also be the result of cellular intelligence. Your dogmatic insistence that you are right, although nobody can know which version is true, does not entitle you to dismiss the hypothesis as unworthy of serious consideration. Ts, ts!-dhw: Since you know as well as I do that Shapiro believes in cellular intelligence, as did McClintock, you can hardly claim that three words removed from their context support your hypothesis. But perhaps you are "having fun"!
DAVID: Yes, fun. I have my point of view developed from my teachings in medical school. Cells are automatic, as are organs such as livers (a cell community). I'd love to interview Shapiro. I think we actually believe the same things.-Organs such as livers act automatically (or appear to act automatically) once they have been invented. They play their part in all the automatic activities that enable organisms to go on living. Cells and cell communities will only have to use their inventive intelligence firstly to create the organ (my hypothesis attempts to solve the mystery of evolutionary innovation), and secondly to solve new problems. As for Shapiro agreeing with you, he explicitly states that “living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities” (Evolution: A View from the 21st Century, p. 143) He dismisses opposition to this as: “Large organisms chauvinism, so we like to think that only we can do things in a cognitive way.” This is one belief you clearly do not share.

Biological complexity: circadian clocks

by David Turell @, Thursday, June 02, 2016, 14:15 (2857 days ago) @ dhw

Our bodies cycle automatically and even has correlations to personality:-https://aeon.co/essays/soon-we-will-see-chrono-attached-to-every-form-of-medicine?utm_source=Aeon+Newsletter&utm_campaign=8c7f17990b-Daily_Newsletter_2_June_20165_31_2016&utm_medium=email&utm_term=0_411a82e59d-8c7f17990b-68942561-"All life on a rotating planet is ruled by circadian rhythms. Chronobiology research has brought the importance of healthy sleep to the fore, and we have made great strides in understanding jetlag. But if we stop there, we're missing the larger point, which is that our bodies in all their complexity live and die by the clock. For decades now, scientists have understood that every bodily function is under the control of the bodyclock. In other words, physiology is four-dimensional - we might as well be different animals during the day than we are at night.-***-"The first circadian clocks originated more than 2 billion years ago, during the Great Oxidation Event. They are found in all plants and animals, and in fact are almost universal in the tree of life. (my bold)-***-"Internal clocks help living beings ready themselves for the daily events that are important to their survival: they act as a conduit between the organism and the environment. A bat's inner alarm clock wakes her at dusk in a cave with no other time cues, and she flies out in time to catch the crepuscular insects that sustain her. Many bacteria shut off their cell division mid-day, regardless of cloud cover, to protect themselves from harmful UV radiation.-***-"With so much of the talk about bodyclocks focused on sleep, it's easy to forget that all of our biological processes around the clock are organised by circadian rhythms. Every day of the internal schedule is full of appointments. Nitrogen-fixing bacteria glean oxygen from the atmosphere, and they also photosynthesise to store energy. But they can't do both at once, so they alternate between nocturnal nitrogen-fixing and daytime photosynthesis. Mammals have many such processes to orchestrate, and just about everything our body does - from metabolism and DNA repair to immune responses and cognition - is under circadian control. In humans, normal organ functioning depends on a harmony in hierarchy: synchrony among molecular rhythms within each cell, among cells in each organ, and among organs in the body. Coordinated functioning ensures that the body doesn't work against itself.-***-"The human body is teeming with clocks, arranged in a hierarchy. At the helm, a master clock in the brain's hypothalamus called the suprachiasmatic nucleus (SCN) sets the overall rhythm of the body. But each organ also has its own rhythm that's generated internally. A clock, in the broadest sense, consists of any type of regular oscillation, and these clocks take the form of a transcription-translation feedback loop that circles back to the beginning in roughly 24 hours. Clock genes activate a process that results in protein synthesis, and once the concentration of those proteins in the cell reach a critical threshold, they come into the nucleus and turn off the clock gene that produced them. Once the proteins have broken down, the gene switches on and the cycle begins again.-"Every day, the body corrects its clock to match its surroundings using daylight. A photoreceptor in the retina - the third photoreceptor after our black-and-white vision rods and colour vision cones - senses only overall light levels and reports directly to that master clock to reset it when it drifts off-course.-***-"The way your body orchestrates its cycles is different from your son's timing or your partner's. For one thing, your avian type - early bird, night owl or humming bird (in between) - is a biological reality. Early birds really do have different physiologies than night owls, because morning people have shorter circadian rhythms that drive them to sleep earlier. Women are more likely to be early birds than men, and introverts are also more likely than extroverts to be up with a smile at the crack of dawn.-"These chronotypes are largely genetic, but they also change with age. Young children and elderly people tend toward the morning, but toward late adolescence our cycles are shifted later in the day."-Comment: This is just the introduction to a long essay on timing in medical therapy, primarily cancer, where it is found that chemotherapy is best tolerated at certain times. The automaticity of cells and the whole body is what I've seen as a physician. As the article shows (see bold) the clock is two billion years old. Cells run automatically through intelligent design. They are given mechanisms they can control as responses to various stimuli.

Biological complexity: protozoa sans mitochondria

by David Turell @, Friday, June 03, 2016, 01:42 (2856 days ago) @ dhw


> dhw: Where does your “therefore” come from? If God put in programmes for every complexification, the complexity mechanism is NOT free, the bush spreads as God wishes and not as “it” wishes, and God does not “only step in to dabble”, he has organized everything!-> dhw: > There is a world of difference between God programming for complexity by creating a mechanism which freely (autonomously) creates its own complexities and God putting in programmes for the creation of every complexity!-God's programming creates complexity which may be free to play with strange results, which would explain the h-p bush. He watches and corrects when necessary. Remember, under my view He controls. Complexity for complexity's sake is not unreasonable.-> dhw: “Can be” fixed reactions, but “can” also be the result of cellular intelligence. Your dogmatic insistence that you are right, although nobody can know which version is true, does not entitle you to dismiss the hypothesis as unworthy of serious consideration. Ts, ts!-You cannot shake my dogma!
> 
> dhw: Organs such as livers act automatically (or appear to act automatically) once they have been invented. They play their part in all the automatic activities that enable organisms to go on living. Cells and cell communities will only have to use their inventive intelligence firstly to create the organ (my hypothesis attempts to solve the mystery of evolutionary innovation), and secondly to solve new problems.-How does the liver community of cells work out all of the cooperative events they have to invent with the kidney cells. Sounds like whole body cellular cooperation.-> dhw: As for Shapiro agreeing with you, he explicitly states that “living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities” -You needn't keep repeating the same quote. I know what he has written. I still consider it hyperbole, emphasis to make a point. The cells care fully endowed as he describes, just automatic.

Biological complexity: protozoa sans mitochondria

by dhw, Friday, June 03, 2016, 13:08 (2856 days ago) @ David Turell

Following on from your agreement, David, that your God may have given organisms an autonomous mechanism to produce the complexities of all the different species: -Dhw: There is therefore no escaping the concept of cellular intelligence […] Why is this argument not to be taken seriously?
DAVID: Because cell intelligent responses can be intelligently planned fixed molecular reactions.
dhw: “Can be” fixed reactions, but “can” also be the result of cellular intelligence. Your dogmatic insistence that you are right, although nobody can know which version is true, does not entitle you to dismiss the hypothesis as unworthy of serious consideration. Ts, ts!
DAVID: You cannot shake my dogma!-That is not a reasonable argument.
 
dhw: Organs such as livers act automatically (or appear to act automatically) once they have been invented. They play their part in all the automatic activities that enable organisms to go on living. Cells and cell communities will only have to use their inventive intelligence firstly to create the organ (my hypothesis attempts to solve the mystery of evolutionary innovation), and secondly to solve new problems.
DAVID: How does the liver community of cells work out all of the cooperative events they have to invent with the kidney cells. Sounds like whole body cellular cooperation.-Of course it has to be whole body cellular cooperation, with the intelligence of each cell community combining forces. We KNOW that the cell communities cooperate now (even if/when their cooperation is “automatic”), and so it is not illogical to assume that when the organs were first invented, they cooperated then. How did they work it all out? Nobody knows. But if you are now willing to concede that your God may have given organisms an autonomous “complexification” mechanism - and you will be the first to agree that the invention of liver and kidneys is a complexification - then instead of marvelling at your God's wonderful dabbles or 3.8 billion-year computer programme, perhaps you can marvel at his ability to endow cell communities with the intelligence to come up with these complexities! You are forever saying how smart “Nature” is, when you can only mean how smart living organisms are.
 
dhw: As for Shapiro agreeing with you, he explicitly states that “living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities” 
DAVID: You needn't keep repeating the same quote. I know what he has written. I still consider it hyperbole, emphasis to make a point. The cells care fully endowed as he describes, just automatic.-You said you would love to interview Shapiro because “I think we actually believe the same things.” I repeated the quote to point out that with regard to the issue we are discussing, you do not believe the same things.

Biological complexity: protozoa sans mitochondria

by David Turell @, Saturday, June 04, 2016, 02:45 (2855 days ago) @ dhw

DAVID: You cannot shake my dogma!
> 
> dhw: That is not a reasonable argument.-You cannot shake my view of cellular function, which I have had for over 50 years. You must be content with the observation that no one outside the cells can tell if they run on intelligently planned information automatically, or have some independent decision making process. All Shapiro shows in his work is the cell's ability to have some simple epigenetic adaptations and responses, which in my view are built in following an algorithmic set of patterns. A bacteria has a limited number of functional responses: approach food, retreat from something noxious, sense others, passively transfer DNA, split into two daughters, etc.
> 
> dhw: But if you are now willing to concede that your God may have given organisms an autonomous “complexification” mechanism - and you will be the first to agree that the invention of liver and kidneys is a complexification - then instead of marvelling at your God's wonderful dabbles or 3.8 billion-year computer programme, perhaps you can marvel at his ability to endow cell communities with the intelligence to come up with these complexities! You are forever saying how smart “Nature” is, when you can only mean how smart living organisms are.-I am getting to like the complexity idea more and more, not your version of course, of free rein cell committees.
> 
> > dhw: You said you would love to interview Shapiro because “I think we actually believe the same things.” I repeated the quote to point out that with regard to the issue we are discussing, you do not believe the same things.-I don't know that we don't. Shapiro was president of his Jewish Temple. He may sound atheistic in his scientific work, but I would not be surprised that he really is agnostic or a believer based on his personal history. He recognizes the epigenetic adaptations in bacteria and shows they turn on of off mechanisms. He does not show any mechanism of speciation, so what he presents is a very limited ability to adapt, not permanent change. His work does not imply your cellular intelligence theory of invention, only that they are seen to make intelligent choices when challenged, which choices may simply be a series of available appropriate fixed responses.

Biological complexity: protozoa sans mitochondria

by dhw, Saturday, June 04, 2016, 11:37 (2855 days ago) @ David Turell

DAVID: You cannot shake my view of cellular function, which I have had for over 50 years. You must be content with the observation that no one outside the cells can tell if they run on intelligently planned information automatically, or have some independent decision making process. -I am quite content with that observation. I only object to the dogmatic dismissal of one of the alternatives, as if 50 years of dogmatism provided some sort of justification! -DAVID: All Shapiro shows in his work is the cell's ability to have some simple epigenetic adaptations and responses…-But as you know, he has come to the opposite conclusion from yours (see below). You are not alone, however, and I only ask for 50/50 instead of your dogmatic 100-0, especially since it has no bearing on theism versus atheism. -dhw: But if you are now willing to concede that your God may have given organisms an autonomous “complexification” mechanism […] then instead of marvelling at your God's wonderful dabbles or 3.8 billion-year computer programme, perhaps you can marvel at his ability to endow cell communities with the intelligence to come up with these complexities! 
DAVID: I am getting to like the complexity idea more and more, not your version of course, of free rein cell committees.-If organisms have an autonomous “complexification” mechanism which results in complex functioning organs, you are left with a choice between the sheer luck of Darwin's random mutations (i.e. organs produced by a non-intelligent mechanism), and design which requires the mechanism's autonomous intelligence. Which do you think it is? -dhw: You said you would love to interview Shapiro because “I think we actually believe the same things.” I repeated the quote to point out that with regard to the issue we are discussing, you do not believe the same things.
DAVID: I don't know that we don't. Shapiro was president of his Jewish Temple. He may sound atheistic in his scientific work, but I would not be surprised that he really is agnostic or a believer based on his personal history. -I would not be surprised either. Our focus, however, is on his belief in cellular intelligence.-DAVID: …His work does not imply your cellular intelligence theory of invention…
-Nobody knows how innovations happen. However, Shapiro suggests that it is the product of what he calls “Natural Genetic Engineering”, and this is guided by the intelligent cell. I have found the following in Wikipedia: -https://en.wikipedia.org/wiki/Natural_genetic_engineering-"Within the context of the article [in the Boston Review] in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making[11] Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)" -You don't have to believe him, but his work certainly does imply my “cellular intelligence theory of invention”. And he obviously got there long before I did!

Biological complexity: protozoa sans mitochondria

by David Turell @, Saturday, June 04, 2016, 15:53 (2855 days ago) @ dhw


> dhw: But as you know, he (Shapiro) has come to the opposite conclusion from yours (see below). You are not alone, however, and I only ask for 50/50 instead of your dogmatic 100-0, especially since it has no bearing on theism versus atheism. -But it does bear on theism. The point is: God implanted the proper intelligent responses for stimuli into bacteria, which makes it look like they are picking and choosing. They either approach and engulf, fight or run away.
> 
> dhw:If organisms have an autonomous “complexification” mechanism which results in complex functioning organs, you are left with a choice between the sheer luck of Darwin's random mutations (i.e. organs produced by a non-intelligent mechanism), and design which requires the mechanism's autonomous intelligence. Which do you think it is? -I think the mechanism would have intelligent construction guidelines coming from God, but act independently in initiating an innovation. Thus the h-p bush would appear. God then steps in to solve resultant problems if any.-> DAVID: Shapiro was president of his Jewish Temple. He may sound atheistic in his scientific work, but I would not be surprised that he really is agnostic or a believer based on his personal history. 
> 
> dhw: I would not be surprised either. Our focus, however, is on his belief in cellular intelligence.-Understood. And we don't know the depth of his belief in CI. He could view it as I do as God-given. But that might be at his personal level, not his scientific persona. 
> 
> DAVID: …His work does not imply your cellular intelligence theory of invention…
> 
> 
> dhw: Nobody knows how innovations happen. However, Shapiro suggests that it is the product of what he calls “Natural Genetic Engineering”, and this is guided by the intelligent cell. I have found the following in Wikipedia: 
> 
> https://en.wikipedia.org/wiki/Natural_genetic_engineering
> 
> "Within the context of the article [in the Boston Review] in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making[11] Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)" 
> 
> You don't have to believe him, but his work certainly does imply my “cellular intelligence theory of invention”. And he obviously got there long before I did!-It won't surprise you that I have read each and every one of his Huff post articles, and his book, and I still have my same view of intelligent cells, as he describes them.

Biological complexity: protozoa sans mitochondria

by dhw, Sunday, June 05, 2016, 13:08 (2854 days ago) @ David Turell

dhw: But as you know, he (Shapiro) has come to the opposite conclusion from yours (see below). You are not alone, however, and I only ask for 50/50 instead of your dogmatic 100-0, especially since it has no bearing on theism versus atheism. 
DAVID: But it does bear on theism. The point is: God implanted the proper intelligent responses for stimuli into bacteria, which makes it look like they are picking and choosing. They either approach and engulf, fight or run away.-Theism versus atheism means whether God exists or not! The intelligence of the cell has absolutely no bearing on that subject. Your God could have made the cell an automaton or could have given it intelligence.-DAVID: I think the mechanism would have intelligent construction guidelines coming from God, but act independently in initiating an innovation. Thus the h-p bush would appear. God then steps in to solve resultant problems if any.-You are back to your nebulous “guidelines”. If organisms have been given a “free complexification mechanism”, act independently in initiating an innovation, and God only dabbles to solve problems, the organisms must have an autonomous intelligence. The alternative is that they haven't a clue what they are doing and yet still manage to produce perfectly functioning organs - which is the same principle as Darwin's random mutations.-DAVID: Shapiro was president of his Jewish Temple. He may sound atheistic in his scientific work, but I would not be surprised that he really is agnostic or a believer based on his personal history. 
dhw: I would not be surprised either. Our focus, however, is on his belief in cellular intelligence.
DAVID: Understood. And we don't know the depth of his belief in CI. He could view it as I do as God-given. But that might be at his personal level, not his scientific persona. -Why must we measure the “depth” of his belief in CI? He says he believes cells are intelligent. Isn't that enough? (Of course he could view it as God-given. As an agnostic I also accept that possibility.)-DAVID: …His work does not imply your cellular intelligence theory of invention…
dhw: ...I have found the following in Wikipedia: 
https://en.wikipedia.org/wiki/Natural_genetic_engineering-"Within the context of the article [in the Boston Review] in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making[11] Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)" 
You don't have to believe him, but his work certainly does imply my “cellular intelligence theory of invention”. And he obviously got there long before I did!-DAVID: It won't surprise you that I have read each and every one of his Huff post articles, and his book, and I still have my same view of intelligent cells, as he describes them.-You said his work did not imply that cellular intelligence was the driving force behind innovation, and I have found a quotation that shows it does. I know you disagree with his view.

Biological complexity: protozoa sans mitochondria

by David Turell @, Sunday, June 05, 2016, 15:43 (2854 days ago) @ dhw

[/i]. 
> DAVID: But it does bear on theism. The point is: God implanted the proper intelligent responses for stimuli into bacteria, which makes it look like they are picking and choosing. They either approach and engulf, fight or run away.
> 
> dhw: Theism versus atheism means whether God exists or not! The intelligence of the cell has absolutely no bearing on that subject. Your God could have made the cell an automaton or could have given it intelligence.-Theism denies that inorganic matter can evolve into intelligently acting cells. They look to the activity of cells as proof of God:-http://townhall.com/columnists/mattbarber/2016/06/05/the-atheist-delusion-ray-comforts-masterpiece-n2173715?utm_source=thdaily&utm_medium=email&utm_campaign=nl&newsletterad=-
> 
> DAVID: I think the mechanism would have intelligent construction guidelines coming from God, but act independently in initiating an innovation. Thus the h-p bush would appear. God then steps in to solve resultant problems if any.
> 
> dhw: You are back to your nebulous “guidelines”. If organisms have been given a “free complexification mechanism”, act independently in initiating an innovation, and God only dabbles to solve problems, the organisms must have an autonomous intelligence. -As long as we are discussing possibilities, why can't God offer guidelines? You look at God as 'nebulous' in your role as an agnostic-> 
> DAVID: Shapiro was president of his Jewish Temple. He may sound atheistic in his scientific work, but I would not be surprised that he really is agnostic or a believer based on his personal history. 
> 
> dhw: He says he believes cells are intelligent. Isn't that enough? (Of course he could view it as God-given. As an agnostic I also accept that possibility.)-Thank you.
> 
> DAVID: …His work does not imply your cellular intelligence theory of invention…
> dhw: ...I have found the following in Wikipedia: 
> https://en.wikipedia.org/wiki/Natural_genetic_engineering
> 
> "Within the context of the article [in the Boston Review] in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making[11] Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)" 
> You don't have to believe him, but his work certainly does imply my “cellular intelligence theory of invention”. And he obviously got there long before I did!
>> 
> dhw: You said his work did not imply that cellular intelligence was the driving force behind innovation, and I have found a quotation that shows it does. I know you disagree with his view.-This phrase fits my interpretation completely: ""guiding intelligence" is to be found within the cell." Not by chance and not from an inorganic beginning.

Biological complexity: protozoa sans mitochondria

by dhw, Monday, June 06, 2016, 12:52 (2853 days ago) @ David Turell

dhw: Theism versus atheism means whether God exists or not! The intelligence of the cell has absolutely no bearing on that subject. Your God could have made the cell an automaton or could have given it intelligence.
DAVID: Theism denies that inorganic matter can evolve into intelligently acting cells. They look to the activity of cells as proof of God:-http://townhall.com/columnists/mattbarber/2016/06/05/the-atheist-delusion-ray-comforts-...-I do not need to hear theists screaming at me that atheists are fools, or to be told that the complexity of the cell is evidence of design. Our discussion concerns the intelligence of the cell, and the question whether the cell is intelligent has nothing to do with whether God exists or not, as explained above.-DAVID: I think the mechanism would have intelligent construction guidelines coming from God, but act independently in initiating an innovation. Thus the h-p bush would appear. God then steps in to solve resultant problems if any.
dhw: You are back to your nebulous “guidelines” [….] 
DAVID: As long as we are discussing possibilities, why can't God offer guidelines? …-Yes, it is possible that God can offer guidelines. Or that he created every single species individually. Or that evolution proceeds through random mutations. What is not possible, as I'm sure you'll agree, is that God created every species individually AND evolution proceeds through random mutations. Similarly, if God gives “guidelines”, how can the mechanism be “FREE” and act INDEPENDENTLY in INITIATING an innovation, while God steps in to solve RESULTANT problems if any? You can't have a free autonomous inventive complexity mechanism that works according to God's guidelines.-DAVID: …[Shapiro's] work does not imply your cellular intelligence theory of invention…
dhw: ...I have found the following in Wikipedia: https://en.wikipedia.org/wiki/Natural_genetic_engineering-"Within the context of the article [in the Boston Review] in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making[11] Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.)" 
You don't have to believe him, but his work certainly does imply my “cellular intelligence theory of invention”. And he obviously got there long before I did!-DAVID: This phrase fits my interpretation completely: ""guiding intelligence" is to be found within the cell." Not by chance and not from an inorganic beginning.-You are having fun again. You know perfectly well that he is referring to the intelligence of the cell, and not to chance or the origin of life (or God's “guidance”). Why else would the article explain his criteria for intelligence? Put your misfiring guns down, hold your hands high in the air, and say after me: 
“The intelligent cell is evolution's hero,
According to the work of James Shapiro.”

Biological complexity: calcium blood level controls

by David Turell @, Thursday, June 09, 2016, 23:25 (2850 days ago) @ dhw

Another discussion of complex biologic processes. In this case calcium control:-http://www.evolutionnews.org/2016/06/how_the_body_co102899.html- "For when it comes to life, real numbers have real consequences. Clinical experience teaches that not just any Ca++ ion concentration in the blood will do. It has to be the right amount. The normal blood level for calcium is between 8 to 10 units and if it rises above or drops below this range by more than 30 percent, the result is often lethal. So how does the body maintain control of its calcium?-***-"The system the body uses to control its blood level of calcium requires calcium sensors on the parathyroid gland cells, the ability for these cells to produce PTH, properly adjusted release of PTH to the change in the calcium blood level, enzymes to limit the effect of PTH, and specific PTH receptors on the bone cells, tubule, and specialized cells of the kidneys. Without any one of these five components being present and doing what they're supposed to do, the whole system would fail and calcium control would be lost.-"But for our earliest ancestors to have survived, not only would they have needed this irreducibly complex system but, in addition, it would have had the natural survival capacity to make sure the blood level of calcium stayed within the right range. In other words, the systems the body uses must do the right thing at the right time and they must do these well enough to survive under the laws of nature. In any realistic perspective, the idea that such a wonder came about by chance and nature's laws alone must be set aside as untenable."-Comment; Note multi-organ involvement for tight control. Not by chance!!

Biological complexity: kidney function is higly complex

by David Turell @, Monday, June 27, 2016, 01:31 (2832 days ago) @ David Turell

I discussed the complexities of the kidney many times but not in great detail because there is not enough room in one entry. Only the brain and the liver are more complex. Rudimentary kidneys undoubtedly appeared in the Cambrian explosion for their current descendants have them:-http://www.evolutionnews.org/2016/06/the_kidneys_irr102933.html-"The functioning unit in the kidney is the nephron, and there are about one million per kidney. The nephron filters fluid out of the blood by squeezing it through a specialized capillary system called the glomerulus. The kidneys filter about 7.5 liters of fluid, with its chemical content, out of circulation per hour. This fluid enters tubules, which wind their way through the tissue of the kidney on its way to becoming urine. As the fluid moves along the cells lining, the tubules reabsorb or secrete different chemicals to the degree that is necessary for body survival. -"The body is always taking in different amounts of various chemicals through the gastrointestinal system, while simultaneously losing them through metabolism. Therefore, the ongoing chemical needs of the body are always in flux and the kidneys must constantly adjust to these changes by changing how much of a given chemical they keep or release from the body through the urine. We will look at the five vital chemicals mentioned above, water, sodium, potassium, calcium, and nitrogen, and explain how the body, through the kidneys, adjusts them to stay alive. -***-"Since blood volume is dependent on water content and water content is dependent on sodium content, this means that the wall motion that takes place as blood flows into a blood vessel or chamber is a reflection of the body's sodium content. One set of sensors, called mechanoreceptors, detect this wall motion within the kidneys, where blood enters to be filtered, and another is in the walls of the atria. The sensory cells in the kidneys release a hormone, called renin. The amount of renin released is inversely related to how much wall motion the sensors detect. The more the walls stretch, indicating more blood volume, the less renin is sent out, and the less the walls stretch, indicating less volume, the more renin is sent out. In contrast, the atrial cells send out a hormone, called Atrial Natriuretic Peptide (ANP), in an amount that is directly related to how much wall motion they detect. The more the walls stretch, indicating more blood volume, the more ANP is sent out, and vice versa.-"Renin results in the formation of a hormone called angiotensin II which binds to specific receptors in the adrenal glands and tells them to release another hormone called aldosterone. Aldosterone travels to the kidneys and attaches to specific receptors on the cells lining some of its tubules. This tells them to bring more sodium back into the body. So, the less blood volume, the more renin, resulting in more angiotensin II and aldosterone, and more sodium the kidneys reabsorb. In contrast, the more blood volume, the more ANP attaches to specific receptorson the same tubules in the kidneys and tells them to release more sodium. In other words, the effects of renin and ANP counterbalance each other.-***-"The body uses sensors in specialized cells within the adrenal glands to detect the ratio between the K+ and Na+ ion concentration in the blood. If the ratio rises, due to an increase in K+ ion concentration or a decrease in Na+ ion concentration, these cells send out more aldosterone. Conversely, if the ratio drops, due to a decrease in K+ ion concentration or an increase in Na+ ion concentration, it sends out less aldosterone. -***-"The cells of the four parathyroid glands have sensors that can detect the calcium level in the blood. In response to a drop in serum calcium, they release more parathormone (PTH). PTH travels in the blood and not only makes the bone release more Ca++ ions into the circulation but tells the kidneys to activate Vitamin D so the gastrointestinal tract can absorb more calcium. It also attaches to specific receptors within the tubules and tells them to bring more calcium back into the body. By using calcium sensors, PTH, and its specific receptors in the kidneys, the body is able to take control of its calcium content. -"Nitrogen is mainly present in the amino acids that make up the proteins of the body. Protein metabolism produces a highly toxic nitrogen-containing molecule called ammonia, which the liver converts into less toxic urea to be released from the body through the kidneys."-Comment: This shows highly complex organization between the kidney, the liver and various hormone producing organs. I've selected out just parts of this long article which should be read in full to really appreciate how complex all of this system has to be. Irreducibly complex for all of it is needed all at once in development within the Cambrian Explosion. We are back to saltation and the recognition that Darwin's ideas don't work. But intelligent design explains it. There is only chance and design to consider, or wish for a third way, for which there is no trace of evidence.

Biological complexity: how to make a whale

by David Turell @, Thursday, June 30, 2016, 02:02 (2829 days ago) @ dhw

Whales developed from land mammals with enormous changes in all parts of the animals. Studies show n ot enough time elapsed for all the mutations needed:-http://www.evolutionnews.org/2016/06/whale_of_a_tale102954.html- "Richard Sternberg considers the number of adaptations required to be "unfathomably complicated" to allow a land animal to live entirely in an aquatic environment. The film lists just a few categories of adaptations for humpback whales:-•Respiratory system-•Locomotive structures-•Musculoskeletal system-•Dentition-•Urinary system-•Cardiopulmonary system-•Thermoregulation-•Sensory organs-•Reproductive organs-
"You can imagine any of these outward changes requiring thousands of genetic changes. "Just think of all the parameters that would have to be modified," Sternberg says, "and then multiply that by, I don't know -- a thousandfold, or more than that. That's the scale of the problem that you're dealing with." In the Q&A feature of the film Icons of Evolution, David Berlinski tried to quantify the number of morphological changes necessary to turn a cow into a whale (like turning a car into a submarine), and stopped counting at 50,000. -***-"In Living Waters, Sternberg showed mathematically that it would take longer to expect just two cooperative mutations to occur than the maximum time expected for the entire evolution of a whale (100 million years vs 9 million years)." -Comment: When chance mutations are considered, there is no way to make a whale without intelligent planning. Only a planning mind can do this.

Biological complexity: automatic breathing controls

by David Turell @, Tuesday, July 05, 2016, 18:07 (2824 days ago) @ David Turell

High or low oxygen and carbon dioxide levels control breathing at the base of the brain. Here is how:-https://www.sciencedaily.com/releases/2016/07/160705111905.htm-"There has been some debate over how the brain controls breathing. Now, a new study in mice, to be published in the journal eLife, shows that when exposed to decreased oxygen or increased carbon dioxide levels, the brain releases a small molecule called Prostaglandin E2 (PGE2) to help protect itself and regulate breathing.-***-"'Our novel brainstem culture first revealed that cells responsible for breathing operate in a small-world network. Groups of these cells work very closely with each other, with each group interconnected by a few additional cells that appear to work as hubs. This networking activity and the rhythmic respiratory motor output it generated were preserved for the full three weeks, suggesting that our brainstem can be used for long-term studies of respiratory neural network activity," explains David Forsberg, PhD student and first author of the study.-"'Secondly, we saw that exposure to different substances made the brainstem breathe faster or slower. Perhaps most interesting was its response to carbon dioxide, which triggered a release of PGE2. Here, PGE2 acted as a signaling molecule that increased breathing activity in the carbon dioxide-sensitive brainstem region, leading to slower and deeper breaths, or 'sighs'."-***-"The study also reveals a novel pathway linking the inflammatory and respiratory systems. PGE2 is released during inflammation and fever, which can dysregulate breathing patterns and interfere with normal responses to carbon dioxide. This can in turn cause disturbed and even dangerous halts in breathing.-"'Our findings go some way to explaining how and why our breathing responses to imbalanced oxygen and carbon dioxide levels are impaired during infectious episodes. It also helps further our understanding of why infection can inhibit breathing so severely in new-born babies," says Eric Herlenius, Professor at Karolinska Institutet's Department of Women's and Children's Health, and senior author of the paper."-Comment: Again one wonders how this develops stepwise by Darwinian theories. Note the brain produces chemical (hormonal) regulators as well as the resultant electrical signals, so we continue breathing without thinking about it. Also our breathing rate increases as we exercise and need more oxygen and to remove more CO2. Respiratory rate and heart rate move consistently in the same direction and have a ratio that is mathematically consistent with the degree of exercise. This is all accomplished by automatic feedback loops. Again I suggest saltation.

Biological complexity: cell communication controls

by David Turell @, Tuesday, July 05, 2016, 18:21 (2824 days ago) @ David Turell

Cells communicate with each other by chemicals on their surfaces that combine with each other, attract or repel: - http://phys.org/news/2016-07-molecules-neuronal-extensions-retract-distance.html - "Eph receptors and their partner proteins, the ephrins, are vital for intercellular communication. In the developing brain, they guide young neurons to the right partner cells by repulsion. They also play important roles in cell migration, regeneration, neurodegenerative diseases and the development of cancer. Until recently, scientists assumed that ephrin/Eph signal transmission could only occur through direct cell-cell contact. However, Rüdiger Klein and his team at the Max Planck Institute of Neurobiology have now shown that cells can also pack and release active ephrins and Eph receptors through extracellular vesicles. - *** - "The human body contains up to 100 billion cells. As they grow, migrate, replicate and move, these cells come into contact with countless other cells and exchange information with them. One way this communication happens is through the ephrin/Eph-receptor system, which is able to guide cell migration and the growth of neuronal extensions. In addition, the ephrin-Eph system also plays a role in plastic processes, such as learning and regeneration, as well as in tumour growth and neurodegenerative diseases. - "Eph receptors and their binding partners, the ephrins, are found on the surface of almost all cell types. When an ephrin meets the Eph receptor of another cell, they join to form an ephrin-Eph complex. This triggers processes in one or both cells that generally lead to internalization of the complex and repulsion of one cell away from the other. The repelled cell then moves or grows in another direction. In the nervous system, many such interactions guide the extensions of young neurons to their right destinations. - *** - "It had always seemed clear that ephrins and Ephs could only trigger a signaling process by direct contact between two cells. Recently, however, ephrins and Eph receptors have also been found in extracellular vesicles/exosomes - small droplets of fat released by cells, used as transport vehicles, signal transmitters or for eliminating cell components. "This has thrown up the interesting question of what business Ephs and ephrins have in exosomes," says Klein. - "Intrigued, the Martinsried-based team set up an elaborate experimental study to purify the exosomes from different cell types, including neurons, and analyse their contents. They revealed that many of these exosomes contained ephrins and Ephs, and decoded the cellular mechanism by which they were packed into the exosomes. Interestingly, further analysis showed that the Eph receptors had not been dumped as waste products, but remained active on the exosomes. Eph receptors on the exosomes were able to bind to ephrin molecules on the surface of growing neurons and repel the neuronal extensions. This proves, for the first time, that cells can send ephrins and Ephs out to transmit signals over a distance." - Comment: This study explains in part how embryology works to make a whole body. It also shows the automaticity of DNA control of cell associations in specific organs as they develop, in this case the brain. Not by chance.

Biological complexity: immune cell stem cell cooperation

by David Turell @, Friday, July 08, 2016, 15:21 (2821 days ago) @ David Turell

How the body is developed and maintained is slowly being understood. As the body cell population is turned over at a rather high rate stem cells and the various immune cells are programmed to work together"-http://www.the-scientist.com/?articles.view/articleNo/46377/title/Immune-Cell-Stem-Cell-Cooperation/-"We may perceive ourselves as static beings, but the cells of our bodies are in constant flux. The outer layers of our skin and intestinal tract are replaced every few weeks; red blood cells circulate in our bodies for about 100 days before they are replaced; cells in our liver and fat are longer lived—more than a year for a liver cell, 10 years on average for a fat cell—but still turn over repeatedly during our lifetimes. More slowly, up to half our heart cells may be replaced during a normal lifespan. And, of course, when healthy tissue is lost due to injury, new cells are made to patch up the damage. -***-"Stem cells self-renew to maintain their numbers and differentiate into the specialized cell types that make up our tissues and organs—a function that becomes especially important after stress or injury. -***-"One of the best-studied examples of mammalian stem cell environments is the intestinal stem cell (ISC) niche. The small intestine's epithelium is the fastest self-renewing tissue in the body due to ISCs' exceptionally rapid rates of cell division and the rapid migration of their differentiated progeny out of the stem cell niche. But the system would not work without the help of Paneth cells, one of four differentiated cell types produced by ISCs, which remain in the niche and secrete essential proteins that are critical for ISC survival. Indeed, the genetic inactivation of Paneth cells results in a near-total loss of ISCs.-***-"An integral part of homeostasis in diverse tissues is the continuous replacement of differentiated cell types. Research is now showing that the immune cells residing within the stem cell niche are essential to this process. For example, specialized macrophages in the bone marrow remain in direct contact with a red blood stem cell called an erythroblast.-***-"At the start of puberty, ovarian hormones trigger the bifurcation and elongation of the ductal structures towards the outer edges of the fat pad while diverse immune cells—mast cells, eosinophils, and macrophages—migrate to the region around the ducts' tips. Genetic or pharmacological disruption of mast cells and macrophages in mice has revealed that these immune cells are critical for rapid proliferation and normal duct branching during puberty. Mast cells secrete protein-degrading serine proteases, which are necessary for the breakdown and reorganization of collagen fibers surrounding the developing ducts, for example,3 while macrophages phagocytize apoptotic cell debris and directly act on mammary stem cells through an unknown mechanism.-***-"Perhaps the best-understood example of immune- and stem-cell cooperation is in skeletal muscle following an acute injury. Tissue repair begins with the removal of damaged muscle fibers by local and infiltrating immune cells. Rare, circulating immune cells called eosinophils instruct resident progenitor cells known as fibro/adipogenic progenitors (FAPs) to generate the fibroblasts and fat cells that deposit collagen and secrete growth factors to support muscle fiber regeneration.8 Concurrently, T cells secrete a protein called amphiregulin, which instructs resident muscle stem cells known as satellite cells to differentiate into new muscle cells and replace the lost muscle fibers.-***-"When researchers plucked hairs off the backs of mice, they found that damaged hair follicles beneath the skin's surface secrete, in unison, a protein called CCL2. In response to this distress signal, macrophages migrated up the CCL2 gradient and toward hair follicles, where they secreted a protein called tumor necrosis factor (TNF), which instructed hair follicle stem cells to produce new hair.-***-"Tissue-resident stem cells' remarkable ability to self-renew while also giving rise to diverse mature cell types is critical for our existence. In order to carry out their inherent roles in tissue maintenance and regeneration, these stem cells rely on signals provided by diverse cell types, including immune cells, within the local and systemic environments. We are at the dawn of understanding the complex and dynamic roles of the immune system's many cell types and their functional relationships with stem cells—a feat that will be critical to harnessing the power of stem cells to treat or cure disease."-Comment: The complex automated dance between cells to maintain the body is illustrated by the bits of tis article I've reproduced. I've skipped the part on uses in regenerative medicine. This complexity tells me only an intelligent mind could create these mechanisms. Each cell works with purpose, programmed purpose, exhibiting intelligent activity. It is programmed intelligence guiding each cell.

Biological complexity: human male sex function

by David Turell @, Wednesday, July 13, 2016, 19:50 (2816 days ago) @ David Turell

Another example of high complexity:-http://www.evolutionnews.org/2016/07/irreducible_com102983.html-"The first task, of producing enough sperm, relates to his fertility and is accomplished by the testes. This is dependent on having enough of the gonadotropins, Follicle-Stimulating Hormone (FSH) and Luteinizing Hormone (LH), producing enough testosterone and having enough properly functioning specific receptors. The sperm produced in the testes is combined with nutrient fluids from the seminal vesicles and the prostate gland to form semen. During sexual intercourse the semen is released from the erect penis into the woman's vagina. The normal amount of semen usually needed for adequate fertility is at least 2 milliliters and the concentration of sperm per milliliter should generally be greater than 20 million. In addition, the appearance of the sperm (morphology) and their ability to move well (motility) are very important factors that affect fertility as well.-***-"The second task, of being able to deposit the sperm inside the female, refers to his potency. This involves having a firm enough normally shaped erection to penetrate deep enough into the vagina and ejaculate semen which is dependent on having a normal penis and normal nerve and vascular function. A penile erection is achieved by hydraulic pressure. Running the length of the penis, surrounding the urethra, above and on each side, are the corpus spongiosa and the corpus cavernosa. These tube-shaped venous chambers are surrounded by strong fibrous tissue. Sex-related thoughts and sensory stimulation of the penis and pelvic region activates the parasympathetic nerves which signals them to send out a neurohormone called acetylcholine. The acetylcholine attaches to specific receptors on the blood vessels in the penis which causes an increase in arterial blood flow into these chambers while at the same time reducing the venous outflow. This combination results in blood collecting within these chambers resulting in penile erection. After erection takes place, with continued stimulation the sympathetic nervous system swings into action and sends out a neurohormone called norepinephrine. The norepinephrine attaches to specific receptors on the associated pelvic muscles causing coordinated contraction and ejaculation of the semen from the penis, which is usually accompanied by the pleasurable sensation of orgasm. As sympathetic nerve stimulation brings on climax and ejaculation to complete the sexual act, the parasympathetic stimulation that caused the erection in the first place turns off and the penis becomes flaccid soon afterwards. -***-"In summary, the two main tasks of male fertility (producing enough sperm and depositing them inside the female) require much more than just having male sexual organs. He must be able to produce enough healthy and vigorous sperm which is dependent on having, not only properly working testes, but the right amount of hormones and properly working receptors as well. In addition, it isn't enough that he has a properly built male internal genital duct system and external genitalia. He must also have proper neurovascular function in the pelvis, which involves the neurohormones acetylcholine and norepinephrine and their specific receptors, to achieve enough of an erection to penetrate deep into the vagina and deposit his semen."-Comment: As usual this human function is highly complex and raises the issue of how it developed during evolution. It involves the coordination of the circulation of the penis, hormones, sperm production, prostatic fluids, nervous controls, and sexual thoughts hat stimulate the process.

Biological complexity: human male sex function

by David Turell @, Friday, May 03, 2019, 20:49 (1792 days ago) @ David Turell

How sperm sense the egg is found in a molecule that opens a calcium channel:

https://phys.org/news/2019-05-molecule-sperm-track.html


'Sperm start their sprint to the ovum when they detect changes in the environment through a series of calcium channels arranged like racing stripes on their tails. A team of Yale researchers has identified a key molecule that coordinates the opening and closing of these channels, a process that activates sperm and helps guides them to the egg.


"When the gene that encodes for the molecule is removed through gene editing, male mice impregnate fewer females, and females who are impregnated produce fewer pups. Also, the sperm of the altered male mice are less active and fertilize fewer eggs in lab experiments, the Yale researchers report May 2 in the journal Cell.

"The calcium channel complex aligned on a sperm's tail, called CatSper, is evolutionarily conserved across many species and consists of multiple subunits, but "we didn't know what each did," said Jean-Ju Chung, assistant professor of cellular and molecular physiology and senior author of the paper.

"Previous studies failed to identify the exact mechanism in CatSper that allows sperm to respond to cues such as acidity levels along the female reproductive tract and trigger changes in their motility to better navigate to the egg. Chung's lab screened all sperm proteins to identify which ones interacted with the CatSper channel complex. They zeroed in on one, EFCAB9, which acts as a sensor that orchestrates the opening and closing of the channels according to environmental cues.

"'This molecule is a long-sought sensor for the CatSper channel, which is essential to fertilization, and explains how sperm respond to physiological cues," Chung said.

"EFCAB9 seems to play "a dual role in regulating the activity and the arrangement of channels on a sperm's tail, which help regulate sperm motility towards the egg," Chung said.

"Mutations have been found in the CatSper genes of infertile men and could be a target for fertility treatments. Since the CatSper channel is necessary for sperm to function, blocking it could lead to development of non-hormonal contraceptives with minimal side effects in both men and women, Chung said."

Comment: This solution for sperm hunting an egg cannot be developed by chance attempts. When sexual reproduction appeared this process had to be designed and ready from the beginning or reproduction by fertilization would not have occurred.

Biological complexity: intracellular protein delivery

by David Turell @, Friday, August 19, 2016, 23:10 (2779 days ago) @ David Turell

Cells are constantly producing proteins for delivery into themselves or for external transport. All of this is tightly controlled as molecules are handed off:-http://phys.org/news/2016-08-scientists-decades-old-proteins-cells.html-"When things are going right in your body, it's because long strings of brand-new proteins are being folded up into just the right tangles and being delivered to just the right place within the cell at just the right time.-***-"A protein's journey begins when a piece of messenger RNA delivers instructions and a command to a ribosome, one of the tiny bulbous protein factories within the cell. The ribosome follows the recipe encoded on the mRNA - which itself was translated from the genes within your DNA - and manufactures the specific protein. The next step is where things get interesting.-"A "signal recognition particle" (SRP) latches on to the protein signal to help pilot it to the ER-"Using modern techniques and instruments that allowed them to observe the mechanism in higher resolution than previously possible, Frydman and her colleagues found that the mRNA actually contains a little bit of information that the SRP recognizes before protein production begins, and that the SRP actually waits at the exit site of the ribosome before the protein even emerges.-"'It's almost prescient; it already knows before it comes and just steps right in," Frydman said.-***-"Very important processes rely on the fidelity of where proteins have to go, Frydman said, and cells need to secrete proteins faithfully. If a particular protein stays in the cytoplasm, it could aggregate and lead to loss of healthy function or the accidental gain of unhealthy function. These gains or losses are typical of a variety of diseases, such as cystic fibrosis, cancer and Alzheimer's disease."-Comment: Just goes to show you have active the cells are and how precise. This precision is vital to life continuing. To me the systems are irreducibly complex and not explained by evolution.

Biological complexity: intracellular protein delivery

by dhw, Saturday, August 20, 2016, 12:06 (2778 days ago) @ David Turell

QUOTE: "'It's almost prescient; it already knows before it comes and just steps right in," Frydman said.
"Very important processes rely on the fidelity of where proteins have to go, Frydman said, and cells need to secrete proteins faithfully. If a particular protein stays in the cytoplasm, it could aggregate and lead to loss of healthy function or the accidental gain of unhealthy function. These gains or losses are typical of a variety of diseases, such as cystic fibrosis, cancer and Alzheimer's disease."-David's comment: Just goes to show you have active the cells are and how precise. This precision is vital to life continuing. To me the systems are irreducibly complex and not explained by evolution.-The “prescience”, activity and precision of these cells may not be explained BY evolution, but if we grant that these attributes confirm the sentience, cognitive, communicative and cooperative intelligence of cells, we might find ourselves with an explanation OF evolution.

Biological complexity: intracellular protein delivery

by David Turell @, Saturday, August 20, 2016, 16:25 (2778 days ago) @ dhw


> dhw: The “prescience”, activity and precision of these cells may not be explained BY evolution, but if we grant that these attributes confirm the sentience, cognitive, communicative and cooperative intelligence of cells, we might find ourselves with an explanation OF evolution. - It is explained just as well if the cells are automatons.

Biological complexity: how nucleus holds it shape

by David Turell @, Monday, August 22, 2016, 20:09 (2776 days ago) @ David Turell

The nucleus of the cell is the largest object in the cell. when the cell is squeezed the nucleus has a protein mechanism to hold its shape:-https://www.sciencedaily.com/releases/2016/08/160822140523.htm-"'There's a really complex network of proteins that keeps the cell from buckling in on itself when it's faced with a tight squeeze."-"The researchers pinpointed one protein responsible -- fascin -- that is known to be at unusually high levels in cancer cells. Originally, says Parsons, fascin was only thought to exist at the cell's edge as a "bundling protein," where it binds and stabilizes spiky finger-like protrusions called filopodia at the cell's plasma membrane. These structures allow the cell to sense its surrounding environment and pull itself through tissue. Now, the researchers have found that fascin also sits at the periphery of the nuclear envelope (the membrane that surrounds the nucleus), binding to different structures there to add stability and prevent collapse.-***-"'All cells have a cytoskeleton made from lots of filaments of a protein called actin that give the cell its architecture, but without other proteins added on, the skeleton will buckle under stress," says Parsons. "Proteins like fascin that bind onto this cytoskeleton add an element of stability and flexibility -- it makes the cell more mechanically stable and able to rapidly respond to the environment to change shape.-***-"By reducing intercellular levels of the fascin protein, they found that the cells were unable to squish their nuclei enough to fit into small channels."-Comment: Much of this article is about cancer research, but the point is to demonstrate how complex cell structure is. My view is the same. The more complexity, the more likely a mind planned multicellular life.

Biological complexity: how vitamin A enters a cell

by David Turell @, Thursday, August 25, 2016, 20:08 (2773 days ago) @ David Turell

It has to be very careful as too much vitamin A is toxic to cells, but A is vital to vision so the system has to work properly. This finding is currently tentative, but reasonable:-http://phys.org/news/2016-08-electron-microscopy-reveals-vitamin-cell.html-"Using a new, lightning-fast camera paired with an electron microscope, Columbia University Medical Center (CUMC) scientists have captured images of one of the smallest proteins in our cells to be "seen" with a microscope. 
The protein—called STRA6—sits in the membrane of our cells and is responsible for transporting vitamin A into the cell interior. Vitamin A is essential to all mammals and is particularly important for making light receptors in our eyes, and to ensuring normal fetal development.-"Images of the protein, which revealed several unusual features, were published in the August 26th issue of the journal Science,...-***-"STRA6 only interacts with Vitamin A via an intermediary protein that carries the greasy vitamin A in the bloodstream. Revealing the structure of STRA6 may not only give the researchers insight into Vitamin A transport, but may also provide clues about how other related transporters work.-"A new type of camera technology was key to obtaining the images of STRA6. When paired with an electron microscope, the camera allows biologists to see tiny, previously unseen structural details of the inner machinery of our cells.-***-"The researchers used approximately 70,000 individual pictures of STRA6 to generate a 3-dimensional map of the protein, which was used to construct an atomic model accurate to the smallest detail. The images and model revealed that STRA6 is "a bit of a freak," says Dr. Clarke. Even more surprising was the fact that STRA6 does not work alone, but is instead tightly associated with another protein, calmodulin, which plays a key role in calcium signaling.-"Although Vitamin A moves through STRA6 to enter the cell, there is no channel in STRA6 like most transporters. Instead, vitamin A enters the top of STRA6, but then appears poised to exit through a side window that opens directly into the cell membrane, not the cell interior.-"Though this needs to be verified, the mechanism may be a way to protect cells from absorbing too much vitamin A. "Vitamin A is actually somewhat toxic," says Dr. Mancia. "Trapping vitamin A inside the membrane may keep control of the amount that gets into the cell."-"The new model of STRA6 advances the understanding of a critical cellular function and may help researchers understand how other, still mysterious, cellular components work."-Comment: Once again a very complicated transport molecule is seen to fill a very exact purpose. How did 'purposeless' Darwin evolution understand the need to do this? Vitamin A has to be used at exact levels or it becomes dangerous. How did vision develop in view of this difficulty. Again a strong suggestion of saltation, and what is the mechanism for saltation? God is a good answer.

Biological complexity: one receptor, two T cells

by David Turell @, Monday, August 29, 2016, 15:54 (2769 days ago) @ David Turell

Immunity is a requirement for life to survive, but like blood clotting it has to be controlled. Too much chronic inflammation will cause scaring and unnecessary damage. this article describes two T cells that are part of the controls:-http://www.the-scientist.com/?articles.view/articleNo/46887/title/One-Antigen-Receptor-Induces-Two-T-cell-Types/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=33514447&_hsenc=p2ANqtz-9eWRUe3gIYPXx0_Z-aS9ugB2dYncZuLbp5g-5WKFV499r0Fp172U87W8qVdeoGdifD8XbMxl6bLPXO-QX9uaqp5sIYIA&_hsmi=33514447-"Each newly-formed T cell bears a unique T cell receptor (TCR) that recognizes a particular antigen. But how a given TCR shapes the fate of its cell and that cell's progeny was largely unknown. Today (August 26), scientists at MIT report in Science Immunology on their discovery that precursor T cells with precisely the same TCR don't necessarily follow the same developmental path.-“'The main take-home message is that T cells with identical specificity . . . can really differentiate into very distinct subtypes of T cell depending on the environment in which they are located,” -***-"During T cell development, the genes encoding the TCR are shuffled and recombined by special genetic mechanisms to create an individual version of the receptor protein expressed on the cell's surface. A variety of T cell types exist: some, like helper and cytotoxic T cells, promote strong immune responses against foreign invaders, while others. like T regulatory cells (T regs), suppress excessive inflammation. It has been observed that the repertoire of TCRs found on one subtype—for example, T regs—tends not to overlap with that found on others. This finding could indicate that the type of antigen recognized by a particular TCR can influence the type of T cell that subsequently develops.-***-"Thinking it likely that these transnuclear mice would only contain T regs, Bilate was “completely surprised” to find that while the animals did produce a small amount of T regs, they also contained an entirely different type of T cell called intraepithelial lymphocytes (iELs). “It was like a bucket of cold water on me,” she told The Scientist.-"In contrast to T regs' anti-inflammatory nature, iELs can adopt both a cytotoxic phenotype—expressing the proinflammatory cytokine interferon gamma—or an antiflammatory state. T regs and iELs share few similarities, said Mucida. “It's not like a subtle difference in the type of function they can perform. They are very distinct.”-"Bilate and colleagues found that the two cell types also differed in their locations within the intestine. The T regs primarily resided in the mesenteric lymph nodes and lamina propria—the layer of connective tissue at the base of the mucus membrane—while iELs dominated the epithelial layer.-***-"In the mammalian gut, immune cells must perform a delicate balancing act of preventing pathogenic invaders while tolerating dietary antigens and commensal microbes. Occasionally this balance is tipped, such as in food allergies or other inflammatory bowel conditions. But, if you “understand the factors that are involved in the modulation of these cells,” said Mucida, then maybe “you can figure out what is required to correct unbalances that occur under pathological conditions.'”-Comment: Runaway inflammation causes chronic ulcerative colitis or regional enteritis in the small intestine. This research may lead to a cure for them. But the key point here is living tissue must contain feedback loops to stop a beneficial process from overextending itself, just as blood clotting must by confined to the damaged vessel area, not the whole body. And the usual question is how does such a complex arrangement develop itself in a stepwise evolutionary process? The answer is it doesn't. It must develop by saltation, all complete at once when put in place. To think that the cells themselves cooked up such a balanced process stretches credulity.

Biological complexity: one receptor, two T cells

by dhw, Tuesday, August 30, 2016, 11:36 (2768 days ago) @ David Turell

David's comment: Runaway inflammation causes chronic ulcerative colitis or regional enteritis in the small intestine. This research may lead to a cure for them. But the key point here is living tissue must contain feedback loops to stop a beneficial process from overextending itself, just as blood clotting must by confined to the damaged vessel area, not the whole body. And the usual question is how does such a complex arrangement develop itself in a stepwise evolutionary process? The answer is it doesn't. It must develop by saltation, all complete at once when put in place. To think that the cells themselves cooked up such a balanced process stretches credulity.-I agree that all such mechanisms must develop by saltation, and I find that all these complexities in themselves stretch credulity! All the miracles of life, of consciousness, of reproduction, of evolution, of oak trees growing from acorns, of ants building cities, of weaverbirds tying knots, of cell communities cooperating to protect themselves and one another…they are all sources of wonderment. How did they originate? Nobody knows. You explain everything as the work of some unknown, unknowable power with a sourceless mind and boundless power and knowledge, whose very existence stretches credulity. There is NO explanation that does not stretch credulity. But within the explanatory confines of your theism, I personally find my hypothesis - that your God endowed cells/cell communities with a particular type of creative intelligence - at least as likely as your own hypothesis that every single process, innovation and wonder, extant and extinct, was preprogrammed or dabbled directly by himself.

Biological complexity: one receptor, two T cells

by David Turell @, Tuesday, August 30, 2016, 18:58 (2768 days ago) @ dhw


> dhw: I agree that all such mechanisms must develop by saltation, and I find that all these complexities in themselves stretch credulity! All the miracles of life, of consciousness, of reproduction, of evolution, of oak trees growing from acorns, of ants building cities, of weaverbirds tying knots, of cell communities cooperating to protect themselves and one another…they are all sources of wonderment. How did they originate? Nobody knows. You explain everything as the work of some unknown, unknowable power with a sourceless mind and boundless power and knowledge, whose very existence stretches credulity. There is NO explanation that does not stretch credulity.-Why doesn't your incredulity about life forms and styles lead you to accept a mind must be behind this to explain the enormous complexity? It can only be chance or design, no third way.

Biological complexity: one receptor, two T cells

by dhw, Wednesday, August 31, 2016, 13:06 (2767 days ago) @ David Turell

dhw: I agree that all such mechanisms must develop by saltation, and I find that all these complexities in themselves stretch credulity! All the miracles of life, of consciousness, of reproduction, of evolution, of oak trees growing from acorns, of ants building cities, of weaverbirds tying knots, of cell communities cooperating to protect themselves and one another…they are all sources of wonderment. How did they originate? Nobody knows. You explain everything as the work of some unknown, unknowable power with a sourceless mind and boundless power and knowledge, whose very existence stretches credulity. There is NO explanation that does not stretch credulity.-DAVID: Why doesn't your incredulity about life forms and styles lead you to accept a mind must be behind this to explain the enormous complexity? It can only be chance or design, no third way.-Because all explanations stretch my credulity. That is the agnostic's dilemma.

Biological complexity: one receptor, two T cells

by David Turell @, Wednesday, August 31, 2016, 18:21 (2767 days ago) @ dhw


> DAVID: Why doesn't your incredulity about life forms and styles lead you to accept a mind must be behind this to explain the enormous complexity? It can only be chance or design, no third way.
> 
> dhw: Because all explanations stretch my credulity. That is the agnostic's dilemma.-Which leaves you incredulous and without answers. So be it.

Biological complexity: one receptor, two results

by David Turell @, Friday, September 02, 2016, 19:09 (2765 days ago) @ David Turell

Once again looking at immunity we find one receptor that sees two different challenges and produces two different responses:-http://www.the-scientist.com/?articles.view/articleNo/46926/title/One-Receptor--Two-Ligands--Different-Responses/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=33767064&_hsenc=p2ANqtz-_eQg_I-Uqv-T4WYh7McB35w3od2mnYcrBbIsaBUUaPIt_z0XMKVDhZj7Oi6ReJLVNDvUmUJjx11vlhVs_1Vt1PJKSX5g&_hsmi=33767064-"Macrophages detect and kill pathogens, but also recognize and repair damage to host tissues. How the cells determine which response is required, however, is somewhat of a mystery. Now, researchers at the University of Oxford studying the macrophage toll-like receptor 4 (TLR4), which interacts with both bacterial lipopolysaccharide (LPS) and host protein tenascin-C, show that the two molecules trigger different pathways and proteins in the macrophages that govern contrasting responses.-"This is a very interesting paper. It addresses a big overall question of how does the immune system distinguish between infection and non-infectious tissue damage,” said immunologist Cynthia Leifer of Cornell University College of Veterinary Medicine in Ithaca, New York, who was not involved in the study. “The overall conclusion is that, through one innate immune receptor, with two different ligands, you can trigger two different types of outcome.”-"LPS, also known as endotoxin, is a molecule found in the outer membrane of many different types of bacteria. Through its interaction with TLR4, LPS induces a strong inflammatory reaction in humans. Tenascin-C, on the other hand, is a protein found in the extracellular matrices of various host tissues. “There is not very much of it present in a healthy person, but when you get injured its levels go through the roof and that triggers an immune response,” said Kim Midwood of Oxford who led the new study. About seven years ago, Midwood's group made the surprising discovery that tenascin-C also signals via TLR4.-“'So this receptor is sensing infection, but its also sensing damage . . . which is a wholly different type of defense,” Midwood said. “It's actually taken years for people to believe it, because nobody would have ever thought it would.”-But even after the naysayers were silenced, a question remained: Can this receptor actually interpret different danger signals? That is, “Does it know that an infection needs immune response A while tissue damage needs immune response B?” asked Midwood.-"To find out, she and her colleagues treated human macrophages in culture with either LPS or an active fragment of tenascin-C and examined the effects. The researchers found that while both ligands triggered the production of cytokines, the subsets and levels of these cytokines differed. Those induced by LPS were representative of a classic pathogen-killing macrophage state, the team found, while those induced by tenascin-C suggested the cells were in tissue-repair mode.-"The team also found that LPS and tenascin-C triggered phosphorylation of different subsets of cellular proteins. Among the phosphoproteins strongly induced by tenascin-C were members of the collagen family. However, in contrast, LPS induced the expression of collagenases—enzymes that breakdown collagen.-“'In one setting [the macrophages] are ready to chew up tissue,” said immunologist Carl Nathan of Weill Cornell Medical College in New York City who was not involved in the study, and in the other they “secrete building blocks for repair.” Thus, the outcome of the LPS versus tenascin-C signaling “is strikingly different,” he said.-"It is not yet clear how these two ligands induce such disparate effects in the same cell by the same receptor. “That's the million-dollar question,” said Leifer. It might be that the ligands recruit different co-receptors, or induce TLR4 to adopt different conformations, she suggested."-Comment: I view this as two automatic molecular responses, as Leifer also seems to in her statement re' mechanism. This is an either/or reaction involving a so far unknown molecular change.

Biological complexity: respiratory mitochondrial form

by David Turell @, Tuesday, September 06, 2016, 19:20 (2761 days ago) @ David Turell

This is another of the huge complex molecules necessary for multicellular life. In a blind search of possible functional molecular structure, as proposed by 'Darwin chance', just how was this found? This is one example of thousands of huge complex molecules necessary for life if one adds up all the different enzymes at work with all the different parts of a cell, especially the energy engines, the mitochondria:-https://www.sciencedaily.com/releases/2016/09/160906131616.htm-"The respiratory chain is responsible for most energy production in humans. Several large protein assemblies are embedded in the mitochondrial lipid membrane. The mitochondrial Complex I is the first and largest complex in this chain. Metabolites derived from food are processed by this enzyme complex in order to contribute to the electron transfer and proton translocation. So far, research groups were only able to reveal mostly poly-alanine models lacking necessary full atomic details due to the fact that huge and complex molecules are difficult to examine with current methods. Cryo-electron microscopy made huge advances in recent years due to the development of new direct electron detectors, allowing high-resolution studies.-"The resolution of the structure at an atomic level now allows the understanding of the intricate arrangements and interactions of all 45 subunits (14 conserved core and 31 mitochondria-specific supernumerary subunits) with implications for the coupling mechanism and its regulation. The insight into mechanism, assembly, maturation, and dysfunction of Complex I allows a detailed molecular analysis of disease-causing mutations and affected enzyme activity."-Comment: See my initial statement, and be sure to look at the diagram. As techniques of resolution improve the complexity will only become more obvious and the odds of chance dwindle to nothingness. The research road ahead is clear, more and more complexity: chance has no chance of being the correct solution to the question of why is there life.

Biological complexity: how cells attach or repel

by David Turell @, Tuesday, September 06, 2016, 20:40 (2761 days ago) @ David Turell

Another complex molecular mechanism by which cells can form parts of a body, either staying attached or separating:-http://phys.org/news/2016-09-pathway-enables-cells-destinations-repulsion.html-"When cells grow and divide, they come into contact with other cells. This happens not only during development and regeneration and after injury, but also during cancer growth and the formation of metastases. When cells come into contact with each other in this way, information is exchanged by proteins, which are embedded in the cell membranes and form tight lock-and-key complexes with each other. These connections must be severed if the cells want to transmit a repulsion signal. It appears that the fastest way to do this is for the cells to engulf the protein complex from the membrane of the neighbouring cell. Scientists from the Max Planck Institute of Neurobiology in Martinsried have now identified the molecules that control this process.-"Development is an extremely rapid process. Increasing numbers of cells are formed which must find their correct position in the body, clearly demarcate themselves from each other to form tissue, or - as is the case in the nervous system - establish contact with partner cells in remote locations. "The crowding is accompanied by orderly pushing and shoving," says Rüdiger Klein, whose Department at the Max Planck Institute of Neurobiology studies how cells get their bearings. "A popular way for one cell to show another which direction to take is for it to repel the other cell following brief contact." According to the scientists' observations, the cells do not exactly treat each other with kid gloves and even go so far as to engulf entire pieces from the membranes of other cells.-"When cells come into contact with each other, ephrin and Eph receptors are often involved. These proteins are located on the surface of almost all cells. When two cells meet, their ephrin and Eph receptors connect to form tight ephrin/Eph complexes. These complexes then trigger the repulsion process through intracellular signalling pathways. "This is where the problem arises, as it appears that the cells then want to separate as quickly as possible - however, the two cells are attached to each other through the tight ephrin/Eph complex," explains Klein. So the cells do something else: they extend their own cell membranes so far over the individual complexes that the complex and the surrounding membrane detaches from the neighbouring cell and is fully incorporated into the cell.-"With the help of a series of genetic modifications and the targeted deactivation of individual cell components, the scientists succeeded in demonstrating that Tiam signalling proteins are activated through the formation of the ephrin/Eph complex. As a result, Rac enzymes become active which, in turn, cause the engulfment of the ephrin/Eph complexes by the cell membrane through the local restructuring of the actin cytoskeleton. If one of these components is missing, this engulfing process through endocytosis is blocked and the cells do not repel each other but remain attached."-Comment: Again molecular automatic activity is demonstrated.

Biological complexity: how cells remove garbage

by David Turell @, Wednesday, September 14, 2016, 23:57 (2753 days ago) @ David Turell

There is lots because cells are constantly in production:-http://www.agnosticweb.com/index.php?mode=posting&id=22780&back=entry-"Proteins are synthesized on ribosomes as linear chains of amino acids and must fold into unique three-dimensional structures to fulfill their biological functions. Protein folding is intrinsically error-prone, and how it is accomplished efficiently represents a problem of great biological and medical importance. During folding, the nascent polypeptide must navigate a complex energy landscape. As a result, misfolded molecules may accumulate that expose hydrophobic amino acid residues and thus are in danger of forming potentially toxic aggregates. To ensure efficient folding and prevent aggregation, cells in all domains of life express various classes of proteins called molecular chaperones. These proteins receive the nascent polypeptide chain emerging from the ribosome and guide it along a productive folding pathway. Because proteins are structurally dynamic, constant surveillance of the proteome by an integrated network of chaperones and protein degradation machineries, the proteostasis network (PN), is required to maintain protein homeostasis in a range of external and endogenous stress conditions. - "'Chaperones are a kind of Technical Inspection Authority for cells," Phys.org explains. "They are proteins that inspect other proteins for quality defects before they are allowed to leave the cell." When molecular chaperones cannot fold a protein properly in time, the surveillance crew must make a go/no-go decision, because some amino acids might clump into toxic aggregates. The "Proteostasis Network" involves cleanup crews like the proteasome system, autophagy, and the lysosome system.-***-"molecular chaperones are involved in a plethora of cellular processes by playing key roles in nascent protein chain folding, transport and quality control. Their molecular functions range from stabilizing stress-susceptible molecules and membranes to assisting the refolding of stress-damaged proteins, thereby acting as protective barriers against cellular damage.-***-"Aberrant proteins are tagged with ubiquitin, a small protein, by two independent surveillance crews. A shredding machine called the proteasome recognizes the tags and provides docking points for them. These quality-control measures ensure that only the bad proteins are degraded.-***-"A large number of different proteins in a cell have to be degraded -- some 30 percent of all cellular protein structures formed by folding of amino acid chains are faulty. The problem for the cells is that these incorrectly folded proteins do not have a uniform structure, making it difficult to identify all of them correctly. If breakdown of these "useless" proteins goes wrong, they are deposited in the cell and disturb its homeostasis. This can lead to death of the cell.-***-" The proteasome is composed of 33 subunits assembled in two sub-complexes, the 20S core particle (CP), flanked at one or both ends by the 19S regulatory particle (RP) to form the 26S proteasome. Proteasome assembly requires the assistance of proteasome assembly chaperones. Four evolutionarily conserved 19S RACs [regulatory particle assembly chaperones]: Nas2, Nas6, Hsm3 and Rpn14 in yeast, and p27 (also known as PSMD9), p28 (also known as PSMD10), S5b (also known as PSMD5) and Rpn14 (also known as PAAF1) in mammals are needed for regulatory particle assembly. In addition, yeast cells have Adc17, a stress-inducible RAC, which is vital for cells to survive conditions, such as accumulation of misfolded proteins, which overwhelm the proteasome. This suggests that cells have evolved adaptive signalling pathways to adjust proteasome assembly to arising needs, but how this is achieved is unknown.(
(My bold suggests a feedback mechanism for tight control.)-***-" Deficient proteasome function can lead to a buildup of unneeded and potentially toxic proteins, so cells usually respond to proteasome dysfunction by increasing production of its component parts. Now two Massachusetts General Hospital (MGH) investigators have identified key molecules in the pathway by which cells in the C. elegans roundworm sense proteasome dysfunction, -***-"After an egg cell is fertilized, the sperm cell's mitochondria need to be digested to prevent a condition called heteroplasmy. Maternal inheritance of mitochondria and mitochondrial genes is a major developmental paradigm in mammals. Propagation of paternal, sperm-contributed mitochondrial genes, resulting in heteroplasmy, is seldom observed in mammals, due to postfertilization targeting and degradation of sperm mitochondria, referred to as "sperm mitophagy." Our and others' recent results suggest that postfertilization sperm mitophagy is mediated by the ubiquitin-proteasome system, the major protein-turnover pathway that degrades proteins and the autophagic pathway.... Our findings provide the mechanisms guiding sperm mitochondrion recognition and disposal during preimplantation embryo development, which prevents a potentially detrimental effect of heteroplasmy.-Comment: A high speed continuous process. We stay alive because the garbage is spotted, removed or destroyed, at 99.99% efficiency. Otherwise we die! Cells are in constant production of product or replacement molecules of cell structure. Developed by chance? Never!

Biological complexity: sensory receptors everywhere

by David Turell @, Friday, September 16, 2016, 15:40 (2751 days ago) @ David Turell

Not just where they are expected to be: - http://www.the-scientist.com/?articles.view/articleNo/46831/title/What-Sensory-Receptor... - " In 2012, Johns Hopkins University's Berkowitz had just moved to a lab space where the lights were motion-activated, and his postdoc Gautam Sikka soon began to observe a curious response in the blood vessels he had isolated for study: whenever he walked in and the lights turned on, the vessels exerted less pressure on the force transducer the researchers had attached to constantly stream data. - "A literature search revealed that the relaxation of blood vessels in response to light, called photorelaxation, had been described almost 50 years earlier, but the underlying mechanisms had never been fully elucidated. Berkowitz wondered if these effects were mediated by resident light-sensing pigments. If so, it wouldn't be the first time that a sensory receptor had been found outside of a sense organ. - "The light, odor, and taste receptors located in our eyes, noses, and tongues flood our brain with information about the world around us. But these same sensory receptors are also present in unexpected places around the body, where they serve a surprising range of biological roles. In the last decade or so, researchers have found that the gut “tastes” parasites before initiating immune responses, and the kidneys “smell” fatty acids, regulating blood pressure in response. Sure enough, upon further investigation Berkowitz found that it was melanopsin, a light-sensing pigment that serves circadian entrainment and other nonvisual functions in the eye, that modulated the relaxation of blood vessels when the lab lights came on. - "In contrast to the early days of the field, the idea of sensory receptors outside of sensory organs is no longer unusual. “They're all just chemoreceptors, and you can use them in lots of different contexts in physiologically different systems,” says University of Colorado Denver neurobiologist Thomas Finger. - "Now researchers are characterizing such sense receptors present in different tissues around the body and working to understand their functions, with the eventual goal of using these receptors for various diagnostic or therapeutic applications." - Comment: A very long article, telling about all the different studies, follows the above excerpt. Here is an example, very complex: - "In a few cases, researchers may have identified the natural ligands responsible for activating olfactory receptors around the body. In the kidney, for example, Johns Hopkins University's Pluznick found that certain short-chain fatty acids produced by gut bacteria can activate olfactory receptor 78 (Olfr78), which in mice triggers changes in blood pressure. When researchers injected mice lacking the gene for Olfr78 with short-chain fatty acids, the animals' blood pressure dropped, suggesting that Olfr78 by itself normally increases blood pressure in response to the compounds. But blood pressure regulation is complicated, and Pluznick found another, nonolfactory receptor called Gpr41 that decreased blood pressure in response to short-chain fatty acids and had a stronger effect than Olfr78.8 Pluznick suggests that the two receptors might act together to produce a buffering effect that protects against wild swings in blood pressure as fatty-acid levels fluctuate."

Biological complexity: automatic molecular switches

by David Turell @, Monday, September 19, 2016, 18:52 (2748 days ago) @ David Turell

No consciousness involved, just molecules that give signals:-http://medicalxpress.com/news/2016-09-molecular-immune-suppression-immunotherapies.html-"The researchers identified a molecular switch that controls immune suppression, opening the possibility to further improving and refining emerging immunotherapies that boost the body's own abilities to fight diseases ranging from cancer to Alzheimer's and Crohn's disease. -***-"When confronted by pathogens, injury or disease, the initial response of the body's immune system comes in the form of macrophages, a type of white blood cell that express pro-inflammatory proteins called cytokines that, in turn, activate T cells, another immune cell, to attack the health threat. The macrophages then switch gears to express other cytokines that dampen T cell activation, stimulating tissue repair.-***-"In the Nature paper, Varner and colleagues pinpoint a key, suspected player: an enzyme in macrophages called PI-3 kinase gamma (PI3Ky). In mouse studies, they found that macrophage PI3Ky signaling promotes immune suppression by inhibiting activation of anti-tumor T cells. Blocking PI3Ky activated the immune response and significantly suppressed growth of implanted tumors in animal models. It also boosted sensitivity of some tumors to existing anti-cancer drugs and synergized with existing immune therapy to eradicate tumors. Varner and her colleagues at the Moores Cancer Center also identified a molecular signature of immune suppression and response in mice and cancer patients that may be used to track the effectiveness of immunotherapy.-***-"In a December 2015 paper published online in Cancer Discovery, Varner and colleagues described animal studies that revealed how disrupting cross-talk between B cells (another type of immune cell) and tumor-associated macrophages inhibited PDAC growth and improved responsiveness to standard-of-care chemotherapy.
Specifically, that research team, which included scientists in San Francisco, Oregon and Switzerland, reported that inhibiting Bruton tyrosine kinase, an enzyme that plays a crucial role in B cell and macrophage functions, restored T cell-dependent anti-tumor immune response. In other words, it reactivated the natural, adaptive immune response in tested mice."-Comment: Once again giant enzyme molecules are part of an automatic control system which encourage or stop the expression of responses. Another example of feedback loop control. How did evolution find those huge complex molecules out of millions available for specific function? Not chance.

Biological complexity: automatic neuron controls

by David Turell @, Thursday, September 22, 2016, 14:54 (2745 days ago) @ David Turell

This study of spinal neurons shows how hey maintain local control of pH levels, while overall body control is mainly through lung gas exchange changes and whart the kidney chooses to keep or remove:-http://www.agnosticweb.com/index.php?mode=posting&id=22898&back=entry-"Bodies like to keep their pH close to 7.4, whether that means hyperventilating to make the blood alkaline, or burning energy, shifting to anaerobic metabolism, and producing lactate to make the blood acidic. The lungs and kidneys can regulate pH changes systemically, but they may not act quickly on a local scale. Because even small pH changes can dramatically affect the nervous system, a study led by Sten Grillner of Karolinska Institute in Sweden looked for a mechanism for pH homeostasis in the spinal cord.-
"Using the lamprey as a model system, the researchers observed that a type of spinal canal neuron, called CSF-c, fired more rapidly when they bathed it with high pH (7.7) or low pH (7.1) media. They could suspend the elevated activity by blocking two ion channels: PKD2L1 channels, which stimulate neurons in alkaline conditions, or ASIC3 channels, which, the team showed previously, do the same in acidic states.-"As the neurons fired, they released the hormone somatostatin, which inhibited the lamprey's locomotor network. These results suggest that, whichever direction pH deviates, “the response of the system is just to reduce activity as much as possible,” Grillner says. The pH-regulating role of CSF-c neurons is likely conserved among animals, the authors suspect, given the presence of these neurons across vertebrate taxa.-“'It's an interesting finding because it adds a level of regulation to maintain homeostasis in the central nervous system,” says Pierre Magistretti of King Abdullah University of Science and Technology in Saudi Arabia who was not involved in the work."-
Comment: Another example of the extreme complexity in the biochemistry of living organisms. Human pH is also kept at 7.4. I would assume the same neurons are in our bodies.

Biological complexity: tracking DNA/RNA activity:

by David Turell @, Monday, October 03, 2016, 14:37 (2734 days ago) @ David Turell

A long article describes using colored fluorescence to follow protein peptide production in cells:-http://www.the-scientist.com/?articles.view/articleNo/47128/title/How-to-Track-Translation-in-Living-Cells/-"More than a decade later, Stasevich and colleagues, alongside three independent groups, have succeeded in devising techniques for visualizing single-molecule translation in living human cells. “The fact that you have four labs working on this is a testament to how hot the topic is,” he says.
Stasevich's group engineered expression vectors that produced an mRNA containing stem-loop epitopes and encoding proteins in which the first few hundred amino acids formed a peptide domain of repeated epitopes called FLAG-tags. This domain, which the team dubbed “the spaghetti monster,” binds multiple FLAG-specific fluorescent antibodies that are injected into the cell, while the mRNA binds its own fluorescent antibodies. Thus, both the mRNA and its newly forming protein are observable at once (Science, 352:1425-29, 2016).-"The groups examined the translation kinetics for individual mRNAs and found that translation initiated roughly twice a minute and that elongation proceeded at 3 to 10 amino acids per second. Singer's crew also found evidence that, at least in neurons, translation proceeds in bursts of activity followed by inactivity—as has been described for transcription (Science, 352:1430-35, 2016). Zhuang's group showed how environmental stresses suppress translation and how the dynamics of translation vary depending on subcellular location (Cell, 165:990-1001, 2016). And Tanenbaum's team observed that individual mRNAs from the same gene in the same cell can vary dramatically in their translation efficiency, with some being practically silent and others translating robustly (Cell, 165:976-89, 2016). “You wouldn't have appreciated that heterogeneity if it weren't for these single-molecule techniques,” says Sonenberg." (my bold)-Comment: I've skipped the long history part of the article which starts with the discovery of DNA. Please note the bolded area, noting the speed of production of a peptide, and remember the amino acids have to be produced also at that speed and they are all left-handed, requiring enzymatic production. The complexity of living biochemistry seen in action demands the conclusion it was developed by an active mind. No chance process can possibly do this.

Biological complexity: Nitrogen fixing

by David Turell @, Wednesday, October 05, 2016, 15:26 (2732 days ago) @ David Turell

Nitrogen is the most common gas in our atmosphere. Plants use it as a mojor component of their structure so it is a primary nutrient, but it must be changed from gas to a more fixed substance:-http://www.calvin.edu/academic/chemistry/faculty/arnoys/arnoys-chem324-leghemoglobin.html-"The reduction of nitrogen to ammonia, known as nitrogen fixing, is vital to agriculture: 
N2 + 3H2 ? 2NH3-"Whereas the industrial Haber-Bosch process requires temperatures ~500 oC and hundreds of atmospheres of pressure to overcome the activation energy, some bacteria can accomplish the reaction at soil temperatures and atmospheric pressure. (In fact the nitrogenase complex found in these bacteria is responsible for fixing over 1011 kg of nitrogen every year.) These bacteria are symbionts--in exchange for the abundant ammonia they produce for the legume host, the plant provides huge amounts of energy for the reaction.-"However, nitrogenase has a problem with oxygen toxicity. Here again the plant host comes to the rescue by providing leghemoglobin (PDB code 2GDM, structure generated with PyMOL), an oxygen-binding protein:-"Leghemoglobin is able to bind oxygen due to the iron-containing heme held in its center.-"As its name suggests, leghemoglobin belongs to the globin protein family and its structure resembles that of the mammalian oxygen-binding protein myoglobin.-" Though the structures and functions of the two proteins are quite similar, their sequences have little in common. Furthermore, myoglobin is not found in plants, so it would be a stretch to suggest that leghemoglobin arose from myoglobin. Instead, what we see here is a wonderful example of convergent evolution in which the optimum oxygen-binding structure is found in two very different types of organisms."-Comment: All hemoglobin/myoglobin-like molecular structures employ iron and bind oxygen. In this case it is used for protection from oxygen, which is a very dangerous element, as shown in forest fires, for example. We have antioxidants in our bodies for the same reason. The symbiotic plant example of nitrogen-fixing is a nice demonstration of convergent evolution. Note how complex the human process is to do what bacteria do easily. Another explanation of convergence is God's pre-planning, setting up similar chemical structures for similar purposes in many places in the bush of life. Also note nitrogenase, as an enzyme, is a giant molecule. Did evolution discover/invent all of this complexity by chance? Not in my view.

Biological complexity: 60 million proteins in a cell

by David Turell @, Thursday, October 06, 2016, 02:32 (2731 days ago) @ David Turell

These molecules are polypeptides which are strings of amino acids, generally 200 or more, with folding that is required to be exact in 3-D form to be functional:-http://www.evolutionnews.org/2016/10/imagine_60_mill103182.html-"Here are some "wow" facts they share about the proteins in a tiny yeast cell:-"Collectively, proteins catalyse and control essentially all cellular processes. They form a highly structured entity known as the proteome, the constituent proteins of which carry out their functions at specific times and locations in the cell, in physical or functional association with other proteins or biomolecules. A proliferating Schizosaccharomyces pombe cell contains about 60 million protein molecules, which have abundances that range from a few copies to 1.1 million copies per expressed gene. Across the species, proteins constitute about 50% of the dry mass of a cell and reach a remarkable total concentration of 2-4 million proteins per cubic micrometre or 100-300 mg per ml. The extensive proteome network of the cell adapts dynamically to external or internal (that is, genetic) perturbations and thereby defines the cell's functional state and determines its phenotypes. Describing and understanding the complete and quantitative proteome as well as its structure, function and dynamics is a central and fundamental challenge of biology.-***-"All these millions of proteins cooperate to contribute to the life and health of the cell, responding dynamically to perturbations, each playing its role to provide energy from nutrients, deliver cargo, translate and maintain genetic information, remove waste, and replicate. -***
" Axe estimated the prevalence of sequences that could fold into a functional shape by random combinations. It was already known that the functional space was a small fraction of sequence space, but Axe put a number on it based on his experience with random changes to an enzyme. He estimated that one in 10^74 sequences of 150 amino acids could fold and thereby perform some function -- any function. -***-"It is useful to begin by considering the fraction of protein sequence space that is occupied by naturally occurring proteins. The number of distinct sequences that are possible for a protein of typical length is 20200 sequences (because each of the protein's 200 residues can be one of 20 amino acids), and the number of distinct proteins that are produced by extant organisms is on the order of 10^12. Evidently, evolution has explored only a tiny region of the sequence space that is accessible to proteins.-***-"Since 20^200 is about 10^260, and the space actually sampled by living organisms is 1012, the numbers differ by at least 240 orders of magnitude for proteins of length 200, or about 183 orders of magnitude the 150-amino-acid chains Axe used. No wonder the authors say that "the natural evolutionary process has sampled only an infinitesimal subset" of sequence space.-***-"Any random search has no possible chance, using all the atoms in the universe for the entire age of the universe, of finding a functional cluster in such a vast space. Dembski said that any search for a target that has less than 1 chance in 10^150 exceeds the universal probability bound; it will never happen anywhere in the entire history of the universe. (my bold)-***-"Functions that naturally occurring proteins mediate include: the use of solar energy to manufacture complex molecules; the ultrasensitive detection of small molecules (olfactory receptors) and of light (rhodopsin); the conversion of pH gradients into chemical bonds (ATP synthase); and the transformation of chemical energy into work (actin and myosin). Not only are these functions remarkable but they are encoded in sequences of amino acids with extreme economy. Such sequences specify the three-dimensional structure of the proteins, and the spontaneous folding of extended polypeptide chains into these structures is the simplest case of biological self-organization." (my bold)-Comment: This article once again shows that blind chance search of all available protein molecule sizes and shapes cannot create life. What has been created is too economical in function for a random process. Life comes from only 10^12 of the possibilities. How were they selected to efficiently run life? Not by chance!

Biological complexity: Using micro-nutrient Selenium

by David Turell @, Thursday, October 06, 2016, 18:38 (2731 days ago) @ David Turell

Selenium is poisonous in large amounts, a strong anti-oxidant, and yet entirely required in nutrition. Only Camelids like Llamas handle very large amounts because they developed on volcanic soil which carried large amounts into plant foods. It must be put into proteins to work, and is handled very carefully:-http://phys.org/news/2016-10-selenium-incorporated-proteins.html-"Humans need eight essential trace elements for good health, and one of them is selenium - a powerful antioxidant that is important for thyroid and brain function as well as metabolism. -"In humans, elongation factor eEF1A helps string together amino acids at the ribosome - that is, all amino acids except selenocysteine, the amino acid that holds selenium.In humans, selenocysteine is incorporated into proteins with help of a unique elongation factor called eEFSec that works very differently from eEF1A.-"We've known that selenium is special when it comes to protein synthesis, because there is a whole other set of rules and tools in use," says Miljan Simonovic, associate professor of biochemistry and molecular genetics in the UIC College of Medicine and corresponding author on the paper. "Not only does it have its own elongation factor, but selenocysteine is also very unusual because it is represented in the genetic code by the same three-letter key, or codon, that signals for protein synthesis to stop."-"Normally, as the ribosome reads the messenger RNA—or mRNA—and reaches this stop codon, it detaches from the mRNA because its work is done, although the full-length protein may still be modified through other processes.
But sometimes the ribosome runs the stop sign and adds selenocysteine instead—and continues to elongate the protein until it reaches another stop sign.-"When the stop codon means 'bring in a selenocysteine,' additional protein factors together with structural features in the mRNA around that stop codon, such as loops, indicate to the ribosome not to stop selenoprotein production," said Malgorzata Dobosz-Bartoszek, postdoctoral research associate in biological sciences, who is lead author on the paper. "The selenocysteine elongation factor, eEFSec, plays a key role in helping to recognize the stop codon as actually coding for selenocysteine." (my bold)-"Simonovic thinks that the reason selenocysteine is handled so differently during protein synthesis traces back to the Great Oxygenation Event. This was the period about 2.3 billion years ago when free oxygen in Earth's atmosphere suddenly spiked, due to the evolutionary emergence of plants and photosynthesis as a way to derive energy from the sun. Organisms needed to evolve ways to prevent cellular damage caused by oxidation, and selenium, a powerful antioxidant, would have been available. But already-existing processes for incorporating trace elements into proteins may not have worked for selenium, which is extremely reactive.-"'We know that eEFSec has a unique domain that helps it safely interact with selenocysteine," Simonovic said.-"Simonovic said the eEFSec elongation factor also stands apart in how it changes shape when it delivers selenocysteine to the ribosome. The researchers showed that eEFSec bends about 20 degrees when delivering selenocysteine, while eEF1A bends "much more dramatically—more like 90 degrees" when it drops off the other amino acids."-Comment: With selenium being so poisonous in large amounts, how did chance evolution develop complex genome mechanisms to incorporate it? Note my bold. Saltation.

Biological complexity: Sodium levels and thirst controls

by David Turell @, Sunday, October 09, 2016, 01:53 (2728 days ago) @ David Turell

The level of sodium in body fluids is tightly controlled, not only by the kidney but also by thirst:-http://medicalxpress.com/news/2016-10-idea-mandatory-intake.html-"A multi-institute study led by Monash University has revealed for the first time the mechanism that regulates fluid intake in the human body and stops us from over-drinking, which can cause potentially fatal water intoxication. The study challenges the popular idea that we should drink eight glasses of water a day for health. -"The study showed that a 'swallowing inhibition' is activated by the brain after excess liquid is consumed, helping maintain tightly calibrated volumes of water in the body.-"Building on a previous study, the researchers asked participants to rate the amount of effort required to swallow water under two conditions; following exercise when they were thirsty and later after they were persuaded to drink an excess amount of water.
The results showed a three-fold increase in effort after over-drinking. -"'Here for the first time we found effort-full swallowing after drinking excess water which meant they were having to overcome some sort of resistance," Associate Professor Farrell said.-"'This was compatible with our notion that the swallowing reflex becomes inhibited once enough water has been drunk."-"Associate Professor Farrell, who works in the Monash University Department of Medical Imaging and Radiation Sciences, used functional magnetic resonance imaging (fMRI) to measure activity in various parts of the brain, focusing on the brief period just before swallowing.-"The fMRI showed the right prefrontal areas of the brain were much more active when participants were trying to swallow with much effort, suggesting the frontal cortex steps in to override the swallowing inhibition so drinking could occur according to the researchers' instructions.-"'There have been cases when athletes in marathons were told to load up with water and died, in certain circumstances, because they slavishly followed these recommendations and drank far in excess of need," he said.-"Drinking too much water in the body puts it in danger of water intoxication or hyponatremia, when vital levels of sodium in the blood become abnormally low potentially causing symptoms ranging from lethargy and nausea to convulsions and coma.-Comment: Thirst is a sensation mediated by the brain and the concentration of saliva. This study raises the issue that the kidney and the brain may signal back and forth and the salivary glands are tied into the network of control. Overhydration can kill. This must be a very old mechanism in land animals

Biological complexity: engulfing photosynthesis

by David Turell @, Monday, October 10, 2016, 20:22 (2727 days ago) @ David Turell

Just as mitochondria were engulfed so was the mechanism of photosynthesis:-http://phys.org/news/2016-10-scientists-reveal-little-known-amoeba-engulfed.html-"About 100 million years ago, a lowly amoeba pulled off a stunning heist, grabbing genes from an unsuspecting bacterium to replace those it had lost. -"Now Rutgers and other scientists have solved the mystery of how the little amoeba, Paulinella, committed the theft. It engulfed the bacterium, kept that cell alive and harnessed its genes for photosynthesis, the process plants and algae use to convert carbon dioxide into oxygen and sugar via solar energy.-"The major finding of the study is the microbial world, which we know is full of valuable genes, can move these genes between organisms according to need," said Debashish Bhattacharya, a study co-author and distinguished professor in the Department of Ecology, Evolution and Natural Resources at Rutgers. "When a microbe has a gene deficit, it can in some cases fill that deficit by grabbing the same gene from the environment. This shows how fluid microbial genomes really are."-***-"The engulfing process is known as primary endosymbiosis, and it altered life on Earth by allowing the rise of animals that depend on plant life.
The theory of endosymbiosis has an interesting scientific history. In 1895, German naturalist Robert Lauterborn wrote a paper on Paulinella chromatophora, an amoeba he discovered, and his finding of plant cells inside the amoeba. It has two large, sausage-shaped plastids called chromatophores, which facilitate photosynthesis. Lauterborn suggested that this could represent the symbiosis, or collaboration, of two cells, and this discovery aided the development of the endosymbiosis theory.-***-"In the new study, scientists led by Eva Nowack examined Paulinella to learn the rules of genome evolution that allowed photosynthesis to take hold and flourish. The rules could be revealed because the Paulinella endosymbiosis took place 100 million years ago, using the same process that unfolded about 1.5 billion years ago.-"Using this unique model, the researchers asked a critical question about endosymbiosis that had dogged scientists for many years. It has long been known that cells kept inside other cells can no longer share DNA with their own species and tend to build up a lot mutations in their genome, leading to their demise.-"This decay process is called Muller's ratchet. So how did the captured plastid escape the ratchet after millions of years of imprisonment? Analysis of Paulinella genomic data showed that every time it lost a gene, the amoeba replaced it with another gene with the same function from bacteria.-"'Evolution can find a way, in this case by solving the problem of broken genes by gathering replacement genes from the environment," Bhattacharya said. "Who knows, in a 100 million years or so, the descendants of Paulinella might become the dominant plants on our planet.'"-Comment: The same process that resulted in mitochondria being made from engulfed bacteria. Could God have provided this mechanism to help evolution advance. Less dabbling for Him as a result.

Biological complexity: evolution of mammalian pregnancy

by David Turell @, Saturday, October 15, 2016, 01:47 (2722 days ago) @ David Turell

This article discusses how placental pregnancy developed. it is complex story featuring a reto virus who entered the animals germ line:

http://www.pbs.org/wgbh/nova/next/evolution/endogenous-retroviruses/

"The critter—already the product of some 100 million years of evolution—looked like a modern mammal, with body hair and mammary glands, except for one tiny detail: according to a recent genetic study, it didn’t have a placenta. And its kind might never have evolved one if not for a chance encounter with a retrovirus.

Unlike most viruses, which infect, replicate, and then leave their host, retroviruses elbow their way into their host’s genome where they are copied and passed on to daughter cells for the life of the host. This retrovirus, however, managed to sneak its way into one of our ancestor’s sperm or egg cells, able to be passed on to every cell in every subsequent generation. Virus and host had become one.

***

"Early mammals used the spare viral parts left in the junk drawers of the genome to use a viral gene to help create the placenta, and other symbiotic viruses help turn us from a ball of cells into a fully-formed squalling infant and protect us from pathogens.

"Scientists are discovering that the so-called “junk DNA”—a significant portion of which is from symbiotic viruses—is actually a potent force in the evolution of new species. Although the evolution of pregnancy via the placenta might be some of the most persuasive evidence that viruses stashed deep within the genome can help give rise to new species, it’s not the only proof. New studies revealing the role of endogenous retroviruses in the more recent evolution of humans show that these snippets of DNA are helping to blur the boundary between human and virus. Humans are, in a very real sense, part virus. (my bold)

***

"Although most symbiosis research has focused on the role of the microbiome, the viruses tucked into our DNA can play a similar role in splitting apart two populations, turning one species into two. The first wedge scientists discovered was a protein called syncytin.

***

"Syncytin is produced only by certain cells in the placenta, and it directs the formation of the cellular boundary between the placenta and maternal tissue. Approximately one week after fertilization, the egg, now a hollow ball of cells called a blastocyst, implants itself into the uterus, stimulating the formation of the placenta, which provides the fetus with oxygen and nutrients while removing carbon dioxide and other wastes. .. The cells in the outer layer of the blastocyst form the outer layer of the placenta, and those in direct contact with the uterus are the only ones that made syncytin.

"When the scientists looked closer at the DNA sequence of syncytin, they found that it was nearly identical to a viral protein called env that caused the virus to fuse with its host cell. In the placenta, syncytin performed helped the fetus fuse with its mother. At last McCoy, Howe, and Mi knew what syncytin did.

“'This was a bona fide retroviral envelope protein that had somehow been captured during evolution and been trained to operate in human biology,” McCoy says.
The two other retroviral genes next to syncytin, gag and pol, were completely non-functional, McCoy says. Only env remained intact. “Everything else about that retrovirus had been trashed,” he says.

***

"An important step in mammalian evolution was accomplished by capturing this viral envelope gene,” McCoy says. “There’s plenty of examples of viruses picking up human genes, but this is one of the first examples of the reverse.”

"Humans aren’t the only species with a placenta, however. All mammals have placentas, including marsupials and egg-laying mammals. Although all of these mammals have a syncytin gene, they don’t all have the same syncytin gene. The syncytin produced by mice is completely different from the two syncytins found in humans and other primates. At numerous points in mammalian evolution, symbiotic retroviruses entered the genome and steered different groups of mammals along different evolutionary paths,

"The team identified genes derived from the human endogenous retrovirus HERV-K that were active around the time when the embryo was just eight cells. Of the many known edogenous retroviruses in humans, HERV-K is the newest—it inserted itself as recently as 200,000 years ago. ...But far from being detrimental, HERV-K activates key genes that help transform a single cell into a fully-formed infant.

***

"HERV-K may also have played an important role in separating some of the first humans from their primate ancestors by making small adjustments in when certain genes were switched on or off, according to Reijo Pera’s research."

Comment: Perhaps God invented and used retroviruses to drive evolution. Note my bold. Giant article worth reading for full details of research.

Biological complexity: circadian muscle oxygen use

by David Turell @, Friday, October 21, 2016, 18:37 (2716 days ago) @ David Turell

It is logical to have a way to use oxygen more efficiently in muscles in the daytime when we are active. There is such a mechanism:

https://www.sciencedaily.com/releases/2016/10/161020144129.htm

"Northwestern Medicine scientists have discovered circadian clocks in muscle tissue that control the muscle's metabolic response and energy efficiency depending on the time of day.

"The finding in mice sheds light on the time-of-day differences in muscle's ability to adapt to exercise and use oxygen for energy. Muscle cells are more efficient during an organism's normal waking hours, the study found.

"All cells in the body, including those in muscle, contain a clock that regulates how cells adapt to changes in the environment and activity across the 24-hour day.

"'Oxygen and the internal clock are doing a dance together inside muscle cells to produce energy, and the time of day determines how well that dance is synchronized," said senior author Dr. Joseph Bass. "The capacity for a cell to perform its most important functions, to contract, will vary according to the time of day."

***

"In the research, scientists performed studies in mice, which were exercised on a treadmill at different times of day, as well as in isolated muscle fibers in which the circadian clock was genetically mutated.

"The scientists analyzed mouse muscle tissues and muscle fibers for expression of genes that are important for exercise. In this way, they determined the impact of deregulation of the circadian clock on muscle fibers in terms of how muscle processes fuel, like sugar and fat, when oxygen levels are low.

"'When we manipulated the clock genetically, we noticed there were profound abnormalities in the muscle," Bass said. "That set us on a course to understand how the inner muscle clock is important in regulating how well the muscle cell can mobilize energy."

"When mice, which are nocturnal, are exercised during the night, their muscles are better at turning on genes to help them adapt to exercise, scientists found. Since these genes also exist in humans, this suggests humans may also be able to respond better to exercise during the daytime.

"The muscle clocks control the metabolic response by interacting with proteins called HIFs that change metabolism when oxygen concentrations get too low in order to allow muscle cells to continue to make energy.

"Normally when we rest or do low-level exercise, our muscles consume oxygen to make energy. When we start to sprint or exercise strenuously, we consume oxygen faster and quickly run out. That's when the dip in oxygen triggers HIFs and signals muscles to switch to sugar for energy -- which in turn increases lactic acid.

"Turning off the muscle clock prevented the normal capacity of exercise to induce sugar consumption and generation of lactic acid. These findings suggest that better exercise capacity may be tied to specific times of day."

Comment: A very reasonable relationship with day and activity. Another addition to biological complexity which raises the bar much higher for chance development of multicellular biochemical mechanisms.

Biological complexity:plants sense light and temperature

by David Turell @, Friday, October 28, 2016, 00:33 (2709 days ago) @ David Turell

Recently discovered cells sense light in the daytime and temperature at night:

http://phys.org/news/2016-10-thermometer-triggers-springtime-budding-night-time.html

"Researchers have revealed that molecules called phytochromes - used by plants to detect light during the day - actually change their function in darkness to become cellular temperature gauges that measure the heat of the night.

"The new findings, published today in the journal Science, show that phytochromes control genetic switches in response to temperature as well as light to dictate plant development.

"At night, these molecules change states, and the pace at which they change is "directly proportional to temperature" say scientists, who compare phytochromes to mercury in a thermometer. The warmer it is, the faster the molecular change - stimulating plant growth.

***

"The latest research pinpoints for the first time the molecular mechanism in plants that reacts to temperature - often triggering the buds of spring we long to see at the end of winter.

***

"If a plant finds itself in shade, phytochromes are quickly inactivated - enabling it to grow faster to find sunlight again. This is how plants compete to escape each other's shade. "Light driven changes to phytochrome activity occur very fast, in less than a second," says Wigge.

" At night, however, it's a different story. Instead of a rapid deactivation following sundown, the molecules gradually change from their active to inactive state. This is called "dark reversion".

"'Just as mercury rises in a thermometer, the rate at which phytochromes revert to their inactive state during the night is a direct measure of temperature," says Wigge.

"'The lower the temperature, the slower phytochromes revert to inactivity, so the molecules spend more time in their active, growth-suppressing state. This is why plants are slower to grow in winter.

"Warm temperatures accelerate dark reversion, so that phytochromes rapidly reach an inactive state and detach themselves from DNA - allowing genes to be expressed and plant growth to resume."

Additional information about how the molecules convert:

https://www.sciencedaily.com/releases/2016/10/161027094826.htm

"Plants contain specialized light-sensitive proteins that change shape when they absorb light, much as do the photopigments in the human eye. All plants have three main red-light photoreceptors, called phytochrome A, B and C.

"Vierstra explains that phytochrome proteins work by switching between two forms, called Pr and Pfr.

"The Pr form is best at absorbing red light, which is plentiful in full sun. When it absorbs red light, phytochrome converts to the Pfr state, which is better at absorbing far-red light that dominates in shade. When the Pfr absorbs far-red light, it switches back to the Pr form.

"This clever little system is able to detect many different qualities of light, including the light intensity (encoded in the speed at which the molecule bounces from one form to another), and the color of the light (encoded by the ratio of the Pfr form to the Pr form). Intensity tells a seed when to emerge from the soil and color tells the seeding when to grow tall to avoid shade."

Comment: How were these specialized molecules found and developed? Plants had to start equipped with them to take advantage of light and heat. Saltation?

Biological complexity: how cell structure functions

by David Turell @, Sunday, November 06, 2016, 00:38 (2700 days ago) @ David Turell

The endoplasmic reticulum is a highly complex network of membranes that holds the internal cell structure together, but is moveable for passage of molecules:

https://www.sciencenews.org/article/scientists-need-redraw-picture-cells-biggest-organe...

"The ER is a snaking network of membranes that stretches from the nucleus of the cell to its edge. A sort of cellular jack-of-all-trades, it provides scaffolding for protein-producing ribosomes and makes sure those proteins are folded properly. It churns out lipids. And it stores and releases calcium, which sends messages within and between cells. Endoplasmic reticulum stress or malfunction can contribute to neurodegenerative diseases like Alzheimer’s and Parkinson’s.

"Scientists have peered at this organelle under microscopes many times before. But newer super-resolution microscopy techniques reveal details just tens of nanometers wide, far smaller than what conventional microscopes can see. That resolution upgrade showed that apparently flat sheets of membranes actually consisted of dense clusters of tubules vibrating and shifting.

"Instead of being made of a mixture of sheets and tubes, the outer region of the ER turns out to be made mostly just of tubes.

"Those tiny tubules come together in three-way junctions, linking into a mesh network that resembles a stretchy spider web. When the ER needs to move into a new part of the cell, the tubes can expand or contract. And the junctions can also slide up and down the tubes like curtains on a rod, the team found.

“'You can’t pull a sheet apart very easily except by breaking it,” Lippincott-Schwartz says, but the tubes are far more adaptable.

"The tubes are packed to different densities throughout the ER, perhaps reflecting the various jobs that different parts of the sprawling organelle take on.

"The team still saw bona fide sheets in the part of the ER closest to the cell’s nucleus, a feature other scientists have also reported. Those sheets were stacked on top of each other like pancakes."

Comment: These cells are a wet environment in which manufacture of protein products is constant. The structure molecules must react with shifting and folding rapidly and automatically in response to stimuli. Within these molecules there is no thinking involved, just automatic changes in form and shape. The protein scaffolding must be pliant to allow for movement within the cell of the reactive molecules, while the protein components of the cell must give way simultaneously and synchronously. This describes a protein factory in which everything is moving, both the manufacturing machines and the interior of the factory itself. It is reasonable that the first living cells were like this. How did that all happen at once? Only if planned by a mind, that is, by God.

Biological complexity: how cell structure functions

by dhw, Sunday, November 06, 2016, 13:52 (2700 days ago) @ David Turell

DAVID: The endoplasmic reticulum is a highly complex network of membranes that holds the internal cell structure together, but is moveable for passage of molecules:

https://www.sciencenews.org/article/scientists-need-redraw-picture-cells-biggest-organe...

DAVID: This describes a protein factory in which everything is moving, both the manufacturing machines and the interior of the factory itself. It is reasonable that the first living cells were like this. How did that all happen at once? Only if planned by a mind, that is, by God.

The more details scientists uncover about the cell, the clearer it becomes that each cell is a microcosmic body in itself, with all its parts interacting just like the parts of our macrocosmic body. In both cases, the majority of the parts will respond automatically to the needs of the moment. But just like our own body, the cell also needs instructions before its different parts go into action. It is the source of the instructions that remains open to debate. How did it all happen in the first place? Nobody knows the origin of the mechanisms for life and evolution, and I am not going to argue against the possibility that they were planned by your God.

Biological complexity: how cell structure functions

by David Turell @, Sunday, November 06, 2016, 15:02 (2700 days ago) @ dhw


DAVID: This describes a protein factory in which everything is moving, both the manufacturing machines and the interior of the factory itself. It is reasonable that the first living cells were like this. How did that all happen at once? Only if planned by a mind, that is, by God.

dhw: The more details scientists uncover about the cell, the clearer it becomes that each cell is a microcosmic body in itself, with all its parts interacting just like the parts of our macrocosmic body. In both cases, the majority of the parts will respond automatically to the needs of the moment. But just like our own body, the cell also needs instructions before its different parts go into action. It is the source of the instructions that remains open to debate. How did it all happen in the first place? Nobody knows the origin of the mechanisms for life and evolution, and I am not going to argue against the possibility that they were planned by your God.

With the evidence now of extreme cellular complexity, what alterative is there but God.

Biological complexity: breathing controls

by David Turell @, Wednesday, November 09, 2016, 17:38 (2697 days ago) @ David Turell

It is found there are three neural networks to control each phase of breathing:

http://www.the-scientist.com/?articles.view/articleNo/47266/title/Neural-Network-Found-...


"There are three stages to mammalian breathing: inspiration, passive expiration (postinspiration), and active expiration—a conditional phase used during labored breathing. Inspiration and active expiration have been linked to rhythm-generating excitatory neural circuits in the medulla: the pre-Bötzinger complex and the lateral parafacial region, respectively. A recent study has revealed a third excitatory network—the postinspiratory complex (PiCo)—that drives postinspiration, suggesting that the coordination of breathing may rely on alternating inhibitory interactions between three networks.

"A lot can happen after we take a breath—from swallowing a sip of coffee to singing in the shower—and the nervous system has to coordinate all these behaviors without sending fluids into the lungs or disrupting airflow. But studying the neural control of breathing has been a challenge, not least because researchers haven’t found all the circuitry involved.

"Two breathing phases, inspiration and active expiration (the forced expulsion of air during labored breathing), have each been linked to rhythm-generating excitatory networks in the medulla, the lowest portion of the brainstem. But scientists have been stumped as to the source of excitation generating the third: the passive release of air from the lungs after breathing in, or postinspiration. From this incomplete picture, most models of breathing have assumed that just two rhythm-generating circuits—inspiratory and expiratory—set the timing of all three breathing phases, with coordination coming about as each active phase inhibits the other two.

***

" Using this preparation, the team has finally discovered the excitatory network that generates postinspiration, which the group has named the postinspiratory complex (PiCo).

***

"Through pharmacological and optogenetic experiments, the researchers demonstrated that the PiCo is necessary and sufficient to generate postinspiration in vitro and in adult transgenic mice. What’s more, like the networks driving inspiration and active expiration, the PiCo appears to generate its own rhythm. “That was astonishing to us,” Ramirez says. The team is now exploring a model of breathing coordinated by the interactions of three, not two, rhythm-generating excitatory networks."

Comment: Another precise example of feedback loops for tight control of biologic processes. This cannot be developed stepwise, but must come all at once all parts working.

Biological complexity: blood vessel controls

by David Turell @, Friday, November 11, 2016, 01:29 (2695 days ago) @ David Turell

Every function in life is tightly controlled. This one relates to blood flow, blood pressure and the fact that the pipes are elastic and constantly pulsate:

https://www.sciencedaily.com/releases/2016/11/161110123943.htm

"Physical forces like blood pressure and the shear stress of flowing blood are important parameters for the tension of blood vessels. Scientists have been looking for a measurement sensor for many years that enables the translation of mechanical stimuli into a molecular response, which then regulates the tension in blood vessels.

***

"Unlike water pipes, which are often used as a model for explaining the functioning of blood vessels, the latter are anything but rigid and lifeless. Instead, they consist of an elastic vessel wall comprising different layers of highly sensitive tissue. This tissue is able to respond to the changing requirements of the body by increasing the vessel diameter and intensifying the blood flow as a result.

"The blood vessel receives the information necessary for this process from the blood stream itself: "One of the most important control mechanisms is the physical forces exerted by the blood on the interior of the blood vessels," says Stefan Offermanns. "The blood vessel interior is lined with endothelial cells. These register the intensity of the blood flow using molecular antennae." In response to this stimulus, the endothelial cells release nitric oxide, among other things. This causes the vessel musculature to relax and the blood vessel expands.

"In addition to the level of the blood pressure, the mechanical shear forces are the main factor that affects the endothelium via the bloodstream and are crucial for the regulation of blood flow. "Previously, we knew very little about how endothelial cells register the mechanical forces of the flowing blood at molecular level. With PIEZO1, we have now discovered a cation channel that forms the interface that transposes the physical stimulus into a molecular reaction. This, in turn, controls the tension of the blood vessel wall," explains Shengpeng Wang, first author of the study.

"The Max Planck researchers initially observed in cultivated endothelial cells that PIEZO1 triggers a signalling cascade when it is exposed to shear stress: "PIEZO1 is activated by the mechanical stimulus. It causes calcium cations to flow through the channel into the endothelial cells and thereby trigger a chain reaction," says Wang. This signalling cascade culminates in the release of nitric oxide and the expansion of the blood vessel. (my bold)

"The Max Planck researchers were able to confirm what they had observed in the laboratory in the living organism using genetically modified mice. Mice with an inactive PIEZO1 gene had higher blood pressure than the control animals. "Due to the lack of the PIEZO1 molecular sensor, the shear forces were not correctly perceived by the endothelial cells and the entire signalling cascade was scarcely activated at all," explains Wang. The cells then released less nitric oxide and the blood vessel musculature remained tense. This, in turn, caused permanently raised blood pressure in the animals.

"If PIEZO1 proves to be the long-sought sensor with which the endothelial cells register the mechanical forces of the flowing blood column so as to regulate the tension of blood vessels, it could be of therapeutic importance."

Comment: The bolded area discusses a cascade, which means in biochemistry that a series of protein molecules trigger each next molecule in the cascade to react and produce the proper control levels with the final products. In blood clotting close to 20 molecules are in the cascade. Since reactions of this sort are stepwise, one should wonder how they develop in evolution by chance. This must be an all-at-once saltation.

Biological complexity: how stressed bacteria go dormant

by David Turell @, Friday, November 11, 2016, 22:59 (2695 days ago) @ David Turell

Another layer of genetic controls is found to control the process of dormancy, as a way of surviving threatening stress such as loss of oxygen:

http://phys.org/news/2016-11-newly-genetic-code-bacterial-survival.html

"MIT researchers have now discovered another layer of control that helps cells to rapidly divert resources in emergency situations. Many bacteria, including strains that cause tuberculosis, use this strategy to enter a dormancy-like state that allows them to survive in hostile environments when deprived of oxygen or nutrients.

***

"Dedon and colleagues have previously shown that stresses such as radiation or toxic chemicals provoke yeast cells to turn on a system that makes chemical modifications to transfer RNA (tRNA), which diverts the cells' protein-building machinery away from routine activities to emergency action.

***

"Once a tRNA molecule is manufactured, it is altered with dozens of different chemical modifications. These modifications are believed to influence how tightly the tRNA anticodon binds to the mRNA codon at the ribosome.

"In this study, Dedon and colleagues found that certain tRNA modifications went up dramatically when the bacteria were deprived of oxygen and stopped growing.
One of these modifications was found on the ACG threonine anticodon, so the researchers analyzed the entire genome of Mycobacterium bovis in search of genes that contain high percentages of that ACG codon compared to the other threonine codons. They found that genes with high levels of ACG included a family known as the DosR regulon, which consists of 48 genes that are needed for a cells to stop growing and survive in a dormancy-like state. (my bold)

"'When oxygen is lacking, these bacterial cells begin churning out large quantities of the DosR regulon proteins, while production of proteins from genes containing one of the other codons for threonine drops. The DosR regulon proteins guide the cell into a dormancy-like state by shutting down cell metabolism and halting cell division.

"'The authors present an impressive example of the new, emerging deep biology of transfer RNAs, which translate the genetic code in all living organisms to create proteins," says Paul Schimmel, a professor of cell and molecular biology.

***

"The researchers also showed that when they swapped different threonine codons into the genomic locations where ACG is usually found, the bacterial cells failed to enter a dormant state when oxygen levels were diminished. Because making this tRNA modification switch is critical to bacterial cells' ability to respond to stress, the enzymes responsible for this switch could make good targets for new antibiotics, Dedon says.

"Dedon suspects that other families of genes, such as those required to respond to starvation or to develop drug resistance, may be regulated in a similar way by other tRNA modifications.

"'It is really an alternative genetic code, in which any gene family that is required to change a cell phenotype is enriched with specific codons" that correspond to specific modified tRNAs, he says.'

Comment: this is another example of the many layers of the genome, showing how complex the genome really is. Further note the bolded area that described how many genes are needed to control this process of dormancy. Recognize that when this system developed in bacteria it required multiple genes, and strongly suggests it developed by saltation. The other takeaway is that when a new process is developed, just as when a new species develops, large families of cooperating genes must be developed simultaneously.

Biological complexity: describing the nuclear pore

by David Turell @, Saturday, November 12, 2016, 20:26 (2694 days ago) @ David Turell

RNA molecules made in the cell nucleus must be able to get out to carry their message. The construction of the pore is found:

http://phys.org/news/2016-11-rna-journey-cell-nucleus.html

"After cells make an RNA version of DNA, they must package it, and ship it through a portal known as the nuclear pore. Once on the other side, some of that packaging has to come off. "We already understood bits and pieces of this aspect of flux into and out of the nucleus, but not the complete picture," says co-corresponding author Brian T. Chait's Laboratory of Mass Spectrometry and Gaseous Ion Chemistry.

"'To better understand the end of RNA's journey through the pore, we examined the protein complex responsible for receiving RNA and helping to unwrap it," says co-corresponding author Michael P. Rout, head of the Laboratory of Cellular and Structural Biology. "Next, we determined how this structure attached to the rest of the nuclear pore."

"Scientists typically crystallize proteins in order to determine their structure. But that approach didn't work well for this component because it is relatively large and has flexible parts. So the team pieced a variety of data together as if assembling a jigsaw puzzle. They found that the core of the complex takes a triangular shape, shown in solid red in the image above. This triangle sits atop a Y-shaped piece, shown in lighter red, creating an arm that extends, cranelike, over the pore.

"This configuration came as a surprise; previously these proteins were thought to stick out further from the pore, like antennae.

"Although the team performed their research on yeast, their work likely has relevance for humans, who possess a similar protein complex. In humans, mutations that affect the complex, as well as other parts of the RNA-catching arm, have been linked to cancer and other diseases. This new blueprint may help to explain why these mutations are harmful, the researchers say."

Comment: Complex protein construction like this cannot be made bit by bit. They must appear all put together, as an irreducibly complex structure. Again, saltation is the only answer.

Biological complexity: how stressed bacteria go dormant

by David Turell @, Sunday, November 13, 2016, 00:10 (2693 days ago) @ David Turell

Another comment on this study with a different point of view, pointing out alternative pathways used by bacteria when in stress:

http://www.uncommondescent.com/intelligent-design/antibiotic-resistance-evolution-at-work/

"Over at PhysOrg they have a story about how certain bacteria, when under stress conditions, shut themselves down and put themselves into a persistent state. They do it by modifying the chemicals involved in t-RNA. No, it’s not a “point mutation”—which is touted as an icon of Darwinian evolution, but the utilization of an “alternate genetic code.” IOW, it’s regulated and ‘directed,’ and is ready-at-hand when needed.

"So, with this new information, the whole story of bacterial resistance now needs to be rethought. And, guess what, instead of pointing to “point mutations” (no pun intended), it points rather to “design.'”

Comment: A good example of alternatives mechanisms bacteria have on board. This is why they have survived since the beginning.

dhw: Biological complexity: how stressed bacteria go dormant

by dhw, Sunday, November 13, 2016, 13:21 (2693 days ago) @ David Turell

DAVID: Another comment on this study with a different point of view, pointing out alternative pathways used by bacteria when in stress:

http://www.uncommondescent.com/intelligent-design/antibiotic-resistance-evolution-at-work/

"Over at PhysOrg they have a story about how certain bacteria, when under stress conditions, shut themselves down and put themselves into a persistent state. They do it by modifying the chemicals involved in t-RNA. No, it’s not a “point mutation”—which is touted as an icon of Darwinian evolution, but the utilization of an “alternate genetic code.” IOW, it’s regulated and ‘directed,’ and is ready-at-hand when needed.
"So, with this new information, the whole story of bacterial resistance now needs to be rethought. And, guess what, instead of pointing to “point mutations” (no pun intended), it points rather to “design.'”

David's comment: A good example of alternatives mechanisms bacteria have on board. This is why they have survived since the beginning.

Or if you follow the work of such experts in the field as James A. Shapiro, a good example of the manner in which intelligent bacteria take decisions and change their own chemicals in order to cope with different environmental conditions. (Not an argument against design, since God may have given them this ability in the first place.)

dhw: Biological complexity: how stressed bacteria go dormant

by David Turell @, Sunday, November 13, 2016, 15:59 (2693 days ago) @ dhw


David's comment: A good example of alternatives mechanisms bacteria have on board. This is why they have survived since the beginning.

dhw: Or if you follow the work of such experts in the field as James A. Shapiro, a good example of the manner in which intelligent bacteria take decisions and change their own chemicals in order to cope with different environmental conditions. (Not an argument against design, since God may have given them this ability in the first place.)

What is involved is a mechanism which puts them into a dormant state and then allows them to wake up when the danger is past. This has to be fully planned in one step when the mechanism is set up at the beginning. Lots of intelligent thought is required to plan this out properly, or they will never wake up in survival. Shapiro has shown simple adaptations with DNA manipulation, not something this complex.

Biological complexity: how stressed bacteria go dormant

by dhw, Monday, November 14, 2016, 12:01 (2692 days ago) @ David Turell

David's comment: A good example of alternatives mechanisms bacteria have on board. This is why they have survived since the beginning.

dhw: Or if you follow the work of such experts in the field as James A. Shapiro, a good example of the manner in which intelligent bacteria take decisions and change their own chemicals in order to cope with different environmental conditions. (Not an argument against design, since God may have given them this ability in the first place.)

DAVID: What is involved is a mechanism which puts them into a dormant state and then allows them to wake up when the danger is past. This has to be fully planned in one step when the mechanism is set up at the beginning. Lots of intelligent thought is required to plan this out properly, or they will never wake up in survival. Shapiro has shown simple adaptations with DNA manipulation, not something this complex.

Lots of intelligent thought is required for most processes of survival. Your superb list of Nature’s Wonders bears testimony to that. This one sounds rather like a form of hibernation. What I find quite simply unbelievable is your insistence that the millions upon millions of such processes, plus the innovations, plus the natural wonders at every level of organic existence all had to be preprogrammed in the very first cells or personally dabbled by your God.

Biological complexity: how stressed bacteria go dormant

by David Turell @, Monday, November 14, 2016, 17:32 (2692 days ago) @ dhw


dhw: Lots of intelligent thought is required for most processes of survival. Your superb list of Nature’s Wonders bears testimony to that. This one sounds rather like a form of hibernation. What I find quite simply unbelievable is your insistence that the millions upon millions of such processes, plus the innovations, plus the natural wonders at every level of organic existence all had to be preprogrammed in the very first cells or personally dabbled by your God.

As I've stated in another thread, the first cells had to have a group of alternative survival pathways onboard from the beginning or there would be no life.

Biological complexity: complex glucose controls

by David Turell @, Monday, November 14, 2016, 18:34 (2692 days ago) @ David Turell

Blood vessels produce chemical reactions that control glucose levels:

https://www.sciencedaily.com/releases/2016/11/161114103909.htm

Research led by a Johns Hopkins University biologist demonstrates the workings of a biochemical pathway that helps control glucose in the bloodstream, a development that could potentially lead to treatments for diabetes.

***

It has been known for some time that neurons and the pancreatic beta cells, or β-cells, that reside in clusters called islets of Langerhans and produce insulin, have many similarities in molecular makeup and signaling receptors. Receptors are proteins on cell surfaces that respond to particular chemicals and have critical roles in biochemical pathways. Both neurons and pancreatic β-cells have the receptors for neurotrophins. (my bold)

***

It turns out that NGF performs a function in the mature pancreas that has nothing to do with supporting neurons. Specifically, the research team traced a chain of biochemical signals showing that elevated blood glucose causes NGF to be released from blood vessels in the pancreas, and that the NGF signal then prompts pancreatic β-cells to relax their rigid cytoskeletal structure, releasing insulin granules into the blood stream. Although β-cells also make NGF, Kuruvilla and her team found that it was the NGF released from the blood vessels that is needed for insulin secretion. (my bold)

Using genetic manipulation in mice and drugs to block NGF signaling in β-cells, they were able to disrupt distinct elements of this signaling sequence, to show that this classical neuronal pathway is necessary to enhance insulin secretion and glucose tolerance in mice. Importantly, Kuruvilla and colleagues found that NGF's ability to enhance insulin secretion in response to high glucose also occurs in human β-cells.

Comment: This is another example of a system that cannot develop in small steps. It must appear all put together. Also look at the bolded portions describing how receptors receive information and how a chain of molecular reactions produce directions for results. All automatic, no thought involved.

Biological complexity: automatic cellular switches

by David Turell @, Tuesday, November 15, 2016, 00:00 (2691 days ago) @ David Turell

Cells manufacture at a high rate and they use switches to change activities in which molecules act automatically. This is a study of a bacterial switch:

http://phys.org/news/2016-11-x-ray-laser-real-time-snapshots-chemical.html

"And because this particular type of RNA switch, known as a riboswitch, is found only in bacteria, a deeper understanding of its function may offer a way to turn off protein production and kill harmful germs without causing side effects in the humans they infect.

"'Previous experiments at SLAC's X-ray laser have studied biological reactions like photosynthesis that are triggered by light. But this is the first to observe one that is triggered by the chemical interaction of two biomolecules in real time and at the atomic scale," said Yun-Xing Wang, a structural biologist

***

"both DNA and RNA also contain extensive regions that don't code for any protein - the so-called genetic "dark matter." Scientists thought for many years that these regions didn't do anything. Now they know that they play an important role in determining where and when genes turn on and off and otherwise fine-tuning their function.

***

"Wang's team studied a riboswitch from Vibrio vulnificus, a bacterium related to the one that causes cholera. The riboswitch sits in a long strand of messenger RNA (mRNA), which copies DNA's instructions for making a protein so they can be read and carried out by the ribosome. The switch acts like a thermostat that regulates protein production

"In this case, the mRNA guides production of a protein that in turn helps to produce a small molecule called adenine. When there is too much adenine in the bacterial cell, adenine molecules enter pockets in the riboswitches and flip the riboswitches into a different shape, and this changes the pace of protein and adenine production.

"For the LCLS experiments, the researchers made nanocrystals that incorporated millions of copies of the riboswitch and mixed them with a solution containing adenine molecules. Each crystal was so small that adenine could quickly and uniformly penetrate into every corner of it, enter riboswitch pockets and flip them almost instantaneously, as if they were millions of synchronized swimmers executing a single flawless move.

"The scientists took snapshots of this interaction by hitting the crystals with X-ray laser pulses at carefully timed intervals after the mixing started. This gave them the first glimpse of a fleeting intermediate stage in the process, which occurred 10 seconds in. Separately, they obtained the first images of the riboswitch in its initial, empty-pocket state, and discovered that it existed in two slightly different configurations, only one of which participates in switching.

"The researchers were surprised to discover that the sudden change in the shape of the riboswitches was so dramatic that it changed the shape of the entire crystal, too. Normally a major change like this would crack the crystal and spoil the experiment. But because these crystals were so small they held together, so the X-ray laser could still get structural information from them."

Comment: This is a beautiful piece of research into how a piece of cellular machinery works. Be sure to look at the diagrams. Note this is in the 'junk' DNA area. Certainly as research advances most of the junk designation areas will disappear.

Biological complexity: complex glucose controls

by David Turell @, Friday, August 16, 2019, 19:00 (1687 days ago) @ David Turell

Another set of controls of insulin production; Delta cells:

https://medicalxpress.com/news/2019-08-indirect-glucose-homeostasis.html

"The hormone secreting islets of Langerhans in the pancreas have a unique cyto-architecture that allows functional interrelationships between the different cell types. Somatostatin is secreted by the delta cell and is an effective inhibitor of the insulin-secreting beta cell and the glucagon-secreting alpha cell. According to a novel study from Sweden's Karolinska Instiutet, published in the journal Nature Communications, the delta cell can thereby indirectly affect glucose homeostasis in health and disease.

"Our results provide important insight into the activity of the delta cell in health and pre-diabetes and a possible mechanism for how somatostatin can so effectively exert its potent suppressive effects within the islet of Langerhans," says senior author Professor Per-Olof Berggren of the Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet in Sweden,

"Most delta cells are elongated and have a well-defined cell soma and a filopodia-like structure. Using in vivo optogenetics and high-speed Ca2+ imaging, Per-Olof Berggren and his colleagues show that these filopodia are dynamic structures that contain a secretory machinery, enabling the delta cell to reach large numbers of beta cells within the islet.

"This provides for efficient regulation of beta cell activity and is modulated by endogenous IGF-1/VEGF-A signaling. In pre-diabetes, delta cells undergo morphological changes that may be a compensation to maintain paracrine regulation of the beta cell.

"'It has long been a mystery how delta cells so effectively regulate the function of alpha and beta cells, only constituting a minority among the hormone secreting cells," says Per-Olof Berggren. "These are fundamental data explaining an important structure/function relationship between delta cells and other hormone-secreting cells, and provides the basis for how delta cells, despite being in minority, can act as efficient modulators of glucose homeostasis.'"

Comment: Additional complexity in the insulin secretion system. Not by chance.

Biological complexity: controlled cell death

by David Turell @, Monday, February 11, 2019, 17:22 (1873 days ago) @ David Turell

Cells are constantly being replaced after old tired ones are removed under tight controls:

https://www.sciencedaily.com/releases/2019/02/190211105405.htm

"Cellular death is vital for health. Without it, we could develop autoimmune diseases or cancers. But a cell's decision to self-destruct is tightly regulated, so that it only happens to serve the best interests of the body. Now researchers have discovered a novel role for a signaling molecule that was once considered a dispensable player, a discovery that could inform fields of research as diverse as cancer, autoimmunity, and in-utero development.

***

"Years ago, researchers in the field discovered receptors on the surfaces of cells they called "death receptors." These molecules would send the cell into a cascade of cellular reactions that ended in death. Soon after, three molecules were discovered that contained "death domains," areas on the molecule that directly interacted with the death receptors and helped relay the message. These molecules proved so essential that without them mice lacking these death-domain molecules died young. At least that was the case in two of the three molecules.

"Of the three major death-relaying molecules, RIPK1, FADD, and TRADD, it seemed TRADD was less essential. Without FADD, mice died in utero. Without RIPK1, mice die shortly before or after birth. Without TRADD, mice seemed to do just fine. TRADD had a death domain -- it clearly was connected to cell-death pathways -- but its main purpose was unclear.

***

"Through the work of Dr. Zhang and others, it became clear that the roles of these molecules wasn't simply to turn on the death signal. Rather, in certain combinations they could protect a cell from death, rather than spur suicide.

"Through the work of first author and postdoctoral fellow John Dowling, their most recent paper, the researchers showed that TRADD serves a dual function. In cells lacking the RIPK1 protein, having two copies of the gene TRADD or no copies of it would result in cell death. On the other hand, when only one copy of TRADD gene was present in cells lacking RIPK1, the cells tended to turn off the death signal, and promote cell survival.

"'The work sheds new light on the regulation of cell death and survival," said Dr. Zhang. "In certain contexts, such as in cells that have naturally low RIPK1 expression, TRADD could drive death or promote survival.'"

Comment: Another very precise feedback mechanism with go or no go decisions about life and death. This cannot be developed or adjusted stepwise, but must be put in place all at once or cell death will not be properly controlled. This is irreducibly complex and must be designed from the beginning.

Biological complexity:pregnancy alters immunity

by David Turell @, Saturday, September 02, 2017, 19:35 (2400 days ago) @ David Turell

New studies show how immune cells are changed during each trimester of pregnancy:

https://medicalxpress.com/news/2017-09-immune-pregnancy-precisely.html

"The findings, which will be published Sept. 1 in Science Immunology, reveal that there is an immune clock of pregnancy and suggest it may help doctors predict preterm birth.

"'Pregnancy is a unique immunological state. We found that the timing of immune system changes follows a precise and predictable pattern in normal pregnancy," said the study's senior author, Brice Gaudilliere, MD.

***

"Although physicians have long known that the expectant mother's immune system adjusts to prevent her body from rejecting the fetus, no one had investigated the full scope of these changes, nor asked if their timing was tightly controlled. "Ultimately, we want to be able to ask, 'Does your immune clock of pregnancy run too slow or too fast?'" said Gaudilliere.

***

"The study confirmed immune features of pregnancy that were already known. For instance, the scientists saw that natural killer cells and neutrophils have enhanced action during pregnancy. The researchers also uncovered several previously unappreciated features of how the immune system changes, such as the finding that activity of the STAT5 signaling pathway in CD4+T cells progressively increases throughout pregnancy on a precise schedule, ultimately reaching levels much higher than in nonpregnant individuals. The STAT5 pathway is involved in helping another group of immune cells, regulatory T cells, to differentiate. Interestingly, prior research in animals has indicated that regulatory T cells are important for maintaining pregnancy.

***

"'We're especially interested in understanding more precisely what is happening very early and very late in pregnancy," Gaudilliere said. "We'd like to see if there is really a switch we can catch, a sweet spot where deviation from the norm would be maximal with pathology."

"'The immune system does not act in isolation, and we're now very interested in profiling its interplay with other aspects of mothers' biology, such as their genetics, metabolism and the body's microbial communities to come up with a holistic biological clock of pregnancy," Aghaeepour added.

Comment: The problem is easy to understand. The baby is not the mother, and is really foreign to her genetically. Therefore the immune system must adapt to tolerate the fetus. For example, in an Rh incompatibility pregnancy an Rh- mother carries a blood-type Rh+ baby and reacts to it since the immune system is not blocked from reacting as part of the overall protection. Obviously, the development of intrauterine pregnancy had to have this system in place beforehand or we would not be here. Only a designer could accomplish this. God exists.

Biological complexity: mammalian pregnancy is a war

by David Turell @, Saturday, November 30, 2019, 22:35 (1581 days ago) @ David Turell

The problem with placental pregnancy is that the Mother and the fetus are different animals with different antigens causing immune problems, with different needs, and it is a designed battle royal:

https://aeon.co/essays/why-pregnancy-is-a-biological-war-between-mother-and-baby?utm_so...

The cells of the human endometrium are tightly aligned, creating a fortress-like wall around the inside of the uterus. That barrier is packed with lethal immune cells. As far back as 1903, researchers observed embryos ‘invading’ and ‘digesting’ their way into the uterine lining. In 1914, R W Johnstone described the implantation zone as ‘the fighting line where the conflict between the maternal cells and the invading trophoderm takes place’. It was a battlefield ‘strewn with… the dead on both sides’.

When scientists tried to gestate mice outside the womb, they expected the embryos to wither, deprived of the surface that had evolved to nurture them. To their shock they found instead that – implanted in the brain, testis or eye of a mouse – the embryo went wild. Placental cells rampaged through surrounding tissues, slaughtering everything in their path as they hunted for arteries to sate their thirst for nutrients. It’s no accident that many of the same genes active in embryonic development have been implicated in cancer. Pregnancy is a lot more like war than we might care to admit.

***

The situation becomes a tug-of-war. Some genes fall silent, while others become more active, counterbalancing them.

That insight led Haig to found the theory of genomic imprinting, which explains how certain genes are expressed differently depending on whether they come from your father or your mother. Armed with this theory, we can see how conflicts of genetic interest between parents play out within the genomes of their offspring.

Because both parental genomes drive each other to keep ramping up their production of powerful hormones, should one gene fail, the result can be disastrous for both mother and infant. Normal development can proceed only as long as both parental genotypes are correctly balanced against one another. Just as in a tug-of-war, if one party drops its end, both fall over. This is one reason why mammals cannot reproduce asexually, and why cloning them is so difficult: mammalian development requires the intricate co-ordination of paternal and maternal genomes. A single misstep can ruin everything.

***

The invading placental cells paralyse the vessels so they cannot contract, then pump them full of growth hormones, widening them tenfold to capture more maternal blood. These foetal cells are so invasive that colonies of them often persist in the mother for the rest of her life, having migrated to her liver, brain and other organs. There’s something they rarely tell you about motherhood: it turns women into genetic chimeras.

Perhaps this enormous blood supply explains why primates have brains five to ten times larger than the average mammal. Metabolically speaking, brains are extremely expensive organs, and most of their growth occurs before birth. How else is the fetus to fund such extravagance?

***

Fascinatingly, the intensity of the invasion does seem to correlate with brain development. Great apes, the largest-brained primates, seem to experience deeper and more extensive invasion of the maternal arteries than other primates. In humans – the largest-brained ape of all – placental cells invade the maternal bloodstream earlier even than in other great apes, allowing the foetus unprecedented access to oxygen and nutrients during early development. (my bold)

***

The second major consequence of the foetus’s direct access to maternal nutrients is that the foetus can also release its own hormones into the mother’s bloodstream, and thus manipulate her. And so it does. The mother counters with manipulations of her own, of course. But there is a strong imbalance: while the foetus freely injects its products into the mother’s blood, the mother is granted no such access to foetal circulation.

Comment: Note the bold paragraph. One can certainly see the advanced preparation in the great apes for the oncoming humans. The energy needs for the giant brain started in the small brained apes, by God's preplanning. Read the whole article. I've presented only a tiny portion of the battles that rage and the designed complexity that was involved in the back and forth between fetus and mother. And please remember the other birth problem that had to be solved: a growing baby head in humans requiring a bigger opening in the mothers pelvis and the two involved individuals are genetically different adversaries. Choosing a chance mechanism to develop all of this is not reasonable.

Biological complexity: mammalian pregnancy is a war

by dhw, Sunday, December 01, 2019, 08:52 (1580 days ago) @ David Turell

DAVID: One can certainly see the advanced preparation in the great apes for the oncoming humans. The energy needs for the giant brain started in the small brained apes, by God's preplanning.

One can certainly see how one evolutionary step may lead to another. What I don’t understand, taking this in the context of your theory, is why a God whose one and only purpose is to design H. sapiens, and who “knows exactly what he is doing”, should take 3.X billion years designing billions of other life forms etc., and then, even when he does start designing the only thing he wants to design, goes about it in such a roundabout, itty-bitty fashion.

DAVID: I've presented only a tiny portion of the battles that rage and the designed complexity that was involved in the back and forth between fetus and mother. And please remember the other birth problem that had to be solved: a growing baby head in humans requiring a bigger opening in the mothers pelvis and the two involved individuals are genetically different adversaries. Choosing a chance mechanism to develop all of this is not reasonable.

I agree. The whole process requires intricate design, and requires synchronized adjustments between cells and cell communities. Whether 3.8 thousand million years ago your God provided the very first cells with programmes for all these itty-bitty adjustments, or he came down to earth and personally conducted itty-bitty dabbling on all the great apes, or he provided cells/cell communities with the intelligence to do their own adjusting (theistic version of Shapiro’s theory) is open to discussion.

Biological complexity: mammalian pregnancy is a war

by David Turell @, Sunday, December 01, 2019, 14:41 (1580 days ago) @ dhw

DAVID: One can certainly see the advanced preparation in the great apes for the oncoming humans. The energy needs for the giant brain started in the small brained apes, by God's preplanning.

dhw: One can certainly see how one evolutionary step may lead to another. What I don’t understand, taking this in the context of your theory, is why a God whose one and only purpose is to design H. sapiens, and who “knows exactly what he is doing”, should take 3.X billion years designing billions of other life forms etc., and then, even when he does start designing the only thing he wants to design, goes about it in such a roundabout, itty-bitty fashion.

Surprise. It's caused evolution by common descent. If one assumes God is in charge of every thing, it was His choice to do it this way.


DAVID: I've presented only a tiny portion of the battles that rage and the designed complexity that was involved in the back and forth between fetus and mother. And please remember the other birth problem that had to be solved: a growing baby head in humans requiring a bigger opening in the mothers pelvis and the two involved individuals are genetically different adversaries. Choosing a chance mechanism to develop all of this is not reasonable.

dhw: I agree. The whole process requires intricate design, and requires synchronized adjustments between cells and cell communities. Whether 3.8 thousand million years ago your God provided the very first cells with programmes for all these itty-bitty adjustments, or he came down to earth and personally conducted itty-bitty dabbling on all the great apes, or he provided cells/cell communities with the intelligence to do their own adjusting (theistic version of Shapiro’s theory) is open to discussion.

Intricate design requires a designer. Evidence is seen in creation of this universe, creation of a perfect planet for life (Earth), fine tuning for life, creation of life, and then evolving a creature with consciousness. If all of this happened by chance, we are lucky to an infinite degree. Luck or purposeful?

DAVID: Biological complexity: mammalian pregnancy is a war

by dhw, Monday, December 02, 2019, 13:41 (1579 days ago) @ David Turell

DAVID: One can certainly see the advanced preparation in the great apes for the oncoming humans. The energy needs for the giant brain started in the small brained apes, by God's preplanning.

dhw: One can certainly see how one evolutionary step may lead to another. What I don’t understand, taking this in the context of your theory, is why a God whose one and only purpose is to design H. sapiens, and who “knows exactly what he is doing”, should take 3.X billion years designing billions of other life forms etc., and then, even when he does start designing the only thing he wants to design, goes about it in such a roundabout, itty-bitty fashion.

DAVID: Surprise. It's caused evolution by common descent. If one assumes God is in charge of every thing, it was His choice to do it this way.

One should assume nothing. If your God’s one and only purpose was to design H. sapiens, and he was in charge of everything, it makes no sense that he should have designed billions of non-human life forms beforehand, or that he should have fiddled around itty-bitty with ape anatomies and all the different hominids first. The history and this particular purpose fit together far more comfortably if your God was experimenting (one of several logical alternatives to your theory).

DAVID: I've presented only a tiny portion of the battles that rage and the designed complexity that was involved in the back and forth between fetus and mother. And please remember the other birth problem that had to be solved: a growing baby head in humans requiring a bigger opening in the mothers pelvis and the two involved individuals are genetically different adversaries. Choosing a chance mechanism to develop all of this is not reasonable.

dhw: I agree. The whole process requires intricate design, and requires synchronized adjustments between cells and cell communities. Whether 3.8 thousand million years ago your God provided the very first cells with programmes for all these itty-bitty adjustments, or he came down to earth and personally conducted itty-bitty dabbling on all the great apes, or he provided cells/cell communities with the intelligence to do their own adjusting (theistic version of Shapiro’s theory) is open to discussion.

DAVID: Intricate design requires a designer. Evidence is seen in creation of this universe, creation of a perfect planet for life (Earth), fine tuning for life, creation of life, and then evolving a creature with consciousness. If all of this happened by chance, we are lucky to an infinite degree. Luck or purposeful?

You have skipped from evolution of life to evolution of the universe, thereby glossing over your particular theory concerning divine dabbling and first cells being provided with billions of programmes for the whole of life’s history, as opposed to (perhaps divinely designed) cellular intelligence. The latter theory is every bit as “purposeful” as the former.

DAVID: Biological complexity: mammalian pregnancy is a war

by David Turell @, Monday, December 02, 2019, 14:42 (1579 days ago) @ dhw

DAVID: One can certainly see the advanced preparation in the great apes for the oncoming humans. The energy needs for the giant brain started in the small brained apes, by God's preplanning.

dhw: One can certainly see how one evolutionary step may lead to another. What I don’t understand, taking this in the context of your theory, is why a God whose one and only purpose is to design H. sapiens, and who “knows exactly what he is doing”, should take 3.X billion years designing billions of other life forms etc., and then, even when he does start designing the only thing he wants to design, goes about it in such a roundabout, itty-bitty fashion.

DAVID: Surprise. It's caused evolution by common descent. If one assumes God is in charge of every thing, it was His choice to do it this way.

dhw: One should assume nothing. If your God’s one and only purpose was to design H. sapiens, and he was in charge of everything, it makes no sense that he should have designed billions of non-human life forms beforehand, or that he should have fiddled around itty-bitty with ape anatomies and all the different hominids first. The history and this particular purpose fit together far more comfortably if your God was experimenting (one of several logical alternatives to your theory).

It is your agnosticism that assumes nothing. If God had not produced the bush of life, but only humans, they would not have survived! Again you are expecting a God with the ability to directly create humans without the bush, or create the whole bush. On the other hand you seem to accept evolution as God's work in experimentation, the same God who created the universe, the special Earth, and started life. You never look at the whole picture of why I believe from all the evidence.


DAVID: I've presented only a tiny portion of the battles that rage and the designed complexity that was involved in the back and forth between fetus and mother. And please remember the other birth problem that had to be solved: a growing baby head in humans requiring a bigger opening in the mothers pelvis and the two involved individuals are genetically different adversaries. Choosing a chance mechanism to develop all of this is not reasonable.

dhw: I agree. The whole process requires intricate design, and requires synchronized adjustments between cells and cell communities. Whether 3.8 thousand million years ago your God provided the very first cells with programmes for all these itty-bitty adjustments, or he came down to earth and personally conducted itty-bitty dabbling on all the great apes, or he provided cells/cell communities with the intelligence to do their own adjusting (theistic version of Shapiro’s theory) is open to discussion.

DAVID: Intricate design requires a designer. Evidence is seen in creation of this universe, creation of a perfect planet for life (Earth), fine tuning for life, creation of life, and then evolving a creature with consciousness. If all of this happened by chance, we are lucky to an infinite degree. Luck or purposeful?

dhw: You have skipped from evolution of life to evolution of the universe, thereby glossing over your particular theory concerning divine dabbling and first cells being provided with billions of programmes for the whole of life’s history, as opposed to (perhaps divinely designed) cellular intelligence. The latter theory is every bit as “purposeful” as the former.

Cells are driven by intelligently designed processes and responses., They look intelligent. Shapiro's bacteria are forerunners of stem cells in my theory.

DAVID: Biological complexity: mammalian pregnancy is a war

by dhw, Tuesday, December 03, 2019, 10:43 (1578 days ago) @ David Turell

DAVID: If one assumes God is in charge of every thing, it was His choice to do it this way.

dhw: One should assume nothing. […] The history and this particular purpose [to design H. sapiens] fit together far more comfortably if your God was experimenting (one of several logical alternatives to your theory).

DAVID: It is your agnosticism that assumes nothing.

Correct.

DAVID: If God had not produced the bush of life, but only humans, they would not have survived! Again you are expecting a God with the ability to directly create humans without the bush, or create the whole bush.

They wouldn’t have survived without those parts of the bush of life that have enabled them to survive! Why do you ignore the 3.X billion years’ worth of bush that had nothing to do with humans? This is the illogical part of your theory, bearing in mind your claim that your always-in-control God’s only purpose was to create H. sapiens!

DAVID: On the other hand you seem to accept evolution as God's work in experimentation, the same God who created the universe, the special Earth, and started life. You never look at the whole picture of why I believe from all the evidence.

If your God exists, then I have no problem with any of the above. My quarrel is with your theory that his sole purpose for all of it was to design H. sapiens, and you have no idea why he spent 3.X billion years specially designing anything but H. sapiens! Experimentation would cover the whole of the above, as would humans as a late arrival in his thinking, but “you never look at the whole picture”.

DAVID: Intricate design requires a designer. Evidence is seen in creation of this universe, creation of a perfect planet for life (Earth), fine tuning for life, creation of life, and then evolving a creature with consciousness. If all of this happened by chance, we are lucky to an infinite degree. Luck or purposeful?

dhw: You have skipped from evolution of life to evolution of the universe, thereby glossing over your particular theory concerning divine dabbling and first cells being provided with billions of programmes for the whole of life’s history, as opposed to (perhaps divinely designed) cellular intelligence. The latter theory is every bit as “purposeful” as the former.

DAVID: Cells are driven by intelligently designed processes and responses. They look intelligent.

Your usual statement of subjective opinion disguised as fact.

DAVID: Shapiro's bacteria are forerunners of stem cells in my theory.

This is very interesting. I have frequently mentioned my suspicion that stem cells are the key to evolution, but you are in a far better position than I am to develop this idea. If you do so, please start a new thread.

DAVID: Biological complexity: mammalian pregnancy is a war

by David Turell @, Tuesday, December 03, 2019, 16:19 (1578 days ago) @ dhw

DAVID: If God had not produced the bush of life, but only humans, they would not have survived! Again you are expecting a God with the ability to directly create humans without the bush, or create the whole bush.

dhw: They wouldn’t have survived without those parts of the bush of life that have enabled them to survive! Why do you ignore the 3.X billion years’ worth of bush that had nothing to do with humans? This is the illogical part of your theory, bearing in mind your claim that your always-in-control God’s only purpose was to create H. sapiens!

Your complaint is just a denial that evolution happened under the control of God. My plain belief is God started life with bacteria and eventually evolved humans as He increased the complexity of living beings.

DAVID: On the other hand you seem to accept evolution as God's work in experimentation, the same God who created the universe, the special Earth, and started life. You never look at the whole picture of why I believe from all the evidence.

dhw: If your God exists, then I have no problem with any of the above. My quarrel is with your theory that his sole purpose for all of it was to design H. sapiens, and you have no idea why he spent 3.X billion years specially designing anything but H. sapiens! Experimentation would cover the whole of the above, as would humans as a late arrival in his thinking, but “you never look at the whole picture”.

Total distortion. I have perfect ideas as to why God evolved humans in the time it took. that is history. Your 'no idea' jib is a twisted version of my intention not to question God's thinking or his choice. You have every right to question a god ( small 'g' intentional) you do not believe in from you humanistic view.


DAVID: Intricate design requires a designer. Evidence is seen in creation of this universe, creation of a perfect planet for life (Earth), fine tuning for life, creation of life, and then evolving a creature with consciousness. If all of this happened by chance, we are lucky to an infinite degree. Luck or purposeful?

dhw: You have skipped from evolution of life to evolution of the universe, thereby glossing over your particular theory concerning divine dabbling and first cells being provided with billions of programmes for the whole of life’s history, as opposed to (perhaps divinely designed) cellular intelligence. The latter theory is every bit as “purposeful” as the former.

DAVID: Cells are driven by intelligently designed processes and responses. They look intelligent.

dhw: Your usual statement of subjective opinion disguised as fact.

I only do it to show both sides are only opinion


DAVID: Shapiro's bacteria are forerunners of stem cells in my theory.

dhw: This is very interesting. I have frequently mentioned my suspicion that stem cells are the key to evolution, but you are in a far better position than I am to develop this idea. If you do so, please start a new thread.

Thank you. I'll dig into the idea when I have more time.

Biological complexity:photosynthesis not understood

by David Turell @, Monday, November 21, 2016, 20:59 (2685 days ago) @ David Turell

The mechanism of photosynthesis contains quantum mechanisms described earlier but is so complex with trace metals it is still not understood how it separates water into hydrogen and oxygen and at the same time the plant uses CO2 in the process of manufacturing plant material:

http://phys.org/news/2016-11-oxygen.html

"The living machinery responsible for photosynthesis - while commonplace and essential to life on Earth - is still not fully understood. One of its molecular mysteries involves how a protein complex, photosystem II, harvests energy from sunlight and uses it to split water into hydrogen and oxygen. This process generates the oxygen in the air that we all breathe.

***

"Previously, the resting state of photosystem II had been seen in detail using samples that were frozen. In this latest study, the researchers were able to see two key steps in photosynthetic water splitting under conditions as it occurs in nature, a big step to decoding how the process works in detail. A damage-free, room temperature study means there are fewer artifacts in the images, and this gives a clearer picture of how photosystem II works in nature.

***

"The water-splitting reaction takes place at a metal catalyst within the photosystem II protein, known as the oxygen-evolving complex, that is made up of four manganese atoms and one calcium atom. The complex uses the energy from light to form pure oxygen from two water molecules. The four manganese atoms are critical in shuffling electrons through the cycle, but it is unknown where exactly in the complex the involved water is located or where the oxygen formation occurs.

"To sort this out, the researchers used ammonia, a water substitute, to narrow down where oxygen atoms from two water molecules combine to form an oxygen molecule. If the ammonia was bound to a site, and the reaction still proceeded, that site is unlikely to be part of the oxygen molecule formation. The results from this study offered a surprise - the data do not seem to support two leading theories for how the reaction proceeds within the oxygen-evolving complex.

"In future studies using this same technique, the researchers hope to capture more images at different steps of the process, which will allow them to further refine the details of the water-splitting reaction.

"'The chemistry is so unusual," co-principal investigator and senior scientist, Vittal Yachandra at Berkeley Lab, said "Learning how exactly this water-splitting process works will be a breakthrough in our understanding, and it can help in the development of solar fuels and renewable energy.'"

Comment: This is part of a perfect balance between plants and animals. We use Oxygen for energy production and plants use CO2. This highly complex quantum reaction is so complex it is very difficult to understand and requires very advanced precise measurements described in the article. Be sure to see the diagram of what is known so far. This had to appear all at once in evolution. it is certainly not clear how any form of partial photosynthesis would work.

Biological complexity:one enzyme two hormones

by David Turell @, Wednesday, November 23, 2016, 22:23 (2683 days ago) @ David Turell

Tight controls are necessary for all levels of hormones, which are very active biologically. This plant has one enzyme that controls the levels of two plant hormones:

http://phys.org/news/2016-11-enzyme-hormones.html

"the research team of Joseph Jez, professor of biology in Arts & Sciences and a Howard Hughes Medical Institute Professor, reports that the enzyme GH3.5 can control the levels of two plant hormones, auxin and salicylic acid. It is the first enzyme of its kind known to control completely different classes of hormones.

"Auxin controls a range of responses in the plant, including cell and tissue growth and normal development. Salicylic acid, on the other hand, helps plants respond to infections, which often take resources away from growth. Plants must tightly control the levels of auxin and salicylic acid to properly grow and react to new threats.

"'Plants control hormone levels through a combination of making, breaking, modifying and transporting them," said Corey Westfall, a former graduate student who led this Jez lab work along with current graduate student Ashley Sherp.

"By stitching an amino acid to a hormone, GH3.5 takes the hormones out of circulation, reducing their effect in the plant.

***

"The scientists were expecting to find key differences between GH3.5 and related proteins that would account for its unique ability to modify multiple hormones.
To their surprise, the part of the enzyme that binds and modifies hormones looked almost identical to related enzymes that can only modify auxin. The surprising similarities between the multi-purpose GH3.5 and its single-use relatives suggests that unrecognized elements of these proteins influence which molecules they can bind and transform.

"'These surprising results mean there's something going on that we're not seeing in the sequence or the structure of these enzymes," Jez said.

"Solving this mystery could tell us more about how enzymes distinguish among similar molecules, a discriminatory ability that is critical for all life, including people as well as plants."

Comment: Enzymes are the workhorses of biological chemistry. They cause reactions to happen quickly. The molecules are giant and very specific in form in order to do their job. How does evolved life find them in a landscape of possible forms?

Biological complexity:how toxoplasmosis parastizes

by David Turell @, Friday, November 25, 2016, 01:15 (2681 days ago) @ David Turell

The parasite produces a protein to block antibodies from its host:

http://phys.org/news/2016-11-toxoplasma.html

"The parasite Toxoplasma gondii is a silent success. It infects up to 95% of people in many regions of the world, and most of them never know it, due to the parasite's artful manipulation of its host's immune response. Toxoplasma keeps the immune response low enough so that it can thrive, but high enough so that its human hosts generally live healthy lives and can incubate parasites.

***

"'The parasite rewires the host's inflammatory response," says Matthew Bowler, who led the research at EMBL. "It completely subverts the chain reaction that would normally trigger our body's defenses."

"When a cell in your body detects a parasite, it sets off a chain reaction. Inside that cell, a series of molecules activate each other until a protein called p38α is activated and moves into the cell's nucleus. There, it turns on the genes that trigger the inflammatory response. Among other things, the purpose of that response is to eliminate the pathogen. One would expect parasites like Toxoplasma to want to subdue that response, but Mohamed-Ali Hakimi and colleagues at IAB discovered a few years ago that Toxoplasma secretes a protein, GRA24, which does just the opposite: it activates and controls our inflammatory response.

"Bowler and Hakimi discovered that GRA24 bypasses the cell's chain reaction, activating p38α directly, and pulling it into the nucleus to turn on inflammatory response genes. Using a combination of techniques, they found that the Toxoplasma protein attaches itself much more strongly to p38α than the cell's own proteins do. So by producing a protein that binds directly, and very tightly, to p38α, Toxoplasma controls the level of the inflammatory response and sustains it by making it inaccessible to the proteins that would usually turn it off. This is why Toxoplasma isn't considered a serious health threat except for pregnant women and people with compromised immune system."

Life cycle:

http://web.stanford.edu/group/parasites/ParaSites2006/Toxoplasmosis/lifecycle.html

"T. gondii primarily exists in three forms: oocysts, tachyzoites, and bradyzoites. Oocysts are only produced in the definitive host, members of the family Felidae. When passed in feces and then ingested, the oocysts can infect humans and other intermediate hosts. They develop into tachyzoites, which are the rapidly multiplying trophozoite form of T. gondii. They divide rapidly in cells, causing tissue destruction and spreading the infection. Tachyzoites in pregnant women are capable of infecting the fetus. Eventually tachyzoites localize to muscle tissues and the CNS where they convert to tissue cysts, or bradyzoites. This is thought to be a response to the host immune reaction. Ingestion of cysts in contaminated meat is also a source of infection, as bradyzoites transform back into tachyzoites upon entering a new host."

Comment: The primary host is cats where eggs are developed, but the parasite cycles through other animals. Look at the diagram in the Stanford site. Ask yourself how this could have evolved step by step. Toxoplasmosis needs the blocking molecule to survive throughout the lifecycle. Logically it had to have this defensive molecule when it started its lifestyle. Note also the giant molecule it uses seen in the first article given here. How did the parasite develop this molecule before entering its first host and experience the immune system present? It has to be saltation.

Biological complexity:how toxoplasmosis parastizes

by dhw, Friday, November 25, 2016, 12:21 (2681 days ago) @ David Turell

David’s comment: The primary host is cats where eggs are developed, but the parasite cycles through other animals. Look at the diagram in the Stanford site. Ask yourself how this could have evolved step by step. Toxoplasmosis needs the blocking molecule to survive throughout the lifecycle. Logically it had to have this defensive molecule when it started its lifestyle. Note also the giant molecule it uses seen in the first article given here. How did the parasite develop this molecule before entering its first host and experience the immune system present? It has to be saltation.

It really is amazing how all these different organisms find all these different ways of surviving. How each way originates we don’t know, but each one must have had a first. No disagreement from me over saltation, but what are you implying? Do you think your God preprogrammed the first cells to pass on this particular lifestyle to the toxoplasma gondii, or personally intervened to guide little toxy into its first cat? If not, what is your alternative?

Biological complexity:how toxoplasmosis parastizes

by David Turell @, Friday, November 25, 2016, 15:44 (2681 days ago) @ dhw


dhw: It really is amazing how all these different organisms find all these different ways of surviving. How each way originates we don’t know, but each one must have had a first. No disagreement from me over saltation, but what are you implying? Do you think your God preprogrammed the first cells to pass on this particular lifestyle to the toxoplasma gondii, or personally intervened to guide little toxy into its first cat? If not, what is your alternative?

Another alternative: God programmed kitties to present the proper immunity info to the toxies and invited them in for beneficial reasons not apparent to us now. The why cats only (?) is itself a mystery. Pregnancy and immune deficiency are the only bad side effects for humans. So far this defies theological theories.

Biological complexity:how toxoplasmosis parastizes

by dhw, Saturday, November 26, 2016, 13:03 (2680 days ago) @ David Turell

DAVID:(Under "fine tuning"): Billions of solar systems follow a design for solar systems. Why does that design exist? A reason for their existence is not yet apparent from our scientific observations, but like the human retina which looks totally wrong, reason may be found.

Dhw: Sometimes theists and atheists seem to me like mirror images of each other. Here is Dawkins: he says there is nothing beyond the physical world “except in the sense of natural phenomena we don’t yet understand. If there is something that appears to lie beyond the natural world as it is now imperfectly understood, we hope eventually to understand it and embrace it within the natural.” (God Delusion, p. 14)
Not yet apparent…may be found…don’t yet understand…we hope eventually…Faith is a wonderful leveller. However, one of you must be groping through the right fog!

DAVID: Don't leave yourself out of the mix, groping or not from your picket fence! ;-)

Quite right. I am groping. But if I'm groping through a fog, I can't be sitting on a fence. Sometimes metaphors just don't work, do they!

dhw (under "toxoplasmosis"): It really is amazing how all these different organisms find all these different ways of surviving. How each way originates we don’t know, but each one must have had a first. No disagreement from me over saltation, but what are you implying? Do you think your God preprogrammed the first cells to pass on this particular lifestyle to the toxoplasma gondii, or personally intervened to guide little toxy into its first cat? If not, what is your alternative?

DAVID: Another alternative: God programmed kitties to present the proper immunity info to the toxies and invited them in for beneficial reasons not apparent to us now. The why cats only (?) is itself a mystery. Pregnancy and immune deficiency are the only bad side effects for humans. So far this defies theological theories.

A lovely response! I reckon it applies to all the natural wonders, including my favourite nest. I like your “so far” too, which fits in nicely with the Dawkins-Turell sequence above. Of course, I can offer you a theological theory, but I know you don’t want to hear it.;-)

Biological complexity:how toxoplasmosis parastizes

by David Turell @, Saturday, November 26, 2016, 15:39 (2680 days ago) @ dhw

DAVID: Another alternative: God programmed kitties to present the proper immunity info to the toxies and invited them in for beneficial reasons not apparent to us now. The why cats only (?) is itself a mystery. Pregnancy and immune deficiency are the only bad side effects for humans. So far this defies theological theories.

dhw: A lovely response! I reckon it applies to all the natural wonders, including my favourite nest. I like your “so far” too, which fits in nicely with the Dawkins-Turell sequence above. Of course, I can offer you a theological theory, but I know you don’t want to hear it.;-)

I like to hear your theological theories benighted as they often are. :-)

Biological complexity:how toxoplasmosis parastizes

by dhw, Tuesday, November 29, 2016, 11:26 (2677 days ago) @ David Turell

DAVID: Another alternative: God programmed kitties to present the proper immunity info to the toxies and invited them in for beneficial reasons not apparent to us now. The why cats only (?) is itself a mystery. Pregnancy and immune deficiency are the only bad side effects for humans. So far this defies theological theories.

dhw: A lovely response! I reckon it applies to all the natural wonders, including my favourite nest. I like your “so far” too, which fits in nicely with the Dawkins-Turell sequence above. Of course, I can offer you a theological theory, but I know you don’t want to hear it. :-)

DAVID: I like to hear your theological theories benighted as they often are.;-)

As for the weaverbird, so too for the toxy. The theory: your God gave life to the first cells, and with life he gave them an intelligence that enabled them to work out their own ways of coping with (= adaptation) AND exploiting (= innovation) the changing environmental conditions that all the different regions of the Earth have undergone. This explains why, over thousands of millions of years, so many species and so many natural wonders have come and, in most cases, gone. Occasionally, he may have intervened to change the course of the great ongoing spectacle.

Benighted? Yes, of course. None of us know how life originated and diversified. And if there is a God, none of us know what he is like or how he works. We CAN only theorize.

Biological complexity:how toxoplasmosis parastizes

by David Turell @, Tuesday, November 29, 2016, 19:16 (2677 days ago) @ dhw


DAVID: I like to hear your theological theories benighted as they often are.;-)

dhw: As for the weaverbird, so too for the toxy. The theory: your God gave life to the first cells, and with life he gave them an intelligence that enabled them to work out their own ways of coping with (= adaptation) AND exploiting (= innovation) the changing environmental conditions that all the different regions of the Earth have undergone. This explains why, over thousands of millions of years, so many species and so many natural wonders have come and, in most cases, gone. Occasionally, he may have intervened to change the course of the great ongoing spectacle.

Benighted? Yes, of course. None of us know how life originated and diversified. And if there is a God, none of us know what he is like or how he works. We CAN only theorize.

If we can find the intelligence you think your version of God put onboard then you win! But some of us can think we know how He works by looking at his works!

Biological complexity:how toxoplasmosis parastizes

by dhw, Wednesday, November 30, 2016, 12:16 (2676 days ago) @ David Turell

DAVID: I like to hear your theological theories benighted as they often are. ;-)

dhw: As for the weaverbird, so too for the toxy. The theory: your God gave life to the first cells, and with life he gave them an intelligence that enabled them to work out their own ways of coping with (= adaptation) AND exploiting (= innovation) the changing environmental conditions that all the different regions of the Earth have undergone. This explains why, over thousands of millions of years, so many species and so many natural wonders have come and, in most cases, gone. Occasionally, he may have intervened to change the course of the great ongoing spectacle.
Benighted? Yes, of course. None of us know how life originated and diversified. And if there is a God, none of us know what he is like or how he works. We CAN only theorize.

DAVID: If we can find the intelligence you think your version of God put onboard then you win! But some of us can think we know how He works by looking at his works!

Isn’t that a coincidence! I also look at the realities we think we know and which, if God exists, he must have created. And I also extrapolate ideas from those “realities” about how he works. If you can find the 3.8-billion-year computer programme or a signed statement from God that he dabbles, then you win! But of course those would be absolute proof, which is impossible, whereas you cannot even consider my hypothesis until I can provide absolute proof, which is impossible. That’s what we call double standards.

Biological complexity:how toxoplasmosis parastizes

by David Turell @, Wednesday, November 30, 2016, 15:29 (2676 days ago) @ dhw


dhw: I also look at the realities we think we know and which, if God exists, he must have created. And I also extrapolate ideas from those “realities” about how he works. If you can find the 3.8-billion-year computer programme or a signed statement from God that he dabbles, then you win! But of course those would be absolute proof, which is impossible, whereas you cannot even consider my hypothesis until I can provide absolute proof, which is impossible. That’s what we call double standards.

Not so fast. You are sitting atop your picket fence which looks down on two sides, neither of which you accept. That is your double standard of disbelief. I am not forbidden to make a choice, and have. Just as you reject both sides, I've rejected one!

Biological complexity:how toxoplasmosis parastizes

by dhw, Thursday, December 01, 2016, 13:05 (2675 days ago) @ David Turell

DAVID: If you can find the intelligence you think your version of God put onboard then you win! [...]

dhw: [...] If you can find the 3.8-billion-year computer programme or a signed statement from God that he dabbles, then you win! But of course those would be absolute proof, which is impossible, whereas you will not even consider my hypothesis until I can provide absolute proof, which is impossible. That’s what we call double standards.

DAVID: Not so fast. You are sitting atop your picket fence which looks down on two sides, neither of which you accept. That is your double standard of disbelief. I am not forbidden to make a choice, and have. Just as you reject both sides, I've rejected one!

You are misrepresenting both my position and the meaning of double standards! Firstly, I do not have disbelief, and I do not reject both sides. I am an agnostic. That means I neither believe nor disbelieve in God. In terms of how evolution works, I offer a theistic hypothesis which I actually find more convincing than your own, though I would not go so far as to call it a belief. As regards double standards, although I accept the possibility of God’s existence, you accuse me of wanting absolute proof, which is impossible. However, you refuse even to consider the possibility of cellular intelligence without absolute proof, which is also impossible. Your hypothesis does not require absolute proof, but mine does. Double standards.

Biological complexity:how toxoplasmosis parastizes

by David Turell @, Thursday, December 01, 2016, 18:57 (2675 days ago) @ dhw


dhw: You are misrepresenting both my position and the meaning of double standards! Firstly, I do not have disbelief, and I do not reject both sides. I am an agnostic. That means I neither believe nor disbelieve in God. In terms of how evolution works, I offer a theistic hypothesis which I actually find more convincing than your own, though I would not go so far as to call it a belief. As regards double standards, although I accept the possibility of God’s existence, you accuse me of wanting absolute proof, which is impossible. However, you refuse even to consider the possibility of cellular intelligence without absolute proof, which is also impossible. Your hypothesis does not require absolute proof, but mine does. Double standards.

My decision is based on the cellular complexities I have been presenting, and I believe they provide proof beyond a reasonable doubt that cellular intelligence, if any existed, cannot be complex enough to invent the complex biochemistry I present. Later today I will bring the latest diagrams on nuclear membrane pores which are still only partially understood and fantastically complex as far as hey are described.

Biological complexity:how toxoplasmosis parasitizes

by dhw, Friday, December 02, 2016, 10:47 (2674 days ago) @ David Turell

dhw: You are misrepresenting both my position and the meaning of double standards! Firstly, I do not have disbelief, and I do not reject both sides. I am an agnostic. That means I neither believe nor disbelieve in God. In terms of how evolution works, I offer a theistic hypothesis which I actually find more convincing than your own, though I would not go so far as to call it a belief. As regards double standards, although I accept the possibility of God’s existence, you accuse me of wanting absolute proof, which is impossible. However, you refuse even to consider the possibility of cellular intelligence without absolute proof, which is also impossible. Your hypothesis does not require absolute proof, but mine does. Double standards.

DAVID: My decision is based on the cellular complexities I have been presenting, and I believe they provide proof beyond a reasonable doubt that cellular intelligence, if any existed, cannot be complex enough to invent the complex biochemistry I present. Later today I will bring the latest diagrams on nuclear membrane pores which are still only partially understood and fantastically complex as far as they are described.
David's comment (on membrane pores): Any reasonable person will see that these pores are extraordinarily complex in structure and function. They obviously require exquisite planning that only a great mind can accomplish. And the complete architecture is not fully elucidated at this time. How much complexity is required to make this point obvious? Not by chance!

As always, you present the most convincing case against chance, and I agree that any reasonable person will accept it. Indeed, that is a major argument against atheism, which I have accepted from the very beginning. However, it is totally irrelevant to the argument for cellular intelligence, and from the very beginning I have agreed that cellular intelligence may be God-given. You are conflating two issues. The evidence for cellular intelligence comes from scientists who have observed the behaviour of cells. You disagree with them, which is your right, but please don’t try to defend your double standards by pretending that the complexity of the cell precludes the possibility that the cell is intelligent.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Saturday, December 03, 2016, 01:00 (2673 days ago) @ dhw


DAVID: My decision is based on the cellular complexities I have been presenting, and I believe they provide proof beyond a reasonable doubt that cellular intelligence, if any existed, cannot be complex enough to invent the complex biochemistry I present. Later today I will bring the latest diagrams on nuclear membrane pores which are still only partially understood and fantastically complex as far as they are described.
David's comment (on membrane pores): Any reasonable person will see that these pores are extraordinarily complex in structure and function. They obviously require exquisite planning that only a great mind can accomplish. And the complete architecture is not fully elucidated at this time. How much complexity is required to make this point obvious? Not by chance!

dhw: As always, you present the most convincing case against chance, and I agree that any reasonable person will accept it. Indeed, that is a major argument against atheism, which I have accepted from the very beginning. However, it is totally irrelevant to the argument for cellular intelligence, and from the very beginning I have agreed that cellular intelligence may be God-given. You are conflating two issues. The evidence for cellular intelligence comes from scientists who have observed the behaviour of cells. You disagree with them, which is your right, but please don’t try to defend your double standards by pretending that the complexity of the cell precludes the possibility that the cell is intelligent.

Cellular intelligence is not the issue. I present complexity, as you state, to raise this issue: how much complexity will it take for you to recognize that intense mental planning is required to produce that complexity. Primarily there are only two choices, chance development or design of the complexity. Your 'third way' with cellular intelligence assumes cells themselves can work out the exquisite complexity. By offering the 'God-given intelligence' you are not taking a 'third way', you are just coming back to God and joining me. I've agreed God may have provided them with an inventive mechanism. Note we are back to simply chance or God!

Biological complexity:how toxoplasmosis parasitizes

by dhw, Saturday, December 03, 2016, 13:59 (2673 days ago) @ David Turell

The start of this discussion was:
Dhw: “you refuse even to consider the possibility of cellular intelligence without absolute proof, which is also impossible. Your hypothesis does not require absolute proof, but mine does. Double standards.”

DAVID: My decision is based on the cellular complexities I have been presenting, and I believe they provide proof beyond a reasonable doubt that cellular intelligence, if any existed, cannot be complex enough to invent the complex biochemistry I present. Later today I will bring the latest diagrams on nuclear membrane pores which are still only partially understood and fantastically complex as far as they are described.[…]

dhw: You are conflating two issues. The evidence for cellular intelligence comes from scientists who have observed the behaviour of cells. You disagree with them, which is your right, but please don’t try to defend your double standards by pretending that the complexity of the cell precludes the possibility that the cell is intelligent.
DAVID: Cellular intelligence is not the issue.

Yes it is, but you are fudging the issue. You insist that cells are automatons. Shapiro says they are sentient intelligent beings, but you demand absolute proof before you will even consider it as a possibility. Hence my reference to your double standards. I use cellular intelligence as the basis for a hypothesis that maybe cells/cell communities are intelligent enough to create the innovations that drive evolution. You have every right not to believe that, but here you are conflating the issue of cellular intelligence with the issue of whether cells are intelligent ENOUGH to create the complexities of evolution, as below:

DAVID: I present complexity, as you state, to raise this issue: how much complexity will it take for you to recognize that intense mental planning is required to produce that complexity. Primarily there are only two choices, chance development or design of the complexity.

Again you are fudging the issue. WHICH complexity – the complexity of the cell, or the complexities of evolutionary innovations? Your post dealt with the cell, and I agree: chance v design. Complexities of evolutionary innovations leading to speciation: I offer cellular intelligence (perhaps God-given) v divine preprogramming and/or dabbling. A totally different issue.

DAVID: Your 'third way' with cellular intelligence assumes cells themselves can work out the exquisite complexity. By offering the 'God-given intelligence' you are not taking a 'third way', you are just coming back to God and joining me.

I am not offering a third way. I am disputing your account of how evolution works (= God planned absolutely everything in order to produce humans) in favour of God (theistic version) planning a free-for-all through autonomous cellular intelligence, with possible dabbling.

DAVID: I've agreed God may have provided them with an inventive mechanism.

There is no agreement between us on this, because you insist that the mechanism for invention is always guided by God. My hypothesis depends on it being autonomous. An inventor is not someone who obeys instructions.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Saturday, December 03, 2016, 14:59 (2673 days ago) @ dhw

dhw: but here you are conflating the issue of cellular intelligence with the issue of whether cells are intelligent ENOUGH to create the complexities of evolution, as below:

DAVID: I present complexity, as you state, to raise this issue: how much complexity will it take for you to recognize that intense mental planning is required to produce that complexity. Primarily there are only two choices, chance development or design of the complexity.

dhw: Again you are fudging the issue. WHICH complexity – the complexity of the cell, or the complexities of evolutionary innovations? Your post dealt with the cell, and I agree: chance v design. Complexities of evolutionary innovations leading to speciation: I offer cellular intelligence (perhaps God-given) v divine preprogramming and/or dabbling. A totally different issue.

No fudging. The complexities of bacteria are not the same as animals with nucleated cells. Bacteria are very complex in that they must be entirely intact to function, so that we cannot imagine a 'first' cell only partially intact. This is the origins of life aspect of evolution you keep dodging as part of the continuum of living evolution. I presented the complexities of the nuclear pores to show that this one innovation alone requires exquisite planning for the pore to function properly, which means the necessary future functions had to be understood in advance to develop the design. You use demonstrated intelligent activity of bacteria to justify your hypothesis that a committee of cells can understand this project and work it out. And yet the possibility of bacterial intelligence is a 50/50 proposition: either they can act intelligently or they follow intelligent instructions they contain, and no one on Earth can tell the difference, me or especially Shapiro. Did you really look at the diagrams of the pores? I come from a view of incredulity. Aren't you incredulous?


DAVID: Your 'third way' with cellular intelligence assumes cells themselves can work out the exquisite complexity. By offering the 'God-given intelligence' you are not taking a 'third way', you are just coming back to God and joining me.

dhw: I am not offering a third way. I am disputing your account of how evolution works (= God planned absolutely everything in order to produce humans) in favour of God (theistic version) planning a free-for-all through autonomous cellular intelligence, with possible dabbling.

Come on, having God give them intelligence and possible dabbling, is bringing God back into the picture. There is only chance or design! You can't escape it!


DAVID: I've agreed God may have provided them with an inventive mechanism.

dhw: There is no agreement between us on this, because you insist that the mechanism for invention is always guided by God. My hypothesis depends on it being autonomous. An inventor is not someone who obeys instructions.

Cells with God's inventiveness on board is still design: God's activity. How agnostic are you, really? Is chance out the window?

Biological complexity:how toxoplasmosis parasitizes

by dhw, Sunday, December 04, 2016, 12:23 (2672 days ago) @ David Turell

DAVID: Primarily there are only two choices, chance development or design of the complexity.
dhw: Again you are fudging the issue. WHICH complexity – the complexity of the cell, or the complexities of evolutionary innovations?
DAVID: No fudging. The complexities of bacteria are not the same as animals with nucleated cells.

Nobody is saying they are. The point of all this research is that cells/cell communities are intelligent, not that they are all the same!

DAVID: This is the origins of life aspect of evolution you keep dodging as part of the continuum of living evolution.

No dodging. Nobody knows the ORIGIN, and your God designing the first intelligent cells is one option.

DAVID: You use demonstrated intelligent activity of bacteria to justify your hypothesis that a committee of cells can understand this project and work it out. And yet the possibility of bacterial intelligence is a 50/50 proposition: either they can act intelligently or they follow intelligent instructions they contain, and no one on Earth can tell the difference, me or especially Shapiro. Did you really look at the diagrams of the pores? I come from a view of incredulity. Aren't you incredulous?

Yes, and yes. That is why I accept the possibility of a God who designed the cell in the first place. However, if the chances of the cell/cell community being intelligent are 50/50, we have good reason not to reject the hypothesis, which is your stance. I do not expect you to believe it, but what happened to open-mindedness? Outright rejection of a 50/50 hypothesis is prejudice, not science.

DAVID: Come on, having God give them intelligence and possible dabbling, is bringing God back into the picture. There is only chance or design! You can't escape it!

Once again, you are conflating issues. Of course God is in the picture, and so is chance. I am a 50/50 agnostic, and find both hypotheses equally difficult to believe. That is why I leave open the question of the ORIGIN of the intelligent cell. Once again, that has no bearing on the question of whether evolution is the result of God’s total control, planning, preprogramming and dabbling, or is a free-for-all, possibly designed as such by your God.

DAVID: I've agreed God may have provided them with an inventive mechanism.
dhw: There is no agreement between us on this, because you insist that the mechanism for invention is always guided by God. My hypothesis depends on it being autonomous. An inventor is not someone who obeys instructions.
DAVID: Cells with God's inventiveness on board is still design: God's activity. How agnostic are you, really? Is chance out the window?

We are not arguing about design. We are arguing about what does the designing/ inventing. I say Frank Whittle designed/invented the jet engine. Perhaps you will agree. I say the weaverbird designed/invented the weaverbird’s nest. You disagree and say God designed/invented it.

I am 50/50 agnostic. I do not believe in God or in chance. I do not disbelieve in God or in chance.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Sunday, December 04, 2016, 17:43 (2672 days ago) @ dhw


DAVID: You use demonstrated intelligent activity of bacteria to justify your hypothesis that a committee of cells can understand this project and work it out. And yet the possibility of bacterial intelligence is a 50/50 proposition: either they can act intelligently or they follow intelligent instructions they contain, and no one on Earth can tell the difference, me or especially Shapiro. Did you really look at the diagrams of the pores? I come from a view of incredulity. Aren't you incredulous?

dhw" Yes, and yes. That is why I accept the possibility of a God who designed the cell in the first place. However, if the chances of the cell/cell community being intelligent are 50/50, we have good reason not to reject the hypothesis, which is your stance. I do not expect you to believe it, but what happened to open-mindedness? Outright rejection of a 50/50 hypothesis is prejudice, not science.

The 50/50 odds I give are based on the fact that we are not inside the bacterial cell. In my opinion, from the outside, there is much more to consider. The bacterial reactions are all molecular responses when they are studied. The movement of the architecture within the bacteria (flagellum) is all mechanical. All of it is perfectly consistent with automatic response guided by automatic messages from the genome. This is the way cells act in our bodies, and I see no difference in lone bacteria. Therefore I am 99% sure that bacteria are automatons. I don't just look at the obvious 50/50 odds. I go much deeper.

dhw:Of course God is in the picture, and so is chance. I am a 50/50 agnostic, and find both hypotheses equally difficult to believe. That is why I leave open the question of the ORIGIN of the intelligent cell. Once again, that has no bearing on the question of whether evolution is the result of God’s total control, planning, preprogramming and dabbling, or is a free-for-all, possibly designed as such by your God.

I am 50/50 agnostic. I do not believe in God or in chance. I do not disbelieve in God or in chance.

I understand your position which avoids the evidence of purpose.

Biological complexity:how toxoplasmosis parasitizes

by dhw, Monday, December 05, 2016, 14:09 (2671 days ago) @ David Turell

Dhw: …if the chances of the cell/cell community being intelligent are 50/50, we have good reason not to reject the hypothesis, which is your stance. I do not expect you to believe it, but what happened to open-mindedness? Outright rejection of a 50/50 hypothesis is prejudice, not science.

DAVID: The 50/50 odds I give are based on the fact that we are not inside the bacterial cell. In my opinion, from the outside, there is much more to consider. The bacterial reactions are all molecular responses when they are studied. The movement of the architecture within the bacteria (flagellum) is all mechanical. All of it is perfectly consistent with automatic response guided by automatic messages from the genome. This is the way cells act in our bodies, and I see no difference in lone bacteria. Therefore I am 99% sure that bacteria are automatons. I don't just look at the obvious 50/50 odds. I go much deeper.

As we have said over and over again, science can only study the physical means whereby organisms perform their actions. You complain when neuroscientists try to reduce human activity to the automaticity of cell responses. Human cells and bacteria automatically respond to instructions. But the question with ALL organisms is how the instructions are given to them in the first place. You are convinced that autonomous intelligence is not possible without a brain – and yet you are also convinced that autonomous intelligence IS possible without a brain (NDEs and the afterlife). The deeper you go, the more confusing your arguments become. I accept your odds of 50/50, but I do not accept the argument that automatic responses in one organism (bacteria) must denote automatic instructions, whereas in others (with brains) they denote autonomous intelligence. The odds are 50/50 regardless of how deep you think you are going.

dhw: Of course God is in the picture, and so is chance. I am a 50/50 agnostic, and find both hypotheses equally difficult to believe. That is why I leave open the question of the ORIGIN of the intelligent cell. Once again, that has no bearing on the question of whether evolution is the result of God’s total control, planning, preprogramming and dabbling, or is a free-for-all, possibly designed as such by your God.
DAVID: I understand your position which avoids the evidence of purpose.

Dealt with under “Life’s biologic complexity”. But I’d like to remind you that apart from a possible divine, overall purpose for life itself, there is also the individual purpose (whether God-given or not) of organisms to survive and/or improve, which I have suggested is the driving force behind evolution.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Monday, December 05, 2016, 17:51 (2671 days ago) @ dhw


DAVID: The 50/50 odds I give are based on the fact that we are not inside the bacterial cell. In my opinion, from the outside, there is much more to consider....I am 99% sure that bacteria are automatons. I don't just look at the obvious 50/50 odds. I go much deeper.

dhw: As we have said over and over again, science can only study the physical means whereby organisms perform their actions. ... But the question with ALL organisms is how the instructions are given to them in the first place.

Exactly the question about the information that runs the processes of life. That information cannot appear de novo by chance. Life originated from a rocky inorganic planet Complex organic molecules had to appear and then coalesce into living forms by some magical process we do no understand at all: 60 years of research is no closer to an understanding.

dhw:You are convinced that autonomous intelligence is not possible without a brain – and yet you are also convinced that autonomous intelligence IS possible without a brain (NDEs and the afterlife).

Quite a mix-up of my theories. YES, no planning for the future without a brain in living organisms wanting to speciate to continue evolution. But NDE's involve death, and I believe there is a special arrangement in the living brain to create a quantum- based soul mechanism to survive death, and return to a universal consciousness. You are poo-pooing my theories just as I do yours. Tit-for tat, double standards.

dhw: The deeper you go, the more confusing your arguments become. I accept your odds of 50/50, but I do not accept the argument that automatic responses in one organism (bacteria) must denote automatic instructions, whereas in others (with brains) they denote autonomous intelligence. The odds are 50/50 regardless of how deep you think you are going.

Confusing to you. I have separate theories, not one all-inclusive theory to cover everything which you always seem try to do. I see no need for that all-inconclusiveness. In each area of thought I follow the known research findings. A brain allows for some integration of received stimuli and responsive alteration. Most of the intelligent planning I refer to is God's in relation to speciation. Again 50/50 is an external assessment, with no insight from the inside of organisms where only molecular reactions are found, the guidance from DNA not understood. You want DNA to think!

DAVID: I understand your position which avoids the evidence of purpose.

dhw: Dealt with under “Life’s biologic complexity”. But I’d like to remind you that apart from a possible divine, overall purpose for life itself, there is also the individual purpose (whether God-given or not) of organisms to survive and/or improve, which I have suggested is the driving force behind evolution.

Preservation of life is implanted in all organism that struggle, or don't have to struggle, to survive. That doesn't explain why the original land mammals became whales at great complications to their original physiology. Defies all logic. You are back to Darwin and the concept of competition as the driving force. I reject that idea. It is back to the tautology of survival of the fittest.

Biological complexity:how toxoplasmosis parasitizes

by dhw, Tuesday, December 06, 2016, 10:22 (2670 days ago) @ David Turell

dhw: As we have said over and over again, science can only study the physical means whereby organisms perform their actions. ... But the question with ALL organisms is how the instructions are given to them in the first place.
DAVID: Exactly the question about the information that runs the processes of life. That information cannot appear de novo by chance. Life originated from a rocky inorganic planet… [etc.]

Your ellipsis (…) leaves out two sentences: ”You complain when neuroscientists try to reduce human activity to the automaticity of cell responses. Human cells and bacteria automatically respond to instructions.” We are not talking about the origin of life, but the origin of the instructions that lead each individual organism to behave the way it does: you say that for humans the origin is our intelligence, but for bacteria every instruction has to come from God. That is the issue here.

dhw: You are convinced that autonomous intelligence is not possible without a brain – and yet you are also convinced that autonomous intelligence IS possible without a brain (NDEs and the afterlife).
DAVID: Quite a mix-up of my theories. YES, no planning for the future without a brain in living organisms wanting to speciate to continue evolution.

You go much further than the ability to speciate, which I keep explaining is a hypothesis. You claim that single cells such as bacteria (which have not advanced evolution through speciation) have no intelligence at all because they do not have a brain, and the same applies to cell communities. I have dealt with “planning for the future” on the other thread.

DAVID: But NDE's involve death, and I believe there is a special arrangement in the living brain to create a quantum- based soul mechanism to survive death, and return to a universal consciousness. You are poo-pooing my theories just as I do yours. Tit-for tat, double standards.

I have never pooh-poohed NDEs or even the concept of life after death. I have even offered you a hypothesis reconciling materialism and dualism, which you applauded, with the brain producing the energy and identity that might possibly survive death (very different from your original claim that the brain is only the receiver and not the producer of consciousness). What I pooh-pooh is your assumption that intelligence is impossible without a brain. The behaviour of cells suggests that this may not be true. 50/50.

DAVID: I have separate theories, not one all-inclusive theory to cover everything which you always seem try to do. I see no need for that all-inconclusiveness. In each area of thought I follow the known research findings.

If your separate theories contradict one another (see the massive gaps in your interpretation of evolutionary history), I think it is only right to question them. I am surprised to hear that “the known research findings” you claim to follow include a 3.8-billion-year computer programme installed by God in the first living cells for every evolutionary innovation and every natural wonder in the history of life (apart from those he dabbled).

DAVID: A brain allows for some integration of received stimuli and responsive alteration. Most of the intelligent planning I refer to is God's in relation to speciation. (dhw: Following which known research findings?) Again 50/50 is an external assessment, with no insight from the inside of organisms where only molecular reactions are found, the guidance from DNA not understood. You want DNA to think!

We can’t even get inside other people – or for that matter, inside ourselves – to find out the source of thought, ideas, decisions etc. All we can see inside are the molecular reactions. We assume some sort of intelligence in ourselves, other people and other organisms by observing their behaviour, not their molecules.

dhw: …I’d like to remind you that apart from a possible divine, overall purpose for life itself, there is also the individual purpose (whether God-given or not) of organisms to survive and/or improve, which I have suggested is the driving force behind evolution.
DAVID: Preservation of life is implanted in all organism that struggle, or don't have to struggle, to survive. That doesn't explain why the original land mammals became whales at great complications to their original physiology. Defies all logic. You are back to Darwin and the concept of competition as the driving force. I reject that idea. It is back to the tautology of survival of the fittest.

As usual you ignore the second drive, which is for improvement. You also ignore the all-important contribution Margulis and others made to the debate by stressing the importance to evolution of cooperation, which of course is absolutely essential to the whole process of improvement and hence innovation.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Tuesday, December 06, 2016, 16:34 (2670 days ago) @ dhw

dhw: We are not talking about the origin of life, but the origin of the instructions that lead each individual organism to behave the way it does: you say that for humans the origin is our intelligence, but for bacteria every instruction has to come from God. That is the issue here.

You are gain skipping the point that original life HAD to come with instruction for how to run a living mechanism. Information of that sort requires origination in a mind.

dhw:What I pooh-pooh is your assumption that intelligence is impossible without a brain. The behaviour of cells suggests that this may not be true. 50/50.

My 50/50 which you are subverting is simply the possibilities of a view from outside the cell. Once inside it is obvious automaticity is what is going on.


DAVID: I have separate theories, not one all-inclusive theory to cover everything which you always seem try to do. I see no need for that all-inconclusiveness. In each area of thought I follow the known research findings.

dhw: If your separate theories contradict one another (see the massive gaps in your interpretation of evolutionary history), I think it is only right to question them. I am surprised to hear that “the known research findings” you claim to follow include a 3.8-billion-year computer programme installed by God in the first living cells for every evolutionary innovation and every natural wonder in the history of life (apart from those he dabbled).

I start with the observation above that first life had to have information to run on. Isn't DNA an intricate code? That is information which cannot develop by chance on a rocky planet.


dhw: …I’d like to remind you that apart from a possible divine, overall purpose for life itself, there is also the individual purpose (whether God-given or not) of organisms to survive and/or improve, which I have suggested is the driving force behind evolution.
DAVID: Preservation of life is implanted in all organism that struggle, or don't have to struggle, to survive. That doesn't explain why the original land mammals became whales at great complications to their original physiology. Defies all logic. You are back to Darwin and the concept of competition as the driving force. I reject that idea. It is back to the tautology of survival of the fittest.

dhw: As usual you ignore the second drive, which is for improvement. You also ignore the all-important contribution Margulis and others made to the debate by stressing the importance to evolution of cooperation, which of course is absolutely essential to the whole process of improvement and hence innovation.

Whales are not improvement, but the initiation of a complex life style requiring enormous physiologic and anatomic changes. A drive to complexity is what that signals.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Friday, January 24, 2020, 21:31 (1526 days ago) @ David Turell

They produce a protein chemical to lower the immune reaction in their hosts:

https://phys.org/news/2020-01-protein-delivery-parasite-suppress-host.html

"Toxoplasma's "success," scientists believe, owes in part to its ability to evade the immune response of its host, whichever warm-blooded vertebrate it has infected. Now a new study suggests the parasite employs a sophisticated manipulation to suppress that immune response.

"The work, ... shows that T. gondii parasites inject their host's macrophages, a type of immune cell, with a protein that changes the activity of the macrophage itself, creating what is known as an M2 macrophage. Those changes, the team showed, rein in the response of T cells that are normally responsible for killing parasites.

"'This is the first time that it's been shown that injection alone is sufficient to drive the creation of M2 macrophages," says Christopher A. Hunter, an immunologist at Penn Vet and senior author of the paper.

***

"For T. gondii, infection is a careful balancing act. It wants to spread far and wide within a host—and eventually be passed on to other hosts—but protective immunity is needed to prevent the death of the host. Scientists have long known that macrophages are critical players in maintaining this balance.

"Macrophages are the cells normally responsible for cleaning up infections by consuming foreign invaders. Around a decade ago, scientists found that they come in different "flavors."

"'Some macrophages are profoundly pro-inflammatory and kill pathogens; these are known as M1 macrophages." Hunter says. "M2 macrophages are profoundly anti-inflammatory but are less able to kill parasites. So M1 macrophages induce inflammation, and M2s help clear it up."

***

"'In an infected cell you see nearly 2,000 genes are changed," says Hunter. "But if they're only injected, you still see about 600 genes changing in expression."

"These changes alone were enough to sway macrophages over to the M2 type and to suppress the activity of T cells that normally act to kill parasites.

"Finally, to investigate the effect of ROP16 on the parasite itself and its ability to infect mice, Josh Kochanowsky of the University of Arizona engineered a ROP16-deficient strain of T. gondii.

"'If you put these parasites in immune-deficient mice, they grow normally" says Christian, "but if you put them in immune competent mice you get a reduced amount of M2s and a reduced parasite burden. So, we're seeing that taking away ROP16 leads to a more effective immune response.'"

Comment: finding just the right protein to adjust the immune system cannot be by chance. The toxoplasma organisms rely on an active life cycle and must have had this ability from the beginning. Only design fits.

Biological complexity:how toxoplasmosis parasitizes

by David Turell @, Friday, October 28, 2022, 20:11 (518 days ago) @ David Turell

A new study of the immune system effects:

https://phys.org/news/2022-10-identity-theft-secret-cat-parasite.html

"In order to fight infections, the various roles of immune cells in the body are very strictly regulated. Scientists have long wondered how Toxoplasma manages to infect so many people and animal species and spread so efficiently.

"'We have now discovered a protein that the parasite uses to reprogram the immune system," says Arne ten Hoeve, researcher at the Department of Molecular Biosciences, Wenner-Gren Institute at Stockholm University.

"The study shows that the parasite injects the protein into the nucleus of the immune cell and thus changes the cell's identity. The parasite tricks the immune cell into thinking it is another type of cell. This changes the gene expression and behavior of the immune cell. Toxoplasma causes infected cells that normally should not travel in the body to move very quickly and in this way the parasite spreads to different organs.

"The phenomenon has been described as Toxoplasma turning immune cells into Trojan horses or wandering "zombies" that spread the parasite. The newly published study provides a molecular explanation for the phenomenon, and also shows that the parasite is much more targeted in its spread than previously thought.

***

"'It is astonishing that the parasite succeeds in hijacking the identity of the immune cells in such a clever way. We believe that the findings can explain why Toxoplasma spreads so efficiently in the body when it infects humans and animals," says Professor Antonio Barragan, who led the study, which was carried out in collaboration with researchers from France and the U.S.

***

"Toxoplasmosis is probably the most common parasitic infection in humans globally. Toxoplasma also infects many animal species (zoonosis), including our pets. The WHO has estimated that at least 30% of the world's human population is a carrier of the parasite. Studies indicate that 15–20% of the Swedish population carry the parasite (the vast majority without knowing it). The incidence is higher in several other European countries.

"Felines, not just domestic cats, have a special place in the life cycle of Toxoplasma: it is only in the cat's intestine that sexual reproduction takes place. In other hosts, for example humans, dogs or birds, reproduction takes place by the parasite dividing.

"Toxoplasma is spread through food and contact with cats. In nature, the parasite spreads preferentially from rodents to cats to rodents and so forth. The parasites are "sleeping" in the rodent's brain and when the cat eats the mouse, they multiply in the cat's intestine and come out via the feces. The parasite ends up in the vegetation and when the rodent eats the vegetation it becomes infected. Humans become infected through meat consumption or through contact with cats, specifically cat feces.

"The parasite causes the disease toxoplasmosis. When a person is infected for the first time, mild flu-like symptoms occur that can resemble a cold or a flu. After the first infection phase, the parasite transitions to a "sleeping" stage in the brain and begins a chronic silent infection that can last for decades or for life. The chronic infection usually causes no symptoms in healthy individuals. Toxoplasma can, however, cause a life-threatening brain infection (encephalitis) in people with a weakened immune system (HIV, organ transplant recipients, after chemotherapy) and can be dangerous to the fetus during pregnancy. Eye infections can occur in otherwise healthy individuals."

Comment: We have a barn cat who occasionally gets a mouse. We both feel OK, so I guess we fit the pattern of either not being infected or not showing symptomology.

Biological complexity:photosynthesis controls

by David Turell @, Monday, July 17, 2017, 22:27 (2447 days ago) @ David Turell

Too much sunlight can cause an over reactive photosynthetic process and damage the plant. There are built in controls:

https://phys.org/news/2017-07-reveals-mechanisms-protein-moss-green.html

"Photosynthesis, which allows energy from the sun to be converted into life-sustaining sugars, can also be hazardous to green plants. If they absorb too much sunlight, the extra energy destroys their tissue.

"To combat this, green plants have developed a defense mechanism known as photoprotection, which allows them to dissipate the extra energy. Researchers from MIT and the University of Verona have now discovered how the key protein in this process allows moss and green algae to protect themselves from too much sun.

"The researchers found that the protein, embedded in the membranes in the chloroplast, can switch between different states in response to changes in sunlight. When moss and green algae absorb more sunlight than they need, this protein releases the energy as heat, preventing it from building up and damaging the cells. The protein can act within seconds of a change in sun exposure, such as when the sun appears from behind a cloud.

***

"Most plants absorb far more sunlight than they can actually use. In very sunny conditions, they convert only about 30 percent of the available sunlight into sugar, while the rest is released as heat.

"Under sunny conditions, the plants have energy sitting around that is too much for the capacity of the rest of the molecular machinery," Schlau-Cohen says.

"If this energy is allowed to remain in the plant cells, it creates harmful molecules called free radicals that can damage proteins and other important cellular molecules.

***

"It was discovered several years ago that a protein called light-harvesting complex stress-related 1 (LHCSR1) is the major player in photoprotection that occurs over short timescales (seconds to minutes) in green algae and moss. This protein is embedded in the membranes in the chloroplast and interacts with chlorophyll and carotenoids, another type of light-absorbing pigment. However, the mechanism of how this photoprotection works was not known.

"Under cloudy or shady conditions, LHCSR1 simply absorbs photons and passes the energy on into the rest of the photosynthetic machinery. When the sun comes out and energy intake rises, LHCSR1 switches to another conformation within seconds. This switch is caused by a decrease in pH, which occurs when too many hydrogen ions are generated by water-splitting during photosynthesis.

"When this occurs, the protein becomes locked into a rigid structure that allows it to convert more of the absorbed light energy into heat, through a mechanism that is not fully known.

"Photoprotection can also be turned on more gradually by another feedback mechanism involving pH. A decrease in pH activates an enzyme that changes the molecular composition of a carotenoid that interacts with LHCSR1. This leads the protein to favor and stabilize its photoprotective state.

"Both of these states are controlled by a feedback loop within the organism. The pH is a short timescale response, and the molecular composition is a longer timescale response," Schlau-Cohen says." (my bold)

Comment: Once again we see a complex mechanism controlled by a feedback loop. This complex mechanism had to be developed in one step or the plants would have destroyed themselves. Again saltation designed by God.

Biological complexity:photosynthesis new research

by David Turell @, Thursday, July 27, 2017, 20:00 (2437 days ago) @ David Turell

The origin of photosynthesis and how it works has been newly studied:

https://phys.org/news/2017-07-picture-emerges-photosynthesis-sun-loving-bacteria.html

"'Nature's invention of photosynthesis is the single most important energy conversion process driving the biosphere, and photosynthesis forever changed the Earth's atmosphere,"

***

"More than 3 billion years ago our planet had an atmosphere without oxygen. At this time, nature figured out a way to capture the sunlight and convert it food to take advantage of this everlasting energy source.

"Now, a research group led by Fromme has gained important new insights by resolving with near-atomic clarity, the very first core membrane protein structure in the simplest known photosynthetic bacterium, called Heliobacterium modesticaldum (Helios was the Greek sun god).

"By solving the heart of photosynthesis in this sun-loving, soil-dwelling bacterium, Fromme's research team has gained a fundamental new understanding of the early evolution of photosynthesis, and how this vital process differs between plants systems.

***

"At the heart of photosynthesis is a reaction center; it's an elaborate complex of pigments and proteins that turn light into electrons to power the cell.

"Chlorophyll is the pigment that makes plants green. In plants, chlorophyll captures the sun's energy and uses it to make sugars out of carbon dioxide from the air and water.
Oxygenic photosynthesis in higher plants, green algae and cyanobacteria make use of Photosystem I (PSI), which is a Type I RC, and Photosystem II (PSII), which is a Type II RC.

"These work together to extract electrons from water to ferredoxin and finally reduce an energy carrier NADP+ to NADPH.

"In contrast, anoxygenic phototrophic bacteria, such as Heliobacterium modesticaldum, use a single RC to drive a cyclic electron transfer (ET) pathway that creates a proton-motive force across the membrane, which is used to drive energy production and metabolism by ATP synthesis.

"The reaction centers enclose these participants like a cage to efficiently capture all the available energy and photons of light by bringing all the elements together in the same vicinity.

"Reaction centers (RC) come in two main flavors of cofactors: iron (Type I) or quinone (Type II).

***

"The heliobacteria RC has been proposed to be the closest thing alive to the earliest common ancestor of all photosynthetic reaction centers, when, around 3 billion years ago, the early Earth contained sulfur rich seas and little oxygen.

"But successfully purifying an RC protein and growing crystals needed for X-ray experiments can be a lengthy, difficult process.

***

"They found an almost perfect symmetry in the heliobacter RC.

First, the amino acid composition of a pair of proteins was identical, called a homodimer.
This was the very first time that a RC was found to contain just a single pair of protein homodimers to drive photosynthesis.

"Finally, they mapped about 60 chlorophylls onto the RC protein complex, which was finally a way higher number than his colleague John Golbeck from Pennstate University who was part of the study predicted.

"The core polypeptide dimer and two small subunits coordinate 54 (bacterio)chlorophylls and 2 carotenoids that capture and transfer energy to the core at the reaction center, which performs charge separation, stabilization and electron transfer it consists of 6 (bacterio)chlorophylls and an iron-sulfur cluster; unlike other reaction centers, it lacks a bound quinone.

"Thus, the structure supports the hypothesis that electron transport in the HbRC does not require an intermediate cofactor.

"'High-resolution structures have been obtained from multiple heterodimeric (more than one protein) RCs (Purple bacteria RC, PSI, and PSII), but no homodimeric RC structure have been solved until now," said Fromme.

***

"In evolutionary terms, this means that the heliobacteria RC may have first come from a single gene."

Comment: Without the production of oxygen, advanced life would not be here. This highly complex process did not appear by chance.

Biological complexity:photosynthesis new research

by David Turell @, Friday, October 20, 2017, 18:35 (2352 days ago) @ David Turell

More complexity unearthed:

https://www.quantamagazine.org/simple-bacteria-offer-clues-to-the-origins-of-photosynth...

"But in terms of function and structure, the photosystem reaction centers fall into two categories that differ in almost every way. Photosystem I serves mainly to produce the energy carrier NADPH, whereas photosystem II makes ATP and splits water molecules. Their reaction centers use different light-absorbing pigments and soak up different portions of the spectrum. Electrons flow through their reaction centers differently. And the protein sequences for the reaction centers don’t seem to bear any relation to each other.

"Both types of photosystem come together in green plants, algae and cyanobacteria to perform a particularly complex form of photosynthesis — oxygenic photosynthesis — that produces energy (in the form of ATP and carbohydrates) as well as oxygen, a byproduct toxic to many cells. The remaining photosynthetic organisms, all of which are bacteria, use only one type of reaction center or the other.

***

"After carefully taking images of the crystallized reaction centers, the team found that although the reaction center is officially classified as type I, it seemed to be more of a hybrid of the two systems. “It’s less like photosystem I than we thought,” Redding said. Some people might even call it a “type 1.5,” according to Gisriel.

"One reason for that conclusion involves greasy molecules called quinones, which help transfer electrons in photosynthetic reaction centers. Every reaction center studied so far uses bound quinones as intermediates at some point in the electron transfer process. In photosystem I, the quinones on both sides are tightly bound; in photosystem II, they are tightly bound on one side, but loosely bound on the other. But that’s not the case in the heliobacterium reaction center: Redding, Fromme and Gisriel did not find permanently bound quinones among the electron transfer chain’s stepping stones at all. That most likely means its quinones, although still involved in receiving electrons, are mobile and able to diffuse through the membrane. The system might send electrons to them when another, more energetically efficient molecule isn’t available.

***

"When an organism is exposed to too much light, electrons build up in the transfer chain. If oxygen is around, this buildup can lead to a harmfully reactive oxygen state. Adding a firmly bound quinone to the complex not only provides an additional slot to deal with potential traffic jams; the molecule, unlike others used in the transfer chain, also does not pose any risk of producing that deleterious form of oxygen. A similar explanation works for why reaction centers became asymmetric, Gisriel added: Doing so would have added more stepping stones as well, which would have similarly buffered against damage caused by the accumulation of too many electrons. (my bold)

***

"That hypothesis contradicts one of the widely held ideas about the origins of photosynthesis: that species incapable of photosynthesis suddenly obtained the capacity through genes passed laterally from other organisms. According to Cardona, in light of the new discoveries, horizontal gene transfer and gene loss may both have played a role in the diversification of reaction centers, although he suspects that the latter may have been responsible for the earliest events. The finding, he said, might suggest that “the balance skews toward the gene-loss hypothesis” — and toward the idea that photosynthesis was an ancestral characteristic that some groups of bacteria lost over time.

"Not everyone is so sure. Blankenship, for one, is skeptical. “I don’t buy that,” he said. “I don’t see any data here that suggests that oxygenic photosynthesis occurred that much earlier.” To him, the work by Redding, Fromme and their collaborators has not answered these questions; it has only conjectured about what may have happened. To solve that puzzle, scientists will need the reaction center structures of other bacteria, so they can continue evaluating the structural differences and similarities to refine the twisting roots of their evolutionary trees."

Comment: Photosynthesis is vital for multicellular life to evolve. How it arrived is still a puzzle as this article shows. But note my bold. Producing oxygen, unless there are existing protections (antioxidant factors), is dangerous. Brings me to the usual point. It all had to be developed with all parts in place, not stepwise. Obviously an argument for God.

Biological complexity:photosynthesis new research

by David Turell @, Tuesday, March 20, 2018, 17:57 (2201 days ago) @ David Turell

Without photosynthesis our atmosphere would not contain the level of oxygen it has, and more than likely life would not have evolved beyond single cells. We still don't know fully how it works, because the photon action responses are so fast:

https://phys.org/news/2018-03-givin-uncovers-photosynthesis.html

"In photosynthesis, light strikes colored molecules that are embedded within proteins called light-harvesting antenna complexes. These same molecules give trees their beautiful fall colors in Michigan. From there, the energy is shuttled to a photosynthetic reaction center protein that starts to channel energy from light through the photosynthetic process. The end product? Oxygen, in the case of plants, and energy for the organism.

***

"'In photosynthesis, the basic architecture is that you've got lots of light-harvesting antennae complexes whose job is to gather the light energy," Ogilvie said. "They're packed with pigments whose relative positions are strategically placed to guide energy to where it needs to go for the first steps of energy conversion."

"The differently colored pigments wrestle with different energies of light and are adapted to gather the light that is available to the bacteria. Photons excite the pigments, which triggers energy transfer in the photosynthetic reaction centers.

"'The antennae take solar energy and create a molecular excitation, and in the reaction center, the excitation is converted to a charge separation," Ogilvie said. "You can think of that kind of like a battery."

"But it is this moment—the moment of charge separation—that scientists do not yet have clearly pictured. Ogilvie and her team were able to take snapshots to capture this moment, using a state-of-the-art "camera" called two-dimensional electronic spectroscopy.


"In particular, Ogilvie and her team were able to clearly identify a hidden state, or energy level. This is an important state to understand because it's key to the initial charge separation, or the moment energy conversion begins during photosynthesis. They were also able to witness the sequence of steps leading up to charge separation.

"The finding is a particular achievement because of how impossibly quickly this energy conversion takes place—over the span of a few picoseconds. Picoseconds are one trillionth of a second, an unimaginable timescale. A honey bee buzzes its wings 200 times a second. The first energy conversion steps within purple bacteria take place before the bee has even thought about the downward push of its first flap."

Comment: Previous research has shown that quantum mechanics are necessary. try and tell me this is not deigned!

Biological complexity:photosynthesis new research

by David Turell @, Wednesday, March 28, 2018, 18:34 (2193 days ago) @ David Turell

Photosynthesis occurs very rapidly. We are still unraveling its complexity:

https://phys.org/news/2018-03-photosynthesis-vibrations-traffic.html

"Plants and algae soak up sunlight and transfer the energy using proteins holding colored pigments. A pigment energized by a photon can pass that excitation energy to another nearby pigment—like passing the baton between runners in a relay. By repeating this process the photon's energy is carried to the reaction center where it is used to produce oxygen and power plant growth.

"Scientists have long wondered how plants move this energy so quickly and efficiently across the large collections of pigments surrounding each reaction center.

"In this study, researchers focused on one photosynthetic protein known as PC645. Using computer simulations and experimental data, they found that PC645 controls where energy goes by tuning the vibrations of pigments to enhance energy transport along specific routes.

"'You can imagine these proteins using the vibrations of different pigments like traffic signals that send excitations in one direction or another," explains Bennett, who was in Toronto for the CIFAR Bio-inspired Solar Energy program meeting.

"For example, when a 'blue' pigment is excited it could pass the excitation to a number of different neighboring pigments with similar energies. By controlling the vibrations, proteins can direct the 'blue' pigment to pass the excitation to a specific 'red' pigment thereby skipping over pigments with intermediate colours.

"'The weird thing is that when you run the experiments, the excitation doesn't step down an energy ladder. It jumps from the very highest rung to the very lowest rung and never touches anything in the middle. It makes you wonder—why? And more importantly, how?" says Bennett.

"Previously, researchers thought this could only be explained by quantum effects like entanglement. Vibronic coherence—the entanglement between electron and vibrational motion—was thought to be necessary for the fast jumps between very different energy levels. However, this new research suggests that what is needed is not vibronic coherence, but a large band of vibrations that bridge the energy gap between two pigments.

"'From a material perspective, this kind of classical mechanism is more useful because it's robust to reasonable levels of disorder that current synthetic techniques can achieve," Bennett says."

Comment: this energy transfer system is very complex. When this process appeared in cyanobacteria and algae it is so irreducibly complex it had to be p=put together all at once or it would not have worked. It had to be designed.

Biological complexity:photosynthesis new research

by David Turell @, Tuesday, June 12, 2018, 01:38 (2117 days ago) @ David Turell

A secondary form of producing oxygen is now found in the mechanics of a giant enzyme:

https://phys.org/news/2018-06-oxygen-photosynthesis-mechanism-exposed.html

"Though chlorophyll is the best-known part, for the vivid green it colors nature, many compounds work together in photosynthesis. And Georgia Tech chemists devised clever experiments to inspect players intimately involved in the release of O2 from water in what's known as photosystem II (PSII).

"PSII is a complex protein structure found in plants and algae. It has a counterpart called photosystem I, an equally complex light-powered producer of oxygen and biomaterials.

***

"Many details are still unknown, but here are some basic workings.
PS II is a biochemical complex made mostly of large amino acid corkscrew cylinders and some smaller such cylinders strung together with amino acid strands. The reaction cycle that extracts the O2 from H2O occurs at a tiny spot, which the study focused on.

"For scale, if PSII were a fairly tall, very wide building, the spot might be the size of a large door in about the lower center of the building, and the metal cluster would be located there. Intertwined in the proteins would be sprawling molecules that include beta-carotene and chlorophyll, a great natural photoelectric semiconductor.

***

"Photons from sunlight bombard photosystem II and displace electrons in the chlorophyll," Barry said. "That creates moving negative charges.

"What is the metal catalyst?

"The metal catalyst acts like a capacitor, building up charge that it uses to expedite four chemical reactions that release the O2 by removing four electrons, one-by-one, from two water molecules. In the process, water also spins off four H+ ions, i.e. protons, from two H2O molecules.

"An additional highly reactive compound acts as a "switch" to drive the electron movement in each step of the reaction cycle.

"Near the metal cluster is a common amino acid called tyrosine, a little building block on that mammoth protein building. The light reactions remove one electron from tyrosine, making it what's called an unstable radical, and the radical version of tyrosine strongly attracts a new electron.

"It very quickly gets that new electron from the metal cluster. As PSII absorbs photons, the taking of an electron from tyrosine and its radical's grabbing of a new one from the cluster repeats rapidly, making the tyrosine a kind of flickering switch.

"'The tyrosine radical drives the cycle around, and what they (Guo and He) did in the lab was to develop a way of seeing the radical reaction in the presence of the metal cluster," Barry said.

"Guo and He also found that the calcium atom in the cluster has key interactions with tyrosine.

***

"The researchers observed the processes via vibrational spectroscopy, which revealed qualities of tyrosine's chemical bonds. The researchers also examined the calcium and discovered a special interaction between it and tyrosine.

"'A new thing we saw was that the calcium ion made the tyrosine twist a certain way," Barry said. "It turns out that the tyrosine may be a very flexible switch."

"The researchers also swapped out calcium for other metals and found that the calcium fulfills this role quite optimally."

Comment: Another very complex system that demands a recognition of design.

Biological complexity:photosynthesis molecule

by David Turell @, Friday, December 21, 2018, 22:24 (1925 days ago) @ David Turell

Its structure in transferring electron is outlined:

https://www.sciencedaily.com/releases/2018/12/181221123848.htm

"An international team of researchers has solved the structure and elucidated the function of photosynthetic complex I. This membrane protein complex plays a major role in dynamically rewiring photosynthesis.

***

"Complex I is found in most living organisms. In plant cells it is used in two places: one is in mitochondria, the cell's power plants, the other is in chloroplasts, where photosynthesis occurs. In both instances, it forms part of an electron transport chain, which can be thought of as biology's electrical circuit. These are used to drive the cells molecular machines responsible for energy production and storage. The structure and function of mitochondrial complex I as part of cellular respiration has been well investigated, whereas photosynthetic complex I has been little studied so far.

"Using cryoelectron microscopy, the researchers were able to solve for the first time the molecular structure of photosynthetic complex I. They showed that it differs considerably from its respiratory relative. In particular, the part responsible for electron transport has a different structure, since it is optimised for cyclic electron transport in photosynthesis.

"Cyclic electron transport represents a molecular short circuit in which electrons are reinjected into the photosynthetic electron transport chain instead of being stored. Marc Nowaczyk explains: "The molecular details of this process have been unknown and additional factors have not yet been unequivocally identified." The research team simulated the process in a test tube and showed that the protein ferredoxin plays a major role. Using spectroscopic methods, the scientists also demonstrated that the electron transport between ferredoxin and complex I is highly efficient.

"In the next step, the group analysed at the molecular level which structural elements are responsible for the efficient interaction of complex I and ferredoxin. Further spectroscopic measurements showed that complex I has a particularly flexible part in its structure, which captures the protein ferredoxin like a fishing rod. This allows ferredoxin to reach the optimal binding position for electron transfer."

Comment: It is amazing how protein molecules walk around, move and bend like a fishing rod. Just like teh machines we make, only in this case it is individual protein molecules. Not by chance.

Biological complexity:photosynthesis molecule

by David Turell @, Friday, February 15, 2019, 19:45 (1869 days ago) @ David Turell

Another complex photosynthesis molecule's structure is outlined:

https://www.sciencedaily.com/releases/2019/02/190214174229.htm

Discovered decades ago, the protein complex targeted by the researchers, called NADH dehydrogenase-like complex (NDH), is known to help regulate the phase of photosynthesis where the energy of sunlight is captured and stored in two types of cellular energy molecules, which are later utilized to power the conversion of carbon dioxide into sugar. Past investigations revealed that NDH reshuffles the energized electrons moving among other protein complexes in the chloroplast in a way that ensures the correct ratio of each energy molecule is produced. Furthermore, NDH of cyanobacteria performs several additional roles including increasing the amount of carbon dioxide (CO2) available for sugar production by linking CO2 uptake with electron transfer.

***

"Research on this enzyme has been difficult and experimental results confounding for the last 20 years or so because we have lacked complete information about the enzyme's structure," said Davies. "Knowing the structure is important for generating and testing out hypotheses of how the enzyme functions. The resolution we obtained for our structure of NDH has only really been achievable since the commercialization of the direct electron counting camera, developed in collaboration with Berkeley Lab."

***

In the current study, first author Thomas Laughlin, a UC Berkeley graduate student with a joint appointment at MBIB, isolated NDH complexes from membranes of a photosynthetic cyanobacterium provided by the Junko Yano and Vittal Yachandra Lab in MBIB and imaged them using a state-of-the-art cryo-TEM instrument fitted with the latest direct electron detector. Located on the UC Berkeley campus, the cryo-TEM facility is managed by the Bay Area CryoEM consortium, which is partly funded by Berkeley Lab.

The resulting atom density map was then used to build a model of NDH that shows the arrangement of all the protein subunits of NDH and the most likely position of all the atoms in the complex. By examining this model, Davies' team will be able to formulate and then test hypotheses of how NDH facilitates sugar production by balancing the ratio of the two cellular energy molecules.

"While the structure of NDH alone certainly addresses many questions, I think it has raised several more that we had not even thought to consider before," said Laughlin.

Comment: Be sure to look at this monster molecule which is an enzyme. The preceding entry here was of a different giant molecule which is part of the photosynthesis process. (December 21, 2018, 22:24) It was 'complex 1' which uses iron in its processing role. There is no way such a complex biological process arrived by chance, considering the size of these molecules and their complexity, which is so difficult for scientists to figure them out.

Biological complexity: new complex photosynthesis molecule

by David Turell @, Monday, May 27, 2019, 22:39 (1768 days ago) @ David Turell

Very large, very complex group of photosynthetic proteins described:

https://phys.org/news/2019-05-scientists-photosynthetic-supercomplex.html

The paper is titled "The structure of the stress induced photosystem I—IsiA antenna supercomplex."

"'Supercomplexes are associations between antennae proteins and photochemical reaction centers that exist in all photosynthetic organisms," explained Yuval Mazor, an assistant professor in the School of Molecular Sciences and the Biodesign Institute's Center for Applied Structural Discovery. "This particular one comes from cyanobacteria, the class (phyla) of bacteria in which oxygenic photosynthesis first appeared (a few billion years ago) and later evolved, into all types of oxygenic photosynthesis that we know today."

***

"In the lab, this particular super-complex is produced by cyanobacteria under low iron environment or excessive light fluxes. However, in the "real world" iron exists at very low concentrations and high light can be the rule rather than the exception, so ultimately PSI-IsiA is a very common form of photosystem I, one of the two essential engines of photosynthesis.

"The complex is unique in size, the largest photosynthetic supercomplex with a known molecular structure, and in complexity with more than 700 different molecules (mostly light-harvesting molecules) making up the complete structure.

"There are 591 chlorophylls in the PSI-IsiA supercomplex, by far the largest number of bound pigments in any of the photosynthetic super-complexes with known structures.

"The ability of cyanobacteria to express this complex when they are under stress plays an important role in their survival under these conditions. This complex also represents a large class of antennae that are very common in marine cyanobacteria, which are responsible for a considerable fraction of the total global photosynthesis output (estimates vary between 15% and 25%). Mazor emphasizes that their work was done on a common laboratory strain, not on one of the marine species.

"The current structure uncovers the most crucial details of this enormous machine. As the first example from the cyanobacterial branch of the membrane embedded antenna proteins, it lays a path for evaluating the light-harvesting and photoprotection mechanism (from excess or fluctuating light conditions) in cyanobacteria."

Comment: Unfortunately no diagram, but the enormous complexity is obvious from the description. There is no way this arrangement could be developed by chance. It must be designed

Biological complexity: cellular quality control

by David Turell @, Thursday, May 30, 2019, 20:03 (1765 days ago) @ David Turell

How proteins are manufactured in the cell is quality controlled automatically:

https://phys.org/news/2019-05-bacteria-protein-quality-agent-insight.html

"Our cells' process for transforming genes into useful proteins works much like an automobile factory's assembly line; there are schematics, parts, workers, motors, quality control systems and even recycling crews. If the cell's recycling process falters, abnormal protein fragments accumulate, potentially causing the cell's death.

***

"'One of the problems with this is that the accumulation of partially formed proteins may be toxic. So in our lab, we're asking how do cells sense this, and how do they disassemble these proteins and recycle the building blocks?"

"Organelles called ribosomes serve as the protein-assembly motors within cells. If they stall during the process of piecing together the parts—amino acids—cells have a variety of systems for responding. In human and other eukaryotic cells, when a ribosome jams, rescue factors split it open. A protein called Rqc2, also known as NEMF, zooms in and recruits another protein—the ubiquitin ligase Ltn1, also called listerin. The Joazeiro lab previously discovered that Ltn1 marks the truncated protein fragment on ribosomes with a destruction tag called ubiquitin. Protease saws then handle the demolition.

"Underscoring the importance of this recycling process, Joazeiro discovered in 2009 that mutations in Ltn1 can cause the death of nerve cells in mice, resulting in ALS-like symptoms. Bacteria have related, but somewhat more direct systems for addressing halted ribosomes and their protein fragments, according to the Cell report. Studying the bacterium B. subtilis, the Joazeiro team found that Rqc2 itself marks the protein fragment with a flag—a polymer made of the amino acid alanine. Thus flagged, proteases come to cut up the bad fragment.

"Previous studies had suggested that in some pathogenic bacteria, Rqc2 proteins had a different job, one that functioned outside the cell, helping attach the microbes to hosts.
"We have found this is not the complete story," Joazeiro says. "Rqc2 plays a more fundamental role inside of bacterial cells."

***

"Equally important to Joazeiro is the realization that Rqc2 serves as a "living" molecular fossil, illuminating new insights about the ancient ancestral organism that emerged some 4 billion years ago to form the very base of the tree of life that evolved into the planet's biodiversity today.

"'Shortly after cells invented how to make proteins, they were also faced with determining how to deal with incompletely made proteins," Joazeiro says. "The analyses suggest that an Rqc2 homolog in the last universal common ancestor already carried out this task.'" (my bold)

Comment: The story implies the automaticity of cells while manufacturing, which is constant. Also the final bolded comment is what I always point out: when the first cell is originated (designed), these defense mechanism against mistakes have to also be created at the same time or life would not survive. Step-by-step evolution is impossible.

Biological complexity: cellular DNA repair

by David Turell @, Thursday, May 30, 2019, 23:27 (1765 days ago) @ David Turell

A new complex mechanism is described:

https://phys.org/news/2019-05-mechanism-accessing-dna.html

"It has been unclear, however, how repair proteins work on DNA tightly packed in chromatin, where access to DNA damage is restricted by protein packaging. Using cryo electron microscopy, researchers from the Thomä group at the Friedrich Miescher Institute for Biomedical Research (FMI) have identified a new mechanism whereby repair proteins detect and bind to damaged DNA that is densely packed in nucleosomes.

"Ultraviolet (UV) light damages DNA, producing small lesions. These UV lesions are first detected by a protein complex known as UV-DDB and—once the lesions have been identified—the rest of the DNA repair machinery swings into action. The question is, how can UV-DDB bind to lesions when the DNA is coiled around the histone protein core of the so-called nucleosome (the basic unit of chromatin—the DNA packaging of eukaryotic chromosomes)?

"To gain access, UV-DDB was previously thought to require the assistance of additional proteins that shift the nucleosome. Researchers from the group led by Nicolas Thomä have now found that additional proteins are not necessarily needed to detect UV-induced lesions; instead, the UV-DDB complex takes advantage of the intrinsic dynamics of nucleosomal DNA. The DNA repair factor appears to catch the UV lesions when they are temporarily accessible.

"In their study published in Nature, the scientists determined various three dimensional (3-D) structures of UV-DDB bound to lesions at different locations around the nucleosome, using cryo-electron microscopy—a technique that allows the 3-D structure of biomolecules to be visualized with atomic detail. The researchers concluded that damage detection strategies depend on where the DNA lesion is located. In the case of "accessible" lesions, which can be directly contacted, UV-DDB binds to the lesion tightly. The recognition of "occluded" lesions (facing the histone protein core of the nucleosome) requires additional steps: UV-DDB binds the UV lesions when they are exposed temporarily through the natural dynamics of the nucleosome. One of the lead authors, Syota Matsumoto, explains: "To visualize what happens at the molecular level, imagine a piece of string wrapped around a spool, which becomes accessible when it is pulled forwards or backwards a little bit."

"The researchers called the mechanism of DNA damage read-out "slide-assisted site-exposure." This new mechanism operates independently of chromatin remodelers and does not require chemical energy to slide or dislodge nucleosomes.

"Thomä comments: "In the past, nucleosomes were thought to be a major obstacle for DNA-binding proteins. In our study, we show that they are not, and that the system is tailored to bind UV lesions wherever they are. What makes this study really powerful is the fact that the mechanism we identified could very well be used by many other types of DNA-binding proteins. Accessing nucleosomal DNA is not only fundamental for DNA repair, but is relevant for all proteins that bind to chromatin. With our study, we define a previously unknown strategy for protein access to chromatinized DNA templates."

Comment: Just as in the last entry, the earliest life forms had to have these defenses for life to continue. Only design fits these requirements.

Biological complexity: cellular DNA repair

by David Turell @, Tuesday, March 24, 2020, 23:26 (1465 days ago) @ David Turell

A new study shows the complexity of this necessary process:

https://phys.org/news/2020-03-scientists-reveal-proteins-team-dna.html

"One of the main DNA repair processes is called homologous recombination (HR). This repairs a severe form of DNA damage where both strands of DNA are broken. A protein called Rad51 orchestrates HR, and Rad51 itself is supported by several 'helper' proteins.

***

"Previous genetic studies have shown that there are two HR sub-pathways in yeast—one that depends on Swi5-Sfr1 and another that relies on molecules called Rad51 paralogs. To test whether it was this other HR pathway that was rescuing DNA repair, the team used yeast that lacked the Rad51 paralogs. The results were striking: in yeast with mutant Swi5-Sfr1 and no Rad51 paralogs, the DNA damage was much more severe. This suggests that the damaging effects of mutations to the Swi5-Sfr1 helper complex are suppressed by a second group of helper proteins.

"'Although these two groups of helper proteins were previously thought to function independently, our study shows that they actually work together to activate Rad51 in DNA repair," explains senior author Hiroshi Iwasaki, Professor at the Tokyo Institute of Technology. "The fundamental mechanisms of DNA repair are highly conserved from yeast to humans. Our new insight into DNA repair in yeast may serve as a template for understanding why DNA repair processes do not function properly in human disease.'"

Comment: Only a designer would see to it that more than one system was available to back up the vital repair process. Not by chance.

Biological complexity:plants control breathing and CO2

by David Turell @, Monday, August 26, 2019, 18:15 (1677 days ago) @ David Turell

Depending on water balance, plants open and close pores to breathe and take in CO2 or slow photosynthesis when pores must be closed:

https://phys.org/news/2019-08-carbon-dioxide-uptake.html

"When water is scarce, plants can close their pores to prevent losing too much water. This allows them to survive even longer periods of drought, but with the majority of pores closed, carbon dioxide uptake is also limited, which impairs photosynthetic performance and thus plant growth and yield.

"Plants accomplish a balancing act—navigating between drying out and starving in dry conditions—through an elaborate network of sensors.

***

"When light is abundant, plants open the pores in their leaves to take in carbon dioxide (CO2) which they subsequently convert to carbohydrates in a process called photosynthesis. At the same time, a hundred times more water escapes through the microvalves than carbon dioxide flows in.

"This is not a problem when there is enough water available, but when soils are parched in the middle of summer, the plant needs to switch to eco-mode to save water. Then plants will only open their pores to perform photosynthesis for as long as necessary to barely survive. Opening and closing the pores is accomplished through specialised guard cells that surround each pore in pairs.

"The guard cells must be able to measure the photosynthesis and the water supply to respond appropriately to changing environmental conditions. For this purpose, they have a receptor to measure the CO2 concentration inside the leaf. When the CO2 value rises sharply, this is a sign that the photosynthesis is not running ideally. Then the pores are closed to prevent unnecessary evaporation. Once the CO2 concentration has fallen again, the pores reopen.


"The water supply is measured through a hormone. When water is scarce, plants produce abscisic acid (ABA), a key stress hormone, and set their CO2 control cycle to water saving mode. This is accomplished through guard cells which are fitted with ABA receptors. When the hormone concentration in the leaf increases, the pores close.

***

"The two experts found out that the gene expression patterns differed significantly at high CO2 or ABA concentrations. Moreover, they noticed that excessive CO2 also caused the expression of some ABA genes to change. These findings led the researchers to take a closer look at the ABA signalling pathway. They were particularly interested in the ABA receptors of the PYR/PYL family (pyrabactin receptor and pyrabactin-like). Arabidopsis has 14 of these receptors, six of them in the guard cells.

***

"Why does a guard cell need as many as six receptors for a single hormone? To answer this question, we teamed up with Professor Pedro Luis Rodriguez from the University of Madrid, who is an expert in ABA receptors," says Hedrich. Rodriguez's team generated Arabidopsis mutants in which they could study the ABA receptors individually.

***

"'We conclude from the findings that the guard cells offset the current photosynthetic carbon fixation performance with the status of the water balance using ABA as the currency," Hedrich explains. "When the water supply is good, our results indicate that the ABA receptors evaluate the basic hormonal balance as quasi 'stress-free' and keep the stomata open for CO2 supply. When water is scarce, the drought stress receptors recognise the elevated ABA level and make the guard cells close the stomata to prevent the plant from drying out.'"

Comment: This system of controls had to be present when leafy plants appeared or they would have died of dehydration. The systems are irreducibly complex, and must have been designed.

Biological complexity: proteins that maintain cell shape

by David Turell @, Monday, August 26, 2019, 18:25 (1677 days ago) @ David Turell

A group of proteins that anchor cell shape and nucleus position are identified:

https://phys.org/news/2019-08-fundamental-properties-cells-affect-tissue.html

"...Virginia Commonwealth University researchers, in collaboration with researchers from the University of Florida, identify a fundamental factor in maintaining a stable multicellular structure: the LINC complex.

"The LINC complex—a group of proteins known as the nuclear linker of nucleoskeleton to cytoskeleton—anchors the nucleus to the cell. The study, using 3-D culture models of cell clusters known as acini, suggests that mechanically disrupting the LINC complex destabilizes the clusters.

"'If these main connections that help anchor the nucleus are disrupted, the cells try their best to compensate in order to keep things normal," said Vani Narayanan, a doctoral candidate in the Department of Biomedical Engineering in the VCU College of Engineering and lead co-author of the study. "Unfortunately, this compensation becomes over-compensation. Various proteins that should ideally remain in nominal amounts within the cell for proper cellular function get unregulated, causing rapid movement of cells within the acinus, abnormal cell division and migration and, hence, the system collapses."

***

"'The mechanics of the cells affect how tissue structures form," said Daniel Conway, Ph.D., associate professor in the Department of Biomedical Engineering and co-author of the study. "If you change the mechanical properties of individual cells, they lose the ability to form more complex tissue or to stay organized. ... The structures actually aren't that stable, [therefore] disruptions in physical connections between or within cells can result in these structures collapsing.'"

Comment: This shape-holding structure must have been designed as multicellular forms appeared in evolution. Otherwise how did they maintain proper functions?

Biological complexity: new complex photosynthesis molecule

by David Turell @, Wednesday, November 13, 2019, 20:20 (1598 days ago) @ David Turell

Another enormous photosynthesis molecule described:

https://phys.org/news/2019-11-experts-key-photosynthesis-food-demands.html

"Scientists have solved the structure of one of the key components of photosynthesis, a discovery that could lead to photosynthesis being 'redesigned' to achieve higher yields and meet urgent food security needs.

"The study, led by the University of Sheffield and published today in the journal Nature, reveals the structure of cytochrome b6f—the protein complex that significantly influences plant growth via photosynthesis.

"Photosynthesis is the foundation of life on Earth providing the food, oxygen and energy that sustains the biosphere and human civilisation. (my bold)

"Using a high-resolution structural model, the team found that the protein complex provides the electrical connection between the two light-powered chlorophyll-proteins (Photosystems I and II) found in the plant cell chloroplast that convert sunlight into chemical energy.

"Lorna Malone, the first author of the study and a Ph.D. student in the University of Sheffield's Department of Molecular Biology and Biotechnology, said: "Our study provides important new insights into how cytochrome b6f utilises the electrical current passing through it to power up a 'proton battery'. This stored energy can then be then used to make ATP, the energy currency of living cells. Ultimately this reaction provides the energy that plants need to turn carbon dioxide into the carbohydrates and biomass that sustain the global food chain."

"The high-resolution structural model, determined using single-particle cryo-electron microscopy, reveals new details of the additional role of cytochrome b6f as a sensor to tune photosynthetic efficiency in response to ever-changing environmental conditions. This response mechanism protects the plant from damage during exposure to harsh conditions such as drought or excess light.

"Dr. Matt Johnson, reader in Biochemistry at the University of Sheffield and one of the supervisors of the study added: "Cytochrome b6f is the beating heart of photosynthesis which plays a crucial role in regulating photosynthetic efficiency."

Comment: Photosynthesis is the source of life on Earth. The giant molecules required had to be found and applied. Only a designer can do this. Chance cannot. Look at the diagram to appreciate this point.

Biological complexity: how photosynthesis controls electrons

by David Turell @, Friday, January 10, 2020, 03:26 (1540 days ago) @ David Turell

A very complex new aspect of photosynthesis regulation is found:

https://phys.org/news/2020-01-ancient-iron-sulfur-based-mechanism-electron-photosynthes...

"[Research] professor[s] of biochemistry, have shown that the chloroplast sensor kinase (CSK) protein is equipped with an evolutionarily conserved iron-sulfur cluster. The cluster helps it to sense the presence of electrons and thereby send signals to the gene expression machinery in plant chloroplasts to turn photosystem genes on and off.

"'CSK is an ancient protein found in both cyanobacteria and chloroplasts. More than a billion years ago a cyanobacterium took up residence inside a eukaryotic host cell and became the chloroplast of plants and algae," Puthiyaveetil said. "By examining the cyanobacterial, plant and diatom CSK proteins, we've discovered that CSK uses an iron-sulfur cluster to sense the electron transport, assessing how well the electrons are flowing, and make adjustments in the relative abundance of plant photosystems to keep photosynthesis working correctly and protect the plant from oxidative stress."

***

"During photosynthesis, plants turn sunlight into energy via two photosystems. Photosystem I utilizes long wavelength light efficiently while photosystem II prefers mostly short wavelength light, with the two photosystems connected by the plastoquinone pool. As the systems work, photosystem II sends electrons into the plastoquinone pool while photosystem I removes and utilizes them.

"But if a plant is exposed to shorter wavelength light, the electron balance can be lost. In that case, photosystem II would send electrons into the plastoquinone pool, but photosystem I wouldn't be able to draw them efficiently. Those electrons could linger in the plastoquinone pool and produce dangerous free radicals.

"'The two photosystems are like two photovoltaic cells connected in series," Puthiyaveetil said. "They should convert light energy at equal rates for optimal electron transport. If the electron transport is not balanced, you get free radicals that can damage the plant's photosynthetic machinery and hurt or kill the plant."

"Purdue scientists determined that CSK's iron-sulfur cluster acts as a sort of magnet for those extra electrons. When the plastoquinone pool becomes reduced, meaning it has excess electrons, those electrons leak into CSK and turn off its kinase activity.

"When kinase activity is interrupted, CSK stops transferring phosphate groups to the chloroplast gene expression machinery, turning on photosystem I genes and increasing its amount and therefore activity in short wavelength light. In essence, when CSK's kinase activity is on, it serves as a brake pedal for photosystem I gene expression.

"The CSK is redox-reactive, meaning it's using the iron and sulfur to sense the electron flow, and that's keeping the two photosystems working at the same rate in photosynthesis.

"The findings illuminate an elegant regulatory mechanism in the photosynthetic processes of plants. It's possible, Puthiyaveetil said, that one day this regulatory circuit could be modified to increase photosynthetic efficiency in crop plants by improving light capture in shaded conditions." (my bold)

Comment: Photosynthesis is a vital source of the level of oxygen now present in this atmosphere. Without it evolution could not have passed beyond the very small animal stage.
Note my bold: without this precise regulatory system photosynthesis would not work. It is so complex is cannot be built by step by step testing of each advance, that is, it is irreducibly complex, a logical concept introduced by Dr. Behe, one of the leading scientists in the ID group, of whom there are many with important papers in publication. Such design requires a designing mind behind it to create it all at once. Any Darwin approach fails to explain it. How long would it take to develop it by chance?

Biological complexity: how photosynthesis controls electrons

by David Turell @, Thursday, February 06, 2020, 00:14 (1513 days ago) @ David Turell

More new research:

https://www.sciencedaily.com/releases/2020/02/200205132347.htm

"Scientists recently solved a critical part of this age-old mystery, homing in on the initial, ultrafast events through which photosynthetic proteins capture light and use it to initiate a series of electron transfer reactions.

"'In order to understand how biology fuels all of its engrained activities, you must understand electron transfer," said Argonne biophysicist Philip Laible. "The movement of electrons is crucial: it's how work is accomplished inside a cell."

"In photosynthetic organisms, these processes begin with the absorption of a photon of light by pigments localized in proteins.

"Each photon propels an electron across a membrane located inside specialized compartments within the cell.

"'The separation of charge across a membrane -- and stabilization of it -- is critical as it generates energy that fuels cell growth," said Argonne biochemist Deborah Hanson.

***

"The scientists' recent article, "Switching sides -- Reengineered primary charge separation in the bacterial photosynthetic reaction center," published in the Proceedings of the National Academy of Sciences, shows how they discovered an engineered version of this protein complex that switched the utilization of the pathways, enabling the one that was inactive while disabling the other.

"'It is remarkable that we have managed to switch the direction of initial electron transfer," said Christine Kirmaier, Washington University chemist and project leader. "In nature, the electron chose one path 100 percent of the time. But through our efforts, we have been able to make the electron switch to an alternate path 90 percent of the time. These discoveries pose exciting questions for future research.'"

Comment: The electron transfer is critical and very complex. Design required.

Biological complexity: how photosynthesis controls energy

by David Turell @, Friday, April 10, 2020, 23:26 (1449 days ago) @ David Turell

Still sorting it out. Energy must be controlled in the process:

https://phys.org/news/2020-04-team-mechanism-toggle-photosynthesis.html

"'There's a lot of potential danger with photosynthesis," said Helmut Kirchhoff, professor in WSU's Institute of Biological Chemistry. "If plants take in light energy that isn't used properly for their metabolism, it can poison the plant and kill cells. The switch of light-harvesting proteins is essential to protect the system when there's too much light available."

"Until now, nobody knew for sure how plants avoided that toxicity on sunny days. It's an important scientific breakthrough.

***

"In the paper, the researchers developed a method for studying how lipids, which are molecules in cell membranes that perform a variety of functions, interact with proteins in chloroplasts, the part of green plant cells that photosynthesize light.

"They found that one specific type of lipid, called a nonbilayer lipid, seems to control the switch that the light harvesting protein makes when the plant has enough light and needs to dissipate some of the energy being received.

"'We were suspicious that this nonbilayer lipid had a role in controlling the structure and function of membrane proteins," Kirchhoff said. "We knew it had to have a function to be there because it's the most abundant lipid in photosynthetic membranes. We just didn't know exactly what that role would be.'"

Comment: a necessary control mechanism, which cannot be developed by chance. The system must be designed and set up all at once.

Biological complexity: photosynthesis makes O2 from water

by David Turell @, Thursday, June 04, 2020, 21:35 (1394 days ago) @ David Turell

Still not fully understood:

https://www.sciencedaily.com/releases/2020/06/200604111643.htm

"Life depends on the oxygen that plants and algae split from water; how they do it is still a mystery,

***

"'With this technique, we get the overall picture of how the entire protein structure dynamically changes and we see the chemical intricacies occurring at the reaction site," said co-lead author Junko Yano, a chemist senior scientist in Berkeley

***

"Traditional crystallography methods often require the sample proteins to be frozen; consequently, they can only generate snapshots of static proteins. This limitation makes it difficult for scientists to get a handle on how proteins actually behave in living organisms, because the molecules morph between different physical states during chemical reactions.

***

"'The water-splitting reaction in photosynthesis is a cyclical process that needs four photons and cycles between four stable 'states,'" said Yano. "Previously, we could only take pictures of these four states. But by taking multiple snapshots in time, we now can visualize how one state goes to the other."

"'We saw, really nicely, how the structure changes step-by-step as it transforms from one state to the next state," said Jan F. Kern, MBIB chemist and co-author. "It is pretty exciting, because we can see the 'cause and effect' and the role that each moving atom plays in this transition.'"

Comment: Imagine the complexity of a giant enzyme molecule changing its shape as if it can think and conform to the next needed posture! Just following instructions. But remember we wouldn't be here unless this highly complex process didn't appear. Not by magic.

Biological complexity:transfer of electrons photosynthesis

by David Turell @, Tuesday, June 16, 2020, 22:31 (1382 days ago) @ David Turell

Another complexity of photosynthesis:

https://phys.org/news/2020-06-small-protein-electrons-photosystems-involved.html

"By utilizing solar energy to turn carbon dioxide into sugars, while also generating molecular oxygen from water, photosynthesis provides the basis for both plant and animal life. These two processes are carried out by distinct, but functionally connected complexes called photosystems I and II (PSI and PSII). In cyanobacteria, algae and plants, these photosystems—all of which employ chlorophyll pigments to capture light energy—are embedded in specialized lipid membranes called thylakoids. Moreover, the thylakoids that contain PS I and PSII differ in their organization, which effectively enables the two systems to convert light of different wavelengths into chemical energy.

"The functional link between the two reaction complexes is provided by soluble proteins that serve as electron transporters. Biologists led by Professor Dario Leister (Chair of Plant Molecular Biology) at LMU's Biocenter, in collaboration with international colleagues, have now taken a closer look at the role of one of these proteins—plastocyanin, a small copper-containing protein. Their findings, which appear in the journal PNAS, reveal that the efficacy of electron transport is critically dependent on the architecture of the membrane systems. "Function shapes" The functional link between the two reaction complexes is provided by soluble proteins that serve as electron transporters. Biologists led by Professor Dario Leister (Chair of Plant Molecular Biology) at LMU's Biocenter, in collaboration with international colleagues, have now taken a closer look at the role of one of these proteins—plastocyanin, a small copper-containing protein. Their findings, which appear in the journal PNAS, reveal that the efficacy of electron transport is critically dependent on the architecture of the membrane systems. "Function shapes architecture," says Leister.

"So the courier's level of performance depends on the architecture of the thylakoids. Both the tower blocks and the walkways between them are congested. Not only the membranous structures, but the aqueous phase that surrounds them, is densely packed with proteins and small molecules. "And that reduces the mobility of the couriers significantly," Leister notes.

"Earlier work done by his research group had shown that the architecture of the thylakoids has a crucial impact on the efficiency of photosynthesis under fluctuating light intensities. "When light levels are low, thylakoid membranes have to be stacked in order to maintain the efficiency of photosynthesis, and only land plants can perform this trick," he says. "Furthermore, to make things easier for the couriers, the width of the individual tower blocks must be restricted. These architectural specifications are observed in essentially all plants.'"

Comment: Unpeeling the layers of the onion shows how complexly the process of photosynthesis is designed. Not by chance.

Biological complexity: photosynthesis controls overload

by David Turell @, Thursday, June 25, 2020, 19:37 (1373 days ago) @ David Turell

Too much energy can damage cells:

https://phys.org/news/2020-06-green-team-photosynthesis.html

"When sunlight shining on a leaf changes rapidly, plants must protect themselves from the ensuing sudden surges of solar energy. To cope with these changes, photosynthetic organisms—from plants to bacteria—have developed numerous tactics.

***

"'Our model shows that by absorbing only very specific colors of light, photosynthetic organisms may automatically protect themselves against sudden changes—or 'noise'—in solar energy, resulting in remarkably efficient power conversion," said Gabor, an associate professor of physics and astronomy, who led the study appearing today in the journal Science. "Green plants appear green and purple bacteria appear purple because only specific regions of the spectrum from which they absorb are suited for protection against rapidly changing solar energy."

***

"'Excitingly, we were then able to show that the model worked in other photosynthetic organisms besides green plants, and that the model identified a general and fundamental property of photosynthetic light harvesting," he said. "Our study shows how, by choosing where you absorb solar energy in relation to the incident solar spectrum, you can minimize the noise on the output—information that can be used to enhance the performance of solar cells."

***

"Gabor explained that plants and other photosynthetic organisms have a wide variety of tactics to prevent damage due to overexposure to the sun, ranging from molecular mechanisms of energy release to physical movement of the leaf to track the sun. Plants have even developed effective protection against UV light, just as in sunscreen.

"'In the complex process of photosynthesis, it is clear that protecting the organism from overexposure is the driving factor in successful energy production, and this is the inspiration we used to develop our model," he said. "Our model incorporates relatively simple physics, yet it is consistent with a vast set of observations in biology. This is remarkably rare. If our model holds up to continued experiments, we may find even more agreement between theory and observations, giving rich insight into the inner workings of nature.'"

Comment: Very clever design. Not by chance

Biological complexity: photosynthesis energy controls

by David Turell @, Tuesday, June 30, 2020, 20:02 (1368 days ago) @ David Turell

Another study increases the knowledge of the overwhelming complexity involved:

https://phys.org/news/2020-06-revisiting-energy-photosynthetic-cells.html

"Photosynthesis utilizes light as an energy source for plant chloroplasts to synthesize carbohydrates from water and CO2 molecules. ATPplays an important role in this process, as it promotes plant growth and supply energy for various cellular activities. It had been a general belief that mature plant chloroplasts can import ATP from cytosol since 1969, but it was shown to be untrue by Dr. Lim and his team in 2018, through introducing a novel ATP sensor in the subcellular compartments of a C3 model plant, Arabidopsis thaliana. This finding has revised our understanding on chloroplast bioenergetics during daytime and nighttime and how mature chloroplasts optimize energy efficiency.

"Another unresolved problem in photo-energy is that the source of NADH as a fuel for mitochondria (the major ATP synthesizing organelle in cells) to produce ATP during photosynthesis is unclear. Some researchers suggested that excess reducing equivalents carried by surplus NADPH (Reduced Nicotinamide adenine dinucleotide phosphate) can be exported to the cytosol in the form of malate, which can then enter mitochondria through the malate-OAA shuttle, and converted into OAA and NADH in the mitochondrial matrix.

"On the other hand, some researchers proposed that during photorespiration glycine decarboxylase generates a large amount of NADH in mitochondria for ATP production and surplus reducing equivalents carried by NADH is exported by the mitochondrial malate-OAA shuttle to the cytosol.

***

"...we found that photorespiration supplies a large amount of NADH to mitochondria during photosynthesis, which exceeds the NADH-dissipating capacity of the mitochondria. Consequently, the surplus NADH must be exported from the mitochondria to the cytosol through the mitochondrial malate-OAA shuttle," said Ms Sheyli Lim, a Ph.D. student and the first author of a manuscript published in Nature Communications. "Solving this question allows us to understand more about the energy flow between chloroplasts and mitochondria during photosynthesis, which could help us to booth the efficiency of photosynthesis in the future."

Comment: It is difficult to follow this verbiage without looking at the diagram which I cannot reproduce here. Only a designer could produce this complex system.

Biological complexity: photosynthesis molecular controls

by David Turell @, Monday, July 06, 2020, 18:33 (1362 days ago) @ David Turell

A new description of an active molecule in the process:

https://phys.org/news/2020-07-quench-role-cyanobacterial-photosystem-protein.html

"...the details of photosynthesis—the key process that supports all forms of advanced lives on earth—have been studied for many decades. And all studies, despite their differences, reveal one thing: that it is an astonishingly precise process, consisting of numerous small reactions run by many proteins and their combinations. However, the molecular-level details of many of these steps are still not understood very well.

***

"In the cyanobacterial membrane, IsiA appears in low iron level conditions, and combines with a trimeric core of PSI to perform the light-harvesting step. Much akin to a runner in a relay race, IsiA "donates" or transfers the captured energy to the trimeric core of PSI that performs the subsequent step in the photosynthesis process. It has been believed that in addition to functioning an "energy harvester," IsiA also works as a "quencher" that gets rid of excess energy as heat when light intensity is too high for the cells to grow.

***

"The result of this study ruled out the possibility of any energy-quenching taking place in the IsiA-PSI core supercomplex, confirming IsiA's role as an energy harvester and donor.
Highlighting the significance of this exciting study, Dr. Akita states, "These structural and spectroscopic findings provide important insights into the molecular arrangement and energy-transfer mechanisms in the photosystems of cyanobacteria. A deeper understanding of how photosynthetic energy transfer takes place will help to develop new energy devices based on photosynthesis.'"

Comment: Be sure to see the diagram of the molecule. Obviously a designed process.

Biological complexity: photosynthesis & green plant color

by David Turell @, Friday, July 31, 2020, 21:00 (1337 days ago) @ David Turell

This range of the light spectrum is a oer energy form to protect the delicate process:

https://www.quantamagazine.org/why-are-plants-green-to-reduce-the-noise-in-photosynthes...

"Why green, and not blue or magenta or gray? The simple answer is that although plants absorb almost all the photons in the red and blue regions of the light spectrum, they absorb only about 90% of the green photons. If they absorbed more, they would look black to our eyes. Plants are green because the small amount of light they reflect is that color.

"But that seems unsatisfyingly wasteful because most of the energy that the sun radiates is in the green part of the spectrum. When pressed to explain further, biologists have sometimes suggested that the green light might be too powerful for plants to use without harm, but the reason why hasn’t been clear.

***

"Their findings point to an evolutionary principle governing light-harvesting organisms that might apply throughout the universe. They also offer a lesson that — at least sometimes — evolution cares less about making biological systems efficient than about keeping them stable.

***

"The first step of photosynthesis happens in a light-harvesting complex, a mesh of proteins in which pigments are embedded, forming an antenna. The pigments — chlorophylls, in green plants — absorb light and transfer the energy to a reaction center, where the production of chemical energy for the cell’s use is initiated. The efficiency of this quantum mechanical first stage of photosynthesis is nearly perfect — almost all the absorbed light is converted into electrons the system can use.

***

"For the cell, a steady input of electrical energy coupled to a steady output of chemical energy is best: Too few electrons reaching the reaction center can cause an energy failure, while “too much energy will cause free radicals and all sorts of overcharging effects” that damage tissues, Gabor said.

***

"The best light for the pigments to absorb, then, was in the steepest parts of the intensity curve for the solar spectrum — the red and blue parts of the spectrum.

"The model’s predictions matched the absorption peaks of chlorophyll a and b, which green plants use to harvest red and blue light. It appears that the photosynthesis machinery evolved not for maximum efficiency but rather for an optimally smooth and reliable output.

"Cogdell wasn’t fully convinced at first that this approach would hold up for other photosynthetic organisms, such as the purple bacteria and green sulfur bacteria that live underwater and are named for the colors their pigments reflect. Applying the model to the sunlight available where those bacteria live, the researchers predicted what the optimal absorption peaks should be. Once again, their predictions matched the activity of the cells’ pigments.

“'When I realized how fundamental this was, I found myself looking in the mirror and thinking: How could I be so dumb not to think about this before?” Cogdell said."

Comment: This system protects against damage. How did it develop stepwise? Not likely as damage would have stopped the plants from evolving. Had to be designed to make any sense.

Biological complexity: photosynthesis, new control found

by David Turell @, Tuesday, March 09, 2021, 22:30 (1116 days ago) @ David Turell

A new enzyme location is discerned:

https://www.sciencedaily.com/releases/2021/03/210309114304.htm

"Scientists have pinpointed the location of an essential enzyme in plant cells involved in photosynthesis, according to a study published today in eLife.

"The findings overturn conventional thinking about where the enzyme resides in plant cells and suggest a probable role in regulating energy processes as plants adapt from dark to light conditions.

"During photosynthesis, plants convert carbon into energy stores through 'electron transport', involving an enzyme called ferredoxin:NADP(H) oxidoreductase, or FNR.

Plants can switch rapidly between two types of electron transport -- linear electron flow (LEF) and cyclic electron flow (CEF) in response to environmental conditions. The transfer of FNR between membrane structures in the chloroplast, where photosynthesis takes place, has been linked to this switch.

"'Current dogma states that FNR carries out its function in the soluble compartment of the chloroplast, but evidence suggests that the activity of FNR increases when it is attached to an internal membrane," explains first author Manuela Kramer, a PhD student at the School of Biological and Chemical Sciences, Queen Mary University of London, UK. "We needed to find out precisely where FNR is located in the chloroplast, how it interacts with other proteins, and how this affects its activity in order to understand its role in switching between electron transport processes."

***

"To understand more about FNR's location, the team generated plants where the enzyme is specifically bound to different proteins called 'tether proteins'...They found that rescue with maize FNR types that strongly bound to the Tic62 tether protein resulted in much higher density of gold FNR labelling in specific, lamellar membrane regions of the thylakoids. This suggests that the distribution of FNR throughout the chloroplast in plant cells is dependent on binding to the tether proteins.

***

"After light acclimatisation, both the wild-type and mutant plants had similar, decreased CEF activity, suggesting that the impact of FNR is related to light-dependent changes in the interactions between the enzyme and tether proteins.

"'Our results show a link between the interaction of FNR with different proteins and the activity of an alternative photosynthetic electron transport pathway," concludes senior author Guy Hanke"

Comment: photosynthesis is a highly complex process which is vital for oxygen production. Design required.

Biological complexity: photosynthesis, new control found

by David Turell @, Wednesday, March 10, 2021, 18:03 (1115 days ago) @ David Turell

Quantum usage in green sulfur bacteria:

https://phys.org/news/2021-03-bacteria-exploit-quantum-mechanics.html

"'This is the first time we are seeing biology actively exploiting quantum effects."

"The scientists studied a type of microorganism called green sulfur bacteria. These bacteria need light to survive, but even small amounts of oxygen can damage their delicate photosynthetic equipment. So they must develop ways to minimize the damage when the bacterium does encounter oxygen.

"To study this process, researchers tracked the movement of energy through a photosynthetic protein under different conditions—with oxygen around, and without.

"They found that the bacterium uses a quantum mechanical effect called vibronic mixing to move energy between two different pathways, depending on whether or not there's oxygen around. Vibronic mixing involves vibrational and electronic characteristics in molecules coupling to one another. In essence, the vibrations mix so completely with the electronic states that their identities become inseparable. This bacterium uses this phenomenon to guide energy where it needs it to go.

"If there's no oxygen around and the bacterium is safe, the bacterium uses vibronic mixing by matching the energy difference between two electronic states in an assembly of molecules and proteins called the FMO complex, with the energy of the vibration of a bacteriochlorophyll molecule. This encourages the energy to flow through the 'normal' pathway toward the photosynthetic reaction center, which is packed full of chlorophyll.

"But if there is oxygen around, the organism has evolved to steer the energy through a less direct path where it can be quenched. (Quenching energy is similar to putting a palm on a vibrating guitar string to dissipate energy.) This way, the bacterium loses some energy but saves the entire system.

"To achieve this effect, a pair of cysteine residues in the photosynthetic complex acts as a trigger: They each react with the oxygen in the environment by losing a proton, which disrupts the vibronic mixing. This means that energy now preferentially moves through the alternative pathway, where it can be safely quenched. This principle is a bit like blocking two lanes on a superhighway and diverting some traffic to local roads where there are many more exits.

"'What's interesting about this result is that we are seeing the protein turn the vibronic coupling on and off in response to environmental changes in the cell," said Jake Higgins, a graduate student in the Department of Chemistry and the lead author of the paper. "The protein uses the quantum effect to protect the organism from oxidative damage." (my bold)

***

"This phenomenon is likely not limited to green sulfur bacteria, the scientists said. As Higgins explained, "The simplicity of the mechanism suggests that it might be found in other photosynthetic organisms across the evolutionary landscape. If more organisms are able to dynamically modulate quantum mechanical couplings in their molecules to produce larger changes in physiology, there could be a whole new set of effects selected for by nature that we don't yet know about.'"

Comment: Note my bold. There is no way this could develop stepwise by chance. Why? The produced oxygen is too dangerous, if not controlled from the beginning. Try to deny the designer in this case. This is the best evidence for God, as designer, I've ever found.

Biological complexity: photosynthesis, use of red spectrum

by David Turell @, Sunday, March 21, 2021, 20:59 (1104 days ago) @ David Turell

Involves more complexity:

https://www.sciencedaily.com/releases/2021/03/210318111430.htm

"Photosynthesis represents the only biological process, which converts the energy of sunlight into chemically stored energy. On molecular level, the photosynthetic key enzymes called photosystems are responsible for this conversion process. Photosystem I (PSI), one of the two photosystems, is a large membrane protein complex that can be present in different forms -- as monomers, dimers, trimers or even tetramers. New isolation technique helps revealing the structure of monomeric PSI.

***

"The atomic structure of monomeric PSI provides novel insights into the energy transfer inside the protein complex as well as on the localization of so-called red chlorophylls -- specially arranged chlorophylls, closely interacting with each other and thus enabling the absorption of low-energy far red light, which normally cannot be used for photosynthesis. Interestingly, the structure revealed that the red chlorophylls seem to interact with lipids of the surrounding membrane. This structural arrangement might indicate that additional thermal energy is used to make far red light accessible for photosynthesis. Long-run cooperation bears further fruits."

Comment: Without photo synthesis there would be no oxygen-using life. It didn't come to being by accident considering how highly complex are all the parts, still not fully understood.

Biological complexity:photosynthesis new research

by David Turell @, Saturday, March 25, 2023, 18:32 (370 days ago) @ David Turell

New details of this very complex system:

https://phys.org/news/2023-03-high-precision-quantum-chemistry-super-efficient-energy.html

"Photosynthesis drives all life on Earth. Complex processes are required for the sunlight-powered conversion of carbon dioxide and water to energy-rich sugar and oxygen. These processes are driven by two protein complexes, photosystems I and II. In photosystem I, sunlight is used with an efficiency of almost 100%. Here a complex network of 288 chlorophylls plays the decisive role.

"A team led by LMU chemist Regina de Vivie-Riedle has now characterized these chlorophylls with the help of high-precision quantum chemical calculations—an important milestone toward a comprehensive understanding of energy transfer in this system. This discovery may help exploit its efficiency in artificial systems in the future.

***

"The chlorophylls in photosystem I capture sunlight in an antenna complex and transfer the energy to a reaction center. There, the solar energy is used to trigger a redox process—that is to say, a chemical process whereby electrons are transferred. The quantum yield of photosystem I is almost 100%, meaning that almost every absorbed photon leads to a redox event in the reaction center.

***

"The results of the study, which is featured on the cover of the journal Chemical Science, reveal so-called "red chlorophylls" that absorb light at slightly lower energies than their neighbors due to ambient electrostatic effects. As a result, their absorption spectrum is red-shifted. Analogously, the researchers also identified energy barriers between the antenna complex and the reaction center, among other places. "This seems surprising at first glance because there is no obvious gradient along which energy is transferred from the antenna complex to the reaction center," explains lead author Sebastian Reiter.

"Under physiological conditions, however, the entire photosystem I is subject to thermal fluctuations that overcome these energy barriers, as the relative energies of the chlorophylls change with respect to each other. In this way, new pathways into the reaction center can constantly open up, while others close. This, according to the core thesis of the authors, could be the key to the high efficiency of photosystem I."

Comment: without the great oxygenation event most forms of life would not exist. A natural event or a system guided by God? It looks designed to me.

Biological complexity: removing Dad's mitochondria

by David Turell @, Thursday, March 23, 2017, 19:22 (2563 days ago) @ David Turell

Male mitochondria must be destroyed in sperm to maintain the inheritance of maternal mitochondria as the rule. This is the first example found:

http://www.the-scientist.com/?articles.view/articleNo/48891/title/Enzyme-Required-for-M...

"Most animals inherit mitochondria from their mothers. Now, at team of scientists has shown that, in Drosophila, the paternal contribution of mitochondrial DNA (mtDNA) is degraded in the sperm in a process that depends on a subunit of the fruit fly mitochondrial DNA polymerase called Tamas.

“'What’s striking about this study is that this gene, tamas, encodes a subunit of the mitochondrial DNA polymerase, which is the enzyme responsible for replicating the mtDNA,” said Damian Dowling of Monash University in Melbourne, Australia, who did not participate in the work. “It’s a completely new function for this gene that was not known prior to this study."

"The role for Tamas is “surprising,” said Eli Arama of the Weizmann Institute of Science in Rehovot, Israel, who was not involved in the study. “Instead of replicating the DNA, basically it is required to degrade it,” he explained.

***

"The researchers hypothesized that the capability of the Tamas enzyme to degrade nucleotides would be responsible for the destruction of paternal mtDNA, but they showed that a Tamas protein without exonuclease activity still resulted in sperm without mtDNA. They also found that the replication function of Tamas did not appear to play a role in eliminating paternal mtDNA.

“'It seems that the catalytic activity of this subunit of mitochondrial DNA polymerase is not required for the degradation of the mitochondrial DNA, which leaves us with a lot of questions about the mechanism,” said Arama. “It’s not the canonical polymerase or exonuclease [functions], but probably another function that this protein has, which remains to be discovered.” Arama noted that Tamas may act in a complex with other proteins to facilitate the elimination of paternal mtDNA.

“'More evidence is required to make sure that Tamas is directly involved in the degradation,” Hansong Ma of the Gurdon Institute at the University of Cambridge in the U.K., who was not involved in the study, wrote in an email to The Scientist.

"According to coauthor Patrick O’Farrell of UCSF, another open question is how general the role for a mitochondrial DNA polymerase in elimination of paternal mtDNA is. “Maternal inheritance is really widespread,” he said. “There are a few exceptions, but for the most part it’s found throughout the entirety of phylogeny, and we don’t know whether exactly the same mechanisms are used.”

“'Typically when we find these sorts of outcomes in fruit flies, they’re broadly applicable across animals,” Dowling told The Scientist. “I wouldn’t be surprised at all if this extends to our own species.”

"Ma also noted that mtDNA destruction may take place outside of sperm. “This paper provides good evidence that Tamas is required for the elimination of mtDNA during spermatogenesis,” she wrote, “but we don’t know whether this role of Tamas is specific to testis, where mtDNA is purposefully eliminated to ensure maternal inheritance of mtDNA, or [if the enzyme performs this function] in other tissues.'”

Comment: Such a removal mechanism must be present and it will be fully discovered as research continues. We still don't know why mitochondria must be maternal. That is one of he mysteries.

Biological complexity: amazing cell pore complexity

by David Turell @, Friday, December 02, 2016, 00:40 (2674 days ago) @ David Turell

Here are two articles about the highly complex nuclear membrane pores. Since the nucleus carries the codes for cellular function the entrance and exit through the membrane pores is highly protected for accuracy. The first article is a summary of the number of proteins involved in just one cell nucleus:

http://www.the-scientist.com/?articles.view/articleNo/47478/title/Doors-and-Pores/&...

"The awesome architecture of the gateways to the nucleus:

"Nuclear pore complexes raise jigsawing to a far more rarified level. In their feature, Daniel Lin and André Hoelz describe these “massive molecular machines” as put together from “more than 1,000 protein subunits with a total molecular mass of approximately 120 million daltons—the equivalent of more than 6.5 million water molecules.” The subunits self-assemble to form more than 30 types of nucleoporin proteins, 17 of which constitute the beautifully symmetric three-ringed core of the nuclear pore complex. Through the pore’s central channel smaller molecules enter and exit by diffusion while proteins or ribosomal units in their native states hop a ride on cargo ships known as karyopherins."

The second article shows the diagrams and there is a link to a very long descriptive article for further review:

http://www.the-scientist.com/?articles.view/articleNo/47560/title/Infographic--The-Nucl...

Descriptions of diagrams: Be sure to look at them

"Macromolecules—including proteins, tRNAs, and even fully assembled pre-ribosomal subunits—are transported through the NPC in their native states with the help of proteins called karyopherins that bind to both target molecules and to FG repeats. Upon entering the nucleus, incoming karyopherins release their cargo when they are bound by RanGTP, the GTP-bound conformation of a small GTPase protein called Ran. For cargoes leaving the nucleus, RanGTP is often incorporated into karyopherin transport complexes inside the nucleus, but encounters the Ran-activating protein RanGAP after exiting. RanGAP triggers Ran to hydrolyze GTP into GDP, causing a conformational change and the release of the cargo into the cytoplasm.

"Messenger RNAs (mRNAs) transcribed in the nucleus are loaded with diverse proteins to form messenger ribonucleoproteins (mRNPs) that are exported through the NPC. These proteins include Nxf1 and Nxt1, which bind to FG repeats in the central channel. Nucleoporins on the cytoplasmic side of the pore recruit and activate an ATPase to remove Nxf1/Nxt1, freeing the mRNA to be translated by the ribosome."

Comment: Any reasonable person will see that these pores are extraordinarily complex in structure and function. They obviously require exquisite planning that only a great mind can accomplish. And the complete architecture is not fully elucidated at this time. How much complexity is required to make this point obvious? Not by chance!

This is the link to the very long article:

http://www.the-scientist.com/?articles.view/articleNo/47529/title/Nuclear-Pores-Come-in...

Biological complexity:maintaining membrane integrity

by David Turell @, Tuesday, December 06, 2016, 19:25 (2670 days ago) @ David Turell

Cells in the body are constantly turning over and replaced. This is a study as to how membranes are maintained:

https://www.sciencedaily.com/releases/2016/12/161206110102.htm

"Scientists from the National Centre for Biological Sciences (NCBS), Bangalore, and the Babraham Institute in UK have recently found a critical player essential for proper membrane recycling. Using the light-sensitive membranes of fruit-fly eyes as a model system, the researchers have discovered that the enzyme Phospholipase D or PLD is necessary for membrane recycling to sustain normal sight.

"The resetting of rhodopsin molecules begins with a process called endocytosis, where the cell pinches off parts of its surface membranes into structures called endosomes. The rhodopsin in these endosomes is eventually recycled back onto the cell surface for further events of light detection. Since a photoreceptor's sensitivity depends on how many rhodopsin molecules it has on its surface, membrane turnover in these cells is critical in preserving normal eyesight.

***

"Using fruit fly photoreceptor cells as a model system, the team has found that when these cells are exposed to light, PLD is switched on, and that its activity is essential in coupling endocytosis with recycling of rhodopsin back to the cell surface.

***

"'The enzyme PLD converts a molecule called phosphatidylcholine into phosphatidic acid or PA, which is implicated in membrane turnover. However, PA is also produced by other enzymes, and our study conclusively shows that the PA regulating membrane turnover was produced by PLD," says Rajan Thakur, a researcher from Padijat's group and the primary author of a publication in the journal eLife that reports these results.

"Despite identifying a key player in the membrane turnover process, Padinjat's team believe that many more gaps need filling in understanding the phenomenon. For example, the work shows that the PLD activity in photoreceptors is light-activated, but how this happens is still unresolved.

"'The light receptor, rhodopsin is on the membrane surface, and can detect light when the surface of the cell is illuminated. But PLD, which is also light-activated, is somewhere inside the cell. So how is the information about perceived light conveyed to PLD for it to get activated?" asks Thakur. "We also need to fill in blanks about how PA actually affects membrane recycling and the turnover process. Our finding has opened up more questions to answer in the membrane turnover process," he adds.

"But the results from this study are not limited only to membrane turnover in the light-sensitive membranes of the eyes. Membrane turnover is a critical mechanism that maintains cell surface area. In cells that have expanded cell surfaces such as those lining the airways of the lungs or the nutrition-absorbing cells of the gut, maintaining cell surface area is essential for their normal function. Even processes such as cell migration have extensive endocytosis and membrane recycling events that must be tightly regulated. (my bold)

"'Therefore, regardless of what the cell type is, there need to be mechanisms to couple endocytosis with recycling of membrane," says Padinjat. "And that is the importance of our work -- we define a mechanism by which cell membrane size is regulated," he adds."

Comment: Two points: first, the need for tight regulation is obvious as noted in the bold area. Secondly, once again a giant enzyme molecule is used. How did the evolutionary process find it? Not by chance!

Biological complexity:cells are factories with roadways

by David Turell @, Wednesday, December 07, 2016, 01:32 (2669 days ago) @ David Turell

Cells are high speed protein producers with product carried along roadway within the cell and with guidance:

http://phys.org/news/2016-12-scientists-motors-maneuver-cells-roadways.html

"Cell motors travel an extensive network of roadways that are actually part of the physical structure, or cytoskeleton, which helps give our cells strength and shape, said Dr. Graydon B. Gonsalvez, cell biologist in the Department of Cellular Biology and Anatomy at the Medical College of Georgia at Augusta University.

"Microtubules and actin are the major roadways motors travel. The motors kinesin and dynein typically travel on microtubules; myosin is the motor running the actin roadway. To help make the math work with so few motors and so much cargo to move, there are adaptors that essentially help connect motor to cargo. The main adaptor for the kinesin motor is something called kinesin light chain; kinesin heavy chain is the motor part.

***

"Gonsalvez is corresponding author of a study featured on the cover of the Journal of Cell Science that provides evidence of an adaptor running these roads that previously seemed to stay on actin.

"'It's switching parties, if you will," Gonsalvez said. "They are thought to not cross react. We found these systems have crosstalk."

"His research team used mass spectroscopy to analyze the proteins associated with the motor kinesin in the fruit fly. They looked specifically at oskar mRNA, a messenger RNA that makes proteins, which, in this case, help direct the orientation of the head and tail of a developing fruit fly embryo.

"They found among the protein crowd what appeared to be an outlier, a form of tropomyosin that they would have suspected would only show up as an adaptor for the actin roadway. "Here is a different kind of tropomyosin that is binding directly to a kinesin motor and functioning as the adaptor between this kinesin motor and the cargo," Gonsalvez said.

***

"And, while motors do move proteins along with other cell inhabitants, it's more efficient to move the mRNA so the mRNA makes the protein right where it's needed, Gonsalvez said. The movement of motors seems to increase when they have a cargo, an apparent energy-conserving approach.

"Our 30,000 genes can make about 100,000 different proteins and are constantly at work. One of the many things that means is that a single gene can often make multiple different proteins. In a single cell at a single moment, there might be several thousand different proteins; and for each of those different proteins, there can be a hundred or more copies, Gonsalvez said.

"In a reinforcement of the concept that location is everything, misdirected mRNA and proteins can cause damage both because they aren't doing what's intended and because they likely are doing additional damage wherever they end up, Gonsalvez said.

"Gonsalvez likens the compartmentalization that occurs inside our cells to a house: Everything may be under the same roof, but very different things need to happen in the kitchen versus the bathroom."

Comment: Highly complex protein manufacturing factories with rope like roadways carrying product to the right spots, rarely an error. High complexity, not by chance!

Biological complexity: controlling cellular potassium

by David Turell @, Friday, December 23, 2016, 21:33 (2653 days ago) @ David Turell

Another complex mechanism controlling the cellular potassium levels has yielded to research:

http://phys.org/news/2016-12-molecular-reveals-cells-spew-potassium.html

"New research from Roderick MacKinnon's Laboratory of Molecular Neurobiology and Biophysics at The Rockefeller University has determined, for the first time, the complete structure of an ion channel that plays an important role in cellular electrical signaling by sending potassium ions out of the cell at an extremely rapid rate.

"By revealing new insights into how the molecule works, this research leads to a deeper understanding of the link between the membrane and processes inside the cell, including calcium regulation of electrical signals, which is central to muscle contraction and neural activity.

***

"Potassium channels both regulate the occurrence of electrical impulses and terminate the impulses once they are generated. One such potassium channel, known as the BK or "big potassium" channel, conducts ions up to a level 20 times that of other potassium channels. To do so, BK responds to two separate triggers—electrical activity on the cell membrane and levels of calcium—that it ties together

***

"The pore within BK is much wider than those of other potassium channels. In fact, it forms a wide funnel that opens up to the interior of the cell," Tao says. "And the funnel's surface bears a negative charge, which attracts positively charged potassium ions from within the cell toward the pore."

"In order for potassium to flow through BK, the channel's pore must open, and it does so in response to two triggers: calcium, another ion important to cellular signaling; and a change in voltage across the cellular membrane, which occurs when a cell generates an electrical impulse."

After binding to calcium ions, the channel compresses itself, changing shape in such a way that its pieces are pulled outward and the pore widens.

While the researchers could not directly observe how the channel responds to a change in voltage, the structure did provide clues to explain this opening mechanism. Sensitivity to both calcium and voltage most likely allows the channel to fine-tune its responses, the researchers say.

Comment: Rapid movement of potassium is essential to the speed impulses travel along nerves and the speed of response of contracting muscles. Remember this is just pore shape and control, and dos not address the other chemical mechanisms that determine when to flush the potassium. this is all highly complex, and like all other integrated functions must have developed by saltation. Bit-by-bit or trial and error just doesn't lend itself to developing this sort of complexity. Look at the moving diagram of the pore, and marvel at the size of the molecules involved.

Biological complexity: complexity of the human body

by David Turell @, Wednesday, December 28, 2016, 15:13 (2648 days ago) @ David Turell

The overwhelming complexity of the human body defies a chance production. It requires planned design:

http://townhall.com/columnists/robertknight/2016/12/28/the-complexity-of-creation-n2263...

"As walking miracles, we comprise trillions of cells, each of which is a marvel of engineering with its own millions of moving parts.

“'Think of the cell as a miniature society,” Reference.com offers in this accessible description. “Within its walls are factories, power plants, a leader, a packaging plant, a central gathering place and recycling stations. All work together to sustain the community.”

"Now, you can argue that this all happened as a result of random, unguided accidents, or you can make the argument for design, which rests largely on irreducible complexity. That term, championed by Lehigh University biologist Michael Behe, means something that must be fully assembled and cannot logically come together gradually.

"He uses a simple mousetrap as an example. Without all its parts – spring, platform, snap bar – it is useless. Mousetraps are an invention, the result of a guided process. How much more so are the fathomlessly complex cells whose parts must all work precisely together in order to allow our fathomlessly complex bodies and brains to function?

"In “More than Meets the Eye,” Richard A. Swenson, M.D. has assembled a mind-boggling array of facts about the human body and brain that should leave any reader in a state of awe, regardless of theology.

"The body has 10 to 100 trillion cells, with each cell having a trillion atoms. They are all coming and going at astronomical speed. “Every couple of days, we replace all the cells that line the intestine – faster if we eat Mexican food,” Swenson quips.

"That person sitting next to you? Her eyes have retinas that contain 120 million rods and 7 million cones. “The rods accomplish dim vision, night vision, and peripheral vision. The cones are for color vision and fine detail.” The human eye can recognize literally millions of shades of colors.

"Now, here’s the really astounding part: “To simulate 10 milliseconds of the complete processing of even a single nerve cell from the retina would require the solution of about 500 simultaneous nonlinear differential equations 100 times and would take at least several minutes of processing time on a Cray supercomputer. Keeping in mind that there are 10 million or more such cells interacting with each other in complex ways, it would take a minimum of 100 years of Cray time to simulate what takes place in your eye many times every second.”

"Sort of gives the phrase “in the blink of an eye” new meaning, doesn’t it?"

Comment: The real meaning is that only a superior mental capacity could create this degree of complexity. Logically it requires God, but absolute proof is lacking.

Biological complexity: immune cells reach infections

by David Turell @, Wednesday, January 18, 2017, 17:46 (2627 days ago) @ David Turell

They travel in the blood stream, are attracted by inflammatory molecules and must leave the vessels to reach the tissue that is inflamed to be effective in the battle. How does the cell leave the vessel without making a leak of blood? It squeezes out:

https://cosmosmagazine.com/biology/watch-immune-cells-squeeze-through-blood-vessel-wall...

"A team from Israel and the UK watched different types of immune cell shimmy through a blood vessel wall. And instead of the blood vessel cells contracting to let them through, it appears immune cells squeeze their way through, breaking a few cell structures which are rapidly replaced.

"Thousands of immune cells, such as white blood cells (also called leukocytes), are nudging their way through your blood vessels each second. When a part of your body becomes inflamed, for instance, molecules signal for help to leukocytes passing by in the bloodstream.

"When they come across such a signal, leukocytes stop and slip between cells that line your capillaries called epithelial cells. Epithelial cells are tightly wedged together to form a physical line of defence. But the damage leukocytes leave behind is insignificant. How?

"Sagi Barzilai and Sandeep Kumar Yadav, both from the Weizmann Institute of Science in Israel, and colleagues decided to see what was going on.

" They stopped the contracting machinery of the epithelial cells but found leukocytes were still able to penetrate. "That was our big surprise," says Ronen Alon, also from the Weizmann Institute.

"So using other cellular tweaks and microscopy, they eventually saw the leukocytes used their nucleus (which harbours important genetic information and, in leukocytes, is particularly pliable) prodded by their own cell machinery to squeeze between cells.
The leukocyte extended a thin protrusion between endothelial cells – think of it as the salesperson's foot. As more of the cell squeezed through, eventually a lobe of the nucleus was squashed through too (our salesperson's leg).

"As the nucleus lobe deformed the surrounding cells, endothelial cell scaffolding called actin snapped and stress fibres stretched, signalling the cells to open the gap. The leukocyte's own internal machinery pushed the nucleus forwards until it – and the rest of the cell – popped through.

"The gaps were only four or five microns wide – the width of the nucleus – and any bits of broken actin was quickly and easily replaced.:

Comment: Responses to infectious attack must be immediate. The blood white cells act intelligently. But they are acting under intelligent instructions, not that they are innately intelligent on their own. I view bacteria the same way, because they are the progenitors in evolution of these cells in our bodies.

Biological complexity: immune cells reach infections

by dhw, Thursday, January 19, 2017, 12:56 (2626 days ago) @ David Turell

David's comment: Responses to infectious attack must be immediate. The blood white cells act intelligently. But they are acting under intelligent instructions, not that they are innately intelligent on their own. I view bacteria the same way, because they are the progenitors in evolution of these cells in our bodies.

Please explain “under intelligent instructions”. Do you mean your God preprogrammed this intelligent behaviour 3.8 billion years ago, to be passed down by the very first cells, or your God intervenes whenever the cells have a problem?

Biological complexity: immune cells reach infections

by David Turell @, Thursday, January 19, 2017, 14:41 (2626 days ago) @ dhw

David's comment: Responses to infectious attack must be immediate. The blood white cells act intelligently. But they are acting under intelligent instructions, not that they are innately intelligent on their own. I view bacteria the same way, because they are the progenitors in evolution of these cells in our bodies.

dhw: Please explain “under intelligent instructions”. Do you mean your God preprogrammed this intelligent behaviour 3.8 billion years ago, to be passed down by the very first cells, or your God intervenes whenever the cells have a problem?

I have the same old problem trying to differentiate between pre-planning or dabbling. No matter, God is in control.

Biological complexity: wet noodle proteins

by David Turell @, Friday, January 20, 2017, 20:41 (2625 days ago) @ David Turell

The past teaching was that all proteins functioned only of they were fixed in amino acid sequences and folded in certain required ways. Not true. There are very important proteins that are as floppy as wet noodles and they have very important functions:

https://www.quantamagazine.org/20170118-disordered-proteins/?utm_source=Quanta+Magazine...

"Proteins are chains of strung-together amino acids, and recent studies estimate that up to half of the total amino acid sequence that makes up proteins in humans doesn’t fold into a distinct shape. (While some of the proteins that make up this total are unstructured from end to end, others contain long unstructured regions side-by-side with structured ones.) “Partly, people didn’t realize how big that number was, and that’s why they ignored it,” said Julie Forman-Kay, a biochemist at the Hospital for Sick Children and the University of Toronto. “And partly they just didn’t know what to think of it.”

"This fluidity — dubbed “intrinsic disorder” — endows proteins with a set of superpowers that structured proteins don’t have. Folded proteins tend to bind to their targets firmly, like a key in a lock, at just one or two spots, but their more stretched-out wiggly cousins are like molecular Velcro, attaching lightly at multiple locations and releasing with ease. This quick-on-quick-off binding’s effect in the cell is huge: It allows intrinsically disordered proteins — or IDPs, for short — to receive and respond to a slew of molecular messages simultaneously or in rapid succession, essentially positioning them to serve as cellular messaging hubs, integrating these multiple signals and switching them on and off in response to changes in the cell’s environment and to keep cellular processes ticking along as they should.

***

" Through their signaling prowess, IDPs help regulate the gas and brake pedals for producing proteins from the DNA code, according to evidence that has accumulated over the past decade, as well as the process by which cells divide. IDPs may also provide cues that allow cells to take on traits specific to different tissues or parts of the body. In other words, they may somehow help make a blood cell a blood cell and a muscle cell a muscle cell.

***

"Protein disorder occurs along a continuum. At one end of the spectrum lie proteins like p21, which fold on contact with other proteins. At the other end are ones that remain limp and floppy, like wet noodle strands, never taking on a shape. Researchers still don’t know how this range corresponds to their versatile functions, but being more like a string than like a lump with keyholes means that a protein can make many contacts with other molecules to regulate the network of signals that drives the cell. “You have all these on-off switches for all kinds of functions,” said Dunker.

***

"When they examined a database of around 5,000 human proteins, they found that most unstructured proteins were expressed in small quantities and quickly destroyed after they had done their job.

"The reason cells regulate their production so tightly and make sure they turn over so quickly is that IDPs pack a huge punch, Babu said. Having too many would be like having a glut of upper management  — with too many people shouting commands, productivity grinds to a halt. Extend that logic to a cell, though, and things can get ugly: Because IDPs regulate how different components of the cell communicate with one another, having extra copies floating around could leave them sending signals that shouldn’t get sent. “These proteins are so dangerous that you can’t afford not to regulate them,” Babu said.

***

"As they continue to explore what disordered proteins do inside the cell, researchers are also pursuing basic questions about how disordered proteins work. If a protein has both disordered and ordered regions, how do the two interact? How did the evolution of disordered proteins differ from that of folded ones? Also, how do molecules figure out where to attach on disordered proteins? Even though both computer analysis and experimental lab tools for probing IDPs have improved over the past five years, studying them directly in a living cell remains a challenge, Wright said.

"Researchers also want to explore how disordered proteins contribute to disease. Most drugs are designed to interfere with a specific disease pathway by elbowing their way into important spots inside the cell. But researchers have only begun to target IDPs."

Comment: This presents a much higher level of cellular complexity than was ever imagined. How much complexity in biology has to be demonstrated before the decision is obvious that it requires creation by a planning mind?

Biological complexity: wet noodle proteins

by David Turell @, Saturday, January 21, 2017, 15:58 (2624 days ago) @ David Turell

The past teaching was that all proteins functioned only of they were fixed in amino acid sequences and folded in certain required ways. Not true. There are very important proteins that are as floppy as wet noodles and they have very important functions:

https://www.quantamagazine.org/20170118-disordered-proteins/?utm_source=Quanta+Magazine...

"Proteins are chains of strung-together amino acids, and recent studies estimate that up to half of the total amino acid sequence that makes up proteins in humans doesn’t fold into a distinct shape. (While some of the proteins that make up this total are unstructured from end to end, others contain long unstructured regions side-by-side with structured ones.) “Partly, people didn’t realize how big that number was, and that’s why they ignored it,” said Julie Forman-Kay, a biochemist at the Hospital for Sick Children and the University of Toronto. “And partly they just didn’t know what to think of it.”

"This fluidity — dubbed “intrinsic disorder” — endows proteins with a set of superpowers that structured proteins don’t have. Folded proteins tend to bind to their targets firmly, like a key in a lock, at just one or two spots, but their more stretched-out wiggly cousins are like molecular Velcro, attaching lightly at multiple locations and releasing with ease. This quick-on-quick-off binding’s effect in the cell is huge: It allows intrinsically disordered proteins — or IDPs, for short — to receive and respond to a slew of molecular messages simultaneously or in rapid succession, essentially positioning them to serve as cellular messaging hubs, integrating these multiple signals and switching them on and off in response to changes in the cell’s environment and to keep cellular processes ticking along as they should.

***

" Through their signaling prowess, IDPs help regulate the gas and brake pedals for producing proteins from the DNA code, according to evidence that has accumulated over the past decade, as well as the process by which cells divide. IDPs may also provide cues that allow cells to take on traits specific to different tissues or parts of the body. In other words, they may somehow help make a blood cell a blood cell and a muscle cell a muscle cell.

***

"Protein disorder occurs along a continuum. At one end of the spectrum lie proteins like p21, which fold on contact with other proteins. At the other end are ones that remain limp and floppy, like wet noodle strands, never taking on a shape. Researchers still don’t know how this range corresponds to their versatile functions, but being more like a string than like a lump with keyholes means that a protein can make many contacts with other molecules to regulate the network of signals that drives the cell. “You have all these on-off switches for all kinds of functions,” said Dunker.

***

"When they examined a database of around 5,000 human proteins, they found that most unstructured proteins were expressed in small quantities and quickly destroyed after they had done their job.

"The reason cells regulate their production so tightly and make sure they turn over so quickly is that IDPs pack a huge punch, Babu said. Having too many would be like having a glut of upper management  — with too many people shouting commands, productivity grinds to a halt. Extend that logic to a cell, though, and things can get ugly: Because IDPs regulate how different components of the cell communicate with one another, having extra copies floating around could leave them sending signals that shouldn’t get sent. “These proteins are so dangerous that you can’t afford not to regulate them,” Babu said.

***

"As they continue to explore what disordered proteins do inside the cell, researchers are also pursuing basic questions about how disordered proteins work. If a protein has both disordered and ordered regions, how do the two interact? How did the evolution of disordered proteins differ from that of folded ones? Also, how do molecules figure out where to attach on disordered proteins? Even though both computer analysis and experimental lab tools for probing IDPs have improved over the past five years, studying them directly in a living cell remains a challenge, Wright said.

"Researchers also want to explore how disordered proteins contribute to disease. Most drugs are designed to interfere with a specific disease pathway by elbowing their way into important spots inside the cell. But researchers have only begun to target IDPs."

Comment: This presents a much higher level of cellular complexity than was ever imagined. How much complexity in biology has to be demonstrated before the decision is obvious that it requires creation by a planning mind?

Further comment: Just as DNA is more than a code for manufacturing proteins, a concept that took years to recognize, these limber proteins are really a total surprise, not following the old man-made rules about functional protein molecules. We are still in our infancy in understanding how living matter works. The layers will get deeper and deeper. Not by chance!

Biological complexity: more irreducible complexity

by David Turell @, Tuesday, January 24, 2017, 01:08 (2621 days ago) @ David Turell

These large molecules are controls over function. They must appear in evolution at the same time the process they control is fully designed and put in place:

https://www.sciencedaily.com/releases/2017/01/170123151408.htm

"By determining the three-dimensional structures of these molecules down to the level of atoms, the researchers have unlocked key details as to how they function in the body.

"Using a state-of-the-art imaging technology in which molecules are deep frozen, scientists in Roderick MacKinnon's lab at Rockefeller University have reconstructed in unprecedented detail the three-dimensional architecture of three channels that provide a path for specific types of ions to travel across a cell's protective membrane. Because such ions are central to biochemical messaging that allows cells to communicate with one another, the findings have implications for understanding how muscles contract, how the heart maintains its rhythm, and many other physiological processes.

***

"The chloride channel, known as CLC, opens to passively allow ions through. However, it has a close relative that moves chloride another way: by exchanging it for protons. In their structural data, Eunyong Park, a postdoc in the MacKinnon laboratory, and Ernest B. Campbell, a research specialist, found a detail that helps to explain how these two similar molecules work so differently: the position of a loop within the pore through which the ions travel. In the exchanger molecule, this loop was already known to partially block the ions' path. In the new CLC structure (above), they saw this loop flipped down, allowing chloride to travel more freely.

"By allowing potassium and sodium to travel through the cell's membrane, the HCN channel contributes to rhythmic electrical signals, including the pacemaker current within the heart. Among similar channels, HCN's contrarian responses to changes in voltage set it apart. While others open as the cell ramps up for a signal, HCN closes. And unlike the others, it opens as the cell returns to rest. Postdoc Chia-Hsueh Lee found features that contribute to this difference, including an extra-long arm within HCN's voltage detecting sensor (blue) as compared to that of a related potassium channel (orange). The longer arm likely stabilizes the pore in a closed position after the start of an electrical impulse.

"To prevent high frequency electrical impulses from running out of control, the channel Slo2.2 puts on the breaks by allowing potassium out of the cell. It does so in response to the sodium that rushes in during a signal. Richard Hite, a postdoc, and his colleagues had already determined what Slo2.2 looks like when it is closed, without sodium around. In new research, published January 19 in Cell, Hite exposed the channel to varying concentrations of its trigger ion, so as to determine the distribution of all the structures that occur simultaneously at a particular sodium concentration -- the first such experiment. It turned out that the channel exists only in two conformations, closed and open. As a result, it undergoes a sharp transition when opening, akin to a light switch being turned on."

Comment: the body uses ions, electrical impulse equivalents, to run various processes and organs like the heart. Think of this: the heart beats and this drives a circulatory pulse of blood. The beat is triggered by electric impulses traveling down biological 'wires' to drive the muscle contractions. Did evolution design a chambered heart and add the impulses later? Of course not. It had to be put all together completely at once. Saltation by God. Be sure to look at the diagrams in the article. Giant molecules. How did chance evolution found those molecules with the proper form for function?

Biological complexity: epigenetics controlled

by David Turell @, Tuesday, January 24, 2017, 01:20 (2621 days ago) @ David Turell

The body has innumerable feedback loop control mechanisms. Epigenetic alterations have to be controlled also. That method is found in one area:

https://www.sciencedaily.com/releases/2017/01/170120100814.htm

"Cells that lack tryptase start to proliferate in an uncontrolled fashion and lose their identity. If tryptase is present, it will cleave the tails of histones, which will protect from certain epigenetic changes," says Gunnar Pejler, Professor at the Department of Medical Biochemistry and Microbiology at Uppsala University.

"Many properties are determined by genetic factors, but we are starting to recognize that also epigenetic factors are of great importance. With epigenetics we mean such changes in genes that are not determined by changes in the actual DNA sequence, but effects that are superimposed on this, caused for example by environmental effects.

"Epigenetic effects include modification of DNA by incorporation of small chemical groups, methyl groups. Another important epigenetic mechanism is that the proteins that are packed together with DNA in the cell nucleus, called histones, can be chemically modified in their tails. Altogether, the different epigenetic mechanisms will lead to either activation or silencing of the respective genes.

"In a new study published in the Journal of Allergy and Clinical Immunology, researchers have now found a new principle for how epigenetic changes can occur. They have showed that one enzyme, tryptase, can be found in the nucleus of cells and that tryptase can cleave off the tails of histones. In this way, certain epigenetic modifications of the histone tails are removed.

"A very interesting finding was that this mechanism is important for maintaining the identity of the cells. Cells that lacked tryptase showed major changes, including a loss of their cellular identity and they also started to proliferate in an uncontrolled way.

"These effects were seen in mast cells which are central in allergic reactions. The researchers propose that this type of epigenetic effect could be of importance in dealing with allergic disease. However, it cannot be excluded that similar epigenetic effects are operative also in other cell types."

Comment: Still only a little of Pandora's box of the genome is known. how much complexity before it is obvious that the genome is designed?

Biological complexity: the brain hwlps fight infections

by David Turell @, Friday, January 27, 2017, 01:22 (2618 days ago) @ David Turell

The brain releases helper proteins to activate immunity active dells such as macrophages:

https://cosmosmagazine.com/biology/how-the-brain-helps-the-body-fight-bacteria?utm_sour...

"The brain may not only control our thoughts and basic physical functions. Recent studies indicate that it also controls the way our body responds to the threat of bacterial infections. It does this by boosting the production of a protective molecule called PCTR1 that helps white blood cells kill the invading bacteria.

"To identify novel avenues to treat bacterial infections we turned our focus to the central nervous system (the brain, spinal cord and optic nerves), as several studies have implicated the brain in orchestrating more than just our thoughts. In our study we found that severing the right vagus nerve in mice, for example, leads to a significant impairment in their ability to clear E. coli infections.

"When we investigated the reason for this delay, we found a significant decrease in the levels of a molecule called “protectin conjugate in tissue regeneration 1”, or PCTR1 for short. PCTR1 is part of a group of molecules called specialised pro-resolving mediators that control how our body responds to inflammation. It is produced by white blood cells from a fish oil-derived essential fatty acid called docosahexaenoic acid.

"We also found that the decrease in PCTR1 reduced the ability of macrophages – a type of white blood cell – to kill E. coli.

"We then investigated how the vagus nerve regulates PCTR1 production in the abdominal cavity of the mice, where this nerve is known to regulate white blood cell behaviour during inflammation. Here we found that the nerve releases a neurotransmitter called acetylcholine which then instructs another type of immune cell (innate lymphoid cells) to increase production of PCTR1. This in turn regulated macrophages’ ability to find and kill bacteria.

'When we injected the mice with the severed vagus nerve with PCTR1, we found that it restored the ability of peritoneal macrophages to get rid of the bacteria as well as dampen the subsequent inflammatory response, accelerating the bacteria’s termination.

"These results are expected to have wide-ranging implications in the fight against bacterial infections, especially in light of the alarming rate at which bacteria are becoming resistant to antibiotics. This is because these findings demonstrate that we can give our body a hand by using PCTR1, and related molecules, to enhance its ability to clear bacteria during infections, reducing our reliance on antibiotics."

Comment: How did evolution develop this setup? Looks designed to me since we are dealing with the brain watching over the presence of infection and producing a specific hormone to support the cells' actions. It certainly looks irreducibly complex.

Biological complexity: the brain hwlps fight infections

by dhw, Friday, January 27, 2017, 12:24 (2618 days ago) @ David Turell

DAVID: The brain releases helper proteins to activate immunity active cells such as macrophages:
https://cosmosmagazine.com/biology/how-the-brain-helps-the-body-fight-bacteria?utm_sour...

QUOTE: "The brain may not only control our thoughts and basic physical functions...

David’s comment: How did evolution develop this setup? Looks designed to me since we are dealing with the brain watching over the presence of infection and producing a specific hormone to support the cells' actions. It certainly looks irreducibly complex.

It certainly does, but I’m surprised that you have not commented on the quote above (later repeated). The assumption that the brain controls our thoughts is as blatant a challenge to your dualism as you could ever have. It may, of course, be true, but this is the insidious way in which folk on both sides of the fence mislead their readers by presenting subjective judgements as if they were facts. Scientists are no more to be trusted than priests!

Biological complexity: the brain hwlps fight infections

by David Turell @, Friday, January 27, 2017, 15:17 (2618 days ago) @ dhw

DAVID: The brain releases helper proteins to activate immunity active cells such as macrophages:
https://cosmosmagazine.com/biology/how-the-brain-helps-the-body-fight-bacteria?utm_sour...

QUOTE: "The brain may not only control our thoughts and basic physical functions...

David’s comment: How did evolution develop this setup? Looks designed to me since we are dealing with the brain watching over the presence of infection and producing a specific hormone to support the cells' actions. It certainly looks irreducibly complex.

dhw: It certainly does, but I’m surprised that you have not commented on the quote above (later repeated). The assumption that the brain controls our thoughts is as blatant a challenge to your dualism as you could ever have. It may, of course, be true, but this is the insidious way in which folk on both sides of the fence mislead their readers by presenting subjective judgements as if they were facts. Scientists are no more to be trusted than priests!

We are very exact here in our discussions. I view that quote as sloppy writing. I control my brain which results in thoughts. I am kind enough to allow that is what the writer means.

Biological complexity: the brain helps burn fat

by David Turell @, Saturday, January 28, 2017, 15:47 (2617 days ago) @ David Turell

The brain seems to get mixed up in all sorts of activities besides thinking, fighting infections and now burning fat:

https://www.sciencedaily.com/releases/2017/01/170127142411.htm

"Biologists at The Scripps Research Institute (TSRI) have identified a brain hormone that appears to trigger fat burning in the gut. Their findings in animal models could have implications for future pharmaceutical development.

***

"Previous studies had shown that the neurotransmitter serotonin can drive fat loss. Yet no one was sure exactly how. To answer that question, Srinivasan and her colleagues experimented with roundworms called C. elegans, which are often used as model organisms in biology. These worms have simpler metabolic systems than humans, but their brains produce many of the same signaling molecules, leading many researchers to believe that findings in C. elegans may be relevant for humans.

***

"This process of elimination led them to a gene that codes for a neuropeptide hormone they named FLP-7 (pronounced "flip 7").

"Interestingly, they found that the mammalian version of FLP-7 (called Tachykinin) had been identified 80 years ago as a peptide that triggered muscle contractions when dribbled on pig intestines. Scientists back then believed this was a hormone that connected the brain to the gut, but no one had linked the neuropeptide to fat metabolism in the time since.

"The next step in the new study was to determine if FLP-7 was directly linked to serotonin levels in the brain. Study first author Lavinia Palamiuc, a TSRI research associate, spearheaded this effort by tagging FLP-7 with a fluorescent red protein so that it could be visualized in living animals, possible because the roundworm body is transparent. Her work revealed that FLP-7 was indeed secreted from neurons in the brain in response to elevated serotonin levels. FLP-7 then traveled through the circulatory system to start the fat burning process in the gut.

***

"Altogether, the newly discovered fat-burning pathway works like this: a neural circuit in the brain produces serotonin in response to sensory cues, such as food availability. This signals another set of neurons to begin producing FLP-7. FLP-7 then activates a receptor in intestinal cells, and the intestines begin turning fat into energy."

Comment: the caloric value of fat is about twice that of carbohydrates and proteins, but it is the fat stored in our bodies that we burn if there is a shortage of energy supply from the food we eat. Our bodies cannot afford to break down carbs and protein of our bodies' structures. As exercise increases energy must come from stored fat. But during evolution food wasn't always easily obtained, so an interesting mechanism appeared: if starving (what we call dieting) our basal metabolism (the cost of daily living at rest) reduced itself, by as much as 300 calories a day. Thus fat is naturally resistant to burning. Fascinating that the brain is geared to step in and prompt fat to burn, as another example of feedback controls in the biology of the body. Again, for me, all of this requires meticulous planning, not chance development. What is apparent is that the brain is automatically managing body processes without our conscious input. Not by chance.

Biological complexity: the brain helps burn fat

by David Turell @, Wednesday, February 08, 2017, 16:06 (2606 days ago) @ David Turell

Plans and fungi exchange genetic elements in their battle:

http://www.the-scientist.com/?articles.view/articleNo/48073/title/RNA-Interference-Betw...

"Plants and fungi can use conserved RNA interference machinery to regulate each other’s gene expression—and scientists think they can make use of this phenomenon to create a new generation of pesticides.

***

"Noncoding RNAs are well known for their ability to control gene expression in cells. And as scientists have demonstrated repeatedly, protein production can be affected not just by RNAs made in the same individual, but by RNAs from altogether different organisms. In recent years, researchers have taken advantage of the ability to traffic RNA between distantly related taxa to selectively inhibit the expression of genes in fungi important for their growth, an approach they say might lead to the development of disease-resistant crops. Scientists have also shown in the lab that this cross-kingdom RNA transfer can go both ways: fungi are also sending RNA dispatches to their plant hosts, and the covert operation could be aiding their invasion.

"In this conversation between plants and fungi, the organisms rely on a well-worn mechanism of gene-expression regulation that has stood the test of evolutionary time: RNA interference (RNAi). Listening in on the RNA crosstalk between plants and their pathogens could reveal previously unknown facets of basic plant biology, and point the way toward a successful strategy to fend off crop pathogens.

***

"RNAi is a widely conserved mechanism used during development, in routine cellular processes, and in response to foreign invaders—especially viruses—entering a cell. The cell produces small RNAs that are then integrated into an aggregation of proteins called the RNA-induced silencing complex (RISC), which targets messenger RNA molecules (mRNAs) containing the small RNA’s complementary sequence. RISC then chops up bound transcripts, thereby tamping down gene expression.

"Over the past decade, scientists have demonstrated RNAi’s ability to protect numerous plants against nonviral pathogenic foes. In 2007, for instance, Monsanto endowed corn with the ability to fend off western corn rootworm by providing the crop with a gene for an RNA that targeted transcripts of an essential gene in the insect. The transgenic plants suffered less damage, presumably because the insects ingested the interfering RNAs and died.1 Around the same time, research groups showed that the approach—called host-induced gene silencing (HIGS)—could also ward off parasitic worms,

***

"While the actions of RNAi against viral pathogens within the plant cell have been appreciated for years, it’s unclear whether plants in the wild send RNA mercenaries into fungi and other invading eukaryotic pathogens.

"A few months ago, scientists reported perhaps the first evidence that small-RNA transfer between plants and fungi does indeed occur without the intervention of genetic engineers. Hui-Shan Guo at the State Key Laboratory of Plant Genomics at the Chinese Academy of Sciences in Beijing discovered that cotton plants ramp up the production of certain small RNAs after infection by a fungal pest, Verticillium dahliae. Not only do these plant RNAs tamp down the expression of two essential genes in the pathogen, but mutating the fungus’s genes to be resistant to the RNAi made the pest more virulent. “Our works are the first direct experimental evidence of the mobility of . . . RNA molecules from plants to fungal cells and inducing target gene silencing in fungal cells,” Guo wrote in an email to The Scientist. "

Comment: This article is presented from the viewpoint of using genetics to modify plants, but I am using it to show the complexity of genetic battling in nature. That complexity is an enemy to Darwin's theories, which come from a simplistic understanding of the biology of life.

Biological complexity: mechanical forces in cells

by David Turell @, Wednesday, February 15, 2017, 18:32 (2599 days ago) @ David Turell

Many cell functions are affected by mechanical stress and forces in cells, and play roles from embryology to adult roles:

http://www.the-scientist.com/?articles.view/articleNo/48096/title/May-the-Force-Be-with...

"Almost all living cells and tissues exert and experience physical forces that influence biological function. Touch, hearing, proprioception, and certain other senses are well-known examples of specialized force sensors. But force detection and sensing are not limited to these special cases; rather, they are shared by all living cells in all tissues and organs.  The underlying mechanisms of force generation and detection are not well understood, however, leaving many open questions about force dynamics; the distance over which a force exerts its impact; and how cells convert mechanical signals into biochemical signals and changes in gene expression.

"In recent years, biologists have begun to uncover the molecular players that mediate force sensation and propagation at the cellular level, and they’re collecting clues as to how mechanical stimuli influence biological function.

***

"Since the early 2000s, my group has demonstrated that forces do propagate across relatively vast cellular distances—on the order of tens of micrometers—in living cells, and that this long-distance signal is dependent on the inherent tension in the cytoskeleton.

"Most recently, we have found that specific signaling molecules—in particular, the tyrosine kinase Src and the GTPase Rac1—can be activated at distances of more than 60 μm away from the site of the local force application via integrins at the cell membrane. Importantly, this activation is fast, taking less than 300 ms from force application to the activation of Src and Rac1, making mechanotransduction much faster than the 10 to 20 seconds it takes a soluble growth factor–induced signal to travel over the same distance.

***

"However, the cytoplasm of a living cell is neither homogeneous nor isotropic; it is heterogeneous and anisotropic, meaning that the material’s mechanical properties do depend on the direction of force. Importantly, there are stiff, prestressed actin bundles (also called stress fibers) in the cell. Applied forces concentrate at these actin bundles and propagate over longer distances in the cytoplasm.

"Since the early 2000s, my group has demonstrated that forces do propagate across relatively vast cellular distances—on the order of tens of micrometers—in living cells, and that this long-distance signal is dependent on the inherent tension in the cytoskeleton. Just as a violin string can only ring with the correct resonance and sound the right note if it has proper tension, when the prestressed actin bundles are disrupted, force propagation becomes short-range (acting over only a few μms). The higher the tension, the farther the force will be propagated.

***

"Belmont’s team used bacterial artificial chromosomes to insert multiple green fluorescent proteins and the gene for dihydrofolate reductase (DHFR), an essential enzyme for the synthesis of thymine, into the same chromatin domain in Chinese hamster ovary (CHO) cells. My lab applied a local force to those modified cells via integrins. Sure enough, we measured an uptick in DHFR transcription in response to the applied force. Conversely, disrupting cytoskeletal tension, or the force transmission pathways from the cell surface to lamins and to the nuclear structural proteins that connect to the chromatin, abolished force-induced DHFR expression.

"This work provides the first evidence that externally applied forces can stretch chromatin and promote gene expression. As expected with physical force–mediated processes, the response was rapid; we were able to quantify DHFR transcription upregulation within 15 seconds after force application. Interestingly, force-triggered transcription is sensitive to the angle and direction of force relative to the actin bundles: the higher the stress angle, the greater the transcription. Because endogenous forces are constantly generated inside a living cell, these findings suggest that gene expression might be incessantly regulated by physical forces via this direct structural pathway and the indirect pathways of matrix rigidity–dependent nuclear translocation of certain factors, such as yes-associated protein (YAP) and TWIST1.

***

"Later, Adam Engler of the University of California, San Diego, and Dennis Discher of the University of Pennsylvania reported that mesenchymal stem cell differentiation can be directed by extracellular matrix stiffness. And my lab has demonstrated that applying local force can spur the differentiation of a single embryonic stem cell. Physical forces also appear critical in the patterning and organization of germ layers during early mammalian embryonic development."

Comment: The layers of complexity increase. What is presented is a logical extension of research. Areas of cell growth will apply force, especially in embryology, implying those forces were planed or understood as organisms were designed.

Biological complexity: mechanical forces in cells (2)

by David Turell @, Wednesday, February 15, 2017, 19:59 (2599 days ago) @ David Turell

Another set of discoveries on mechanical forces that control epithelial cell reproduction to help maintain proper cell numbers in covering sheets of tissue:

https://www.sciencedaily.com/releases/2017/02/170215131543.htm

"Research published in Nature from scientists at Huntsman Cancer Institute (HCI) at the University of Utah shows how epithelial cells naturally turn over, maintaining constant numbers between cell division and cell death.

"Epithelial cells comprise the skin and skin-like linings that coat internal organs, giving organs a protective barrier so they can function properly. Cells turn over very quickly in epithelia. To maintain healthy cell densities, an equal number of cells must divide and die. If that balance gets thrown off, inflammatory diseases or cancers can arise.

***

"'If too many epithelial cells die, you can lose the organ barrier function and inflammatory diseases like asthma and colitis can result. On the other hand, if too many cells divide compared to the number dying, this can cause an overabundance of cells, which can lead to tumor formation. So imbalance on either side is problematic."

***

"'We knew there had to be some kind of regulation to tie the death and division processes together," says Rosenblatt. "What we found boils down to really simple principles. It's all mechanical tension. If the cells get too crowded -- 1.6-fold more crowded -- then they pop some cells out that later die. The extrusion of cells enables the cell sheets to return to densities they like."

"On the flip side, researchers noticed that cells divided in sparser areas. They realized those sparse regions were creating a tension on the cells to stretch.
"If the cells become too sparse, then they activate cells to divide -- and that signal to divide comes from mechanical stretch," explains Rosenblatt. "To test this, we stretched cells and found that stretch could trigger cells to divide within only one hour! The process also showed us that stretch is a normal trigger for cell division."

***

"The next question was figuring out what caused these processes to happen. Rosenblatt's team discovered both cell division and death were controlled by the same protein, Piezo1.

"'Basically this same protein is sensing both crowding and stretch -- but the outcome is very different, depending on what state the cells are in," says Rosenblatt. "Piezo1 is sort of like a thermostat, regulating two different sides. Just like a thermostat regulates both heat and cold, it makes sense to have one sensor measuring crowding and stretch. If there were two separate regulators, things could get out of hand fairly quickly if one sensor breaks."

"In addition to understanding how Piezo1 is involved in regulation, Rosenblatt's team also identified a stage in the cell cycle where cells sit paused for repair.

"'We had always assumed that once cells start a division cycle, they just power through. We didn't know that they take breaks throughout the cell cycle," explains Rosenblatt. "But we found a point where the cells were just stalled, waiting to divide. A lot of things need to happen for cells to divide. The DNA needs to replicate so it can divide in half, providing each new cell with the same DNA as the parent. These cells have everything ready to do that, but they still pause there at a step that we did not expect to be regulated. Cells could be paused waiting to reach a certain size. Once they reach this size, stretch triggers them to divide.'"

Comment: Again is this example mechanical forces are carefully regulating how cells reproduce. In most soft tissues cells are turning over to new cells constantly. Obviously bone is different, and turnover is not as fast in the brain where neurons are more fixed. It is interesting how many controls are outside DNA control. Biologic complexity is great design!

Biological complexity: multiple cell machine

by David Turell @, Thursday, February 23, 2017, 02:09 (2591 days ago) @ David Turell

Our cells are constantly at work producing new product, getting rid of old stuff. this article is a review of a number of new discoveries of complexity:

http://www.evolutionnews.org/2017/02/more_marvels_in103504.html

"Here's another new paper about voltage-gated sodium channels, called Navs. In humans, these are involved in sensory neurons as well as heart and brain cells, but even microbes have them.

"The cycling of Navs through open, closed and inactivated states, and their closely choreographed relationships with the activities of other ion channels lead to exquisite control of intracellular ion concentrations in both prokaryotes and eukaryotes.

***

"the machines that repair double-stranded breaks in DNA are "far more complex than previously assumed." For instance, "The ends of breaks in the double helix are not just joined, they are first changed in a meticulously choreographed process so that the original genetic information can be restored."

***

"'Protein chaperone takes its job seriously." What is it? It's a ribosomal protein's secret service bodyguard, essentially:

"For proteins, this would be the equivalent of the red-carpet treatment: each protein belonging to the complex machinery of ribosomes -- components of the cell that produce proteins -- has its own chaperone to guide it to the right place at the right time and protect it from harm.

"The particular protein they studied, named L4, has a chaperone that fits tightly like a hand and glove. When the protein is produced in the nucleus, the chaperone takes it on a long trip out the nuclear pore and into the cytoplasm, where it has to be fitted into the ribosome at the right place and time.

***

"Building ribosomes is a formidable undertaking for the cell, involving about 80 proteins that make up the ribosome itself, strings of ribosomal RNA, and more than 200 additional proteins that guide and regulate the process. "Ribosome assembly is a dynamic process, where everything happens in a certain order. We are only now beginning to elucidate the many steps involved," says [André] Hoelz.

***

"One more little factoid if you're not impressed yet: "More than a million ribosomes are produced per day in an animal cell."

***

"the 26S Proteosome, "a large multisubunit complex that executes the degradation of intracellular proteins marked for destruction," contains an "engine" with moving parts. This engine "unfolds and translocates substrates into the 20S core particle" where the protein is shredded, allowing its amino acids to be recycled. How does the machine know what to recycle?...Here, we report cryo-EM structures of the yeast 26S proteasome in the presence of different nucleotides and nucleotide analogs, revealing the existence of four distinct conformational states. These structures elucidate the conformational changes underlying substrate translocation and their coupling with gate opening.

***

"'The ability to dispose of proteins that are either aberrant or (in the worst case) toxic is fundamental to a cell's survival, Researchers describe "rescue proteins" that patrol ribosomes, providing the necessary quality control on the assembly line. The next question is: how do they recognize errors?

"Using cryo-electron microscopy to study the structure of such ribosome-mRNA complexes, the researchers were able to show the manner in which special rescue proteins (Dom34 and Hbs1) recognize such stalled ribosomes, thereby initiating the splitting of the arrested complex and the degradation of the faulty mRNA. The rescue proteins recognize arrested ribosomes by detecting, and binding to, conserved locations normally occupied by mRNA. This direct competition-based approach ensures that only ribosomes with aberrant mRNAs are targeted.

***

"an article describes protein machines that attach to mRNAs as they exit the nucleus and stabilizes them for transport. "We were surprised to see that the RNA is not only recognized by these proteins, they also force it to adopt a new form. They staple it together, so to speak." Then the motor proteins "take the mRNA train," carrying the passenger down the cell's "railway lines," the article says picturesquely.

***

"When cells get too sparse, they pull on each other, triggering cell division and the creation of new cells to fill in the gaps. But then, they discovered a protein machine responsible for this balance. It's called Piezo1, named undoubtedly for its mechanosensitive nature, like certain crystals that can spark when compressed. Piezo1 acts like a "thermostat" on both sides of the cell, they found.

"Just like a thermostat regulates both heat and cold, it makes sense to have one sensor measuring crowding and stretch. If there were two separate regulators, things could get out of hand fairly quickly if one sensor breaks."

Comment: Read the article. I can't put in more. Only design can plan this.

Biological complexity: bacterial defend against virus

by David Turell @, Sunday, March 05, 2017, 18:15 (2581 days ago) @ David Turell

They chop up its DNA while defending their own DNA:

http://alliance.nautil.us/feature/155/the-man-who-kicked-off-the-biotech-revolution?utm...

"Wilcox suggested to Smith that the bacteria were destroying the viral DNA. He based his suggestion on a hypothesis proposed a few years earlier by Werner Arber, a microbiologist at the University of Geneva. Arber speculated that enzymes could restrict the growth of viruses by chopping up their DNA, and dubbed these hypothetical molecules “restriction enzymes.”

"Arber recognized that if restriction enzymes went on an unchecked rampage, they could kill the bacteria themselves by chopping up their own DNA. He speculated that bacteria were shielding their own DNA from assault, and thus avoiding suicide, by covering their genes with carbon and hydrogen atoms—a process known as methylation. The restriction enzymes couldn’t attack methylated DNA, Arber proposed, but it could attack the unprotected DNA of invading viruses.

***

"Matthew Meselson and Robert Yuan at Harvard University reported in the paper how they had discovered a protein in E. coli that cut up foreign DNA—in other words, an actual restriction enzyme. With that paper fresh in his mind, Wilcox suggested to Smith that they had just stumbled across another restriction enzyme in Haemophilus influenzae.

***

"Once Smith and his colleagues published the remarkable details of their restriction enzymes, other scientists began to investigate them as well. They didn’t just study the enzymes, though—they began employing them as a tool. In 1972, Paul Berg, a biologist at Stanford University, used restriction enzymes to make cuts in the DNA of SV40 viruses, and then used other enzymes to attach the DNA from another virus to those loose ends. Berg thus created a single piece of DNA made up of genetic material from two species.

***

" Companies sprouted up that were dedicated to using restriction enzymes to modify DNA. The first commercial application of this technology came from Genentech, a company founded in 1976. Genentech scientists used restriction enzymes to create a strain of E. coli that carried the gene for human insulin. Previously, people with diabetes could only purchase insulin extracted from the pancreases of cows and pigs. Genentech sold insulin produced by swarms of bacteria reared in giant metal drums.

"Over the years, scientists have built on Smith’s initial successes by finding new tools for manipulating DNA. Yet even today, researchers make regular use of restriction enzymes to slice open genes. “They’re still absolutely crucial,” said Carlson. “If you want to put a specific sequence of DNA in another sequence, it’s still most often restriction enzymes that you use to do that.'”

Comment: the subject of this entry is a single scientist's research and how it resulted in a whole biotech industry working with DNA. My take is on the genome complexity of bacteria and how they defend themselves with specialized enzymes, giant molecules that must be discovered by the bacteria in order to deploy them and defend their own DNA by learning to deploy methyl radicals to protect their own DNA. Not by chance, only by design.

Biological complexity: protein folding highly complex

by David Turell @, Monday, March 06, 2017, 00:54 (2580 days ago) @ David Turell

New techniques reveal protein folding is much more complex than previously shown. Only precise properly folded proteins can function effectively:

https://www.nist.gov/news-events/news/2017/03/jila-team-discovers-many-new-twists-prote...

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. The results suggest that, until now, much about protein behavior has been hidden to science—happening on faster timescales and with finer changes in structure than conventional methods could detect.

The JILA research revealed many previously unknown states by unfolding an individual protein. For example, the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research.

“The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST) biophysicist working at JILA, a partnership of NIST and the University of Colorado Boulder. “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.”

“If you miss most of the intermediate states, then you don’t really understand the system,” he said.

Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins. Over the last 50 years, protein folding has become the focus of a large, interdisciplinary research field.

***

The JILA team found that intermediate states were not only more numerous than expected but also lasted as little as 8 microseconds. The findings resolved long-standing discrepancies between past experimental data and molecular simulations, giving confidence to using such simulations to further probe the behavior of membrane proteins.

Comment: The complexity of living biochemicals increases by leaps and bounds as research is refined. As Tony just suggested, God is in charge of design. Not by chance.

Biological complexity: protein folding highly complex

by Balance_Maintained @, U.S.A., Monday, March 06, 2017, 13:10 (2580 days ago) @ David Turell

Given this, how do scientist make the leap from chemical soup to DNA/Proteins in a living cell?

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: protein folding highly complex

by David Turell @, Monday, March 06, 2017, 14:54 (2580 days ago) @ Balance_Maintained

Tony: Given this, how do scientist make the leap from chemical soup to DNA/Proteins in a living cell?

They can't. OOL research goes nowhere.

Biological complexity: epigenetic controls in intestine

by David Turell @, Monday, March 06, 2017, 15:01 (2580 days ago) @ David Turell

New research shows how an "epigenetic reader" controls epigenetic marks:

http://www.the-scientist.com/?articles.view/articleNo/48729/title/Key-Regulator-of-Inte...

"Jeffrey and colleagues decided to focus on SP140 because prior genome-wide association studies characterized it as the culprit behind a number of autoimmune disorders, including Crohn’s disease. In the latest study, the researchers used ChiP-seq analysis to isolate the epigenetic reader and the DNA bound to it, and discovered that SP140 occupied transcriptional start sites in human macrophages. They also found that depleting SP140 in macrophages (from both healthy humans and mice) in cell culture severely impaired their abilities to be activated.

"In addition, the team knocked out the SP140 gene in the immune systems of model mice, finding that the loss of this epigenetic reader weakened the rodents’ intestinal barrier defenses, altered the balance of their gut microbes, and exacerbated intestinal inflammation.

“'It’s interesting that [SP140] both changes the response to pathogens and makes colitis worse,” said Alexander Marson, an assistant professor of microbiology and immunology at the University of California, San Francisco, who was not involved in the study. “Figuring out exactly what it does in the context of infection in vivo will be interesting.”

“'Initially, when we found this epigenetic mediator to be immune-restricted, we thought that would make a great therapeutic target because . . . you may not get off-target effects,” Jeffrey said. “But it turns out that you would not want to inhibit this particular epigenetic reader because its loss results in intestinal inflammation.'”

Comment: Obviously the living body must be able to add and subtract epigenetic marks as necessary, adapting and un-adapting. More complexity found.

Biological complexity: how hemoglobin wolrks

by David Turell @, Thursday, March 30, 2017, 01:56 (2556 days ago) @ David Turell

this amazing molecule carries oxygen to the tissues and takes back C02 to the lungs. At either end of the cycle the molecule easily releases its carried gas:

https://www.evolutionnews.org/2017/03/why-understanding-intelligent-design-helps-us-to-...

. Specifically, the hemoglobin molecule has an increased affinity for oxygen (O2) in the alveoli of the lung, where the O2 level is high. But it has a decreased affinity for O2 in the capillaries of the peripheral tissues, where the O2 is low and the high level of carbon dioxide (CO2) makes the tissues more acidic. (This is called the Bohr effect, after Danish physiologist Christian Bohr.) So hemoglobin releases O2 at precisely the point where it has the shortest path to diffuse from the blood to the mitochondria of the cells.

By a different mechanism, hemoglobin in the peripheral capillaries binds to CO2. This converts the molecule to carbaminohemoglobin, which has a low affinity for O2. In the alveolar capillaries of the lung, where the level of CO2 is low and the level of O2 is high, carbaminohemoglobin releases its CO2 and reverts to hemoglobin, with its high affinity for O2. (This is called the Haldane effect, after Scottish physiologist John Haldane.)

We are able to plot an Oxyhemoglobin Saturation curve comparing the degree of oxygen saturation of hemoglobin to the level of oxygen in the blood. Under conditions in the lung represented by the green curve (high O2, low CO2) hemoglobin takes up oxygen more readily; under conditions represented by the red curve in the peripheral tissues (low O2, high CO2), hemoglobin takes up oxygen less readily.

Comment: This is a very large molecule with very special properties. It has a cousin in the muscles of the body where extra oxygen is stored for use. It is called myoglobin and looks a lot like hemoglobin. This arrangement cannot be the result of a chance process. The size of the molecule in terms of the number of amino acids is shown here:

https://www.google.com/?gws_rd=ssl#q=hemoglobin+molecule+size&*&spf=569

"Protein Structure. The hemoglobin molecule is made up of four polypeptide chains: two alpha chains < >of 141 amino acid residues each and two beta chains < > of 146 amino acid residues each. The alpha and beta chains have different sequences of amino acids, but fold up to form similar three-dimensional structures." That is 574 smino acids in a precise structure to make it act as it does.

If anything shows design, this does!

Biological complexity: how hemoglobin works

by David Turell @, Thursday, April 20, 2017, 19:24 (2535 days ago) @ David Turell

A bacterium is difficult to kill because of its osmotic pressure defense mechanism:

https://cosmosmagazine.com/biology/why-a-common-hospital-infection-is-so-hard-to-wipe-o...

"As slimming stories go, it’s pretty spectacular. A bacterium called Pseudomonas aeruginosa can shed 20% of its weight in just 28 milliseconds.

"This unusual ability to super-slim, research shows, is one of the key reasons the species is one of the most resilient in the bacterial world.

"Form a human perspective, P. aeruginosa’s toughness is bad news. The species is resistant to most antibiotics and is the cause of many severe hospital-acquired xinfections. P. aeruginosa is seriously nasty – but a team led by Sergei Sukharev of Maryland University in the US has shown that it is also seriously well adapted.

"The bacterium thrives in a wide variety of environments, including freshwater, soil and – significantly – the moist surfaces of surgical instruments. What’s more, sudden changes in its living arrangements, especially influxes of water, don’t worry it all.
It was this ability to survive inundation that intrigued Sukharev and his colleagues, because it appeared to defy physics.

"Broadly comparable bacteria will swell up and burst when hit by a raindrop. This is because of a process called osmosis. The rain dilutes the media outside each bacterium, causing a pressure disparity. Water rushes into the bacterium through its semi-permeable cell wall, with fatal results.

"Previous research demonstrated that another particularly hardy species of bacteria – E.coli – is able to partially mediate this type of “osmotic downshock” by pushing small solute molecules, called osmolytes, out through the cell wall, thus reducing the pressure gradient.

"E.coli manages this evacuation through two channels – the second of which functions as an emergency measure, kicking in when the first is overwhelmed, pushing out larger osmolytes at a faster rate.

"Sukharev’s team discovered that P. aeruginosa also uses a pair of osmolyte chutes to reduce the effects of osmosis, but also boasts two other adaptations.

"First, its cell wall is less permeable to water, which means it takes longer for the inrushing moisture to build up pressure. Second, its osmolyte release is so concentrated and rapid that it can clear out one-fifth of its starting weight in a flash, thereby providing more room at lower pressure, greatly reducing the destructive power of the osmotic shock.

“'These results move us one step closer to a mechanistic understanding of the physiological response to osmotic downshocks,” says Sukharev."

Comment: the key to understanding this is understanding osmotic pressure. Given a semipermeable membrane, the side with the most concentration of dissolved chemicals will take on water to make both sides equivalent. Obviously the least concentrated side loses water across the membrane. This bacteria has a highly complex solution which it did not invent by a chance mechanism. It is a very specialized organelle.

Biological complexity: how hemoglobin works

by dhw, Friday, April 21, 2017, 14:14 (2534 days ago) @ David Turell

DAVID (under “ants farm fungus”): With bacteria, they pass it on by splitting in two, no societal culture involved.

dhw: Bacteria communicate, and often form groups. In any case, cell memory would explain how information can be passed from one generation to another.

DAVID: They do communicate chemical signals and biochemical processes they contain are passed along automatically in the splitting process.

As usual you slide in the word “automatic”, and once a solution has been found, this may well be so. The question is how bacteria are able to come up with their solutions in the first place.

DAVID: This bacteria has a highly complex solution which it did not invent by a chance mechanism. It is a very specialized organelle.

Yes indeed, the bacterium may have invented the solution by using its possibly God-given intelligence, as opposed to your God having preprogrammed it 3.8 billion years ago, or popped in to tell it what to do. And one can’t help wondering why your God would have preprogrammed or dabbled all these specialized bacterial methods of attacking humans. In your moments of humanization you have suggested that he wanted to see how we solve the problems he set us, but perhaps you have already withdrawn that suggestion. Dangerously close to the concept of God enjoying the spectacle he has created.


--

Biological complexity: how the cell proteasome works

by David Turell @, Tuesday, May 02, 2017, 15:37 (2523 days ago) @ dhw

Cells are constantly producing and degrading protein products. This is how the proteasome does it:

http://www.the-scientist.com/?articles.view/articleNo/49260/title/The-Proteasome--A-Pow...

"Although they are not alive themselves, proteins nonetheless progress through a life cycle of sorts: they are created by the cell, serve a specific purpose in the organism, and ultimately expire either by passive accumulation of structural defects or through active metabolic processes. As in ecological circles of life, the dead are degraded for their core components. But rather than the scavengers and microbial decomposers at work in macroscale habitats, much of the protein recycling work within the cell falls to a barrel-shaped protein complex known as the proteasome.

"Found in most known organisms, the proteasome is the crucial component of ubiquitin-mediated protein degradation. It complements the numerous proteases that degrade proteins in the cell. Protease targets can be very broad, even random, yet at the same time, the proteases themselves can be quite limited in the extent to which they break down those molecules. On the other hand, the substrate selection for the proteasome is a tightly controlled process in which chains of ubiquitins attach to proteins destined for extensive degradation by the proteasome.

***

" This beefy complex is composed of more than 60 protein subunits that act together to
hydrolyze targeted proteins into short peptides of just 3 to 15 amino acids. These peptides are then broken down further into their constituent amino acids by cellular proteases.

"The proteasome can be divided into two main components, the core particle and the regulatory particles. The core particle is formed from four rings, each composed of seven subunits, that are stacked to form the proteasome’s barrel structure, which measures approximately 5 nanometers in diameter—almost as thick as the cell membrane. The two outer rings are constructed of alpha subunits that constrict the ends of the barrel to control access to the lumen. The two inner rings contain proteolytic beta subunits that degrade protein chains as they pass through. The regulatory particles form “lids” on either end of the barrel, unfolding polyubiquitinated target proteins and threading them through the narrowed opening of the core particle into the lumen. The proteasome is a two-way street; proteins can enter and exit either side.

"The proteasome is responsible for three types of ATP-dependent proteolytic activity: chymotrypsin-like, which cleaves on the carboxyl side of a target protein’s hydrophobic amino acids; trypsin-like, which chops up the carboxyl side of basic amino acids; and caspase-like, which cuts the carboxyl side of acidic amino acids. Each of these protease activities is encoded in separate beta subunits in the core particle—β5, β2, and β1 subunits, respectively. Despite targeting different parts of a protein for cleavage, all of these subunits act via a similar mechanism: a threonine residue in each β subunit attacks the peptide bond of its target amino acid.....in order to keep the proteasome from degrading itself during its initial assembly, these reactive threonine residues are masked by protective amino acids that are snipped off in the final assembly step.

"Specialized proteasomes are structurally similar to the constitutive proteasome, but do have some unique alpha and beta subunits that impart functional differences. For example, due to its beta subunits β1i, β2i, and β5i, immunoproteasomes have dramatically reduced caspase-like proteolytic activity and greatly increased chymotrypsin-like activity, which is believed to assist in creating peptide fragments that are better suited for binding to the major histocompatibility complex during antigen presentation.

"Conversely, the thymoproteasome-specific β5 subunit (β5t) gives that complex much lower chymotrypsin-like activity than constitutive proteasomes, a difference that appears to be instrumental for the thymus to select CD8+ T cells for survival and maturation. Knockout mice that lack β5t lose more than 80 percent of their cytotoxic CD8+ T cells and succumb to infections that wild-type mice overcome.2 Finally, the altered alpha subunit composition of the spermatoproteasome may contribute to the degradation of acetylated core histones, an important step in chromosome condensation during spermatid differentiation and spermatogenesis."

Comment: The proteasome protects itself from self-degradation and is specialized for different organ functions and for different immunologic activities. No cell can operate without this organelle. The original cells at the start of life had to have a portion of it that maintained this action. Only design can provide all the interactive parts of the original cells. The complexity shows this.

Biological complexity: how the cell proteasome works

by David Turell @, Wednesday, May 03, 2017, 18:25 (2522 days ago) @ David Turell


David: Comment: The proteasome protects itself from self-degradation and is specialized for different organ functions and for different immunologic activities. No cell can operate without this organelle. The original cells at the start of life had to have a portion of it that maintained this action. Only design can provide all the interactive parts of the original cells. The complexity shows this.

It is important to recognize that the original cells of early life had to be complete units. How would a simple partial cell work? Could one even exist? We really have no experience with that. Viruses are close but they are set up to manage their affairs until they invade a fully living cell to take over the replication part of DNA and reproduce. This means my point above must be taken seriously. The first cells that maintained life after it started were complete units with completely integrated organelles that were protected against mistakes and had controls managed by feedback loops. They were run by a DNA code which rivals any code invented by humans. It is more than reasonable to conclude that only design by a planning mind is the source of the beginning of life.

Biological complexity: how the cell proteasome works

by dhw, Thursday, May 04, 2017, 12:12 (2521 days ago) @ David Turell

DAVID's comment: The proteasome protects itself from self-degradation and is specialized for different organ functions and for different immunologic activities. No cell can operate without this organelle. The original cells at the start of life had to have a portion of it that maintained this action. Only design can provide all the interactive parts of the original cells. The complexity shows this.
DAVID: It is important to recognize that the original cells of early life had to be complete units. How would a simple partial cell work? Could one even exist? We really have no experience with that. Viruses are close but they are set up to manage their affairs until they invade a fully living cell to take over the replication part of DNA and reproduce. This means my point above must be taken seriously. The first cells that maintained life after it started were complete units with completely integrated organelles that were protected against mistakes and had controls managed by feedback loops. They were run by a DNA code which rivals any code invented by humans. It is more than reasonable to conclude that only design by a planning mind is the source of the beginning of life.

Perfectly reasonable. And alongside a variety of psychic experiences, the complexity of the cell is the major reason why I cannot embrace atheism. The problem that leaves me on my agnostic fence is that we cannot solve a mystery by substituting another mystery. All we can say is that the first living cells were produced by an unknown force. We have no idea what that force is or was, how it originated, whether it is singular or plural, absent or present, working from top to bottom or bottom to top...You make great play of not humanizing this force, but you can’t help it – you call it “He”, you see it as an individual mind with individual intentions and interests, a “person like no other person” (why a “person” at all?), and you even pray to it in the belief that it cares about you. With my theist hat on, I can also humanize it (and I take this approach seriously, because your God may indeed exist), but with my agnostic hat on, I cannot go beyond the unknown force. THAT is avoidance of humanization. I shan’t bore you by repeating my panpsychist hypothesis, other than to say that I see it as no more and no less improbable than your sourceless eternal mind and the atheists’ “god” of chance. But in the light of some of your current posts (for which once more many thanks), I will point out the evidence for bottom-up evolution, the point being that rudimentary intelligence can create ever more sophisticated forms of intelligence by combining with other intelligences. This is summed up by the Wikipedia article I referred to earlier:

Microbial intelligence (popularly known as bacterial intelligence) is the intelligence shown by microorganisms. The concept encompasses complex adaptive behaviour shown by single cells, and altruistic or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.”
(Please note that chemical signalling is their form of communication, and does not denote automaticity.)

From “Neurons’ DNA”: “Accepted dogma holds that—although every cell in the body contains its own DNA—the genetic instructions in each cell nucleus are identical. But new research has now proved this assumption wrong. There are actually several sources of spontaneous mutation in somatic (nonsex) cells, resulting in every individual containing a multitude of genomes—a situation researchers term somatic mosaicism....There are reasons to think somatic mosaicism may be particularly important in the brain, not least because neural genes are very active.”

From “Ant queens”: DAVID’S Comment: this is a logical explanation to show how social ant colonies get their cues for activity: chemical signals as well as instinctual behaviour. The ants need queen/worker ratios for proper survival. One can wonder how evolution worked this all out. Certainly not by chance; more likely by design.

The pattern in all these quotes is clear: individual units combine into communities that work out processes far beyond the scope of each individual in isolation. This applies from bacteria right through to ourselves: we are a collection of cell communities (including that of the brain), and all these cell communities have an intelligence of their own. This is not to minimize the problem of the very first cells, but I am simply trying to show that intelligent design does not necessarily mean a single mind that knows and plans everything (top down); intelligent design can be the product of intelligent communities that learn from experience and (bottom up) create ever more complex designs as they build on the work of their predecessors.

Biological complexity: how the cell proteasome works

by David Turell @, Friday, May 05, 2017, 01:44 (2520 days ago) @ dhw

Daavid: This means my point above must be taken seriously. The first cells that maintained life after it started were complete units with completely integrated organelles that were protected against mistakes and had controls managed by feedback loops. They were run by a DNA code which rivals any code invented by humans. It is more than reasonable to conclude that only design by a planning mind is the source of the beginning of life.[/i]

dhw: All we can say is that the first living cells were produced by an unknown force. We have no idea what that force is or was, how it originated, whether it is singular or plural, absent or present, working from top to bottom or bottom to top...

What we can say is design is required. the complexity demands that.

dhw: But in the light of some of your current posts (for which once more many thanks), I will point out the evidence for bottom-up evolution, the point being that rudimentary intelligence can create ever more sophisticated forms of intelligence by combining with other intelligences. This is summed up by the Wikipedia article I referred to earlier:

Microbial intelligence (popularly known as bacterial intelligence) is the intelligence shown by microorganisms. The concept encompasses complex adaptive behaviour shown by single cells, and altruistic or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.”
(Please note that chemical signalling is their form of communication, and does not denote automaticity.)

I will simply repeat that my interpretation and that of the ID scientists is that the cells are totally automatic and contain intelligently implanted information.


dhw: The pattern in all these quotes is clear: individual units combine into communities that work out processes far beyond the scope of each individual in isolation. This applies from bacteria right through to ourselves: we are a collection of cell communities (including that of the brain), and all these cell communities have an intelligence of their own. This is not to minimize the problem of the very first cells, but I am simply trying to show that intelligent design does not necessarily mean a single mind that knows and plans everything (top down); intelligent design can be the product of intelligent communities that learn from experience and (bottom up) create ever more complex designs as they build on the work of their predecessors.

Intelligence had to appear in the first cells. Intelligence is immaterial and requires thoughtful planning to be useful in having evolution progress from simple single celled to complex multicellular, granting that the initial cells are highly complex to begin with. I simply accept that God supplied the intelligence from the beginning.

Biological complexity: how the cell proteasome works

by dhw, Friday, May 05, 2017, 12:40 (2520 days ago) @ David Turell

dhw: All we can say is that the first living cells were produced by an unknown force. We have no idea what that force is or was, how it originated, whether it is singular or plural, absent or present, working from top to bottom or bottom to top...
DAVID: What we can say is design is required. the complexity demands that.

But we have no idea what did the designing. Hence the “unknown force”.

dhw: But in the light of some of your current posts (for which once more many thanks), I will point out the evidence for bottom-up evolution, the point being that rudimentary intelligence can create ever more sophisticated forms of intelligence by combining with other intelligences. This is summed up by the Wikipedia article I referred to earlier:
“Microbial intelligence (popularly known as bacterial intelligence) is the intelligence shown by microorganisms. The concept encompasses complex adaptive behaviour shown by single cells, and altruistic or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.”
(Please note that chemical signalling is their form of communication, and does not denote automaticity.)

DAVID: I will simply repeat that my interpretation and that of the ID scientists is that the cells are totally automatic and contain intelligently implanted information.

There is no need to repeat your interpretation. I made it clear that I am explaining how evolution can proceed from bottom up (intelligent microorganisms combining their intelligences to create ever greater complexity) as opposed to top down (your “God” planning everything). You may not believe this hypothesis, but that does not invalidate the logic, and there is no more proof that your God preprogrammes/dabbles (or indeed exists) than there is that microorganisms are intelligent enough to do their own innovating.

dhw: This is not to minimize the problem of the very first cells, but I am simply trying to show that intelligent design does not necessarily mean a single mind that knows and plans everything (top down); intelligent design can be the product of intelligent communities that learn from experience and (bottom up) create ever more complex designs as they build on the work of their predecessors. (My bold)
DAVID: Intelligence had to appear in the first cells.

Of course it did, and in my hypothesis I allow for your “God” having implanted the intelligence that drives it. (But see below and under “Information”.)

DAVID: Intelligence is immaterial and requires thoughtful planning to be useful in having evolution progress from simple single celled to complex multicellular, granting that the initial cells are highly complex to begin with. I simply accept that God supplied the intelligence from the beginning.

“Accept” is the wrong word. That is what you believe, but you have ignored everything else I have said in my post about the term “God”. Whatever supplied the intelligence from the beginning is an unknown force.

Biological complexity: how the cell proteasome works

by David Turell @, Saturday, May 06, 2017, 00:12 (2519 days ago) @ dhw

DAVID: Intelligence had to appear in the first cells.

dhw: Of course it did, and in my hypothesis I allow for your “God” having implanted the intelligence that drives it. (But see below and under “Information”.)

DAVID: Intelligence is immaterial and requires thoughtful planning to be useful in having evolution progress from simple single celled to complex multicellular, granting that the initial cells are highly complex to begin with. I simply accept that God supplied the intelligence from the beginning.

dhw: “Accept” is the wrong word. That is what you believe, but you have ignored everything else I have said in my post about the term “God”. Whatever supplied the intelligence from the beginning is an unknown force.

At least you admit there has to be a 'force' to supply the intelligence. That is a beginning of what that force might be. Is it in and of itself intelligent? Does it supply raw undeveloped intelligence as in an infant? Can it plan?

Biological complexity: how the cell proteasome works

by dhw, Saturday, May 06, 2017, 10:47 (2519 days ago) @ David Turell

DAVID: Intelligence had to appear in the first cells.

dhw: Of course it did, and in my hypothesis I allow for your “God” having implanted the intelligence that drives it. (But see below and under “Information”.)

DAVID: Intelligence is immaterial and requires thoughtful planning to be useful in having evolution progress from simple single celled to complex multicellular, granting that the initial cells are highly complex to begin with. I simply accept that God supplied the intelligence from the beginning.

dhw: “Accept” is the wrong word. That is what you believe, but you have ignored everything else I have said in my post about the term “God”. Whatever supplied the intelligence from the beginning is an unknown force.

DAVID: At least you admit there has to be a 'force' to supply the intelligence. That is a beginning of what that force might be. Is it in and of itself intelligent? Does it supply raw undeveloped intelligence as in an infant? Can it plan?

Yes, these are the questions we ask and can never answer. Under “Genome complexity” you wrote that “all forms are descended from earlier forms by a totally unknown process”, and the same can be said of whatever force brought life into existence: it is totally unknown. That is why we continue to ask questions and examine the different answers to see whether they make sense or not. To a certain extent, all of them do, which is why different people adhere to different hypotheses. But eventually all of them reach a dead end where they cease to make sense. Some folk can then close their eyes to the senselessness and make a leap of faith, which boils down to choosing between god(s), chance and a nebulous form of panpsychism as the unknown force that originated life, evolution and intelligence. Other folk keep their eyes open and sit on the fence. In ludic terms, the latter - including me, of course - can’t win, but unless there is a life beyond this life in which all will be revealed (who knows?), I suspect there is no possibility of us ever knowing the result!

Biological complexity: how the cell proteasome works

by David Turell @, Saturday, May 06, 2017, 19:54 (2519 days ago) @ dhw


DAVID: At least you admit there has to be a 'force' to supply the intelligence. That is a beginning of what that force might be. Is it in and of itself intelligent? Does it supply raw undeveloped intelligence as in an infant? Can it plan?

dhw: Yes, these are the questions we ask and can never answer. Under “Genome complexity” you wrote that “all forms are descended from earlier forms by a totally unknown process”, and the same can be said of whatever force brought life into existence: it is totally unknown. That is why we continue to ask questions and examine the different answers to see whether they make sense or not. To a certain extent, all of them do, which is why different people adhere to different hypotheses. But eventually all of them reach a dead end where they cease to make sense.

This is where the design argument steps in. The biology of the living cell is too complex for anything but design to be the source of the result. The interdigitation of all the interlocking organelles each doing their own thing yet cooperating with the other parts requires design, and a designer. I see no way around this argument. We can argue who is the designer, but not the necessity for design.

Biological complexity: how the cell proteasome works

by dhw, Sunday, May 07, 2017, 13:26 (2518 days ago) @ David Turell

DAVID: At least you admit there has to be a 'force' to supply the intelligence. That is a beginning of what that force might be. Is it in and of itself intelligent? Does it supply raw undeveloped intelligence as in an infant? Can it plan?

dhw: Yes, these are the questions we ask and can never answer. Under “Genome complexity” you wrote that “all forms are descended from earlier forms by a totally unknown process”, and the same can be said of whatever force brought life into existence: it is totally unknown. That is why we continue to ask questions and examine the different answers to see whether they make sense or not. To a certain extent, all of them do, which is why different people adhere to different hypotheses. But eventually all of them reach a dead end where they cease to make sense.

DAVID: This is where the design argument steps in. The biology of the living cell is too complex for anything but design to be the source of the result. The interdigitation of all the interlocking organelles each doing their own thing yet cooperating with the other parts requires design, and a designer. I see no way around this argument. We can argue who is the designer, but not the necessity for design.

Why “who”? You are immediately jumping to the conclusion that the source of the design is an individual conscious “person”. You may be right, but this assumption raises innumerable and unanswerable questions about the source, composition, nature and intentions of such a “person”, which means you are simply trying to solve one mystery (the origin of life) by creating another. That is the “dead end” I mentioned above. Chance is a far simpler solution, as it does not create any mysteries about identity, but the belief that such complexity can be the result of sheer luck places an intolerable burden on one’s credulity – another dead end. My panpsychist compromise, in which individual materials possess a rudimentary intelligence and gradually complexify through interaction with other rudimentary intelligences (bottom up evolution) avoids the problems of theistic identity but again requires too great a degree of credulity for me to take the leap of faith. And so, as always, we are left with inadequate hypotheses that lead to the dead end of the totally unknown and perhaps unknowable.

Biological complexity: how the cell proteasome works

by David Turell @, Sunday, May 07, 2017, 15:57 (2518 days ago) @ dhw


DAVID: This is where the design argument steps in. The biology of the living cell is too complex for anything but design to be the source of the result. The interdigitation of all the interlocking organelles each doing their own thing yet cooperating with the other parts requires design, and a designer. I see no way around this argument. We can argue who is the designer, but not the necessity for design.

dhw: Why “who”? You are immediately jumping to the conclusion that the source of the design is an individual conscious “person”. You may be right, but this assumption raises innumerable and unanswerable questions about the source, composition, nature and intentions of such a “person”, which means you are simply trying to solve one mystery (the origin of life) by creating another. That is the “dead end” I mentioned above. Chance is a far simpler solution, as it does not create any mysteries about identity, but the belief that such complexity can be the result of sheer luck places an intolerable burden on one’s credulity – another dead end. My panpsychist compromise, in which individual materials possess a rudimentary intelligence and gradually complexify through interaction with other rudimentary intelligences (bottom up evolution) avoids the problems of theistic identity but again requires too great a degree of credulity for me to take the leap of faith. And so, as always, we are left with inadequate hypotheses that lead to the dead end of the totally unknown and perhaps unknowable.

The 'who' is to get around the discussion of imagining God. The key issue is the unimaginable complexity of life and the requirement for a designing mind to produce it. Your panpsychist alternative is a bottom up alternative which parenthetically sneaks in the 'conscious universe' concept, every rock has consciousness, which really is a version of my thought that a universal consciousness exists, God.

Biological complexity: how the cell proteasome works

by dhw, Monday, May 08, 2017, 13:50 (2517 days ago) @ David Turell

DAVID: This is where the design argument steps in. The biology of the living cell is too complex for anything but design to be the source of the result. The interdigitation of all the interlocking organelles each doing their own thing yet cooperating with the other parts requires design, and a designer. I see no way around this argument. We can argue who is the designer, but not the necessity for design.

dhw: Why “who”? You are immediately jumping to the conclusion that the source of the design is an individual conscious “person”. […]

DAVID: The 'who' is to get around the discussion of imagining God.

Then “what” and “it” would be far more appropriate.

DAVID: The key issue is the unimaginable complexity of life and the requirement for a designing mind to produce it. Your panpsychist alternative is a bottom up alternative which parenthetically sneaks in the 'conscious universe' concept, every rock has consciousness, which really is a version of my thought that a universal consciousness exists, God.

Most panpsychist theories are indeed theistic. However, mine is not, and these are very different concepts. Yours is an inexplicable single, eternal mind which is the source of everything, and knows and plans everything in advance – a “person like no other person”. Mine is countless individual consciousnesses (rudimentary) that inexplicably arise in some (not necessarily all) materials which over the course of time combine their limited intelligences to create increasingly complex forms of intelligent matter – just as bacteria, ants etc. form communities whose intelligence far exceeds that of each individual. Two totally different, inexplicable forms of consciousness which, to my mind and for different reasons, are equally unbelievable.

Biological complexity: how the cell proteasome works

by David Turell @, Monday, May 08, 2017, 18:20 (2517 days ago) @ dhw


DAVID: The key issue is the unimaginable complexity of life and the requirement for a designing mind to produce it. Your panpsychist alternative is a bottom up alternative which parenthetically sneaks in the 'conscious universe' concept, every rock has consciousness, which really is a version of my thought that a universal consciousness exists, God.

dhw: Most panpsychist theories are indeed theistic. However, mine is not, and these are very different concepts. Yours is an inexplicable single, eternal mind which is the source of everything, and knows and plans everything in advance – a “person like no other person”. Mine is countless individual consciousnesses (rudimentary) that inexplicably arise in some (not necessarily all) materials which over the course of time combine their limited intelligences to create increasingly complex forms of intelligent matter – just as bacteria, ants etc. form communities whose intelligence far exceeds that of each individual. Two totally different, inexplicable forms of consciousness which, to my mind and for different reasons, are equally unbelievable.

I'm sorry, but I cannot imagine any intelligence existing in the formation of the original rocky Earth that was created 4.5 billion years ago. The only intelligence we see is from the formation of very many complex organic molecules which then become alive through the coordination of their functions. That miracle is due to God's actions. I view anything less as impossible.

Biological complexity: how the cell proteasome works

by dhw, Tuesday, May 09, 2017, 12:07 (2516 days ago) @ David Turell

DAVID: The key issue is the unimaginable complexity of life and the requirement for a designing mind to produce it. Your panpsychist alternative is a bottom up alternative which parenthetically sneaks in the 'conscious universe' concept, every rock has consciousness, which really is a version of my thought that a universal consciousness exists, God.

dhw: Most panpsychist theories are indeed theistic. However, mine is not, and these are very different concepts. Yours is an inexplicable single, eternal mind which is the source of everything, and knows and plans everything in advance – a “person like no other person”. Mine is countless individual consciousnesses (rudimentary) that inexplicably arise in some (not necessarily all) materials which over the course of time combine their limited intelligences to create increasingly complex forms of intelligent matter – just as bacteria, ants etc. form communities whose intelligence far exceeds that of each individual. Two totally different, inexplicable forms of consciousness which, to my mind and for different reasons, are equally unbelievable.

DAVID: I'm sorry, but I cannot imagine any intelligence existing in the formation of the original rocky Earth that was created 4.5 billion years ago. The only intelligence we see is from the formation of very many complex organic molecules which then become alive through the coordination of their functions. That miracle is due to God's actions. I view anything less as impossible.

I cannot imagine intelligent chemicals either, and that is why I do not believe or disbelieve in my panpsychist hypothesis. On the other hand, I cannot imagine a sourceless, individual, eternally conscious mind, a “person like no other person”, creating and encompassing and occupying ALL THAT IS, and that is why I do not believe or disbelieve in your “God” hypothesis. You wrote on this thread: “The ‘who’ is to get around the discussion of imagining God.” You can’t imagine my bottom-up panpsychist hypothesis and so you disbelieve it. And you would prefer to get round the problem of imagining your God hypothesis because you believe it.

Biological complexity: how the cell proteasome works

by David Turell @, Tuesday, May 09, 2017, 18:18 (2516 days ago) @ dhw

DAVID: I'm sorry, but I cannot imagine any intelligence existing in the formation of the original rocky Earth that was created 4.5 billion years ago. The only intelligence we see is from the formation of very many complex organic molecules which then become alive through the coordination of their functions. That miracle is due to God's actions. I view anything less as impossible.

dhw: I cannot imagine intelligent chemicals either, and that is why I do not believe or disbelieve in my panpsychist hypothesis. On the other hand, I cannot imagine a sourceless, individual, eternally conscious mind, a “person like no other person”, creating and encompassing and occupying ALL THAT IS, and that is why I do not believe or disbelieve in your “God” hypothesis. You wrote on this thread: “The ‘who’ is to get around the discussion of imagining God.” You can’t imagine my bottom-up panpsychist hypothesis and so you disbelieve it. And you would prefer to get round the problem of imagining your God hypothesis because you believe it.

Because I believe only a planning mind can produce our life-allowing universe, our life, and our consciousness.

Biological complexity: breathing controls

by David Turell @, Tuesday, May 09, 2017, 21:22 (2516 days ago) @ David Turell

The level of Carbon dioxide in the blood is one of the controls of the rate of breathing. The sensors for this control are in the brain stem. The vessels there constrict when the rest of the body dilates to wash out high CO2:

https://www.sciencedaily.com/releases/2017/05/170509121914.htm

"For more than a century, doctors and scientists have known that blood vessels dilate when cellular waste products like carbon dioxide build up. Widening the vessels allows fresh blood to flush through, carrying in oxygen and washing away the acidic carbon dioxide. This has been shown to be true throughout the body, and is standard dogma in undergraduate physiology classes.

***

"He's shown in the past that RTN neurons respond to rising levels of carbon dioxide in the bloodstream by stimulating the lungs to breathe. But if the blood vessels in the RTN dilated in response to rising carbon dioxide the same way blood vessels do everywhere else, it would wash out that all-important signal, preventing cells in the RTN from doing their job driving us to breathe. It would be as if the drum major didn't notice the percussion section wandering off to left field.

"When Mulkey returned to the lab, he asked his team, including NIH postdoctoral fellow Virginia Hawkins, to see how blood vessels in thin slices of brainstem respond to carbon dioxide. And they saw it was indeed true -- RTN blood vessels constricted when carbon dioxide levels rose. But blood vessels from slices of cortex (the wrinkled top part of the brain) dilated in response to high carbon dioxide, just like the rest of the body.

"But how did the blood vessels know to act differently in the RTN? Mulkey guessed that RTN astrocytes had something to do with it. He suspected that the astrocytes were releasing adenosine triphosphate (ATP), a small molecule cells can use to signal one another. And that was causing the RTN blood vessels to constrict.

"When they tested it, they found the hypothesis was correct. The astrocytes in the RTN were behaving differently than astrocytes anywhere else in the body. When these brainstem astrocytes detected high levels of carbon dioxide, they released ATP signaling to the neurons and blood vessels.

"When the researchers induced the astrocytes artificially to release ATP, they got the same results. Bathing the RTN blood vessels directly in ATP also caused them to constrict. Blocking ATP receptors blocked the ability of blood vessels to respond to carbon dioxide. When the team did the same experiments in live animals, they got the same results. Perhaps most importantly, manipulating blood vessels in the RTN actually influenced how animals breathe, thus linking regulation of blood vessel diameter to behavior."

Comment: Obviously the vessels in the brain stem have to remain constricted to maintain the CO2 level there so the control neurons will continue to signal dilatation and more rapid breathing until the danger from CO2 is over. This is a highly complex coordinated activity, with similar astrocytes acting in different ways. How did evolution work this out? It requires design and planning. Only a thinking mind can do this.

Biological complexity:finding new cells,new functions

by David Turell @, Friday, May 12, 2017, 14:38 (2513 days ago) @ David Turell

In the Zebra fish a new protective brain cell is discovered. We might have them:

https://cosmosmagazine.com/biology/cleaning-up-scavenger-brain-cells?utm_source=Today+i...

"In the brain of a zebrafish, lymphatic “scavenger” cells (shown in red) wrap around blood vessels (shown in green). The scavenger cells, or mural lymphatic endothelial cells, discovered by scientists at the University of Queensland, are believed to protect the brain from cellular waste, such as excess fats, leaking from the bloodstream.

“'It is rare to discover a cell type in the brain that we didn’t know about previously, and particularly a cell type that we didn’t expect to be there,” says lead researcher Ben Hogan, of UQ’s Institute for Molecular Bioscience.

"He and his colleagues hope the discovery will improve understanding of how the human brain functions, since zebrafish share many of the same cell types and organs as humans. The tropical freshwater fish make ideal subjects for such exploration, because the brains of the naturally transparent creatures can be observed directly using advanced light microscopes.

"Hogan says there is reason to be confident that equivalent scavenger cells surround and protect the human brain. Learning how to control them, such as through pharmaceuticals, could lead to breakthroughs in preventing or treating neurological diseases such as stroke and dementia."

Comment: We continue to find new cells with different purposes and specific functions. Multicellular organisms have hundreds of specified cells all working together in a coordinated fashion. Not by chance.

Biological complexity: shape shifting proteins

by David Turell @, Friday, May 12, 2017, 20:31 (2513 days ago) @ David Turell

Not all proteins are fixed in shape. Those that don't have a fixed form are vital to the functions of life:

https://www.quantamagazine.org/20170118-disordered-proteins/?utm_source=Quanta+Magazine...

"...recently, however, biologists have begun paying attention to these shapeshifters. Their findings are tearing down the structure-function dogma.

"Proteins are chains of strung-together amino acids, and recent studies estimate that up to half of the total amino acid sequence that makes up proteins in humans doesn’t fold into a distinct shape.

***

"This fluidity — dubbed “intrinsic disorder” — endows proteins with a set of superpowers that structured proteins don’t have. Folded proteins tend to bind to their targets firmly, like a key in a lock, at just one or two spots, but their more stretched-out wiggly cousins are like molecular Velcro, attaching lightly at multiple locations and releasing with ease. This quick-on-quick-off binding’s effect in the cell is huge: It allows intrinsically disordered proteins — or IDPs, for short — to receive and respond to a slew of molecular messages simultaneously or in rapid succession, essentially positioning them to serve as cellular messaging hubs, integrating these multiple signals and switching them on and off in response to changes in the cell’s environment and to keep cellular processes ticking along as they should.

***

" IDPs help regulate the gas and brake pedals for producing proteins from the DNA code, according to evidence that has accumulated over the past decade, as well as the process by which cells divide. IDPs may also provide cues that allow cells to take on traits specific to different tissues or parts of the body. In other words, they may somehow help make a blood cell a blood cell and a muscle cell a muscle cell.

***

"Dunker’s analysis revealed that disordered proteins had very different sequences of amino acids than structured ones. When he looked for these differences in databases of sequenced proteins, a surprisingly high number of disordered suspects popped out. Even more interesting, a higher percentage of the protein sequence is disordered in more complex organisms — for example, about 20 percent of the amino acids in the bacterium Escherichia coli are disordered, but the percentage is at least twice as high in humans.

***

"Protein disorder occurs along a continuum. At one end of the spectrum lie proteins like p21, which fold on contact with other proteins. At the other end are ones that remain limp and floppy, like wet noodle strands, never taking on a shape. Researchers still don’t know how this range corresponds to their versatile functions, but being more like a string than like a lump with keyholes means that a protein can make many contacts with other molecules to regulate the network of signals that drives the cell. “You have all these on-off switches for all kinds of functions,” said Dunker.

***

"When they examined a database of around 5,000 human proteins, they found that most unstructured proteins were expressed in small quantities and quickly destroyed after they had done their job.

"The reason cells regulate their production so tightly and make sure they turn over so quickly is that IDPs pack a huge punch, Babu said. Having too many would be like having a glut of upper management  — with too many people shouting commands, productivity grinds to a halt. Extend that logic to a cell, though, and things can get ugly: Because IDPs regulate how different components of the cell communicate with one another, having extra copies floating around could leave them sending signals that shouldn’t get sent. “These proteins are so dangerous that you can’t afford not to regulate them,” Babu said.

***

"When a cell produces too many of these proteins, they found, it dies.

***

"For him the turning point came five years ago, when a colleague showed him data suggesting that some disordered proteins can form liquid droplets that briefly exist suspended in the fluid of the cell. Researchers still don’t know exactly how or why this process occurs, but some speculate that it brings molecules together for signaling.

***

"Hurley speculates that these disordered regions act like a weak glue, creating just the right level of cohesion — not too rigid and not too loose — to bring together the molecular components needed for autophagy" [cell death].

Comment: So living cells have both fixed and disordered proteins to run the processes of life. Too complex for chance development. This is different than the Kinesin transport proteins.

Biological complexity: how the cell proteasome works

by David Turell @, Thursday, May 18, 2017, 14:51 (2507 days ago) @ David Turell

The proteasome is a complex structure as shown by this reference of illustrations. One can certainly wonder how evolution created this complex mechanism. It is easier to understand that it requires a functioning mind to plan it:

http://www.the-scientist.com/?articles.view/articleNo/49279/title/Infographic--Proteaso...

Comment: The illustrations show clearly how a large protein is degraded into short peptide parts which can be reused or discarded. Not by chance.

Biological complexity: transient enzyme complexity

by David Turell @, Wednesday, May 31, 2017, 20:01 (2494 days ago) @ David Turell

Without enzymes to speed reactions life would not exist. Now transient enzymes are revealing their evanescent changes and helping to explain how enzymes work:

https://www.sciencedaily.com/releases/2017/05/170531094844.htm

"By modifying the enzyme adenylate kinase, researchers were able to isolate the molecule and study it using the quantitative techniques X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy.

***

"Biological life is dependent on a large number of cellular, chemical reactions that are often extremely slow and can take months or years to complete. For chemical and biological time-scales to match, chemical reactions are sped up in cells with the use of enzymes as efficient biocatalysts.

"Over the last decade of research it has been made clear that enzyme structures that only exist briefly and transiently can be entirely essential for the catalytic function.

***

"The results indicated that the function in one enzyme is entirely dependent on its inherent dynamics, and without dynamics the enzyme would be rendered useless. Furthermore, it turned out that the transient state bound its substrate molecules much stronger than the natural proteins. The results gave us further clues as to how enzymes can speed up reactions with such incredible specificity and efficacy. All the while, the method that we developed can be generally useful in studies of other enzymes.'"

Comment: Enzymes are huge molecules, and perform precise functions. This level of complexity requires design. Please look at the diagrammed structure of the molecule used in this study.

Biological complexity: seed brains?

by David Turell @, Tuesday, June 06, 2017, 14:20 (2488 days ago) @ David Turell

Seeds have two sets of cells which control grow now or wait to germinate. Both must have sensory input which is not yet described. The need for seeds to have these controls is obvious:

https://cosmosmagazine.com/biology/do-plant-seeds-have-brains

"Scientists from the University of Birmingham have discovered that the plants themselves determine when to germinate, effectively making a decision through the interaction of two groups of cells that constitute an analogue of a brain.

"The scientists, led by George Bassel of the university’s School of Biosciences, discovered two types of cell operating in concert in the embryos of a plant called Arabidopsis, or thale cress. One group of cells promotes seed dormancy, while the other drives germination.

"Bassel’s team discovered tat the two groups collectively function as a decision-making centre by moving hormones from one to the other.

"Using a genetically modified variety of the thale cress that amplified chemical signaling, the researchers found that the two exchange hormones between the two cell groups effectively led to a decision of when to trigger germination.

"The interaction between the cells permitted greater control of the timing of germination, ensuring that the process didn’t start too early – when cold conditions might kill the young plant – or too late, when higher levels of competition might starve it.

“'Our work reveals a crucial separation between the components within a plant decision-making centre,” explains Bassel.

“'In the human brain, this separation is thought to introduce a time delay, smoothing out noisy signals from the environment and increasing the accuracy with which we make decisions. The separation of these parts in the seed ‘brain’ also appears to be central to how it functions.'”

Comment: This pattern of divided control is seen all over cellular controls in animals. It is not surprising to see it is seeds, which to evaluate soil temperature and moisture. The specialized cells can evaluate the information received, and obviously run on information contained in the cell. The responses are automatic once the information is received.

Biological complexity: cell ribosome preferences

by David Turell @, Friday, June 23, 2017, 15:49 (2471 days ago) @ David Turell

Ribosomes make proteins. A new study describes differences in them in a single cell:

http://www.the-scientist.com/?articles.view/articleNo/49721/title/Study--Ribosomes-are-...

"Ribosomes, the cell’s protein-building machines that were thought to be indistinguishable from one another, have specialized functions, according to a pair of studies—one published earlier this month (June 1) in Cell and another published last week (June 15) in Molecular Cell.

“'Until now, each of the 1 [million] to 10 million ribosomes within a cell has been thought to be identical and interchangeable,” study coauthor Maria Barna, a developmental biology and genetics professor at Stanford University, said in a statement. “Now we’re uncovering a new layer of control to gene expression that will have broad implications for basic science and human disease.”

"In the first study, Barna and colleagues reported their findings that ribosomes accumulate different types of proteins around their outer shells, and that these proteins are associated with each ribosome’s function. In their latest study, the researchers discovered that ribosomes preferentially translated certain messenger RNAs to create groups of proteins involved in the same task, such as controlling cell metabolism or the cell cycle.

“'This is really an important step in redefining how we think about this central player in molecular biology,” Jonathan Dinman, a molecular biologist at the University of Maryland in College Park who was not involved in either study, tells Science."

Comment: note how may ribosomes exist in one cell. How much complexity must be demonstrated before the need for design is recognized.

Biological complexity: cell life/death hangs by a thread

by David Turell @, Saturday, June 24, 2017, 02:36 (2470 days ago) @ David Turell

An iron sulfur bond must be maintained by some energy or the cell can die:

https://www.sciencedaily.com/releases/2017/06/170622182832.htm

"Slight changes in the machinery of a cell determine whether it lives or begins a natural process known as programmed cell death. In many forms of life -- from bacteria to humans -- a single chemical bond in a protein called cytochrome c can make this call. As long as the bond is intact, the protein transfers electrons needed to produce energy through respiration. When the bond breaks, the protein switches gear and triggers the breakdown of mitochondria, the structures that power the cell's activities.

"For the first time, scientists have measured exactly how much energy cytochrome c puts into maintaining that bond in a state where it's strong enough to endure, but easy enough to break when the cell's life span is ending.

***

"The study marks the first time that anyone has been able to experimentally quantify how the rigid structure of the cytochrome c molecule supports this crucial bond between iron and sulfur atoms in what's known as an entatic state, where the protein maintains a bond that is just strong enough to perform both of its jobs.

"'This was important because we had shown the bond is weak and shouldn't be present at room temperature in the absence of the protein constraints," says Solomon. "But the protein is able to contribute energy to keep this bond intact for electron transfer. In this LCLS experiment, we determined exactly how much energy the rest of the protein contributes to maintaining the bond: about 4 kcal/mol that is derived from an adjacent hydrogen bond network."

"'We were able to show how nature tunes this system to change the properties on a fundamental level and perform two very different functions," Mara says. "The energy contribution by cytochrome c is really at a sweet spot. (my bold)
***

"Scientists knew from earlier studies that a particular iron-sulfur bond is key. When iron in the protein binds to sulfur contained in one of the protein's amino-acid building blocks, cytochrome c participates in electron transfer. By transferring electrons, the protein helps generate energy needed for biological processes that maintain life.

"But when cytochrome c encounters cardiolipin, a lipid present in the membrane of the cell's mitochondria, the iron-sulfur bond breaks, and the protein becomes an enzyme that creates holes in the mitochondria's outer membrane - the first step in programmed cell death.
These changes occur incredibly fast, in less than 20 picoseconds, so the experiment required ultrafast pulses of X-rays generated by LCLS to take snapshots of the process.

***

"Knowledge of cytochrome c's function is also valuable to the fields of bioenergy and environmental science, since it is a critically important protein in bacteria and plants.

Comment: this is a very precise balance. See my bold above. It is a mechanism in all branches of life. This cannot be the result of chance. Cell processes are designed and directed for them to work. Not by chance!

Biological complexity: enzyme acts like a clam

by David Turell @, Tuesday, June 27, 2017, 23:07 (2467 days ago) @ David Turell

Protein molecules can make motions like tiny machines as tghey work in cell metabolism:

https://www.sciencedaily.com/releases/2017/06/170627105458.htm

The adenylate kinase enzyme is crucial to managing the energy budget of cells, accelerating the biochemical process whereby energy is stored or released. The enzyme continuously changes between open and closed states. In its closed form, adenylate kinase is particularly active biochemically and thus able to accelerate the chemical reaction of "docked" molecules that it has encased like a clam. These are called ligands.

***

The adenylate kinase enzyme opens and closes like a clam: it opens to receive a ligand and closes in order to "process" it biochemically. Afterwards, it opens once again to release it and admit the next ligand. This happens 340 times per second -- much too fast to map the individual stages of the process via structural analysis. (my bold)

***

Kovermann's analyses had already shown that the enzyme's affinity for reaction -- the chemical pull between the enzyme and its ligand -- increases many times over in its closed state, whereas its productive turnover decreases at the same rate. In other words: Chemical activity between ligand and enzyme is particularly high during the closed state. But turnover decreases because the ligand cannot escape the closed "clamshell," which means fewer ligands in total pass through the enzyme.

Kovermann was also able to prove that adenylate kinase's structural dynamic strongly depends upon the interaction between enzyme and ligand- i.e. upon the presence or absence of a ligand. To do so, he compared the enzyme's closed state for both variations, with and without a trapped ligand. If there is no ligand, the closed enzyme's dynamic remains unchanged as compared to its open state. However, once a ligand is present, marked changes can be observed. "This behaviour is counter-intuitive, it's not what one would expect," explains Michael Kovermann.

Comment: Once again, the activity of protein molecules is amazing as they act like moving parts. Remember that enzymes are giant molecules that control the speed of individual molecular reactions, this one at 340 time a second. Too complex for chance. Must be designed by a powerful mind.

Biological complexity: extracellular matrix activity

by David Turell @, Tuesday, July 04, 2017, 14:55 (2460 days ago) @ David Turell

Cell culture studies indicate the extracellular matrix is not inert as thought, but actively controls gene expression and cell activity:

http://www.the-scientist.com/?articles.view/articleNo/48909/title/Location--Location--L...

"That thinking led her to propose, in 1982, that the microenvironmental influence is the ECM, which both chemically and physically interacts with cells. According to Bissell’s ‘dynamic reciprocity’ model, signals from the ECM traveled through transmembrane receptors to a cell’s interior and nucleus, altering its gene expression. “I began to think that the ECM played a role in tissue and organ specificity, because the cells all had the same genetic material, but I realized that there is no constitutive gene expression, that the context changes and so do the cells.”

"To provide evidence for the model, Bissell’s lab developed 3-D culture techniques, allowing differentiation and creation of at least partial tissue architecture of the mammary gland in culture. “If the cellular and tissue architecture is so important, I thought we should be able to take a malignant cell and change its structure and make it normal and also vice versa,” says Bissell. By the early 1980s, integrins—proteins that physically attach the ECM to the cell cytoskeleton—had been discovered. Valerie Weaver, a postdoc in Bissell’s lab, showed that blocking integrins with an inhibitory antibody could revert the malignant phenotype of human breast cancer cells in 3-D culture. Then, in collaboration with Zena Werb of the University of California, San Francisco, the labs showed that proteins called matrix metalloproteinases (MMPs), when upregulated, promote tumor formation, providing evidence that the ECM can encourage malignant transformation and proliferation. Six years later, the two labs revealed that signaling from the MMPs resulted in genomic instability in cells that led to malignancy.

" Bissell’s lab is still buzzing with excitement, continuing to bolster the validity of her dynamic reciprocity model. “When I would give talks and say that laminin [a large extracellular protein that is a major component of the basement membrane] is as important as p53, people would laugh. We have been working on the story of what laminin does for the last eight years, and it is almost complete,” says Bissell. “It probably will be considered one of my most important studies.”

"Over a period of 40 years, was instrumental in developing the field of tumor microenvironments
Developed the concepts that phenotype is dominant over genotype, that context matters, and that cellular and tissue architecture relays messages to cells
Used a “steady-state machine” she helped develop to show that the level of sugar in culture media determined whether chicken cells remained normal or displayed malignant metabolic patterns
In her model of dynamic reciprocity, proposed that the extracellular matrix directly signals to the nucleus and chromatin biochemically and mechanically to regulate gene expression  (my bold)
Developed three-dimensional culture techniques using basement membrane gels to study organ specificity in mammary organoids."

Comment: This scientist notes the automaticity of controls (note my bold) in cells from multicellular organisms. I am convinced bacteria are no different, except Shapiro's discovery that bacteria have extra controls over their DNA, since everything is in one cell

Biological complexity: speed of cellular production

by David Turell @, Wednesday, July 12, 2017, 19:15 (2452 days ago) @ David Turell

RNA molecules control protein production and last only two minutes!

https://phys.org/news/2017-07-rna-molecules-short.html

"RNA molecules are individual transcripts of the cell's DNA. They transfer the genetic information of the DNA and provide a template for the production of proteins that regulate all the cell's processes. The small carriers of information are themselves regulated throughout their lifespan, or rather half-life. After being produced, RNA molecules serve as a template for protein production for a limited time, before they are degraded.

***

"The experiments were repeated for some 50 different genes and showed that 80 percent of all RNAs undergo a rapid turnover, living less than 2 minutes and can be classified as short-lived. Only about 20 percent live longer, for about 5 to 10 minutes. "These results are astounding, if you consider that until now it was assumed that on average RNAs survived 20 minutes in the cell", says Becskei."

Comment: this shows the speed of protein production in cells. It shows that life is more amazing than previously thought.

Biological complexity: speed of cellular production

by Balance_Maintained @, U.S.A., Thursday, July 13, 2017, 06:26 (2451 days ago) @ David Turell

RNA molecules control protein production and last only two minutes!

https://phys.org/news/2017-07-rna-molecules-short.html

"RNA molecules are individual transcripts of the cell's DNA. They transfer the genetic information of the DNA and provide a template for the production of proteins that regulate all the cell's processes. The small carriers of information are themselves regulated throughout their lifespan, or rather half-life. After being produced, RNA molecules serve as a template for protein production for a limited time, before they are degraded.

***

"The experiments were repeated for some 50 different genes and showed that 80 percent of all RNAs undergo a rapid turnover, living less than 2 minutes and can be classified as short-lived. Only about 20 percent live longer, for about 5 to 10 minutes. "These results are astounding, if you consider that until now it was assumed that on average RNAs survived 20 minutes in the cell", says Becskei."

Comment: this shows the speed of protein production in cells. It shows that life is more amazing than previously thought.

It also throws a monkey wrench into the idea that RNA was the initial building block for early life by dramatically compressing the time frame for 'evolution' to occur.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: speed of cellular production

by David Turell @, Thursday, July 13, 2017, 15:26 (2451 days ago) @ Balance_Maintained


David: Comment: this shows the speed of protein production in cells. It shows that life is more amazing than previously thought.


Tony: It also throws a monkey wrench into the idea that RNA was the initial building block for early life by dramatically compressing the time frame for 'evolution' to occur.

I never bought the RNA story, but we don't know the reproductive rate of the initial cells.

Biological complexity: new fatty acid antioxidents

by David Turell @, Friday, July 14, 2017, 14:17 (2450 days ago) @ David Turell

A whole new family of protective fatty acid antioxidants is discovered:

https://www.sciencedaily.com/releases/2017/07/170713153049.htm

"Research led by Nicolas Bazan, MD, PhD,...has discovered a new class of mediators, or biochemical triggers that he named elovanoids (ELVs). Elovanoids are the first bioactive chemical messengers made from omega-3 very long chain polyunsaturated fatty acid (VLC-PUFAs,n-3) that are released in response to cell injury or when cells are confronted with adversities for survival. This discovery provides the first evidence of the existence of elovanoids and of their significant role in protecting and sustaining retinal pigment epithelial (RPE) and photoreceptor cell survival.

"Bazan's lab discovered, identified and structurally characterized this new class of molecules in human retinal pigment epithelial cells. Due to their biology, they are classified as mediators and are derived from docosahexaenoic acid (DHA). DHA is present abundantly in the retina and also serves as a precursor of signaling molecules called docosanoids that promote cell stability and equilibrium and act to protect the cell. The DHA- or eicosapentaenoic acid (EPA)-derived 26 carbon fatty acid is a molecule acted upon by the elongating enzyme ELOVL4, which is expressed in photoreceptor cells. ELOVL4 mutations are linked to vision loss and neuronal dysfunction. This has implications for developing new therapies for conditions such as Stargardt's disease and other forms of retinal degeneration.

"Bazan and his team found that ELVs are made from 32 or 34 carbon-length fatty acid precursors produced naturally in human retinal pigment epithelial (RPE) cells. Most of the known lipid mediators or messengers are derived from 18, 20, or 22 carbon-length fatty acid precursors, including prostaglandins, leukotrienes, lipoxyns, endocanabinoids, resolvins and docosanoids. Elovanoids have structures reminiscent of docosanoids but with different physicochemical properties and alternatively regulated biosynthetic pathways. That elovanoids are longer than all known mediators may be the key to their potency. The longer elovanoids may be able to reach and bind for a longer period of time to receptors in cells necessary to induce cell survival."

Comment: A reminder that we use oxygen to create the energy of life, but oxygen is in and of itself very damaging. Evolving life had to learn to use oxygen and protect itself all at the same time. It could not have been stepwise. It requires design.

Biological complexity: understanding the ribosome

by David Turell @, Saturday, July 22, 2017, 15:36 (2442 days ago) @ David Turell

It is throughout life and manufactures proteins at high speed:

https://phys.org/news/2017-07-optimization-self-production-mysterious-features-ribosome...

"In a new study, a team led by Johan Paulsson, professor of systems biology at Harvard Medical School, mathematically demonstrated that ribosomes are precisely structured to produce additional ribosomes as quickly as possible, in order to support efficient cell growth and division.

"The study's theoretical predictions accurately reflect observed large-scale features of ribosomes—revealing why are they made of an unusually large number of small, uniformly sized proteins and a few strands of RNA that vary greatly in size—and provide perspective on the evolution of an exceptional molecular machine.

***

"Every living cell, whether a single bacterium or a human neuron, is a biological system as dynamic and complex as any city. Contained within cells are walls, highways, power plants, libraries, recycling centers and much more, all working together in unison to ensure the continuation of life.

"The vast majority of these myriad structures are made of and made by proteins. And those proteins are made by ribosomes.

***

"Ribosomes are composed of a puzzlingly large number of different structural proteins—anywhere from 55 to 80, depending on organism type. These proteins are not just more numerous than expected, they are unusually short and uniform in length. Ribosomes are also composed of two to three strands of RNA, which account for up to 70 percent of the total mass of the ribosome.

***

"The team calculated that distributing the task of making a new ribosome among many ribosomes—each making a small piece of the final product—can increase the rate of production by as much as 30 percent, since each new ribosome helps make more ribosomes as soon as they are created, accelerating the process.

"This represents an enormous advantage for cells that need to divide quickly, such as bacteria. However, the protein production process takes time to initiate, and this overhead cost limits the number of proteins that a ribosome can be made of, according to the math.

"The team's models predicted that, for maximum self-production efficacy, a ribosome should be made of between 40 and 80 proteins. Each of these proteins should be around three times smaller than an average cellular protein, and they should all be roughly similar in size.

"It turns out that the researchers' theory, developed completely independently of the laboratory, accurately reflects the observed protein composition of the ribosome.

***

"Their analysis showed that, the more RNA a ribosome is made of, the more rapidly it can be produced. This is because cells can make ribosomal RNA much faster than protein. Thus, while RNA enzymes are thought to be less efficient than protein enzymes, ribosomes have enormous pressure to use as much RNA as possible to maximize the rate at which more ribosomes can be made.

***

"Taken together, the team's theory accurately predicts large-scale features of the ribosome that are seen across domains of life. It explains why the fastest growing organisms, such as bacteria, have the shortest ribosomal proteins and the greatest amounts of ribosomal RNA. At the opposite end of the spectrum are mitochondria—the power plants of eukaryotic cells, which are thought to have once been bacteria that entered a permanent symbiotic state.

"Mitochondria have their own ribosomes that do not produce themselves. Without this pressure, mitochondrial ribosomes are indeed made of larger proteins and far less RNA than cellular ribosomes.

***

"Rather than being mere relics of an evolutionary past, the unusual features of ribosomes thus seem to reflect an additional layer of functional optimization acting on collective properties of its parts, the team writes."

Comment: Much too complex for chance development. Also proves common descent.

Biological complexity: understanding the ribosome

by dhw, Sunday, July 23, 2017, 09:42 (2441 days ago) @ David Turell

QUOTES: "Every living cell, whether a single bacterium or a human neuron, is a biological system as dynamic and complex as any city. Contained within cells are walls, highways, power plants, libraries, recycling centers and much more, all working together in unison to ensure the continuation of life."

"At the opposite end of the spectrum are mitochondria—the power plants of eukaryotic cells, which are thought to have once been bacteria that entered a permanent symbiotic state."

DAVID’s comment: Much too complex for chance development. Also proves common descent.

Thank you for this revealing article. I’ve selected the two quotes and your comment, simply because I feel they should all be highlighted and a casual reader might miss them. You and I rarely agree about anything, but the complexity of the cell remains a major reason why I am unable to embrace atheism. The theory of common descent – which is neither theistic nor atheistic – seems to me to provide a beautifully logical explanation of how all the different life forms have developed, namely through the inventive cooperation of intelligent cells from bacteria onwards. Whether this intelligence springs from a god (or in your theistic version has been preprogrammed or dabbled by a god), from chance, or from some form of panpsychism remains open. (Reblak offers another alternative, but we are both waiting to hear a bit more about the nature of Mother Nature!)

Biological complexity: understanding the ribosome

by David Turell @, Sunday, July 23, 2017, 23:11 (2441 days ago) @ dhw

QUOTES: "Every living cell, whether a single bacterium or a human neuron, is a biological system as dynamic and complex as any city. Contained within cells are walls, highways, power plants, libraries, recycling centers and much more, all working together in unison to ensure the continuation of life."

"At the opposite end of the spectrum are mitochondria—the power plants of eukaryotic cells, which are thought to have once been bacteria that entered a permanent symbiotic state."

DAVID’s comment: Much too complex for chance development. Also proves common descent.

dhw: Thank you for this revealing article. I’ve selected the two quotes and your comment, simply because I feel they should all be highlighted and a casual reader might miss them. You and I rarely agree about anything, but the complexity of the cell remains a major reason why I am unable to embrace atheism. The theory of common descent – which is neither theistic nor atheistic – seems to me to provide a beautifully logical explanation of how all the different life forms have developed, namely through the inventive cooperation of intelligent cells from bacteria onwards. Whether this intelligence springs from a god (or in your theistic version has been preprogrammed or dabbled by a god), from chance, or from some form of panpsychism remains open. (Reblak offers another alternative, but we are both waiting to hear a bit more about the nature of Mother Nature!)

You are welcome.I cannot accept chance. And I view panpsychism as a variation on universal consciousness, an equivalent of God

Biological complexity: understanding the ribosome

by dhw, Monday, July 24, 2017, 13:43 (2440 days ago) @ David Turell

dhw: Whether this intelligence springs from a god (or in your theistic version has been preprogrammed or dabbled by a god), from chance, or from some form of panpsychism remains open. (Reblak offers another alternative, but we are both waiting to hear a bit more about the nature of Mother Nature!)

DAVID: You are welcome.I cannot accept chance. And I view panpsychism as a variation on universal consciousness, an equivalent of God.

Some forms of panpsychism are indeed a God equivalent, but you know very well that the form I am proposing is totally different: namely, the evolution of zillions of individual consciousnesses from the bottom up (as opposed to your sourceless top-down, know-it-all single god). In my opinion, this is no more and no less likely than the god and the chance hypotheses.

Biological complexity: understanding the ribosome

by David Turell @, Monday, July 24, 2017, 16:27 (2440 days ago) @ dhw

dhw: Whether this intelligence springs from a god (or in your theistic version has been preprogrammed or dabbled by a god), from chance, or from some form of panpsychism remains open. (Reblak offers another alternative, but we are both waiting to hear a bit more about the nature of Mother Nature!)

DAVID: You are welcome.I cannot accept chance. And I view panpsychism as a variation on universal consciousness, an equivalent of God.

dhw: Some forms of panpsychism are indeed a God equivalent, but you know very well that the form I am proposing is totally different: namely, the evolution of zillions of individual consciousnesses from the bottom up (as opposed to your sourceless top-down, know-it-all single god). In my opinion, this is no more and no less likely than the god and the chance hypotheses.

OK. We can't explain one form of consciousness (ours) and you want zillions. Are they all alike or dissimilar since the organisms are dissimilar?

Biological complexity: specific cell protein production

by David Turell @, Monday, July 24, 2017, 19:03 (2440 days ago) @ David Turell

New techniques studying specific proteins show how complex cellular production actually is, and helps to differentiate subtypes of cells, not apparent when only microscopic studies are done:

https://www.quantamagazine.org/cell-atlases-reveal-biologys-frontiers-20170712/

"Analyzing patterns of gene expression in individual human immune system cells, the researchers refined the definitions of the types known as dendritic cells and monocytes and identified a novel type that had been overlooked. Moreover, they discovered that a cell population thought to comprise one subtype was actually a mixture of two, which perform different functions.

***

"Turning their attention to the single-cell level, they mapped more than 12,000 proteins to 30 subcellular structures, in turn defining the proteomes — the complete sets of expressed proteins — of more than a dozen major organelles. The researchers identified which proteins were found where, explored variations in protein expression from cell to cell and analyzed how cells segregate chemical reactions within themselves.

"One of the paper’s most salient findings, according to its principal investigator, Emma Lundberg, was that as many as half of our proteins can be found in multiple compartments of a cell. “Everything that proteins do is specific within the context of their environment,” Lundberg said. “If one protein is present in the nucleus but also in the plasma membrane, it might have different functions in those compartments.”

***

"As much as 50 percent of the proteins that her group observed were expressed in more than one part of a cell. If that figure indicates how big multi-functionality could be, Lundberg said, “it makes the cell much more complex and the functionality of the proteome greater.”
This heterogeneity offers deeper insights into the fundamentals of protein function, but it may also explain why, for instance, certain drugs result in unwanted side effects.

***

"The team observed that approximately 15 percent of the proteins exhibited single-cell variation: In a tissue that looked superficially uniform, some cells might differ from their neighbors in the amount or spatial distribution of the proteins they expressed, when one would expect them to be the same. The single-cell RNA sequencing approach of the Human Cell Atlas will allow researchers to create cell profiles based on molecules other than proteins."

Comment: the point is that a cell might like exactly like another cell, but the two cells may be in different production modes, with different genes expressed. The finding of living complexity can only increase as new techniques are employed. Not by chance!

Biological complexity: brain receptor in action

by David Turell @, Monday, July 24, 2017, 21:12 (2440 days ago) @ David Turell

A highly complex molecule opens a pore like a camera shutter to allow ions to move creating the connecting synapses to occur and transmit impulses:

https://medicalxpress.com/news/2017-07-scientists-capture-image-major-brain.html

"Columbia University Medical Center (CUMC) researchers have captured the first three-dimensional snapshots of the AMPA-subtype glutamate receptor in action. The receptor, which regulates most electrical signaling in the brain, is involved in several important brain activities, including memory and learning.

***

"'With our new findings, we can now, for the first time, visualize how the neurotransmitter glutamate opens glutamate receptor ion channels," said Alexander Sobolevsky, PhD, associate professor of biochemistry and molecular biophysics at Columbia and senior author of the paper. "This is the fundamental process that directly affects learning and memory.

***

"Most signaling in the brain is triggered by glutamate, a neurotransmitter that activates proteins on the surface of neurons called glutamate receptors. Glutamate receptors underlie a variety of high cognitive functions, including learning and memory. AMPA receptors are glutamate receptors that open and close very quickly—in less than a millisecond—and are involved in fast processes in the brain, such as the rapid perception and reaction of an organism to its surrounding environment.

"Previously, the Sobolevsky lab deciphered the structures of the AMPA receptor alone and in complex with other proteins that regulate the speed and strength of synaptic connections. In the current study, the researchers captured the AMPA receptor in action, as glutamate activates the receptor to allow ions to flow through its channel and initiate signaling in the brain. This provides the first precise insights into how receptors mediate brain function.

"To freeze the AMPA receptor in an active state, the researchers fused it with stargazin, a regulatory protein that prompts the channel to open. The images they captured show that when signaling molecules such as glutamate are present, the entrance to the AMPA receptor, which consists of four units, opens up like a camera's iris, or aperture, to reveal its pore. To shepherd the ions through, the receptor widens the diameter of its channel, and a specialized channel pore lining ushers the ions into the cell.

"'These new fundamental discoveries have implications for our understanding of neurotransmission by glutamate, our brain's major neurotransmitter" says Edward C. Twomey, a PhD candidate at CUMC and first author of the paper. "Understanding these processes will impact future studies on glutamate receptor signaling in neurodegenerative diseases as well as drug design.'"

Comment: be sure to look at the article to see models of the molecule, made up of thousands of amino acids in an exact order and folding for proper function. This complexity is not by chance!

Biological complexity: specific cell protein production

by David Turell @, Wednesday, July 26, 2017, 22:42 (2438 days ago) @ David Turell

Another review of this study in the complexity of cell proteins:

https://darwins-god.blogspot.com/2017/07/subcellular-map-of-human-proteome.html

"New research is using antibodies to map out the spatio-temporal locations of 12,003 different proteins in human cells. The results are another example of how, as Bruce Alberts put it in 1998: “We have always underestimated cells.” Alberts explained how cells were once naively viewed as something of a random affair, where molecules “were thought to diffuse freely, randomly colliding.” The new research reveals the “the highly complex architecture of the human cell” and adds more detail to the fact that the workings of the cell are far from random:

"A total of 12,003 proteins targeted by 13,993 antibodies were classified into one or several of 30 cellular compartments and substructures, altogether defining the proteomes of 13 major organelles.

"Although evolutionists “thought the cell was so simple,” this research is showing that the “cellular proteome is compartmentalized and spatiotemporally regulated to a high degree.” In fact “[m]ore than half of these 12,003 proteins localize in more than one compartment at the same time.” This is consistent with the fact that most proteins are capable of performing multiple functions, and is another indicator of high complexity:

"Moreover, proteins that localize to more than one compartment may have context-specific functions, increasing the functionality of the proteome. The fact that proteins “moonlight” in different parts of the cell is now well accepted. … The more complex a system is, the greater the number of parts that must be sustained in their proper place, and the lesser the tolerance for errors; therefore, a high degree of regulation and control is required.

"Indeed, the degree of regulation and control required for this system is not only enormous, but contrary to evolutionary expectations."

Comment: the complexity of the cell cannot be explained by evolutionary theory, which starts after life appears. The original cells of life were obviously more complex than chance can produce.

Biological complexity: understanding the ribosome

by Balance_Maintained @, U.S.A., Tuesday, July 25, 2017, 07:10 (2439 days ago) @ dhw

dhw: Whether this intelligence springs from a god (or in your theistic version has been preprogrammed or dabbled by a god), from chance, or from some form of panpsychism remains open. (Reblak offers another alternative, but we are both waiting to hear a bit more about the nature of Mother Nature!)

DAVID: You are welcome.I cannot accept chance. And I view panpsychism as a variation on universal consciousness, an equivalent of God.

Some forms of panpsychism are indeed a God equivalent, but you know very well that the form I am proposing is totally different: namely, the evolution of zillions of individual consciousnesses from the bottom up (as opposed to your sourceless top-down, know-it-all single god). In my opinion, this is no more and no less likely than the god and the chance hypotheses.

DHW: Where is the cut off point for this intelligence? Is it cellular? Molecular? Atomic? Where is the demarcation for you to say 'There is no intelligence beyond this point"? I only ask because that is where the discussion needs to start really, not at some nebulous, ill defined point in the transition between chemical soup and single cell. Further, this study would seem on the surface to demolish that concept because getting 50+ atypical proteins and a few RNA together at the same time in the same place to form a Ribosome which is incredibly complex and needed in turn to make the infinitely more complex cell requires a great deal more planning and work then I am prepared to accept as coming from inorganic matter.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: understanding the ribosome

by dhw, Tuesday, July 25, 2017, 13:38 (2439 days ago) @ Balance_Maintained

dhw: Whether this intelligence springs from a god (or in your theistic version has been preprogrammed or dabbled by a god), from chance, or from some form of panpsychism remains open. (Reblak offers another alternative, but we are both waiting to hear a bit more about the nature of Mother Nature!)
DAVID: You are welcome.I cannot accept chance. And I view panpsychism as a variation on universal consciousness, an equivalent of God.
dhw: Some forms of panpsychism are indeed a God equivalent, but you know very well that the form I am proposing is totally different: namely, the evolution of zillions of individual consciousnesses from the bottom up (as opposed to your sourceless top-down, know-it-all single god). In my opinion, this is no more and no less likely than the god and the chance hypotheses.
DAVID: OK. We can't explain one form of consciousness (ours) and you want zillions. Are they all alike or dissimilar since the organisms are dissimilar?

We can’t explain any form of consciousness, and it is not an explanation to argue that there is one unexplained consciousness (God) that invented every other form of consciousness. Since organisms are dissimilar, it is obvious that the zillions are also dissimilar, but if we are talking about the origin of life, we must start with the hypothethical, rudimentary consciousnesses of blobs of inorganic matter which amalgamate and with time and experience increase their degree of consciousness and their range of dissimilarity until they come up with the living cell. No, I don’t believe it. I offer it as an alternative to the other two equally unbelievable hypotheses.

Xxxxx

TONY: DHW: Where is the cut off point for this intelligence? Is it cellular? Molecular? Atomic? Where is the demarcation for you to say 'There is no intelligence beyond this point"? I only ask because that is where the discussion needs to start really, not at some nebulous, ill defined point in the transition between chemical soup and single cell. Further, this study would seem on the surface to demolish that concept because getting 50+ atypical proteins and a few RNA together at the same time in the same place to form a Ribosome which is incredibly complex and needed in turn to make the infinitely more complex cell requires a great deal more planning and work then I am prepared to accept as coming from inorganic matter.

I agree with all your objections. As above, in my response to David, the panpsychist process would have to start at a rudimentary atomic level, and in the course of billions of years build up to the point at which it forms the single cell. The same progression of increasing intelligence as that from the single cell to ourselves (which I do find credible, though not sufficiently so for me to be convinced). I can only repeat that here I am offering alternative hypotheses for the origin of life. I can’t believe in this one, any more than I can believe in chance or in an eternal, inexplicable, sourceless mind with the knowledge and power to create a seemingly infinite universe and all the complexities of life. This scepticism is one main reason why I remain agnostic: I cannot find an explanation that convinces me.

Biological complexity: understanding the ribosome

by David Turell @, Tuesday, July 25, 2017, 16:16 (2439 days ago) @ dhw

dhw: Since organisms are dissimilar, it is obvious that the zillions are also dissimilar, but if we are talking about the origin of life, we must start with the hypothethical, rudimentary consciousnesses of blobs of inorganic matter which amalgamate and with time and experience increase their degree of consciousness and their range of dissimilarity until they come up with the living cell. No, I don’t believe it. I offer it as an alternative to the other two equally unbelievable hypotheses.

Answered below


Xxxxx

TONY: DHW: Where is the cut off point for this intelligence? Is it cellular? Molecular? Atomic? Where is the demarcation for you to say 'There is no intelligence beyond this point"? I only ask because that is where the discussion needs to start really, not at some nebulous, ill defined point in the transition between chemical soup and single cell. Further, this study would seem on the surface to demolish that concept because getting 50+ atypical proteins and a few RNA together at the same time in the same place to form a Ribosome which is incredibly complex and needed in turn to make the infinitely more complex cell requires a great deal more planning and work then I am prepared to accept as coming from inorganic matter.

dhw: I agree with all your objections. As above, in my response to David, the panpsychist process would have to start at a rudimentary atomic level, and in the course of billions of years build up to the point at which it forms the single cell.

You have forgotten the history of life on Earth. Current theory: Earth forms about 4.5 billion years ago; becomes cool enough and calm enough about 4.0 billion years ago to begin to allow for life; first life at 3.8 billion years ago. Result: it took just 200 million years to create life, not billions of years. Surely that suggests agency.

Biological complexity: understanding the ribosome

by dhw, Wednesday, July 26, 2017, 09:41 (2438 days ago) @ David Turell

Dhw (to Tony): I agree with all your objections. As above, in my response to David, the panpsychist process would have to start at a rudimentary atomic level, and in the course of billions of years build up to the point at which it forms the single cell. The same progression of increasing intelligence as that from the single cell to ourselves (which I do find credible, though not sufficiently so for me to be convinced)

DAVID: You have forgotten the history of life on Earth. Current theory: Earth forms about 4.5 billion years ago; becomes cool enough and calm enough about 4.0 billion years ago to begin to allow for life; first life at 3.8 billion years ago. Result: it took just 200 million years to create life, not billions of years. Surely that suggests agency.

Tony’s question concerned the beginning of panpsychist “intelligence”, and my point was that it would have to begin with inorganic matter at an atomic level. In other words, we are talking about the time when the Earth was formed, not the time when conditions became suitable for life. Even today there are bacteria that live in the most hostile conditions, but they mark the beginning of intelligent life. You left out my important third sentence, which offers an analogy. If matter has some rudimentary form of intelligence, it will make no difference whether conditions are suitable for life or not. This would apply to all matter throughout the universe, most of which as far as we know is totally unsuitable for life but which panpsychists still believe to be possessed of some kind of intelligence. As I keep saying, it’s hard to believe. So is a single mind that is big and powerful and knowledgeable enough to create and encompass possible infinity and eternity.

Biological complexity: understanding the ribosome

by David Turell @, Wednesday, July 26, 2017, 16:40 (2438 days ago) @ dhw

Dhw (to Tony): I agree with all your objections. As above, in my response to David, the panpsychist process would have to start at a rudimentary atomic level, and in the course of billions of years build up to the point at which it forms the single cell. The same progression of increasing intelligence as that from the single cell to ourselves (which I do find credible, though not sufficiently so for me to be convinced)

DAVID: You have forgotten the history of life on Earth. Current theory: Earth forms about 4.5 billion years ago; becomes cool enough and calm enough about 4.0 billion years ago to begin to allow for life; first life at 3.8 billion years ago. Result: it took just 200 million years to create life, not billions of years. Surely that suggests agency.

dhw: Tony’s question concerned the beginning of panpsychist “intelligence”, and my point was that it would have to begin with inorganic matter at an atomic level. In other words, we are talking about the time when the Earth was formed, not the time when conditions became suitable for life. Even today there are bacteria that live in the most hostile conditions, but they mark the beginning of intelligent life. You left out my important third sentence, which offers an analogy. If matter has some rudimentary form of intelligence, it will make no difference whether conditions are suitable for life or not. This would apply to all matter throughout the universe, most of which as far as we know is totally unsuitable for life but which panpsychists still believe to be possessed of some kind of intelligence. As I keep saying, it’s hard to believe. So is a single mind that is big and powerful and knowledgeable enough to create and encompass possible infinity and eternity.

If matter has intelligence that fits my proposal that the universe is a part of God's consciousness

Biological complexity: understanding the ribosome

by dhw, Thursday, July 27, 2017, 10:32 (2437 days ago) @ David Turell

dhw: Tony’s question concerned the beginning of panpsychist “intelligence”, and my point was that it would have to begin with inorganic matter at an atomic level. In other words, we are talking about the time when the Earth was formed, not the time when conditions became suitable for life. Even today there are bacteria that live in the most hostile conditions, but they mark the beginning of intelligent life. You left out my important third sentence, which offers an analogy. If matter has some rudimentary form of intelligence, it will make no difference whether conditions are suitable for life or not. This would apply to all matter throughout the universe, most of which as far as we know is totally unsuitable for life but which panpsychists still believe to be possessed of some kind of intelligence. As I keep saying, it’s hard to believe. So is a single mind that is big and powerful and knowledgeable enough to create and encompass possible infinity and eternity.

DAVID: If matter has intelligence that fits my proposal that the universe is a part of God's consciousness

Why are you trying to pretend that my alternative hypothesis is the same as yours? You insist on a single, all-knowing mind, a “person like no other”, who created matter. My (atheistic) panpsychist alternative is zillions of blobs of matter with the most rudimentary of minds which, in the course of time, as matter and energy constantly transform themselves into an infinite number of combinations and forms, increase their knowledge until eventually one product among zillions is the living cell. And the living cell continues the process of combining and increasing knowledge and variety of forms. Bottom up atheistic evolution as opposed to top down theistic evolution. Two equally incredible hypotheses, one of which must be closer to the truth than the other.

Biological complexity: understanding the ribosome

by David Turell @, Thursday, July 27, 2017, 15:20 (2437 days ago) @ dhw


DAVID: If matter has intelligence that fits my proposal that the universe is a part of God's consciousness

dhw: Why are you trying to pretend that my alternative hypothesis is the same as yours? You insist on a single, all-knowing mind, a “person like no other”, who created matter. My (atheistic) panpsychist alternative is zillions of blobs of matter with the most rudimentary of minds which, in the course of time, as matter and energy constantly transform themselves into an infinite number of combinations and forms, increase their knowledge until eventually one product among zillions is the living cell. And the living cell continues the process of combining and increasing knowledge and variety of forms. Bottom up atheistic evolution as opposed to top down theistic evolution. Two equally incredible hypotheses, one of which must be closer to the truth than the other.

I'm not pretending. I think God is universal consciousness and His consciousness is part of everything in the universe.

Biological complexity: understanding the ribosome

by dhw, Friday, July 28, 2017, 11:26 (2436 days ago) @ David Turell

DAVID: If matter has intelligence that fits my proposal that the universe is a part of God's consciousness

dhw: Why are you trying to pretend that my alternative hypothesis is the same as yours? You insist on a single, all-knowing mind, a “person like no other”, who created matter. My (atheistic) panpsychist alternative is zillions of blobs of matter with the most rudimentary of minds which, in the course of time, as matter and energy constantly transform themselves into an infinite number of combinations and forms, increase their knowledge until eventually one product among zillions is the living cell. And the living cell continues the process of combining and increasing knowledge and variety of forms. Bottom up atheistic evolution as opposed to top down theistic evolution. Two equally incredible hypotheses, one of which must be closer to the truth than the other.

DAVID: I'm not pretending. I think God is universal consciousness and His consciousness is part of everything in the universe.

You were pretending that my hypothesis amounted to the same as yours, and I have tried to explain why the two hypotheses are completely different.

Biological complexity: understanding the ribosome

by David Turell @, Friday, July 28, 2017, 18:31 (2436 days ago) @ dhw


DAVID: I'm not pretending. I think God is universal consciousness and His consciousness is part of everything in the universe.

dhw: You were pretending that my hypothesis amounted to the same as yours, and I have tried to explain why the two hypotheses are completely different.

Tiny minds all over the place with no overall control vs. one single mind in control

Biological complexity: understanding the ribosome

by dhw, Saturday, July 29, 2017, 08:29 (2435 days ago) @ David Turell

DAVID: If matter has intelligence that fits my proposal that the universe is part of God’s consciousness.

dhw: Why are you pretending that my alternative proposal is the same as yours?

DAVID: I'm not pretending. I think God is universal consciousness and His consciousness is part of everything in the universe.

dhw: You were pretending that my hypothesis amounted to the same as yours, and I have tried to explain why the two hypotheses are completely different.

DAVID: Tiny minds all over the place with no overall control vs. one single mind in control

Precisely – the complete opposite of your hypothesis (and not a bad description of the higgledy-piggledy history of evolution).

xxxxxx

Tony: If matter at the atomic or subatomic level has intelligence, then aren't you essentially equating intelligence to energy as it is the common component between organic brains and inorganic matter?

DAVID: I think God is pure energy.

The idea that intelligence is a form of energy lies at the heart of my attempt to find a compromise between materialism and dualism. I have had one go at it, and will return to it when I have time. (I can’t actually find my first attempt, but it must be there somewhere!)

Biological complexity: understanding the ribosome

by Balance_Maintained @, U.S.A., Friday, July 28, 2017, 16:50 (2436 days ago) @ David Turell

If matter at the atomic or subatomic level has intelligence, then aren't you essentially equating intelligence to energy as it is the common component between organic brains and inorganic matter?

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: understanding the ribosome

by David Turell @, Friday, July 28, 2017, 18:52 (2436 days ago) @ Balance_Maintained

Tony: If matter at the atomic or subatomic level has intelligence, then aren't you essentially equating intelligence to energy as it is the common component between organic brains and inorganic matter?

I think God is pure energy

Biological complexity: cell division controls

by David Turell @, Sunday, July 30, 2017, 23:44 (2434 days ago) @ David Turell

Our cells are in constant division and reproduction. Chromosomes must be controlled to always keep the same number with the same genes:

https://phys.org/news/2017-07-human-cells-chromosomes.html

"Cell division is an essential process in humans, animals and plants as dying or injured cells are replenished throughout life. Cells divide at least a billion times in the average person, usually without any problem. However, when cell division goes wrong, it can lead to a range of diseases, such as cancer, and problems with fertility and development, including babies born with the wrong number of chromosomes as in Down's syndrome.

***

"During cell division, a mother cell divides into two daughter cells, and during this process the DNA in the mother cell, wrapped up in the form of chromosomes, is divided into two equal sets. To achieve this, rope-like structures called microtubules capture the chromosomes at a special site called the kinetochore, and pull the DNA apart," said Dr Viji Draviam.

***

"We have identified two proteins - tiny molecular machines - that enable the correct attachment between the chromosomes and microtubules. When these proteins don't function properly, the cells can lose or gain a chromosome. This finding gives us a glimpse of an important step in the process of cell division."

***

"Using high resolution microscopes to video the inner workings of live human cells, Dr Draviam and her colleagues at the University of Cambridge (UK) and the European Molecular Biology Laboratory in Heidelberg (Germany), discovered that two proteins - Aurora-B kinase and BubR1-bound PP2A phosphatase - act in opposition to each other, adding or removing phosphate groups respectively, to correctly control the attachment of microtubules to the chromosomes.

"Co-author Duccio Conti, who is Dr Draviam's PhD student, said: "We found that a balance between Aurora-B kinase and BubR1-bound phosphatase is important to maintain correct chromosome numbers in human cells.'"

Comment: A microscopic picture of cell division shows the chromosomes lined up across the median of the cell about to divide. The microtubules stretch in either direction to points at opposite sides like two back to back harps. Then the chromosomes are pulled apart as the cell divides, with DNA equally divided in two. We now know that two enzymes play a major role. How this developed through chance evolution cannot be explained. It has to be put together by design all at once to have any possibility of proper development. Further, old story, enzymes are very exactly designed for their purpose, and are giant molecules made up of exactly sequenced and folded amino acids numbering from the several hundreds to thousands. Life functions only because of thousands of these specialized molecules which have just one function, or occasionally two. Not by chance!

Biological complexity: immunity feedback loop

by David Turell @, Sunday, August 06, 2017, 18:41 (2427 days ago) @ David Turell

A new immune T cell has been found which tends to keep regular T cells under control. All of life's processes has activator and depressor controls to keep everything within proper limits. Both have to be developed simultaneously or new processes would act out of control:

https://www.sciencedaily.com/releases/2017/08/170804124005.htm

"Type 1 regulatory (Tr1) cells are a type of regulatory immune cell that help suppress immune responses, including inflammation and tissue damage, but very few details were known about their development and function.

"A new study with mice and humans, published in the journal Nature Communications, describes how an enzyme called ITK plays a crucial role in the development of Tr1 cells during an immune response. The enzyme offers an entry point for researchers to manipulate the development of Tr1 cells to enhance them to treat allergies, for instance, or block their development to treat viral and bacterial infections.

***

"Doctors employ antigen immunotherapy to treat allergies by administering a regimen that exposes a patient to increasing doses of an allergen over a period of months. Since allergies are caused by an overactive immune response to an allergen, the treatment works because Tr1 cells help suppress the immune system and lower inflammation. In the future, clinicians may want to enhance the pathway to produce more Tr1 cells, August said.

"But when treating viral infections such as the flu, bacterial infections and tumors, clinicians may want to selectively block the pathway to lower the number of Tr1 cells. In experiments with mice, August and colleagues found that Tr1 cells increase when a mouse is infected with viruses or bacteria or when fighting tumors.

***

"This is a balance because these cells are there for a purpose, and we think their purpose is to make sure the immune system doesn't destroy and cause pathology in an immune response," August said. (my bold)

"The danger with flu, for example, is that at a certain point other types of immune system T cells, whose purpose is to kill infected cells, start to destroy tissue. In such cases, an overactive immune response can lead to death.

***

"In the study, August, Huang and their colleagues bred genetically altered mice so they carried a gene that makes Tr1 cells glow green when they develop, which allows for easy tracking. They then bred another type of mouse that had fluorescent Tr1 cells and also allowed the researchers to specifically block the enzymatic activity of ITK. Using the same protocol, they created a third type of mouse that lacked ITK.

"In both the mice where ITK was inhibited and the mice that lacked ITK, Tr1 cells failed to develop. Using blood cells from anonymous human volunteers, they got the same results.

"In a second experiment, the researchers identified a second critical enzyme in the pathway that leads to the development of Tr1 cells. This other enzyme, called IRF4, is a transcription factor that regulates the expression of a number of genes and proved key for controlling whether Tr1 cells developed. The team also confirmed that the same pathway exists in people.:

Comment: To my mind the evidence of design is overwhelming. There are two enzymes to develop Tr1 cells. These specialized giant molecules must be created and the Tr1 feedback control must be put in place for the system to work. All multicellular animal life has inflammatory reactions to fight infections. Only design saltation fits this process.

Biological complexity: platelet glucose metabolism

by David Turell @, Sunday, August 06, 2017, 19:02 (2427 days ago) @ David Turell

Without glucose platelets can be produced but in smaller quantities. The pathways are outlined for glucose use. As usual very complex:

https://www.sciencedaily.com/releases/2017/08/170804123941.htm

"We found that glucose metabolism is very critical across the entire life cycle of platelets -- from production, to what they do in the body, to how they get cleared from the body," says E. Dale Abel, MD, PhD, professor and DEO of internal medicine at the UI Carver College of Medicine and director of the Fraternal Order of Eagles Diabetes Research Center at the UI.

"Two proteins -- glucose transporter (GLUT) 1 and GLUT3 -- are required for glucose to enter platelets. Abel and his colleagues studied genetically engineered mouse models that were missing GLUT1 and GLUT3 or GLUT3 alone and observed how platelet formation, function, and clearance were affected. (my bold)

In the absence of the ability to metabolize glucose, the mice did produce platelets, and the platelets' mitochondria metabolized other substances in place of glucose to do their job of generating the cells' energy. But the mice had platelet counts that were lower than normal.

***

"The researchers were able to pinpoint two causes for the low platelet count in mice lacking GLUT1 and GLUT3: fewer platelets being produced, and increased clearance of platelets.
Platelets are created by cells in the bone marrow called megakaryocytes. The researchers tested the megakaryocytes' ability to generate new platelets by depleting the blood of platelets and observing the subsequent recovery, which was lower than normal. They also tested the megakaryocytes in culture, stimulating them to create new platelets, and found that the generation of new platelets was defective.

"'Clearly, we show that there's an obligate need for glucose to bud platelets off from the bone marrow," Abel says.

"In addition, the team observed that young platelets functioned normally, even in the absence of glucose. But as they aged, the platelets were cleared from the circulation earlier than normal because they were being destroyed.

"We identified a new mechanism of necrosis by which the absence of glucose leads to the cleavage of a protein called calpain, which marks them for this necrotic pathway," Abel says. "If we treated the animals with a calpain inhibitor, we could reduce the increased platelet clearance."

"The team also sought to determine whether platelets could exist and function when mitochondria metabolism is halted. The mice were injected with a mitochondrial poison at a dose that a healthy mouse can tolerate. In the mice deficient in GLUT1 and GLUT3, however, platelet counts dropped to zero within about 30 minutes.

***

"In the related study in ATVB, the research team showed that GLUT3 played the predominant role in platelet activation and that mice with reduced GLUT3 in platelets survived pulmonary embolism and developed less severe arthritis in a model of rheumatoid arthritis.

***

"'We know that in diabetes, platelets are using too much glucose," Abel says. "This increase in glucose metabolism does correlate with the platelet hyperactivity that characterizes many diabetic vascular complications. Reducing the ability of platelets to use glucose could be of therapeutic benefit in the context of diabetes.'"

Comment: Platelets are vital particles. They set off clotting at wounds. Their lifetime is about 10 days, so a constant supply is vital. Note their production and actions depend upon two distinct specialized proteins (note my bold) allowing glucose to enter them. Once again this complexity requires design for initial development.

Biological complexity: wiring taste buds

by David Turell @, Wednesday, August 09, 2017, 18:36 (2424 days ago) @ David Turell

Taste bud cells are constantly remade and have special wiring methods:

https://medicalxpress.com/news/2017-08-rewired-reveals-flavors-tongue-brain.html

"By tangling up bitter- and sweet-sensing cells on the tongues of mice, researchers have teased apart how the taste system wires itself. The results, from Howard Hughes Medical Institute (HHMI) Investigator Charles Zuker at Columbia University and colleagues, reveal how cells constantly reconnect to keep taste abilities running smoothly, allowing flavor information to flow from tongue to brain.

"The ability to sense sweet, bitter, salty, sour, and savory (also called umami) is innate, says Hojoon Lee, a postdoctoral researcher in Zuker's lab who led the study, which is published August 9 in the journal Nature. "We are born to be averse to sour or bitter tastes and attracted to sweet things," he says.

"Although it may seem like taste is merely a matter of pleasure (or mild disgust), those responses can be key to survival, especially for other animals. Sweet tastes can signal nutrient-dense fare, whereas bitter tastes can mark a deadly poison.

"For such an important job, the taste system has remarkably high turnover. Like a string of fritzy Christmas lights, the cells on the tongue that detect tastes are constantly dying and being replaced. These cells, called taste receptor cells, are nestled on the taste buds and live for only about two weeks—which means that stem cells need to churn out new taste receptor cells continually.

"The short life span of taste cells created a conundrum, Zuker says: Amid such high turnover, how does the taste system do its job reliably? Connections between cells in the taste buds and neurons must be re-wired correctly each time for the taste system to work. "If you don't connect properly, you're going to be triggering the wrong behavioral responses," Zuker says. But just how the taste system pulled off this feat was a mystery.

"'Essentially, very little was known about the wiring of the taste system," Lee says. Using sophisticated genetics and single-cell functional imaging, Zuker, Lee, and colleagues created genetically modified mice with mixed-up taste systems. Then, the researchres watched how the miswiring linked bitter taste receptor cells to sweet neurons or sweet receptor cells to bitter neurons.

"Each taste receptor cell is tuned to detect one of the five flavors. When the cell recognizes a chemical taste, it jumps into action. This activity is picked up by a bundle of nerves originating in ganglion neurons located just behind the mice's ears. These neurons send taste messages from the tongue to the brain.

"To figure out how ganglion neurons find and reconnect to the correct newly-born taste receptor cells, Zuker, Lee and colleagues focused on bitter and sweet. Using a method called RNA-seq, they found two molecules that may function as critical signals. Bitter-sensing taste receptor cells produced a molecule called Semaphorin 3A, while sweet-sensing taste receptor cells had an abundance of different one, Semaphorin 7A. Both molecules are known to help neural circuits wire up correctly.

"Next, the researchers tested mutant mice with bitter-sensing taste receptor cells that lacked Semaphorin 3A. Most ganglion neurons usually hook up with receptor cells that all sense the same flavor. But without Semaphorin 3A, previously bitter ganglion neurons expanded their repertoire and reached out to other kinds of taste receptor cells. Nearly half of these ganglion cells also responded to sweet, umami and salty flavors, the researchers found.

***

"The results confirm the idea that specific chemical signals in newborn taste receptor cells can pull the right nerve cell connections toward them, creating cellular links that lead to proper taste sensation. "As new taste cells are born, they provide the right instructions to establish the right connection," Zuker says.

"The experiments were done in mice, but because of the strong similarities between human and mice taste systems, Lee suspects the results may apply to humans too. And by revealing how the taste system continually remakes itself, the work may lead to a deeper understanding of how the senses are assembled and wired, and how their signals make their way to the brain."

Comment: The rapid turnover of this system requires that it was designed all at once. Finding the specific proteins out of the millions possible to have the right functional capacity as a chance process is obviously highly unlikely. This is a saltation.

Biological complexity: make way for hemoglobin

by David Turell @, Friday, August 18, 2017, 22:16 (2415 days ago) @ David Turell

Red blood cells are champion examples of design. They are shaped like donuts but the center is not completely open offering the best shaped surface diffusion area to allow oxygen to be delivered to the tissues and CO2 to be escorted out to the

https://medicalxpress.com/news/2017-08-hemoglobin.html

"Every cell in the body, whether skin or muscle or brain, starts out as a generic cell that acquires its unique characteristics after undergoing a process of specialization. Nowhere is this process more dramatic than it is in red blood cells.

"In order to make as much room as possible for the oxygen-carrying protein hemoglobin, pretty much everything else inside these precursor red blood cells—nucleus, mitochondria, ribosomes and more—gets purged. Jam-packing red blood cells with hemoglobin is essential. Doing so ensures that all the body's tissues and organs are well nourished with oxygen to carry on their normal functions.

"But how does this cell remodeling take place to begin with?

***

"During cell specialization, unwanted parts of a generic, immature cell are removed by the proteasome, protein-gobbling strings of molecules, or the cells' "trash compactors," says study first author Anthony Tuan Nguyen, an HMS MD-PhD student.

"The researchers set out to find the mechanism that controls which parts get destroyed and which parts are spared before the precursor red blood cell becomes a full-fledged one.

"Finley had a hunch that the process was controlled by an enzyme called UBE2O, which he and colleagues identified in the 1990s. The enzyme marks cell parts for destruction by tagging them with a small protein called ubiquitin. This tagging allows the proteasome to recognize cells destined for destruction. The vast machinery, known as the ubiquitin-proteasome system (UPS), is switched on constantly throughout the body to remove unnecessary proteins and keep cells free of clutter.

***

"While studying blood cells, Fleming had identified a mutant mouse that lacked the UBE2O enzyme. Knowing that Finley was interested in the enzyme and its possible role in cell specialization, Fleming contacted him.

"The researchers observed that mice without the enzyme were anemic, a marker of red blood cell deficiency. The observation supported the notion that UBE2O may play a role in red blood cell development.

"Using a series of tests that relied on large-scale protein analyses not available in earlier decades, the researchers confirmed the enzyme's role. Their results revealed that immature red blood cells lacking UBE2O retained hundreds of proteins and failed to become specialized.

"The researchers also demonstrated that when isolated from immature red blood cells and tested in other cell types, UBE2O still marked the right proteins for destruction, suggesting that the enzyme is the primary regulator of red blood cell specialization."

Comment: This is one of the best examples of design I've ever seen: the shape of the red cell, which is basically a bag of hemoglobin, hemoglobin, itself, with its unique properties of carrying oxygen in one direction and CO2 in the other, and its formation with the help a unique enzyme, remembering that all enzymes are huge molecules of a very specialized design. Only a planning mind can create this system.

Biological complexity: beating cilia controls

by David Turell @, Sunday, August 20, 2017, 18:29 (2413 days ago) @ David Turell

Liquids are moved in the body by hair-like cilia all beating in synchronized fashion like rowers in a boat:

https://www.sciencedaily.com/releases/2017/08/170818102316.htm

"Researchers have revealed that a molecule called Daple is essential for the correct orientation and coordinated beating of cilia on the surface of cells lining ventricles in the brain. Without Daple, the cilia develop a random arrangement and cannot produce a uniform flow of CSF. This in turn leads to a build-up of fluid, which is associated with swelling of the head, known as hydrocephalus.

"Some cells in the body contain long thin structures called cilia on their surface, which exhibit a whip-like motion that promotes the flow of fluid past the cell. Although these cilia are known to play vital roles in the body, much remains to be understood about their molecular components and the mechanisms by which they work. This is especially true for the cilia on cells that line the ventricles of the brain, which contain cerebrospinal fluid (CSF) that has various functions including cushioning the brain against potentially damaging impacts.

"A team at Nagoya University has shed light on this issue by revealing that a molecule called Daple is essential for cilia to adopt an arrangement by which they can beat in one direction at the same time, thereby creating a flow of fluid past the cell exterior. This arrangement on cell surfaces all along the lining of ventricles in the brain ensures the correct flow of CSF, which in turn prevents its accumulation associated with brain swelling known as hydrocephalus.

***

"The findings also showed that the lack of Daple stopped cilia all adopting the same orientation on the same side of cells. Without the cilia all beating in the same direction, there would be no directional flow of CSF, leading to its accumulation and subsequent swelling.

"According to Masahide Takahashi, "Daple functions through a cytoplasmic structure called microtubules, which are protein filaments involved in various functions including maintaining the overall structure of cells. When Daple is absent, the microtubules are unable to accurately specify the arrangement of structures called basal bodies, from which the cilia develop."

"The team's findings should lead to a deeper understanding of diseases caused by the dysfunction of cilia. These include not only hydrocephalus, but also asthma and even female infertility, given the structural and functional similarities of cilia in the trachea and oviduct."

Comment: This is an irreducibly complex system that had to be designed from the beginning to be sure that liquid flowed in the proper direction. Has to work in the oviduct or the egg will not move to the uterus to be fertilized.

Biological complexity: zebrafish smell ATP for food

by David Turell @, Friday, September 01, 2017, 16:54 (2401 days ago) @ David Turell

They are shown to smell molecules from organisms they eat:

http://www.the-scientist.com/?articles.view/articleNo/50151/title/Fish-Smell-ATP-to-Fin...

"Studies have shown that fish sense ATP, the cellular unit of energy, and follow concentration gradients of the molecule released by zooplankton to track down their next meal. Testing zebrafish in the lab, neurobiologist Yoshihiro Yoshihara of the RIKEN Brain Science Institute in Japan and colleagues found that ATP appeared to activate a small number of short, pear-shape olfactory sensory neurons at the very tip of the nose.

"When the researchers hunted for ATP receptors in the zebrafish genome, they found a novel receptor called A2c. Cell culture experiments revealed that A2c was not directly activated by ATP, however; two enzymes, tissue-nonspecific alkaline phosphatase (TNAP) and CD73, first broke down ATP to adenosine, which then bound the receptor and triggered the neurons in the nose to fire. Signals from these neurons then activated a single large cluster of nerve endings, or a glomerulus called IG2, in the olfactory bulb of the zebrafish brain.

"A database search of available genomes showed that the A2c receptor is found in fish and amphibian species, but not in terrestrial reptiles, birds, and mammals. “The A2c receptor must serve a very fundamental function in all the aquatic lower vertebrates,” Yoshihara says."

Comment: Even in fairly primitive animals the biologic systems they use are highly complex, as this study shows. To be developed in evolution two large very specific enzymes must be found (or invented) to have it all work. We do not know how this happens, but it did. Design?

Biological complexity: misfolded protein problems

by David Turell @, Monday, September 04, 2017, 18:56 (2398 days ago) @ David Turell
edited by David Turell, Monday, September 04, 2017, 19:02

There are defense mechanisms to handle misfolded non-function protein molecules:

https://medicalxpress.com/news/2017-09-mysterious-protein-folding-molecule-trigger-meta...

"When improperly folded molecules are encountered in cells, the unfolded protein response (UPR) is activated within the endoplasmic reticulum (ER). The ER is in charge of molecular quality control, making sure proteins, lipids and other molecules are folded properly before the cell attempts to use them for metabolic processes. Here, a master protein called grp78 is in contact with three main signaling hubs that make up the control center of the UPR.

"When an unfolded or misfolded protein is encountered by grp78, it breaks contact with those sensors and activates the UPR. The UPR then refolds or disposes of such molecules before they are shipped to the parts of the cell that need them.

"There is a wrinkle in the UPR, however. When too many unfolded proteins build up, the UPR senses that the cell has become overstressed and activates programs to recycle the cell. Yet if a number of cells experience such stress and are similarly retired, whole organs can suffer. This appears to be where the CNPY2 molecule exerts influence during the development of metabolic problems, according to experiments performed by Li and his group.

***

"The investigators examined mouse cells with and without CNPY2 and isolated the PERK protein, and its downstream signaling molecule, CHOP, within them. This interestingly named PERK-CHOP pathway, which is a major enabler of liver stress when the UPR is induced, was not activated in cells without CNPY2. When they added CNPY2 back to those cells, suddenly the pathway was restored. Protein isolation experiments confirmed their hypothesis that CNPY2 and PERK interacted closely when the UPR was again induced by the drug tunicamycin.

"In addition, the master protein grp78 that regulates all three main UPR sensors interacted with CNPY2 under normal conditions. But when the UPR drug was added, grp78 left CNPY2 able to interact closely with PERK, which finally activated the PERK-CHOP pathway. Last, they found that the PERK-CHOP pathway, when activated by free CNPY2, further increased levels of CNPY2 in the liver. In other words, CNPY2 was able to further reinforce itself once activated.

"Taken together, the team's experiments showed that CNPY2 powerfully sustains cellular stress when the unfolded protein response becomes active, providing a link between the UPR and the development of metabolic problems in the liver.

Comment: Not only is the biology of the cell highly complex, it carries protections against mistakes. The normal processes and the protection for mistakes both had to be started at the same time. Since mistakes would be anticipated to occur, this implies planning and design for the entire systems. Chance attempts will not work.

Biological complexity: misfolded protein problems

by dhw, Tuesday, September 05, 2017, 13:43 (2397 days ago) @ David Turell

DAVID’s comment: Not only is the biology of the cell highly complex, it carries protections against mistakes. The normal processes and the protection for mistakes both had to be started at the same time. Since mistakes would be anticipated to occur, this implies planning and design for the entire systems. Chance attempts will not work.

One might ask why your all-powerful designer would create a system that keeps making mistakes but also creates methods of dealing with the mistakes, although these methods frequently fail (all organisms die). It might make sense, however, if we imagine him creating a system in which the components work independently in a grand free-for-all that applies just as much to the living microworld as it does to the living macroworld. To put it more directly: he might have created the first cells with an autonomous mechanism that would provide its own infinite variety of organisms (micro and macro) doing their own thing, i.e. making their own mistakes and corrections.

Biological complexity: misfolded protein problems

by David Turell @, Tuesday, September 05, 2017, 17:40 (2397 days ago) @ dhw

DAVID’s comment: Not only is the biology of the cell highly complex, it carries protections against mistakes. The normal processes and the protection for mistakes both had to be started at the same time. Since mistakes would be anticipated to occur, this implies planning and design for the entire systems. Chance attempts will not work.

dhw: One might ask why your all-powerful designer would create a system that keeps making mistakes but also creates methods of dealing with the mistakes, although these methods frequently fail (all organisms die). It might make sense, however, if we imagine him creating a system in which the components work independently in a grand free-for-all that applies just as much to the living microworld as it does to the living macroworld. To put it more directly: he might have created the first cells with an autonomous mechanism that would provide its own infinite variety of organisms (micro and macro) doing their own thing, i.e. making their own mistakes and corrections.

Cell reproduction is at high speed. Mistakes occur. We see the protections for mistake discovery are in place. You want to cells to invent their own protection while working at high speed. A day dream. It all had to be place at the start.

Biological complexity: misfolded protein problems

by dhw, Wednesday, September 06, 2017, 13:26 (2396 days ago) @ David Turell

DAVID’s comment: Not only is the biology of the cell highly complex, it carries protections against mistakes. The normal processes and the protection for mistakes both had to be started at the same time. Since mistakes would be anticipated to occur, this implies planning and design for the entire systems. Chance attempts will not work.

dhw: One might ask why your all-powerful designer would create a system that keeps making mistakes but also creates methods of dealing with the mistakes, although these methods frequently fail (all organisms die). It might make sense, however, if we imagine him creating a system in which the components work independently in a grand free-for-all that applies just as much to the living microworld as it does to the living macroworld. To put it more directly: he might have created the first cells with an autonomous mechanism that would provide its own infinite variety of organisms (micro and macro) doing their own thing, i.e. making their own mistakes and corrections.

DAVID: Cell reproduction is at high speed. Mistakes occur. We see the protections for mistake discovery are in place. You want to cells to invent their own protection while working at high speed. A day dream. It all had to be place at the start.

Again I wonder why an all-powerful designer, who is always in control, would design a system that makes mistakes. This doesn’t strike you as strange? Do you think he was incapable of designing a system without mistakes? If not, maybe he wanted it to make mistakes, but gave it the potential ability to put things right. ("Potential" because lots and lots of things go wrong and are not put right.) That would fit in very nicely with the history of evolution. Or do you think he was incapable of designing a system potentially enabling organisms to put things right?

Biological complexity: misfolded protein problems

by David Turell @, Wednesday, September 06, 2017, 14:59 (2396 days ago) @ dhw


DAVID: Cell reproduction is at high speed. Mistakes occur. We see the protections for mistake discovery are in place. You want to cells to invent their own protection while working at high speed. A day dream. It all had to be place at the start.

dhw: Again I wonder why an all-powerful designer, who is always in control, would design a system that makes mistakes. This doesn’t strike you as strange? Do you think he was incapable of designing a system without mistakes? If not, maybe he wanted it to make mistakes, but gave it the potential ability to put things right. ("Potential" because lots and lots of things go wrong and are not put right.) That would fit in very nicely with the history of evolution. Or do you think he was incapable of designing a system potentially enabling organisms to put things right?

The biological cell has many moving parts acting at high speed in a liquid environment. If a molecular movement is a split-second off, a mistake can happen. God in His wisdom recognized this obvious problem and put into place the proper corrective mechanisms. Preparing for possible mistakes is perfect designer planning.

Biological complexity: misfolded protein problems

by dhw, Thursday, September 07, 2017, 10:41 (2395 days ago) @ David Turell

DAVID: Cell reproduction is at high speed. Mistakes occur. We see the protections for mistake discovery are in place. You want to cells to invent their own protection while working at high speed. A day dream. It all had to be place at the start.

dhw: Again I wonder why an all-powerful designer, who is always in control, would design a system that makes mistakes. This doesn’t strike you as strange? Do you think he was incapable of designing a system without mistakes? If not, maybe he wanted it to make mistakes, but gave it the potential ability to put things right. ("Potential" because lots and lots of things go wrong and are not put right.) That would fit in very nicely with the history of evolution. Or do you think he was incapable of designing a system potentially enabling organisms to put things right?

DAVID: The biological cell has many moving parts acting at high speed in a liquid environment. If a molecular movement is a split-second off, a mistake can happen. God in His wisdom recognized this obvious problem and put into place the proper corrective mechanisms. Preparing for possible mistakes is perfect designer planning.

Perfect designer planning would exclude the possibility of mistakes.

Biological complexity: misfolded protein problems

by David Turell @, Thursday, September 07, 2017, 14:32 (2395 days ago) @ dhw

DAVID: Cell reproduction is at high speed. Mistakes occur. We see the protections for mistake discovery are in place. You want to cells to invent their own protection while working at high speed. A day dream. It all had to be place at the start.

dhw: Again I wonder why an all-powerful designer, who is always in control, would design a system that makes mistakes. This doesn’t strike you as strange? Do you think he was incapable of designing a system without mistakes? If not, maybe he wanted it to make mistakes, but gave it the potential ability to put things right. ("Potential" because lots and lots of things go wrong and are not put right.) That would fit in very nicely with the history of evolution. Or do you think he was incapable of designing a system potentially enabling organisms to put things right?

DAVID: The biological cell has many moving parts acting at high speed in a liquid environment. If a molecular movement is a split-second off, a mistake can happen. God in His wisdom recognized this obvious problem and put into place the proper corrective mechanisms. Preparing for possible mistakes is perfect designer planning.

dhw: Perfect designer planning would exclude the possibility of mistakes.

Experience tells us it is not possible.

Biological complexity: misfolded protein problems

by dhw, Friday, September 08, 2017, 14:18 (2394 days ago) @ David Turell

There are three posts dealing with the same subject:

DAVID: The biological cell has many moving parts acting at high speed in a liquid environment. If a molecular movement is a split-second off, a mistake can happen. God in His wisdom recognized this obvious problem and put into place the proper corrective mechanisms. Preparing for possible mistakes is perfect designer planning.
dhw: Perfect designer planning would exclude the possibility of mistakes.
DAVID: Experience tells us it is not possible.

So your all-powerful God makes mistakes, and yet his planning is perfect. (See last item.)
xxxxxx

DAVID:(under "3-D DNA packing") […] like a good designer, God recognized the need for backup corrective mechanisms to cover that possibility.
dhw: There is no cure for Down’s syndrome.
DAVID: And there are many others, not as well known. What we have been given has never been completely perfect.

So once again “perfect designer planning” is not perfect. (See last item.)

Xxxxxxx
DAVID's comment: (Under "Cell division DNA controls") With enough advances in research into cell division and reproduction we might be able tp solve the congenital defects like Down's syndrome, an issue dhw raised today. Again this research demonstrates how complex is our biology has to be. Not by chance.

I agree that it’s not by chance: the complexity has been built up by intelligent combinations of individual units. But the issue I raised is that your God’s designs are riddled with mistakes, and if – as you keep insisting – he is all-powerful and in full control, the logical inference has to be that these are not “mistakes” but weaknesses deliberately built into the system. So here’s a theistic alternative: your God planned a system that would make mistakes, and he gave organisms the means to work out solutions. Some did, some didn’t. Some do, some don’t.

Biological complexity: misfolded protein problems

by David Turell @, Friday, September 08, 2017, 20:57 (2394 days ago) @ dhw

Xxxxxxx
DAVID's comment: (Under "Cell division DNA controls") With enough advances in research into cell division and reproduction we might be able tp solve the congenital defects like Down's syndrome, an issue dhw raised today. Again this research demonstrates how complex is our biology has to be. Not by chance.

dhw: I agree that it’s not by chance: the complexity has been built up by intelligent combinations of individual units. But the issue I raised is that your God’s designs are riddled with mistakes, and if – as you keep insisting – he is all-powerful and in full control, the logical inference has to be that these are not “mistakes” but weaknesses deliberately built into the system. So here’s a theistic alternative: your God planned a system that would make mistakes, and he gave organisms the means to work out solutions. Some did, some didn’t. Some do, some don’t.

Perfectly designed systems do make mistakes at times, do break down. This is our human experience, and I think that fits what we see in the genome replication at very high speed; occasional errors. By your way of thinking God should not have made the universe so dangerous, but He didn't.

Biological complexity: misfolded protein problems

by dhw, Saturday, September 09, 2017, 10:39 (2393 days ago) @ David Turell

DAVID's comment: (Under "Cell division DNA controls") With enough advances in research into cell division and reproduction we might be able tp solve the congenital defects like Down's syndrome, an issue dhw raised today. Again this research demonstrates how complex is our biology has to be. Not by chance.

dhw: I agree that it’s not by chance: the complexity has been built up by intelligent combinations of individual units. But the issue I raised is that your God’s designs are riddled with mistakes, and if – as you keep insisting – he is all-powerful and in full control, the logical inference has to be that these are not “mistakes” but weaknesses deliberately built into the system. So here’s a theistic alternative: your God planned a system that would make mistakes, and he gave organisms the means to work out solutions. Some did, some didn’t. Some do, some don’t.

DAVID: Perfectly designed systems do make mistakes at times, do break down. This is our human experience, and I think that fits what we see in the genome replication at very high speed; occasional errors. By your way of thinking God should not have made the universe so dangerous, but He didn't.

I think you mean He did. I’m afraid my definition of perfection would not include a propensity for making mistakes. For someone who objects to any anthropomorphization of his God, you surprise me by arguing that since we humans make mistakes, so does God. But you have missed my point anyway, which is that your God might have deliberately devised a system that made mistakes. If we apply that approach to humans, we might perhaps agree that if every human behaved “perfectly”, and if there were no mistakes of any kind to be corrected, life might become boringly predictable.

Biological complexity: misfolded protein problems

by David Turell @, Saturday, September 09, 2017, 14:40 (2393 days ago) @ dhw


DAVID: Perfectly designed systems do make mistakes at times, do break down. This is our human experience, and I think that fits what we see in the genome replication at very high speed; occasional errors. By your way of thinking God should not have made the universe so dangerous, but He did.

dhw: I’m afraid my definition of perfection would not include a propensity for making mistakes. For someone who objects to any anthropomorphization of his God, you surprise me by arguing that since we humans make mistakes, so does God. But you have missed my point anyway, which is that your God might have deliberately devised a system that made mistakes. If we apply that approach to humans, we might perhaps agree that if every human behaved “perfectly”, and if there were no mistakes of any kind to be corrected, life might become boringly predictable.

I did not say God makes mistakes, you did. He designed the most perfect biological cell division reproduction high speed system could allow. Mechanisms make mistakes. I didn't miss your point.

Biological complexity: misfolded protein problems

by dhw, Sunday, September 10, 2017, 13:50 (2392 days ago) @ David Turell

DAVID: Perfectly designed systems do make mistakes at times, do break down. This is our human experience, and I think that fits what we see in the genome replication at very high speed; occasional errors. By your way of thinking God should not have made the universe so dangerous, but He did.

dhw: I’m afraid my definition of perfection would not include a propensity for making mistakes. For someone who objects to any anthropomorphization of his God, you surprise me by arguing that since we humans make mistakes, so does God. But you have missed my point anyway, which is that your God might have deliberately devised a system that made mistakes. If we apply that approach to humans, we might perhaps agree that if every human behaved “perfectly”, and if there were no mistakes of any kind to be corrected, life might become boringly predictable.

DAVID: I did not say God makes mistakes, you did. He designed the most perfect biological cell division reproduction high speed system could allow. Mechanisms make mistakes. I didn't miss your point.

I am baffled by your logic. Perfect = without mistakes or faults. You say your God’s design of the system was perfect, but the system he designed makes mistakes at times (= is not perfect). So your God’s perfect design is imperfect. Does this mean your God was incapable of a perfect design because the system he created took over and insisted on making mistakes, which meant he had to invent correcting mechanisms which also made mistakes, because not all organisms survive? Ugh, what a whale-like mess! Meanwhile, you have not responded to my point, which would disentangle all this confusion.

Biological complexity: misfolded protein problems

by David Turell @, Sunday, September 10, 2017, 15:26 (2392 days ago) @ dhw


DAVID: I did not say God makes mistakes, you did. He designed the most perfect biological cell division reproduction high speed system could allow. Mechanisms make mistakes. I didn't miss your point.

dhw: I am baffled by your logic. Perfect = without mistakes or faults. You say your God’s design of the system was perfect, but the system he designed makes mistakes at times (= is not perfect). So your God’s perfect design is imperfect. Does this mean your God was incapable of a perfect design because the system he created took over and insisted on making mistakes, which meant he had to invent correcting mechanisms which also made mistakes, because not all organisms survive? Ugh, what a whale-like mess! Meanwhile, you have not responded to my point, which would disentangle all this confusion.

You are a stickler for an exact meaning of words. I've modified my original statement with what I've said above. And yes, He recognized the mistakes that can happen in a high speed biologic mechanism so He designed corrective mechanisms, but I'll agree, biologic mechanisms cannot be absolutely perfect, since we see mistakes.

Biological complexity: misfolded protein problems

by dhw, Monday, September 11, 2017, 13:14 (2391 days ago) @ David Turell

DAVID: I did not say God makes mistakes, you did. He designed the most perfect biological cell division reproduction high speed system could allow. Mechanisms make mistakes. I didn't miss your point.

dhw: I am baffled by your logic. Perfect = without mistakes or faults. You say your God’s design of the system was perfect, but the system he designed makes mistakes at times (= is not perfect). So your God’s perfect design is imperfect. Does this mean your God was incapable of a perfect design because the system he created took over and insisted on making mistakes, which meant he had to invent correcting mechanisms which also made mistakes, because not all organisms survive? Ugh, what a whale-like mess! Meanwhile, you have not responded to my point, which would disentangle all this confusion.

DAVID: You are a stickler for an exact meaning of words. I've modified my original statement with what I've said above. And yes, He recognized the mistakes that can happen in a high speed biologic mechanism so He designed corrective mechanisms, but I'll agree, biologic mechanisms cannot be absolutely perfect, since we see mistakes.

Words are the only instruments we have for expressing our opinions and beliefs, but I am also a stickler for logic, and I can see no logical coherence between your belief in an all-powerful God and the mistakes that happen not only in a high speed biological mechanism but in every other system he has designed. (As a physician you don’t need me to describe those relating to bodies!) Wearing my theist hat, I have suggested that if he is all-powerful, the mistakes are not mistakes at all, but the result of his deliberately inventing a fallible system because a perfect system would be boringly predictable. Once again, you have omitted to comment on this perfectly logical reconciliation between the all-powerful God and the “mistakes” that permeate the system he designed.

Biological complexity: misfolded protein problems

by David Turell @, Monday, September 11, 2017, 17:55 (2391 days ago) @ dhw


DAVID: You are a stickler for an exact meaning of words. I've modified my original statement with what I've said above. And yes, He recognized the mistakes that can happen in a high speed biologic mechanism so He designed corrective mechanisms, but I'll agree, biologic mechanisms cannot be absolutely perfect, since we see mistakes.

dhw: Words are the only instruments we have for expressing our opinions and beliefs, but I am also a stickler for logic, and I can see no logical coherence between your belief in an all-powerful God and the mistakes that happen not only in a high speed biological mechanism but in every other system he has designed. (As a physician you don’t need me to describe those relating to bodies!) Wearing my theist hat, I have suggested that if he is all-powerful, the mistakes are not mistakes at all, but the result of his deliberately inventing a fallible system because a perfect system would be boringly predictable. Once again, you have omitted to comment on this perfectly logical reconciliation between the all-powerful God and the “mistakes” that permeate the system he designed.

Under my discussions of theodicy in my first book I made exactly your point. God knew the universe and the Earth He created had dangerous aspects. He gave us a brain to try to solve those problems. But I don't think the high speed movements and reactions of biochemical molecules, as independent operatives, can be expected to be error free. That is why corrective cleanup measures were designed on top of the reproductive systems. To do the perfect system you desire, God has to be in personal control of each molecule. I doubt He is. He did not produce a fallible system purposely. He gave us our brain to attempt solutions for errors, and we are now manipulating the genome.

Biological complexity: misfolded protein problems

by dhw, Tuesday, September 12, 2017, 12:05 (2390 days ago) @ David Turell

DAVID: You are a stickler for an exact meaning of words. I've modified my original statement with what I've said above. And yes, He recognized the mistakes that can happen in a high speed biologic mechanism so He designed corrective mechanisms, but I'll agree, biologic mechanisms cannot be absolutely perfect, since we see mistakes.

dhw: Words are the only instruments we have for expressing our opinions and beliefs, but I am also a stickler for logic, and I can see no logical coherence between your belief in an all-powerful God and the mistakes that happen not only in a high speed biological mechanism but in every other system he has designed. (As a physician you don’t need me to describe those relating to bodies!) Wearing my theist hat, I have suggested that if he is all-powerful, the mistakes are not mistakes at all, but the result of his deliberately inventing a fallible system because a perfect system would be boringly predictable. Once again, you have omitted to comment on this perfectly logical reconciliation between the all-powerful God and the “mistakes” that permeate the system he designed.

DAVID: Under my discussions of theodicy in my first book I made exactly your point. God knew the universe and the Earth He created had dangerous aspects. He gave us a brain to try to solve those problems. But I don't think the high speed movements and reactions of biochemical molecules, as independent operatives, can be expected to be error free. That is why corrective cleanup measures were designed on top of the reproductive systems. To do the perfect system you desire, God has to be in personal control of each molecule. I doubt He is. He did not produce a fallible system purposely. He gave us our brain to attempt solutions for errors, and we are now manipulating the genome.

So did God deliberately create a dangerous universe so that humans could solve the problems? Or was he incapable of producing a universe that wasn’t dangerous? If it’s the former, he did produce a fallible system purposely. If it’s the latter, he is not in full control.

Biological complexity: misfolded protein problems

by David Turell @, Tuesday, September 12, 2017, 15:25 (2390 days ago) @ dhw


DAVID: Under my discussions of theodicy in my first book I made exactly your point. God knew the universe and the Earth He created had dangerous aspects. He gave us a brain to try to solve those problems. But I don't think the high speed movements and reactions of biochemical molecules, as independent operatives, can be expected to be error free. That is why corrective cleanup measures were designed on top of the reproductive systems. To do the perfect system you desire, God has to be in personal control of each molecule. I doubt He is. He did not produce a fallible system purposely. He gave us our brain to attempt solutions for errors, and we are now manipulating the genome.

dhw: So did God deliberately create a dangerous universe so that humans could solve the problems? Or was he incapable of producing a universe that wasn’t dangerous? If it’s the former, he did produce a fallible system purposely. If it’s the latter, he is not in full control.

We've visited this before. I believe God created the best life-creating universe He could. A much more benign universe might not have been capable of supporting life. For example, exploding stars scattered the proper newly formed elements around the universe. Plate tectonics on earth cause earthquakes but are shown to be vital for life on Earth. I've just touched on hundreds of examples of this approach to what or how God did it.

Biological complexity: misfolded protein problems

by dhw, Wednesday, September 13, 2017, 13:26 (2389 days ago) @ David Turell

DAVID: God knew the universe and the Earth he created had dangerous aspects. He gave us a brain to try to solve those problems.

dhw: So did God deliberately create a dangerous universe so that humans could solve the problems? Or was he incapable of producing a universe that wasn’t dangerous? If it’s the former, he did produce a fallible system purposely. If it’s the latter, he is not in full control.

DAVID: We've visited this before. I believe God created the best life-creating universe He could. A much more benign universe might not have been capable of supporting life. For example, exploding stars scattered the proper newly formed elements around the universe. Plate tectonics on earth cause earthquakes but are shown to be vital for life on Earth. I've just touched on hundreds of examples of this approach to what or how God did it.

“The best he could”...You are definitely limiting his powers. "Might not have been capable of supporting life"...But on the other hand, might have been. You think his prime purpose was to produce the human brain, which he gave us to do what? Solve the problems he couldn’t solve? The same question arises under “Immunity”:

DAVID’s comment: Finding just the right organic molecule to fight viruses cannot be left to chance. Since viruses constantly are invading, survival depends upon an immediate solution to the problem. It must be designed from the beginning.

Why would your God have designed viruses and at the same time designed molecules to fight viruses, especially when his prime purpose was to produce the human brain? Your answer basically seems to be that he had to do whatever he did because it couldn’t be done any other way. So he was always in control except when he wasn’t. I’m sure this will be of great consolation to the victims of viral diseases, pandemics, tsunamis, volcanic eruptions, earthquakes, and hurricane Irma. But your theistic explanation and mine both make sense: yours, that with his limited powers (though he's sometimes all-powerful) this was the best he could do; mine, he chose to do it this way because perfection would have been boring.

Biological complexity: misfolded protein problems

by David Turell @, Thursday, September 14, 2017, 01:29 (2388 days ago) @ dhw

DAVID: God knew the universe and the Earth he created had dangerous aspects. He gave us a brain to try to solve those problems.

dhw: So did God deliberately create a dangerous universe so that humans could solve the problems? Or was he incapable of producing a universe that wasn’t dangerous? If it’s the former, he did produce a fallible system purposely. If it’s the latter, he is not in full control.

DAVID: We've visited this before. I believe God created the best life-creating universe He could. A much more benign universe might not have been capable of supporting life. For example, exploding stars scattered the proper newly formed elements around the universe. Plate tectonics on earth cause earthquakes but are shown to be vital for life on Earth. I've just touched on hundreds of examples of this approach to what or how God did it.

“The best he could”...You are definitely limiting his powers. "Might not have been capable of supporting life"...But on the other hand, might have been. You think his prime purpose was to produce the human brain, which he gave us to do what? Solve the problems he couldn’t solve? The same question arises under “Immunity”:

I don't know if God can create a perfect universe, or should. It may be, as above, that our universe has to be as it is to allow for life. That is a finer point than you are allowing for in regard to God's powers.


DAVID’s comment: Finding just the right organic molecule to fight viruses cannot be left to chance. Since viruses constantly are invading, survival depends upon an immediate solution to the problem. It must be designed from the beginning.

dhw: Why would your God have designed viruses and at the same time designed molecules to fight viruses, especially when his prime purpose was to produce the human brain? Your answer basically seems to be that he had to do whatever he did because it couldn’t be done any other way. So he was always in control except when he wasn’t. I’m sure this will be of great consolation to the victims of viral diseases, pandemics, tsunamis, volcanic eruptions, earthquakes, and hurricane Irma. But your theistic explanation and mine both make sense: yours, that with his limited powers (though he's sometimes all-powerful) this was the best he could do; mine, he chose to do it this way because perfection would have been boring.

There are lots of things we do not know about the origin of life and how speciation works. Viruses may also be good guys and help with speciation. They do add to our DNA. God's limits may be dictated by His goals, as those goals might require the way the universe and Earth work. Perfection may not be the solution.

Biological complexity: misfolded protein problems

by dhw, Thursday, September 14, 2017, 13:15 (2388 days ago) @ David Turell

dhw: Why would your God have designed viruses and at the same time designed molecules to fight viruses, especially when his prime purpose was to produce the human brain? Your answer basically seems to be that he had to do whatever he did because it couldn’t be done any other way. So he was always in control except when he wasn’t. I’m sure this will be of great consolation to the victims of viral diseases, pandemics, tsunamis, volcanic eruptions, earthquakes, and hurricane Irma. But your theistic explanation and mine both make sense: yours, that with his limited powers (though he's sometimes all-powerful) this was the best he could do; mine, he chose to do it this way because perfection would have been boring.

DAVID: There are lots of things we do not know about the origin of life and how speciation works. Viruses may also be good guys and help with speciation. They do add to our DNA. God's limits may be dictated by His goals, as those goals might require the way the universe and Earth work. Perfection may not be the solution.

It is because we don’t know about lots of things that we formulate hypotheses. Yours seem to change from day to day. You now seem to be taking it for granted that God has limits. Not so long ago, he was all-powerful and always in control. Why not acknowledge the possibility (which is all it can be) that what we have IS God’s goal – namely, a massive free-for-all, full of nice and nasty, good and evil, joy and sadness, birth and death, extinction and survival?

Biological complexity: misfolded protein problems

by David Turell @, Thursday, September 14, 2017, 15:59 (2388 days ago) @ dhw


DAVID: There are lots of things we do not know about the origin of life and how speciation works. Viruses may also be good guys and help with speciation. They do add to our DNA. God's limits may be dictated by His goals, as those goals might require the way the universe and Earth work. Perfection may not be the solution.

dhw: It is because we don’t know about lots of things that we formulate hypotheses. Yours seem to change from day to day. You now seem to be taking it for granted that God has limits. Not so long ago, he was all-powerful and always in control. Why not acknowledge the possibility (which is all it can be) that what we have IS God’s goal – namely, a massive free-for-all, full of nice and nasty, good and evil, joy and sadness, birth and death, extinction and survival?

Obviously I don't see that your conclusion fits the arrival of H. sapiens, but yours does include free will and the chaos it creates. Birth and death, extinctions are requirements of evolution. Your view of God's limits may be requirements of evolving life as a method of creation. As for my apparent changeability, it is the result of your probing questions, requiring me to explore my own theories and consolidate ideas.

Biological complexity: mitochondrial protein supply

by David Turell @, Tuesday, September 05, 2017, 00:40 (2397 days ago) @ David Turell

Ribosomes are now found attached to mitochondria to supply needed proteins:

https://www.sciencedaily.com/releases/2017/08/170830114753.htm

"Mitochondria, which exist within human cells but have their own DNA, need many different proteins to function -- but the process of how they get these has never been imaged in detail.

"Now a study led by Dr Vicki Gold, of the University of Exeter, has shown that some ribosomes --the tiny factories of cells which produce proteins -- are attached to mitochondria. This can explain how proteins are pushed into mitochondria whilst they are being made.

"Proteins are responsible for nearly all cellular processes. The cell has to make a huge variety of proteins and target them to the precise location where they are needed to function," said Dr Gold, of Exeter's Living Systems Institute.

"'In the case of mitochondria, proteins have to cross the boundary of two membranes to get inside them.

"'We looked for -- and were able to image at unprecedented detail -- ribosomes attached to mitochondria."

"The images were taken using cutting-edge technology called cryo-electron microscopy."

Comment: As mitochondria were added to cells by being engulfed ( according to theory) they need a source of continuous protein supply, and it is now found. Logically, when mitochondria were recruited, the ribosomes had to be formed and activated, in one designed step. It would not have worked if not formed in one step by design.

Biological complexity: bacteria R' us

by David Turell @, Thursday, September 07, 2017, 15:01 (2395 days ago) @ David Turell

We live in symbiosis with hordes of bacteria everywhere on and in us:

http://nautil.us/issue/52/the-hive/what-the-meadow-teaches-us?utm_source=Nautilus&u...

"It has taken a long time for biology and medicine to arrive at the idea that significant portions of an individual’s own body are foreign to it. Now, however, microbiology in particular is discovering that there is no reposing, solid core within us, but rather a lurking void around which life’s dance unfurls. In the human body, thousands of different players make the meaningful whole possible. We know that our body is colonized by microbes, particularly in the gut, which perform metabolic processes essential to our lives. Within our body, we carry our own, developed ecosystem, without which we could not break down and digest food. There is a reason that biologists call the “biofilm” of microorganisms that cover moist surfaces “bacterial lawns.” With hundreds of species entangled on them—consuming, eliminating, extracting, and synthesizing matter—these bacterial lawns, like the Ligurian pastures, have the characteristic of an undulating meadow in the spring, inside of us. No wonder we have a feeling of recollection on such evenings.

***

"In this age of advanced gene technology, the true abyss of renunciation from which we speak “I” is only now becoming obvious to us. For only a few years, it has been clear that bacteria are completely dominant in a healthy human being: On top of our ten billion body cells, there are one hundred billion microbial cells that play a role in our metabolism. This enormously increases the options for our bodily processes: If we include the microbes’ genes, then we have over 100,000 genes at our disposal, as opposed to just over 20,000. This sort of bacterial aid leads, for example, to children in Papua New Guinea being born with nitrogen-fixing bacteria (like those found in some plants and algae) in their intestinal tissues. This allows them to subsist for years on a plant-based diet without suffering from symptoms of deficiency.

***

"With these symbiotic microbes, our existence joins the ranks of a continuum shared by many other beings that exist outside our bodies. For bacteria are engaged in constant exchange with one another. During times of crisis, they share advantageous genes with one another like children sharing candies. This is why researchers nowadays are speaking less about the various types of bacteria in the world (as they are so transformative) and more about the diversity of their genes and the biological abilities they facilitate. Biologists are regularly stunned by this diversity: The US researcher Norman Pace investigated an ounce of silt from the hot springs of Yellowstone National Park in the 1990s and found more genetic diversity there than scientists had previously assumed to be present in the entire biosphere.

"This diversity is not neatly divided between distinct species or types but is available to all microbes within the context of symbiotic processes of exchange. The late biologist and symbiosis researcher Lynn Margulis believed, for example, that this exchange relationship meant that we should actually speak about all the bacteria on Earth as though they composed a single biological subject—one body swarming with countless cells. Consequently, we who are dominated by a bacterial ecosystem ten times larger than our own body’s cells also belong to the great continuum of life. We are literally, physically, a part of the landscape. The moment we take sustenance from it, we enfold it and its inhabitants into our bodies."

Comment: There is a reason bacteria have survived and been here forever. Look how they join with us and are helpful.

Biological complexity: circadian clock feedback loop

by David Turell @, Thursday, September 07, 2017, 19:16 (2395 days ago) @ David Turell

Not fully worked out. but close. A complex set of proteins:

https://phys.org/news/2017-09-molecular-machines-biochemical-oscillator-bodily.html

"Scientists have long known that circadian clocks—biochemical oscillators that control physiology, metabolism and behavior on a roughly 24-hour cycle—are present in all forms of life, including animals, plants, fungi and some types of bacteria. However, the molecular mechanisms that "run" these systems remain largely unknown.

***

"In the late 1990s, Weitz, the Robert Henry Pfeiffer Professor of Neurobiology at Harvard Medical School, and researchers from other labs discovered several key proteins involved in the clock system. These include three different period proteins (PER), two different cryptochrome proteins (CRY), and casein kinase-1 (CK1). When these proteins accumulate inside cells and enter the cell nucleus, they bind to a protein called CLOCK-BMAL1 that is attached to DNA responsible for making more PER and CRY. The influx and accumulation of these proteins inside the nucleus effectively shut down the production of PER and CRY. However, when the levels of PER and CRY drop, the CLOCK-BMAL1 can once again resume work unhindered so that the DNA responsible for making PER and CRY can do its job.

"The completion of this feedback loop—production of PER and CRY, their attachment to CLOCK-BMAL1, shutting down PER and CRY production so that it can start over again—takes about 24 hours, Weitz explains.

"To figure out precisely how these proteins might run the clock, Weitz and colleagues used a laboratory technique that selectively pulled out proteins from the nuclei of mouse cells at the peak of PER and CRY negative feedback. Their findings turned up a single large protein complex that incorporated each of the six important clock proteins: the three PERs, two CRYs, and CK1, along with about thirty other accessory proteins. Additionally, the protein complex, which electron microscopy showed is quasi-spherical, was associated with CLOCK-BMAL1, the experiments showed.

***

"The results suggest that this complex, which the researchers named the PER complex, is universal in tissues throughout the body. They also suggest that the six key clock proteins probably don't operate individually; instead, they seem to organize themselves to work in concert to run the circadian clock's negative feedback loop.

"To determine when this organization happens, the researchers looked for the presence of the six main clock proteins in the cytoplasm, the gooey liquid inside a cell that surrounds the nucleus and other organelles. There, they found four other complexes composed of different groups of the six proteins—one with all six, named the upper complex—and three others missing one or more of these key proteins. The researchers hypothesized that these complexes were in various states of assembly, but that the six key proteins entered the nucleus as a group.

"The upper complex also had a seventh protein called GAPVD1, known from other studies to help shepherd chemicals to different locations inside cells. Although the role of GAPVD1 in the circadian clock remains somewhat unclear, Weitz said, experiments in which he and his colleagues trimmed this protein out of the upper complex caused disruption in circadian cycle—an observation that suggests GAPVD1 plays a key role in the clock.

***

"'The circadian clock is a very deep timing system that controls a large part of the physiology and behavior in all cells in the body to shape multiple processes," Weitz said. "The more we learn about it, the more links we'll get to certain kinds of disease states that aren't easily amenable to treatment today. Now that we understand how these molecular machines are built, we can start asking questions about how they work.'"

Comment: this is a highly complex feedback loop for the 24 hour clock. It had to be designed all at once. God at work.

Biological complexity: cell division DNA controls

by David Turell @, Thursday, September 07, 2017, 19:32 (2395 days ago) @ David Turell

How the chromosomes are herded into two cells. A control protein is found:

https://phys.org/news/2017-09-chromosome-motor-discovery-dna-loop.html

"How does a cell neatly distribute its replicated DNA between two daughter cells? For more than a century, we have known that DNA in the cell is comparable to a plate of spaghetti—a jumble of intermingled strands. When cells divide, they have to pack two metres of DNA into tidy little packages—chromosomes. This packing is induced by proteins called condensin, but scientists are split regarding the actual mechanism. One argument holds that the protein works like a hook, randomly grasping somewhere in the jumble of DNA and tying it all together. Another holds that the ring-shaped protein pulls the DNA inward to create a loop. In a new study reported in Science, researchers from TU Delft, Heidelberg and Columbia University give the oop-extrusion argument a significant boost, demonstrating that condensin does, indeed, have the putative motor function required for this dynamic.

***

"In their article in Science, the researchers show for the first time that condensin does have a motor function. They positioned DNA molecules that were stretched on a surface and added condensin proteins, each fitted with a light-emitting quantum dot to enable observation. "We observed how condensin does, indeed, translocate along the DNA. This only happened if fuel was present, in this case the molecule ATP – the petrol that powers all processes in a cell," explains Jorine Eeftens, graduate student at Delft and one of the first authors. "The results also show that condensin takes extremely large steps on the DNA, and therefore needs significantly less ATP than previously thought." In the second stage of their research, the researchers replaced the light-emitting quantum dot on the condensin with a light-emitting string of DNA. They once again witnessed condensin moving in the same way. Condensin is therefore able to move a piece of DNA in relation to another, which corresponds with the idea of loop formation.

"'The exact underlying mechanism is still open to discussion. But this discovery is certainly an enormous boost to the loop extrusion camp. We have also shown that the amount of energy used is a lot less than previously thought," says Cees Dekker.

"The research represents a significant step in the fundamental understanding of cells, but it is also relevant for medical research. Problems with the protein family to which condensin belongs, the SMC proteins, are related to hereditary conditions such as Cornelia de Lange Syndrome. Condensin is also crucial in the organisation of the chromosomes during cell division, and errors in the process can result in cancer. A better understanding of these processes is vital for tracking down the molecular origins of serious illnesses."

Comment: With enough advances in research into cell division and reproduction we might be able tp solve the congenital defects like Down's syndrome, an issue dhw raised today. Again this research demonstrates how complex is our biology has to be. Not by chance.

Biological complexity: cell division DNA controls

by David Turell @, Thursday, June 25, 2020, 20:55 (1373 days ago) @ David Turell

New studies show more controls:

https://phys.org/news/2020-06-dynamics-dna-replication-revealed-nanoscale.html

"DNA replication is a process of critical importance to the cell, and must be coordinated precisely to ensure that genomic information is duplicated once and only once during each cell cycle. Using super-resolution technology a University of Technology Sydney led team has directly visualized the process of DNA replication in single human cells.

"This is the first quantitative characterization to date of the spatio-temporal organization, morphology, and in situ epigenetic signatures of individual replication foci (RFi) in single human cells at the nanoscale.

"The results of the study, published in PNAS (Proceedings of the National Academy of Sciences) give new insight into a poorly understood area of DNA replication namely how replication origin sites are chosen from thousands of possible sites.

"Lead author of the study, biophysicist Dr. Peter Su from UTS Institute of Biomedical Materials and Devices (IBMD), explains that it's known DNA replication is initiated at numerous sites along the chromosomes.

"'These are known as replication origins, which are clustered into thousands of replication domains (RDs) across the genome, which in turn cluster within the cell nucleus as RFi " he says.

"'Such organization is critically important for the cell but how replication origins are chosen within individual RDs remains poorly understood, and it is unclear whether the origins are activated randomly or preferentially near certain chromatin features," he says.Chromatin helps package DNA material together so it can fit efficiently within the nucleus of a cell a, thus protecting the DNA from damage.

"The collaboration with scientists from Peking University and National University of Singapore revealed a distinct pattern of replication propagation dynamics that reverses directionality across S-phase of the cell cycle, and is diminished upon knockdown of CTCF, a key regulator of 3-D genome architecture.

"The researchers say that together with simulation and bioinformatic analyses, these findings point to a model in which replication is preferentially activated on CTCF-organized looped chromatin structures, and suggest a non-random selection mechanism for replication activation at the sub-RD level.

"Dr. Su said: "Our findings shed critical insights into the role local epigenetic environment plays in coordinating DNA replication across the genome, and could have wide-ranging implications for our understanding of how multi-scale chromatin architecture controls the organization and dynamics of diverse intranuclear processes in space and time.'"

Comment: Despite this very careful design, we know mistakes happen. This entry applies directly to our discussion about God's control, and lack of control, of mistakes. (Back to David's theory of evolution (Evolution) by David Turell @, Thursday, June 25, 2020, 19:20). The body is not a car, where the only mistakes are wear and tear.

Biological complexity: circadian clock feedback loop

by David Turell @, Monday, October 02, 2017, 21:07 (2370 days ago) @ David Turell

Nobel prize awarded for the research that uncovered how it worked:

https://www.sciencedaily.com/releases/2017/10/171002092603.htm

"Life on Earth is adapted to the rotation of our planet. For many years we have known that living organisms, including humans, have an internal, biological clock that helps them anticipate and adapt to the regular rhythm of the day. But how does this clock actually work? Jeffrey C. Hall, Michael Rosbash and Michael W. Young were able to peek inside our biological clock and elucidate its inner workings. Their discoveries explain how plants, animals and humans adapt their biological rhythm so that it is synchronized with the Earth's revolutions.

***

"With exquisite precision, our inner clock adapts our physiology to the dramatically different phases of the day. The clock regulates critical functions such as behavior, hormone levels, sleep, body temperature and metabolism. Our wellbeing is affected when there is a temporary mismatch between our external environment and this internal biological clock, for example when we travel across several time zones and experience "jet lag."

***
"This year's Nobel Laureates, who were also studying fruit flies, aimed to discover how the clock actually works. In 1984, Jeffrey Hall and Michael Rosbash, working in close collaboration at Brandeis University in Boston, and Michael Young at the Rockefeller University in New York, succeeded in isolating the period gene. Jeffrey Hall and Michael Rosbash then went on to discover that PER, the protein encoded by period, accumulated during the night and was degraded during the day. Thus, PER protein levels oscillate over a 24-hour cycle, in synchrony with the circadian rhythm.

"The next key goal was to understand how such circadian oscillations could be generated and sustained. Jeffrey Hall and Michael Rosbash hypothesized that the PER protein blocked the activity of the period gene. They reasoned that by an inhibitory feedback loop, PER protein could prevent its own synthesis and thereby regulate its own level in a continuous, cyclic rhythm.

"The model was tantalizing, but a few pieces of the puzzle were missing. To block the activity of the period gene, PER protein, which is produced in the cytoplasm, would have to reach the cell nucleus, where the genetic material is located. Jeffrey Hall and Michael Rosbash had shown that PER protein builds up in the nucleus during night, but how did it get there? In 1994 Michael Young discovered a second clock gene, timeless, encoding the TIM protein that was required for a normal circadian rhythm. In elegant work, he showed that when TIM bound to PER, the two proteins were able to enter the cell nucleus where they blockedperiodgene activity to close the inhibitory feedback loop.

***

"Michael Young identified yet another gene, doubletime, encoding the DBT protein that delayed the accumulation of the PER protein. This provided insight into how an oscillation is adjusted to more closely match a 24-hour cycle.

"The paradigm-shifting discoveries by the laureates established key mechanistic principles for the biological clock. During the following years other molecular components of the clockwork mechanism were elucidated, explaining its stability and function. For example, this year's laureates identified additional proteins required for the activation of the period gene, as well as for the mechanism by which light can synchronize the clock.

"The biological clock is involved in many aspects of our complex physiology. We now know that all multicellular organisms, including humans, utilize a similar mechanism to control circadian rhythms. A large proportion of our genes are regulated by the biological clock and, consequently, a carefully calibrated circadian rhythm adapts our physiology to the different phases of the day."

Comment: This tightly controlled system developed to adapt life to our 24 hour day. But it is hard to image a blind evolutionary process finding exactly the right genes and proteins to set up the precise feedback loop of controlling proteins. Why not God at work?

Biological complexity: circadian clock feedback loop

by David Turell @, Tuesday, January 16, 2018, 19:23 (2264 days ago) @ David Turell

Another molecular mechanism to control circadian rhythm is found in the honeybee:

https://www.sciencedaily.com/releases/2018/01/180116095503.htm

"Circadian clocks regulate the behaviour of all living things. Scientists from the University of Würzburg have now taken a closer look at the clock's anatomical structures and molecular processes in the honeybee.

"How does the honeybee manage to visit the flowers that bloom exactly at the right time? How do bees find their way back to the hive even when the sun, which they use as reference point, has changed its position in the sky? How do they communicate this information to other bees? And which molecular processes control this behaviour and in which anatomical structures do they take place?

***

"'In our current study, we focused on the concentration of a specific peptide in the bee's central nervous system," Charlotte Helfrich-Förster explains. This peptide is called "pigment-dispersing factor" or short PDF in scientific language. It has been known to play a central role in the circadian clocks of insects for some time. Previous measurements also revealed that special nerve cells, the so-called clock neurons, produce PDF.

***

"Charlotte Helfrich-Förster sums up the central findings of these experiments as follows: "Our analyses show that PDF neurons head for brain areas that are essential for learning, memory and orientation to the sun. The concentration of the PDF proteins is subject to considerable fluctuations throughout the day with an absolute low early in the morning. When the bees were given artificial PDF, their typical behavioural pattern was postponed by some time."

"For the scientists this is the clue that PDF clock neurons form an anatomical bridge between the different pacemaker cells in the clock network of insects. What is more, they transfer day-night information from the circadian clock to such brain areas that control complex behaviours such as orientation to the sun, temporal memory and organizing the work throughout the day."

Comment: Again communication of information by molecular messanger. How did evolution decide on this particular protein to use? For the honeybee, when it evolved this messenger molecule had to be in place to help them in their hunt for pollen and nector. Evidence of dsign is everywhere.

Biological complexity: circadian clock muscle controls

by David Turell @, Tuesday, August 21, 2018, 17:43 (2047 days ago) @ David Turell
edited by David Turell, Tuesday, August 21, 2018, 18:16

Body tissues have controls outside of the brain controls of the 24 hour day:

https://medicalxpress.com/news/2018-08-muscles.html

"How do muscle cells prepare for the particular metabolic challenges of the day? Scientists at Helmholtz Zentrum München and Ludwig-Maximilians-Universität München (LMU), members of the German Center for Diabetes Research (DZD), have investigated this question and published their results in PLOS Biology. The study has uncovered a metabolic network which is, contrary to expectations, not controlled by the brain but rather by the 'circadian clock' of muscle cells.

"Circadian clocks are present in all cells of the body, and have a pervasive influence on all aspects of human physiology. This is because they regulate homeostasis by anticipating rhythmic changes in behavior and nutritional state, and by compartmentalizing incompatible metabolic pathways within precise temporal windows. "This applies, for example, to the use of nutrients such as fats and carbohydrates," explains Professor Henriette Uhlenhaut.

***

"In their recent work, the team led by Uhlenhaut turned their attention to the 24-hour metabolic rhythm of muscles. "We focused specifically on two proteins that act as master regulators, positive and negative arms of the circadian clock," says Kenneth Dyar, a scientist at the IDO and lead author of the study. "These two opposing molecules bind to DNA and trigger expression of additional proteins known to regulate lipid and protein metabolism." Using muscle cells from mice, the scientists determined the activity of the two proteins over the course of the day and night. "We measured everything, from DNA binding to gene expression and metabolites," says Kenneth Dyar, explaining the researchers' comprehensive approach. Building upon previous studies, the scientists studied the synthesis and breakdown of fats and proteins over 24 hours – an approach that might also be interesting for athletes.

"In collaboration with Italian and Austrian colleagues (from the Venetian Institute of Molecular Medicine and the Universities of Padua, Graz, and Trieste) the researchers identified certain processes that are switched on at night by the regulators of the internal clock: "They include, for example, fat storage, glucose metabolism and insulin sensitivity," explains Henriette Uhlenhaut. At the same time, opposing processes such as fatty acid oxidation and protein breakdown are throttled down, according the authors. These patterns are especially pronounced in the hours before awakening and are thought to prepare the muscles for the day ahead.

"In the final step, the scientists investigated possible ways to intervene in these processes. To this end, they examined mice lacking these master regulators. Without a circadian clock, the animals were leaner, with less fat and more muscle mass. "Taken together, our work has revealed an entire metabolic network at multiple levels," Uhlenhaut explains. "Another biologically exciting finding is that, contrary to expectations, the key regulator is not centrally located in the brain, but is in fact the internal clock of the muscle cells themselves.'"

Comment: Just another example of the enormity of biological complexity. Only design fits.

"Author summary
Circadian clocks are known to regulate local and systemic homeostasis by anticipating rhythmic changes in behavior and nutritional state and by compartmentalizing incompatible metabolic pathways within precise temporal and spatial windows. Yet a precise mechanistic understanding of how the circadian clock in the skeletal muscle controls homeostasis is just beginning to come to light. Here, we investigated how the muscle clock directs 24-hr metabolic rhythms. We compared genome-wide binding of clock transcription factors brain and muscle ARNT-like protein 1 (BMAL1) and REV-ERBα with 24-hr transcriptional and metabolic effects after their loss of function specifically in muscles. We found that the muscle clock plays a major role anticipating the transition from fasting to feeding. This occurs by direct activation of transcriptional programs promoting lipid storage, insulin sensitivity, and glucose metabolism, with coordinated repression of programs controlling lipid oxidation and protein catabolism. Importantly, these gene expression changes occur in the hours prior to systemic metabolic and hormonal cues that arise upon awakening. As such, we find that the muscle clock tips the scales in favor of glucose metabolism, whereas loss of function of the clock transcription factor BMAL1 is associated with persistent lipid metabolism, protein catabolism, and metabolic inefficiency."

Biological complexity:circadian controls of plant breathing

by David Turell @, Tuesday, March 17, 2020, 21:54 (1473 days ago) @ David Turell

It controls how plants use water and save it:

https://phys.org/news/2020-03-clockwork-transpires.html

"Plants are so dependent on daylight that circadian clocks are even more influential, regulating the rate of photosynthesis, gas exchange, and transpiration, which is the flow of water through the stem and evaporation from leaves.

"Now researchers have discovered that these biological clocks play a critical role in the consumption of water, allowing plants to use this precious resource more efficiently.

"They carried out a series of experiments with model laboratory plants in which the genes encoding circadian rhythms had been changed.

"Some changes made plants use more water in relation to growth but, unexpectedly, the experiments revealed that some of these changes to circadian rhythms allowed plants to grow strong and healthily whilst using less water. The study reveals that it is the whole circadian system that affects water use efficiency not just a specific part.

***

"Plants transpire water with a daily rhythm because the stomata, tiny pores on the surface of leaves, generally open only in the day. Previous studies showed that daily opening is regulated by circadian rhythms.

"'We reasoned that circadian rhythms might have a big impact upon the amount of water that plants use. And our experiments show this to be the case," explains Dr. Antony Dodd of the John Innes Centre, who is the senior author of the study."

Comment: All organisms follow the 24 hour daily pattern. What is not described here is how evolution was able to design pores that open and close on schedule. I'm sure there are specific molecular reactions based on sunlight intensity.

Biological complexity: ion channel pores

by David Turell @, Wednesday, March 18, 2020, 19:34 (1472 days ago) @ David Turell

A new discovery of how they work:

https://medicalxpress.com/news/2020-03-ball-and-chain-inactivation-ion-channels-visuali...

"Ion channels, which allow potassium and sodium ions to flow in and out of cells, are crucial in neuronal 'firing' in the central nervous system and for brain and heart function. These channels use a "ball-and-chain" mechanism to help regulate their ion flow, according to a new study led by Weill Cornell Medicine scientists.

***

"Many types of ion channels, including those necessary for neuronal signaling and the beating of the heart, will physically open, allowing a flow of ions in or out of the cell, when a certain stimulus is applied. However, in order to switch ion flow on and off with high enough frequencies to meet the demands of neurons, heart muscle cells and other cell types, some ion channels need an additional, on-the-fly mechanism to stop ion flow—even when the stimulus is still present and the channel structure is in principle in the "open" state.

***

"With low-temperature electron microscopy (cryo-EM), which bounces electrons instead of light off objects to make atomic-resolution images of them, the scientists obtained pictures of the MthK channel when it was switched open by calcium and switched closed. The pictures revealed that even when the MthK channel is in the calcium-activated, "open" state, the pathway through which ions flow was plugged by a flexible element that sticks into the pore of the channel structure.

"The scientists confirmed the function of this plug mechanism by showing that when the 'ball-and-chain' was deleted genetically, the flow of potassium ions through the calcium-activated MthK channel was no longer regulated."

Comment: this irreducibly complex mechanism cannot be developed by chance. Only design achieves this.

Biological complexity: the role of G protein receptors

by David Turell @, Thursday, March 19, 2020, 21:22 (1471 days ago) @ David Turell

A study generally shows how they function at the molecular level:

https://phys.org/news/2020-03-glucagon-receptor-reveal-protein-specificity.html

"G protei"n-coupled receptors (GPCRs) play essential roles in cell signal transduction and serve as important therapeutic targets for a large number of diseases. Upon binding to extracellular agonists, GPCRs stimulate various signaling pathways by recruiting different G proteins (Gs, Gi, Gq, etc.) to mediate a wide variety of physiological functions. The selective coupling between a GPCR and specific G proteins is critical for the biological action of the receptor.

***

"GCGR, a member of the class B GPCR family, is critical to glucose homeostasis by triggering the release of glucose from the liver, making it a potential drug target for type 2 diabetes and obesity.

"Although GCGR canonically exerts its physiological action through Gs signaling, it can also couple to other G proteins such as Gi and Gq, leading to diverse cellular responses. In 2017 and 2018, the scientists at SIMM determined the crystal structures of the full-length GCGR bound to a negative allosteric modulator or a partial peptide agonist, providing insights into signal recognition and modulation of class B GPCRs.

"This time, the scientists made further progress by solving the complex structures of GCGR bound to two transducer proteins with opposing biological activities. This study offers valuable insights into pleiotropic GPCR-G protein coupling and G protein specificity. Notably, it revealed that the sixth transmembrane helix (helix VI) of GCGR adopts a similar outward shift in the two G protein-bound GCGR structures, forming a common binding cavity to accommodate Gs and Gi. This is contrary to the hypothesis based on the previously determined GPCR-G protein complex structures, which proposed that the positional difference of helix VI is a major discriminator in the coupling specificity of Gs and Gi.

"The common G protein binding pocket observed in the GCGR-G protein complex structures is consistent with the signaling pleiotropy of GCGR and allows for maximal efficiency in activating various pathways. Although GCGR couples to both G proteins through the common pocket, it does so with different interaction patterns, which account for G protein specificity. The measured interaction interface between GCGR and Gs is much larger than for Gi, resulting in higher binding affinity of Gs to the receptor. This offers a structural basis for the preferential coupling of GCGR to Gs.***

"The results show that conformational differences of intracellular loops and residue side chains in the receptor are sufficient to guide G protein selectivity. The interactions contributed by the second intracellular loop (ICL2) and helix VII/VIII junction of the receptor play a crucial role in Gs coupling, while the other two intracellular loops, ICL1 and ICL3, and the receptor hydrophobic intracellular binding cavity are more important for Gi recognition."

Comment: Another example of protein molecules automatically reacting to manage a process in glucose metabolism

Biological complexity: miRNA control of plant pores

by David Turell @, Thursday, March 19, 2020, 22:22 (1471 days ago) @ David Turell

More on protein molecule and miRNA controls:

https://phys.org/news/2020-03-sesame-micro-rnas-pores.html

"Plant pores, called stomata, are tiny openings mainly found on the surfaces of leaves. They are bordered by two 'guard cells,' and are involved in gas exchange and water loss between plants and the atmosphere.

"Scientists already have a good idea about many molecular signals involved in turning on and off genes responsible for stem cells becoming guard cells. But, in addition to normal hereditary processes, environmental cues can also affect how stomata develop and are distributed. For example, pathogen infections, high carbon dioxide levels and high temperatures lead to reduced pore density.

"Molecular cell biologist June Kwak of the Daegu Gyeongbuk Institute of Science and Technology (DGIST) and colleagues investigated if RNA segments called micro RNAs (miRNAs) were involved in stomatal formation and distribution triggered by surrounding conditions. miRNAs are gene regulators that give multi-cellular organisms a degree of flexibility to respond and adapt to environmental changes.

"Kwak and his team developed an approach that allowed them to 'see' which miRNAs turned on throughout the transition from stem cell to guard cell. They found that slightly more than half of all known miRNAs in a plant called Arabidopsis turned on during the various stages of guard cell development. Inhibiting or increasing the expression of the miRNAs altered guard cell formation and distribution, indicating that miRNAs play a crucial role in the pore development.

"Importantly, they singled out a miRNA, called miR399, for its involvement in controlling the pattern of stomatal pores. miR399 is already known for its involvement in regulating phosphate transporter proteins inside plant cells, suggesting a link between stomatal development and phosphate homeostasis in plants.

"'This study reveals that miRNAs constitute a crucial component of stomatal development and control," says Kwak."

Comment: This shows how automatic reactions using miRNA's control these pores.

Biological complexity: bacteria R' us

by dhw, Friday, September 08, 2017, 14:22 (2394 days ago) @ David Turell

DAVID: We live in symbiosis with hordes of bacteria everywhere on and in us:
http://nautil.us/issue/52/the-hive/what-the-meadow-teaches-us?utm_source=Nautilus&u...

QUOTE: "This diversity is not neatly divided between distinct species or types but is available to all microbes within the context of symbiotic processes of exchange. The late biologist and symbiosis researcher Lynn Margulis believed, for example, that this exchange relationship meant that we should actually speak about all the bacteria on Earth as though they composed a single biological subject—one body swarming with countless cells. Consequently, we who are dominated by a bacterial ecosystem ten times larger than our own body’s cells also belong to the great continuum of life. We are literally, physically, a part of the landscape. The moment we take sustenance from it, we enfold it and its inhabitants into our bodies."

Thank you for this great article, and as always for your integrity in presenting it. You will know, of course, that Lynn Margulis was a champion of bacterial intelligence. The suggestion is that our bodies are inhabited by other intelligent beings, and this observation can be extended to the whole of life and the whole history of evolution. Your God may be the source of that intelligence, but if this article and Margulis, McLintock, Albrecht-Bühler, Shapiro and others are correct, there is no way you can dismiss cellular behaviour as automatic.

Biological complexity: bacteria R' us

by David Turell @, Friday, September 08, 2017, 21:04 (2394 days ago) @ dhw

DAVID: We live in symbiosis with hordes of bacteria everywhere on and in us:
http://nautil.us/issue/52/the-hive/what-the-meadow-teaches-us?utm_source=Nautilus&u...

dhw: QUOTE: "This diversity is not neatly divided between distinct species or types but is available to all microbes within the context of symbiotic processes of exchange. The late biologist and symbiosis researcher Lynn Margulis believed, for example, that this exchange relationship meant that we should actually speak about all the bacteria on Earth as though they composed a single biological subject—one body swarming with countless cells. Consequently, we who are dominated by a bacterial ecosystem ten times larger than our own body’s cells also belong to the great continuum of life. We are literally, physically, a part of the landscape. The moment we take sustenance from it, we enfold it and its inhabitants into our bodies."

Thank you for this great article, and as always for your integrity in presenting it. You will know, of course, that Lynn Margulis was a champion of bacterial intelligence. The suggestion is that our bodies are inhabited by other intelligent beings, and this observation can be extended to the whole of life and the whole history of evolution. Your God may be the source of that intelligence, but if this article and Margulis, McLintock, Albrecht-Bühler, Shapiro and others are correct, there is no way you can dismiss cellular behaviour as automatic.

My usual answer. The bacteria are following intelligent instructions they have been given.

Biological complexity: homeostasis

by David Turell @, Friday, September 15, 2017, 21:49 (2387 days ago) @ David Turell

Our bodies are in a constant state of disequilibrium called homeostasis, maintaining exact levels at all times by feedback loops. These controls must have all parts set up all at once:

https://evolutionnews.org/2017/09/in-a-new-book-scott-turner-explores-biologys-second-law/

Homeostasis is life as a state of persistent dynamic disequilibrium…

"Matter is flowing through the whole living organism, while the organism is “maintaining a persistent state of highly specified and complex organization.” Work has to be done to maintain this state. This “self-adjusting confluence of forces is precisely what living things do as a routine.” Turner observes, “It’s what distinguishes the living from the inanimate world…homeostasis is an exceedingly strange idea.”

"Homeostasis is a balancing act. The organism responds to environmental cues and adjusts its own chemistry to maintain things at a certain pH, temperature, oxygen level, salinity, ion concentration, glucose level etc. For creatures like us, none of those states are in equilibrium with the environment. Levels must be precisely balanced at a particular point suitable for life. For example, if our blood chemistry goes askew, it will kill us.

***

"Why should we live in this continuous state of flux? We balance as if on a tightrope with hydrogen, oxygen, carbon, and nitrogen flowing through us. Who we are today, molecularly speaking, is not who we were yesterday or will be tomorrow. Yet we as individuals remain as singular points of balance. As Turner says, homeostasis is an exceedingly strange idea.

"Yet without homeostasis there is no life.

***

"When the parathyroid gland senses low levels of calcium in the blood, it releases the hormone PTH. It is counterintuitive, but osteoblasts (cells that take up calcium to build bone) have PTH receptors. These receptors stimulate osteoblasts to pump calcium ions out of the fluid surrounding the bone and into the extracellular fluid. They also produce a signaling molecule that activates osteoclasts (cells that break down bone to produce calcium).

"PTH also stimulates calcium reabsorption in the kidney and the production of 1,25(OH)2D, the active form of vitamin D by the kidney. In the small intestine, 1,25(OH)2D works to promote calcium absorption.

***

"Not to put too fine a point on it, but the existence of complex and specified systems is a hallmark of design. How do you build a system requiring multiple signals and receptors one step at a time when the system does not work until all are present? A receptor is no good without a signal to receive, and the signal will not be sent with a cue.

"Then there is the need for an effector. The parathyroid gland senses low calcium (how?) and produces PTH. PTH travels through the blood stream to its many sites of action. If PTH is high, then receptors on osteoblasts (receptors are usually proteins) receive that signal, and in turn send another signal to osteoclasts (probably a protein), which then receive that signal and effect a change (another protein?) in order to release calcium ions to the blood stream, and restore the calcium levels to where they should be. And that is just one means of regulating calcium.

"To recap, from Claude Bernard:

"The fixity of the [interior] milieu supposes a perfection of the organism such that the external variations are at each instant compensated for and equilibrated…. All of the vital mechanisms, however varied they may be, have always one goal, to maintain the uniformity of the conditions of life in the internal environment…. The stability of the internal environment is the condition for the free and independent life."

Comment: The moment by moment conduct of living organisms (homeostasis as constant disequilibrium) can only result from design. No other theory makes any sense. There is a designer.

Biological complexity: cell division reidentification

by David Turell @, Sunday, September 17, 2017, 18:52 (2385 days ago) @ David Turell

How do cells know how to return to their functional capacity after division? After all they contain all the DNA of all functions, but must active some and suppress others. The mechanism is identified:

https://www.sciencedaily.com/releases/2017/09/170914152248.htm

"Prior to cell division, chromosomes are seemingly a jumbled mess. During cell division, parent cell chromosomes and their duplicates sort themselves out by condensing, becoming thousands of times more compact than at any other time. Researchers have long assumed that genes become "silent" during cell division, not being transcribed into proteins or regulatory molecules. This has left open the question of how genes get properly re-activated after cell division. Now, researchers in the Perelman School of Medicine at the University Pennsylvania have found that gene expression actually continues during cell replication.

***

"First author Katherine C. Palozola, a doctoral candidate in the Zaret lab, is the first to find a way to look at gene activity in a living cell during division. Using a human liver cell line, she labeled the nucleic acid uridine (one of the four gene messenger building blocks) and followed it to see which genes were still active during replication.

"'We were surprised that gene expression was still on -- albeit at a low level -- during replication," Palozola said.

"Although chromosomes are extremely compact during cell division, with sequences for regulatory molecules buried and previously presumed to be unavailable to be transcribed, Palozola found that most genes and their nearby regions that promote gene function are still actively expressed. She discovered how cells wake up after cell division and recall "who they are." What ultimately drives cell differentiation are sequences of enhancer molecules located away from the gene they act on.

"The laboratory of Gerd Blobel at the Children's Hospital of Philadelphia had previously shown that these far-away modifiers "nap" during division, since it only lasts about 30 minutes -- relatively quickly in biological terms -- and come back online after a cell division cycle is complete.

""The most amazing thing about this study is that in the end, we had to throw what we thought we knew about this basic aspect of gene regulation out the window," Zaret said. "The findings indicate that we need to think about how promoters, rather than enhancers, are regulated during cell division. This refocusing will tell us how a cell's identity, as defined by the genes it expresses, is retained through cell division.'

Comment: Cell division is highly complex. Cell division occurred with first life. Therefore the mechanism had to exist from the beginning. It could not develop bit by bit, but was designed all at once. No other conclusion is logical.

Biological complexity: mitochondrial structure found

by David Turell @, Friday, September 22, 2017, 18:56 (2380 days ago) @ David Turell

Take a look at this story. The complexity of the molecules is amazing:

https://phys.org/news/2017-09-mitochondrial-respiratory-supercomplex-decoded.html

"The picture of the megacomplex (MC) that has emerged has the following stoichiometry: MCI2II2III2IV2. This means that complexes I,II,III,& IV are each present in duplicate while complex V is absent. It is configured within the membrane into a circular structure with the dimeric CIII located at the center and fed by peripheral CI and CIV complexes. The CII complexes are apparently not essential requirements to the core structure but rather are theorized to be wedged into gaps as needed. The authors also found evidence for a lightweight rendition of the megacomplex that can sometimes be assembled with just a single CI complex.

"The central positioning of the CIV dimer suggests a certain logic. CIV, or cytochrome oxidase, is the terminal resting ground for electrons entering the chain. Those that make it this far have been lowered down the reduction potential hierarchy as far as they can go. Here, they are sunk into waiting oxygen molecules, which are then exhausted as molecules of water. High potential electrons packaged as NADH enter the complex at its perimeter and are funneled into the center. The absence of C5 complexes may not be so unusual, considering that they are typically found as rows of "V'-shaped dimers that contort the membrane into regions of high curvature at bends in the cristea.

***

"The central positioning of the CIV dimer suggests a certain logic. CIV, or cytochrome oxidase, is the terminal resting ground for electrons entering the chain. Those that make it this far have been lowered down the reduction potential hierarchy as far as they can go. Here, they are sunk into waiting oxygen molecules, which are then exhausted as molecules of water. High potential electrons packaged as NADH enter the complex at its perimeter and are funneled into the center. The absence of C5 complexes may not be so unusual, considering that they are typically found as rows of "V'-shaped dimers that contort the membrane into regions of high curvature at bends in the cristea.

"With the basic structure in hand, the researchers were able to suggest a few basic principles of operation. Their inclusion and placement of CII effectively explains reverse electron transport from succinate to NADH. The proposed geometry also creates a sealed Q-pool (a lipid-soluble electron carrier) which is accessible to both CI and CII. The authors were also able to pinpoint the identity and locations of several lipid molecules that secure the complex within the membrane, specifically, several pivotal several lipid molecules that secure the complex within the membrane, specifically, several pivotal molecules of phosphatidylethanolamine, phosphatidylcholine, and cardiolipin. They were also able to identify preferred or most efficient electron transfer pathways, which in turn constrain how many electrons can simultaneously be transferred among active carriers."

Comment: this is a highly complex article based on an extraordinary piece of research. I've presented it to show the complexity of mitochondria, the size of enzymatic molecules an evolutionary process is supposed to find by chance. Never!

Biological complexity: ion channel complexity

by David Turell @, Friday, October 13, 2017, 23:24 (2359 days ago) @ David Turell

All mammalian cells have this channel to conduct ions properly:

https://phys.org/news/2017-10-d-atomic-trpml1-ion-channel.html

"'Functioning ion channels are needed for the proper movement of electrically charged particles - ions - in and out of cells and organelles to run cellular processes," said Dr. Youxing Jiang, Professor of Physiology and Biophysics, an Investigator in the Howard Hughes Medical Institute (HHMI), and co-corresponding author of the study.

"The TRPML1 channel, which regulates the flow of calcium ions, is found in every mammal. The channel sits in the membrane of organelles inside cells called lysosomes, which contain enzymes that aid in cellular recycling by breaking down large molecules."

The original article abstract:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature24035.html?foxtrotcallbac...

"Transient receptor potential mucolipin (TRPML1) is a cation channel located within endosomal and lysosomal membranes. Ubiquitously expressed in mammalian cells1, its loss-of-function mutations are the direct cause of type IV mucolipidosis, an autosomal recessive lysosomal storage disease3. Here we present the single-particle electron cryo-microscopy structure of the mouse TRPML1 channel embedded in nanodiscs. Combined with mutagenesis analysis, the TRPML1 structure reveals that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2) binds to the N terminus of the channel—distal from the pore—and the helix–turn–helix extension between segments S2 and S3 probably couples ligand binding to pore opening. The tightly packed selectivity filter contains multiple ion-binding sites, and the conserved acidic residues form the luminal Ca2+-blocking site that confers luminal pH and Ca2+ modulation on channel conductance. A luminal linker domain forms a fenestrated canopy atop the channel, providing several luminal ion passages to the pore and creating a negative electrostatic trap, with a preference for divalent cations, at the luminal entrance. The structure also reveals two equally distributed S4–S5 linker conformations in the closed channel, suggesting an S4–S5 linker-mediated PtdInsP2 gating mechanism among TRPML channels."

Comment: Be sure to look at the links to see how highly complex this controlling pore has to be. Certainly not by chance. Design required.

Biological complexity: mitochondrial DNA repair

by David Turell @, Saturday, October 14, 2017, 14:55 (2358 days ago) @ David Turell

It all depends upon an unusual enzyme which has an ancient structure:

https://www.eurekalert.org/pub_releases/2017-10/uoef-sdn101217.php

"Researchers at the University of Eastern Finland have discovered a novel mechanism safeguarding mitochondrial DNA. ...A central part of the protective mechanism is an unusual enzyme, PrimPol, which can re-initiate mitochondrial DNA replication after damage.

"Besides nuclear genomic DNA, mitochondria also contain their own small genomes, mitochondrial DNA (mtDNA), which encodes for thirteen essential parts of the cellular respiration machinery. mtDNA is especially vulnerable to oxidative damage as it is located close to the free radical producing mitochondrial electron transport chain. Cells protect their mitochondria by repairing mtDNA as well as constantly making new copies of it to replace the damaged molecules. Although cells are able to tolerate DNA damage, problems might arise when the DNA is replicated. Certain types of damage can stall the replication machinery before all of the genome has been replicated. This can result in double-strand breaks in DNA, resulting in the loss of partially replicated parts of the genome. In mitochondria this partial loss, or deletion, causes dysfunction of the cellular respiration and is the driving pathological mechanism behind many mitochondrial diseases but also responsible for aging associated decline of cell function.

"Researchers were able to show that a primase enzyme PrimPol can generate a new primer adjacent to the damaged DNA sequence and re-initiate stalled replication in mitochondria. PrimPol itself is a highly unusual, structurally ancient primase, which can synthetize DNA primers in contrast to RNA primers synthetized by all other primases in our cells. Not only does the new study change our perceptions of PrimPol's functions, it also helps us to understand the basic mechanisms of mtDNA maintenance. (my bold)

"'As mtDNA often suffers collateral damage from cytostatins used during cancer treatment or antibiotics targeting bacteria, understanding of the repair mechanisms can help in developing these treatments," says Dr Jaakko Pohjoismäki from the University of Eastern Finland.

"'Heart cells or cardiomyocytes are especially vulnerable to the loss of mitochondrial function, and enhanced protection of mtDNA could also shield diseased hearts," he continues."

Comment: Fits the theory that mitochondria were swallowed bacteria, early in the history of life, that fit into cells to produce energy. A special 'ancient enzyme' is needed. Once again we see that a giant complex molecule (enzyme) manages to appear in evolution to solve a problem. Luck or God? I'll pick God.

Biological complexity: must be discovered

by David Turell @, Monday, October 16, 2017, 17:44 (2356 days ago) @ David Turell

When a mechanic looks at a motor he can quickly understand its functional activity and quickly fix what is wrong. In life we must discover how it works and then learn how to work with it. we can discover reasons, but just looking at living tissue explains nothing. This complexity of life beggars description and requires intelligent design. Look at this study:

https://phys.org/news/2017-10-neutrons-vitamin-b6-dependent-enzyme-drug.html

"Specifically, the team used neutron crystallography to study the location of hydrogen atoms in aspartate aminotransferase, or AAT, an enzyme vital to the metabolism of certain amino acids.

"'We visualized the first neutron structure of a vitamin B6 enzyme that belongs to a large protein family with hundreds of members that exist in nature," said ORNL's Andrey Kovalevsky, a senior co-author of the study, which was published in Nature Communications.

"Vitamin B6-dependent proteins are part of a diverse group of enzymes that conduct over a hundred different chemical reactions in cells. The enzymes are of interest to biomedical, as well as bioenergy, researchers because of their role in metabolizing amino acids and other cell nutrients.

"'These enzymes are unique in that each one performs a specific chemical reaction with exquisite accuracy, while suppressing other viable chemical transformations," Kovalevsky said. "How they accomplish this is not well understood, but it is of great significance for drug design."

"The team's previous research predicted that hydrogen atoms move in and around the enzyme's active site, where the chemical reaction takes place, indicating that the hydrogen atoms' positioning controls the reaction type. Knowing the precise location of hydrogen atoms can explain why the behavior of these enzymes is so specific, but hydrogen is hard to detect with standard methods such as X-ray crystallography.

"The team's previous research predicted that hydrogen atoms move in and around the enzyme's active site, where the chemical reaction takes place, indicating that the hydrogen atoms' positioning controls the reaction type. Knowing the precise location of hydrogen atoms can explain why the behavior of these enzymes is so specific, but hydrogen is hard to detect with standard methods such as X-ray crystallography.

"The data revealed that in one of the enzyme's biomolecular structures the covalent bonds reorganized after a chemical reaction occurred in the active site and, in another, the reaction had not taken place," Kovalevsky said. "Essentially, we were able to obtain two structures in one crystal, which has never been done before for any protein using neutrons.'"

Comment: These delicate studies show how giant enzyme molecules with minor hydrogen ion changes manage biochemical reactions in micro-seconds. Without these intricate changes life could not continue as it does. How did evolution discover these complex molecules? Only design can create them.

Biological complexity: complexity of DNA repair

by David Turell @, Monday, October 16, 2017, 17:56 (2356 days ago) @ David Turell

DNA damage must have exact repair:

https://phys.org/news/2017-10-insights-dna-sites.html

"With their structural data, the FMI scientists provide the missing link between two previously published structures, allowing them to assemble a to-scale composite structural model of Mec1-Ddc2 on ssDNA-RPA at DNA damage sites.

"The ATR kinase has attracted interest for over 20 years. This kinase is one of two central DNA damage sensing kinases in mammalian cells, and it is also a tumor suppressor. Two compounds that inhibit ATR kinase are in clinical trials for the treatment of leukemia and solid tumors. Yet, how this enzyme is regulated on a molecular level has remained elusive.

***

"Mec1 forms a complex with a regulatory subunit called Ddc2 (ATRIP in humans). Upon DNA damage, large stretches of single strand DNA (ssDNA) are exposed, which are rapidly covered by replication protein A (RPA). Mec1-Ddc2 recognizes these ssDNA-RPA stretches and accumulates at these sites to initiate repair mechanisms.

"Deshpande and colleagues have now resolved the 3-D structure of the Ddc2 N-terminus in association with part of RPA thus providing structural data on the link between RPA and Mec1, which had up to now been elusive. We obtained a high-resolution co-crystal structure of the Ddc2 N-terminus together with a subunit of RPA, Deshpande explained. With these data, we could show that Ddc2 forms homodimers and binds RPA by its N-terminus. Interestingly, our Ddc2-RPA structure is the missing link between two previously published structures, and this allows us to assemble a to-scale composite structural model of Mec1-Ddc2 on ssDNA-RPA at DNA damage sites.

"The Ddc2 N-terminus not only facilitates Mec1 interaction with RPA but also functions as a spacer for the Mec1 kinase. Deshpande explains: The elongated Ddc2 N-terminus allows the large Mec1 kinase module to move without encountering the damaged DNA nor the repair machinery working at the lesion. In addition, the Ddc2 spacer may allow Mec1 to phosphorylate multiple spatially distinct substrates while remaining bound to the site of DNA damage. You can think of the Ddc2 N-terminus as a giraffe's neck that allows the giraffe to reach the grass on the ground as well as the leaves on a tall tree."

Comment: Back to the chicken/egg question. In the beginning of life, DNA had to be protected from mistakes and damage. Obviously, life could not continue if these mechanisms provided by giant enzyme molecules were not present to protect the integrity of DNA. Only intelligent design can provide this. My point is material naturalism is not able to invent these necessary giant molecules, yet they exist. Darwinism doesn't work

Biological complexity: producing lipoic acid

by David Turell @, Thursday, October 19, 2017, 19:21 (2353 days ago) @ David Turell

Lipoic acid is necessary to produce energy for cells. How it is generated by enzymes is shown:

https://phys.org/news/2017-10-renewable-resource-vital-lipoic-acid.html

"New research shows how a protein is consumed and then reconstituted during the production of lipoic acid, a compound required by our bodies to convert energy from food into a form that can be used by our cells. The lipoyl synthase enzyme (LipA) removes two hydrogen atoms from an inert carbon chain and replaces them with sulfur atoms from one of its own iron-sulfur clusters to create lipoic acid, rendering itself inactive in the process. The new research ... shows that another protein, an iron-sulfur cluster carrier called NfuA, replaces the destroyed iron-sulfur cluster in LipA, allowing it to continue producing lipoic acid.

***

"'LipA cannibalizes itself to provide the sulfur atoms needed for the production of lipoic acid," said Squire Booker, professor of chemistry and of biochemistry and molecular biology at Penn State University, an investigator of the Howard Hughes Medical Institute, and the corresponding author of the research paper. "When we demonstrated this in 2011, it was perplexing because if LipA is destroyed, how could the cell make enough lipoic acid?"

"LipA is a member of the radical SAM (S-adenosylmethionine) family of enzymes. Like most radical SAM enzymes, it contains a cluster of four iron and four sulfur atoms, which it uses to convert SAM into a high energy radical. In turn, that radical can remove hydrogen atoms from other molecules, a step required to activate many important cellular metabolic reactions. The hydrogen atoms are replaced with sulfur to complete the process.

"Where the sulfur atoms that LipA uses to produce lipoic acid come from and how they are attached have been major questions in the field. How other enzymes attach oxygen atoms to inert carbon centers is fairly well understood. In those instances, oxygen, which is ubiquitously available in the atmosphere, is used to create high-energy radicals and is also the source of the appended oxygen atom. Sulfur, on the other hand, is not similarly available, but unlike most other radical SAM enzymes, LipA has an additional iron-sulfur cluster.

***

"In this second experiment, the researchers showed that after the 32S originally present in LipA was consumed in the chemical reaction to produce lipoic acid, lipoic acid was produced containing 34S, which could only have come from their engineered NfuA.

"'We've been interested for quite some time in both the process that adds sulfur to an inert carbon compound to make lipoic acid and the source of the added sulfur," said Booker. "Lipoic acid is a vital component of the basic metabolic processes that keep our cells alive."

Comment: This is a complex interaction within a giant enzyme molecule and a gene. For cells to use energy this reaction is necessary on a continuous basis, which implies it was present at the beginning of life as a totally intact process. It could not have developed bit by bit. Moe evidence for intelligent design.

Biological complexity: controlling DNA expression

by David Turell @, Monday, October 23, 2017, 16:39 (2349 days ago) @ David Turell

Another giant enzyme is studied and its actions further understood:

https://phys.org/news/2017-10-single-molecule-developmental-gene.html

"Scientists at EPFL and Max Plank have made significant discoveries on how developmental genes are controlled by the methyltransferase enzyme PRC2.

"Polycomb repressive complex 2 (PRC2) is part of a larger system of proteins that work together to repress the expression of developmental genes. PRC2 does this by adding up to three methyl groups to a specific lysine amino acid (lysine 27) of the histone H3 protein. Trimethylation (three methyl groups) of lysine 27 in particular is important, as turns off the expression of specific genes during development.

"Such gene repression requires a high concentration of lysine 27 trimethylation within defined chromatin (DNA wrapped around histones) regions, since mutations that prevent this process result in developmental defects or cancer. For maximum activity, PRC2 needs further "accessory factors", which vary between species. In humans, a main accessory factor is PHF1.

***

"Structural analysis showed that PHF1 contains a previously unknown DNA-binding domain whose interactions with the nucleosomal DNA is critical for anchoring PRC2 to chromatin and for increasing its activity. Essentially, this DNA-binding domain is the key to efficient gene regulation across different species. As the authors write: "...a major part of the binding affinity of PRC2 for nucleosomes comes from interactions of the complex with DNA."

"The authors draw three conclusions from the findings: First, that the binding affinity of PRC2 for chromatin substrate is determined by its interactions with DNA. Second, that increased anchoring of PRC2 to chromatin via PHF1 depends on a newly identified structural unit in PHF1. And third, that stable PRC2 chromatin interactions, mediated by PHF1, are key for increased lysine trimethylation in chromatin - and thus for gene repression."


Comment: Again extreme complexity in the controls of DNA expression. Cannot be accomplished by a chance process of evolution. Without strict control there would be developmental abnormalities. Obviously this whole system had to be developed all at once, intact, not bit by bit.

Biological complexity: controlling intracellular traffic

by David Turell @, Friday, November 10, 2017, 00:33 (2331 days ago) @ David Turell

Expression of certain proteins and enzymes controls speed and direction of traffic along the microtubules in the cells:

https://www.sciencedaily.com/releases/2017/11/171109131223.htm

"The highways inside cells are called microtubules, and proteins called kinesins and dyneins act like motors and are essentially the cargo trucks in cells, O'Hagan said. The motor proteins drive cargoes around microtubule highways, but a central question in cell biology is how intracellular transport and the highway systems are organized. Questions include how the motor proteins know where to go and how fast they need to be.

***

" The scientists found that TTLL-11 is an enzyme that puts traffic signs composed of the amino acid glutamate on the microtubule highways to regulate the speed of the protein cargo trucks. CCPP-1 is an enzyme that takes down these glutamate traffic signs when there are too many of them, according to O'Hagan.

"'Working together, they seem to regulate the speed of the motors that move cargoes on the microtubular highways," he said.

"The scientists also found that the glutamates can also act as a "roadway under construction" sign, changing the highways' structure, he said."

Comment: There is no way to develop this system stepwise. It is too complex with specific enzymes and proteins working in concert. It must be designed and put into effect all at once. Only a designer God can do his.

Biological complexity:fine-tuning neuron transmission

by David Turell @, Tuesday, November 28, 2017, 14:52 (2313 days ago) @ David Turell

The controls over neuronal firing are being discovered:

https://www.the-scientist.com/?articles.view/articleNo/50632/title/Presynaptic-Neurons-...

"Psychiatrist Zachary Freyberg thought he knew the basics of dopamine signaling. When a dopamine neuron fires, vesicles containing the neurotransmitter migrate to the cell membrane, where they fuse and release their cargo into the synapse, all in the course of about a millisecond. But a chance observation by Freyberg a few years ago revealed a new dimension to this critical aspect of neural communication.

"At Columbia University, beginning in 2009, Freyberg had helped develop a technique to observe dopamine signaling in living Drosophila brains. The method used molecules of FFN206, Freyberg says, which “behave like dopamine, but unlike dopamine, they’re fluorescent and therefore can be readily visualized.”

"He and his colleagues expected that when neurons were artificially stimulated with potassium chloride, vesicles would transport FFN206 to the cell membrane and release it into the synapse. That did happen—but the fluorescence indicated something else was going on, too. “You’d expect the dopamine signal to go down,” Freyberg, now at the University of Pittsburgh, explains. “Instead, it was going up before going down.” The vesicles, the team realized, were loading extra cargo before fusing with the membrane—a contradiction of the textbook view that vesicles’ dopamine levels were fixed.

"To investigate further, the researchers looked for signals associated with the boost in vesicle content. They found that before fusion but after cell membrane depolarization—a sign of neuronal activity—the pH inside vesicles dropped. “For dopamine, it’s the pH of the vesicles that creates the driving force for loading,” Freyberg explains, with more-acidic conditions promoting loading.

"However, it was unclear what triggered the extra acidification. The researchers suspected chloride, a negatively charged ion often involved in establishing proton gradients. But experiments didn’t back that theory up. So the team turned to glutamate, a neurotransmitter that is also negatively charged. “When we blocked the entry of glutamate into these dopamine vesicles, they no longer acidified more, and no longer loaded more in response to activity,” Freyberg says.

"The researchers observed similar processes in mice, and in a new paradigm, suggest how this unexpected role for glutamate links neuronal activity to dopamine vesicle content across species. “It’s showing a mechanism by which presynaptic neurons can be regulated,” says Thomas Hnasko, a neurobiologist at the University of California, San Diego. “Most people think about plasticity in the brain as a postsynaptic phenomenon. . . . This is all really quite novel.”

"Freyberg is now investigating how these mechanisms fine-tune the amount of dopamine sent across the synapse, and their effects on neuronal communication in normal and diseased brains. “It’s as if we’ve been thinking all our lives that when you turn on a light, you just flip a switch, and it’s on or off,” he says. “But what this suggests is that neurons are capable of a great deal more subtlety.'”

Comment: Yes, fine-tuned and more subtle. The underlying design cleverness of living cells is always surprising. There is no way for a chance evolutionary process to create this degree of obvious design of controls. It will turn out to be all automatic.

Biological complexity: enzyme stops U_V damage

by David Turell @, Tuesday, December 05, 2017, 22:09 (2306 days ago) @ David Turell

This huge enzyme molecule repairs DNA U-V damage in plants that need to sit in sunshine all day:

https://www.sciencedaily.com/releases/2017/12/171205092220.htm

"By studying this enzyme, called DNA photolyase, with the ultrabright and ultrafast pulses of the LCLS X-ray laser, researchers finally have the opportunity to watch the enzyme in action as it catalyzes a chemical reaction in real time and at the atomic scale to resolve longstanding debates about how these enzymes work. Ultimately, this knowledge could be used to engineer improved synthetic versions of enzymes that drive crucial reactions in biological systems, or to produce novel enzymes that do not exist in nature.

"'The biochemical reactions performed by enzymes are at the heart of the adaptability and efficiency of living things," says Thomas Joseph Lane, an associate staff scientist at LCLS. "But the details of how enzymes work is hidden in chemical processes that occur on extremely short timescales, down to millionths of a billionth of a second, so we needed LCLS to reveal their secrets."

"In just a few seconds, ultraviolet light from the sun can damage DNA by creating hundreds of unwanted links within DNA's double helix. These modifications make the genetic material bulky and unreadable by DNA replication tools, leading to permanent mutations that can cause cancer and other diseases if left unrepaired.

"But the same sunlight that carries damaging UV rays also contains blue light that can induce photolyase to quickly repair any DNA damage.

"Photolyase is thought to be one reason why plants -- that have hours of exposure to the sun each day -- are less susceptible to UV damage than humans, who lack photolyase. Humans and other mammals must fall back on alternative DNA repair mechanisms (or avoid going out into the sun altogether).

***

"'There are still some major gaps in our understanding of how enzymes work, highlighted by the fact that human-made enzymes have yet to match nature's performance," says Lane. "We hope our experiments here at LCLS will help us bridge those gaps, getting us closer to understanding and harnessing the chemistry living things do every day.'"

Comment: Note tgeh bold. Our inventiveness is not equal to natures. This study presents the usual problem, how did chance evolution even find this necessary giant molecule? Only design can do this.

Biological complexity: cell migration motors

by David Turell @, Monday, December 11, 2017, 15:50 (2300 days ago) @ David Turell

Cells in the body have to migrate to heal a wound as one example of the requirement. How the cell moves is described:

https://phys.org/news/2017-12-internal-cell-migration-revealed-live-cell.html

"How do cells move in a certain direction in the body—go to a wound site and repair it, for example, or hunt down infectious bacteria and kill it?

"Two new studies from the Marine Biological Laboratory (MBL) show how cells respond to internal forces when they orient, gain traction, and migrate in a specific direction. The research, which began as a student project in the MBL Physiology Course and was developed in the MBL Whitman Center, is published in Proceedings of the National Academy of Sciences (PNAS) and this week in Nature Communications.

"Both papers focus on the activation of integrins, proteins that allow cells to attach to their external environment and respond to signals coming from other cells. Integrins are transmembrane proteins: part lies on the cell surface and part lies inside the cell. Using a microscope invented at the MBL, the authors showed that when integrins unfurl from the cell surface and bind extracellularly, they simultaneously align in the same direction as a force inside the cell (actin retrograde flow).

"'If you think of a cell as a car, the actin flow is the engine," says Clare Waterman, a Whitman Center Scientist from the National Heart, Lung and Blood Institute. "The cell can sit there, idling its engine. But when the integrins activate and bind externally, they are like the tires hitting the road, providing friction. The engine goes into gear and the car moves."

***

"There are 24 different types of integrins found on human cells. The PNAS paper studies an integrin on fibroblast cells while the Nature Communications paper analyzes an integrin on white blood cells.

"'The two integrins we worked on were about as structurally different as you can get in the integrin family," says Springer, yet both types, when activated, oriented in a direction dictated by intracellular actin flow.

"'This is really beautiful basic research," Springer says. "While we knew a lot about highly purified integrins in solution, this research gives us specific information about their activation state in living cells.'"

Comment: A wonderful depiction of how cells can migrate. The initiation of movement must be a response to a stimulus/stimuli, but that is not part of this study.

Biological complexity: specialized taste proteins

by David Turell @, Tuesday, January 09, 2018, 17:40 (2271 days ago) @ David Turell

There are two specialized proteins necessary to send taste signals to the brain for interpretation:

https://medicalxpress.com/news/2018-01-chemical-pathway-brain-sweet-savory.html

"Until now, many scientists believed that a single protein—TRPM5—acted as a gatekeeper for tasting these delectable foods. Remove TRPM5 from a person's taste cells, and they would no longer be able to identify sweet, bitter or savory (also called umami) foods.

"A new study challenges this thinking. The research, published on Jan. 8 finds that a second protein—TRPM4—performs a similar role in the taste system.

In experiments, mice who had TRPM4 drank sugar water enthusiastically and enjoyed a savory treat. They also recoiled from quinine, a bitter compound. Mice who were missing the protein on their taste cells had a more difficult time detecting sweet, bitter and savory flavors.

"'Our research shows that there is redundancy in the taste system," says lead researcher Kathryn Medler, Ph.D., associate professor of biological sciences in the University at Buffalo College of Arts and Sciences. "This is important because taste is actually central to our survival. If you can't taste something bitter, you might gobble up something that's poisonous without ever knowing that it could be harmful."

***

"Like TRPM5, TRPM4 is a special kind of protein called an ion channel. Found on taste cells, TRPM5 and TRPM4 channels open when sweet, bitter or savory foods land on the tongue. This sets off a chain reaction in which the cells produce an electrical signal that travels to the brain, notifying the organ of which flavors have been detected.

"Banik and Medler's new study found that mice were most sensitive to sweet, bitter and umami stimuli when the animals had both TRPM5 and TRPM4 on their taste cells. Removing either protein caused a decrease in sensitivity, and removing both left the mice unable to detect the flavors at all.

"Though the study was done on mice, the research is likely relevant to humans, Medler says. TRPM5 and TRPM4 are both present in human taste cells, and TRPM5 is known to play a role in how people taste."

Comment: How did evolution as a chance process find these two specific proteins? But more to the point is the magical way the particular stimuli are identified as electrical impulses which can be specifically identified by the brain neurons. All of our sensory input is really a second-hand representation of reality. But it works.

Biological complexity:inflame then implant a placenta

by David Turell @, Wednesday, January 10, 2018, 22:08 (2270 days ago) @ David Turell

Experimentation in animals has shown that molecules that cause inflammation help implant a placenta in mammals:

https://www.scientificamerican.com/article/armadillo-hedgehog-and-rabbit-genes-reveal-h...

a study of gene expression in early pregnancy, when the embryo implants in the uterus, suggests that placental mammals evolved the ability to turn an inflammatory attack on the embryo into an advantage.

***

in placental mammals, the embryo does not simply cling to the uterus. Rather, it destroys the uterine lining as it invades the tissue, triggering a flood of inflammatory proteins. During infection and injury, these proteins normally fight invaders and repair wounds. Some of these proteins could be detrimental to a budding life form, but studies suggest that inflammation is necessary for an embryo. For instance, women who take anti-inflammatory drugs in the earliest days of pregnancy have a higher risk of miscarriage because the embryo does not successfully implant in the uterus. And reproductive biologists argue that certain aspects of inflammation, such as the growth of new blood vessels, help the developing embryo to get the oxygen and nutrients it needs.

***

To find out how placental mammals are able to withstand the protein assault in these early days, Chavan analysed the inflammatory response in three of these species: the rabbit (Oryctolagus cuniculus), armadillo (Dasypus novemcinctus) and hedgehog (Echinops telfairi). An inflammatory protein, interleukin-17, that had been present in high levels in the opossum seemed to be inactive in the placental mammals—as if it had been switched off. The protein normally beckons white blood cells that kill invaders by digesting them or destroying them with enzymes. “It’s probably important to shut those down before they can damage the embryo,” Chavan says.

***

His preliminary studies found that cells lining the uterus of placental mammals suppress the production of interleukin-17. Other aspects of the inflammatory response subside later in pregnancy, although it’s unclear what triggers this. The results suggest that placental mammals have fine-tuned inflammation over the course of pregnancy so that it waxes and wanes. “Mammals have figured out a way to keep some aspects of the inflammatory process that are favourable to the fetus, but stop the destructive parts of the response,” says Gunter Wagner, an evolutionary biologist at Yale and the senior investigator on the studies.

Comment: this finding presents the usual question of how it evolved. All of this process can damage the fetus, so the inflammatory event and its protective mechanism for the fetus must all develop simultaneously. Cannot be stepwise. Design in action.

Biological complexity: how plants stop U_V damage

by David Turell @, Tuesday, April 17, 2018, 18:53 (2173 days ago) @ David Turell

Plants sit out in the sun, needing it for energy , but are exposed to UV radiation, and must protect themselves. They have a mechanism like animals have with slight different proteins employed:

https://www.sciencedaily.com/releases/2018/04/180417085926.htm

"because plants can't come in from the sun or slather on sunblock, they have a super robust DNA repair kit. Today, the UNC School of Medicine lab of 2015 Nobel laureate Aziz Sancar, MD, PhD, has published an exquisite study of this powerful DNA repair system in plants, which closely resembles a repair system found in humans and other animals.

"The study, published in Nature Communications, is the first repair map of an entire multicellular organism. It revealed that the "nucleotide excision repair" system works much more efficiently in the active genes of plants as compared to humans. And this efficiency depends on the day/night cycle.

***

"Sancar, the Sarah Graham Kenan Professor of Biochemistry and Biophysics, was awarded the 2015 Nobel Prize in Chemistry for his studies of excision repair, which is now widely viewed as the major mechanism of DNA repair -- including repair of UV damage -- in living organisms.

***

"For the study, Oztas and colleagues used an excision-repair mapping technique they recently developed, known as XR-seq. The technique enables them to detect and sequence the short lengths of damaged DNA that are cut from chromosomes during the excision repair process. The sequences of these DNA snippets can be matched to corresponding stretches of DNA on a reference genome, in order to map precisely the spots where DNA-damage is under repair.

"The UNC researchers performed XR-seq scans on cells from UV-exposed plants -- Arabidopsis thaliana, the "lab rat" of plant research also known as thale cress or mouse-ear cress. The resulting repair maps revealed that excision repair in Arabidopsis works faster on genes that are active. Genes when active are transcribed into strands of RNA that may then be translated into proteins, the main machinery of cells. Prior studies from the Sancar lab showed that excision repair works more efficiently for actively transcribed genes in animals and bacteria. The phenomenon, called transcription-coupled repair, is thought to have evolved as a way to direct DNA repair where it is most acutely needed.

"'Here we found that the jump in efficiency for transcription-coupled repair is even more pronounced in plants than it is in animals or bacteria," Oztas said.

"Sancar's lab performed XR-seq on UV-exposed Arabidopsis over 24-hour periods to discover that the efficiency of transcription-coupled repair also varies according to the "circadian" day/night cycle for 10 to 30 percent of Arabidopsis's genes. This reflects the normal daily variations of transcription activity in these genes.

"'The results show that excision repair in plants is regulated in much the same way it is in other organisms -- in order to maximize efficiency," Oztas said.

***

"The plant excision repair system also involves a slightly different set of repair proteins than are found in other organisms. The UNC scientists hope to determine why that is and precisely how plants' distinctive set of excision repair proteins work together to keep plant genomes in good repair."

Comment: Since plants must be constantly exposed to sunlight and UV wavelengths, this system must have been designed into plants at the beginning of plants development on Earth. Not by chance.

Biological complexity: complexity of DNA repair

by David Turell @, Tuesday, January 16, 2018, 18:49 (2264 days ago) @ David Turell

Another method of DNA repair with different molecules:

https://www.sciencedaily.com/releases/2018/01/180116093652.htm

"DNA is like the computer code of the body, and it must be preserved for our bodies to survive. Yet, as cells grow and change, DNA is vulnerable to defects, especially double strand breaks (DSBs). In fact, DSBs regularly occur throughout one's lifetime. The DNA is protected, however, by DNA repair machinery. A new study from scientists at Osaka University and The University of Tokyo describes the crystal structure of a crucial part of this machinery, the binding of RNF168 to ubiquitylated proteins and find a unique binding not seen in other ubiquitylated protein interactions.

"To activate the DNA repair machinery, DSBs stimulate ubiquitylation. RNF168 binds to polyubiquitylated proteins and accumulates at the damaged DNA as part of the repair process.

"Ubiquitylation describes the binding of the protein ubiquitin to another protein. Ubiquitin will then further bind to itself through one of its seven lysine amino acid residues to form a ubiquitin chain. RNF168 binds with high specificity to ubiquitin chains linked at lysine 63.

***

"Crystal structures were made of each RNA168 domain bound to a lysine 63 chain two ubiquitin molecules long. The structures revealed that the RNF168-lysine 63 chain interaction is stabilized by many unique hydrogen bonds and hydrophobic interactions not seen in other ubiquitin lysine chains. Furthermore, UDM1 and UDM2 each folded as single α-helices to bind to the distal and proximal ubiquitins, but the specificity for lysine 63 chains by RNF168 depended on the interaction with the distal ubiquitin. This, the study noted, is in striking contrast to other interactions where proximal ubiquitin defines the linkage specificity.

"Using the crystal structures, the researchers could identify which regions in each UDM bound to the two ubiquitin molecules: LRM1 and UMI in UDM1, and UAD and MIU2 in UDM2. However, the conditions for binding were different. For UDM1, the specificity to lysine 63 chains depended on the distance and orientation between LRM1 and UMI while RNF168 was bound to ubiquitin. On the other hand, for UDM2, it was the space between the two ubiquitin molecules while RNF168 was bound to ubiquitin. Subsequent mutant experiments revealed that UDM2 binding was essential for RNF168 recruitment, while UDM1 was auxiliary."

Comment: The complexity of these necessary molecular DNA repair activities demand the recognition that they had to be in place was DNA first appeared. If DNA was not protected from damage in the very beginning of life, life would not survive. Only specific design can accomplish this. God in action.

Biological complexity: complexity of cells

by David Turell @, Thursday, January 18, 2018, 18:09 (2262 days ago) @ David Turell

Each cell has an enormous number of parts:

https://cosmosmagazine.com/biology/how-many-protein-molecules-in-a-single-cell-go-on-guess

"How many protein molecules in a single cell?

"The answer, it turns out, is a remarkably specific 42 million.

"At least, it is if the cell in question belongs to yeast.

***

"Every yeast cell contains 6000 proteins. Brown and colleagues faced the daunting task of taking each one and finding out how many molecules they contained.

"In the end, they discovered that most of the proteins fell into a fairly narrow range, containing between 1000 and 10,000 molecules. A few were enormous – topping half a million molecules – while at the other end of the scale some contained fewer than 10."

Comment: Each cell is a factory in constant motion producing protein molecules to maintain life's homeostasis. We may not have an exact definition of life, but maintaining homeostasis is a key concept.

Biological complexity: intramembrane enzyme cuts proteins

by David Turell @, Saturday, February 03, 2018, 21:02 (2246 days ago) @ David Turell

A recently found enzyme is hydrophobic and chops up proteins into smaller parts for further use:

https://phys.org/news/2018-02-hatchet-enzyme-enabler-sickness-health.html

"Tucked away inside cell membranes, a molecular butcher does the bidding of healthy cells but also of disease agents. It has been operating out of clear view, but researchers just shined a mighty spotlight on it.

"The butcher is a common enzyme called presenilin, which chops lengthy protein building blocks down to useable shorter lengths. It resides in membrane spaces that evade ready experimental detection.

***

"'One third of our genome goes to work to encode intramembrane proteins," said Raquel Lieberman, an associate professor in Georgia Tech's School of Chemistry and Biochemistry. "Some of them are huge and do super complex biochemistry."

"The enzyme presenilin in particular is an intramembrane protease. There are four classes of these, and they are needed, among other things, for: Alerting to and defending against infectors, and cell differentiation and development.

***

"Presenilin (MmIAP) is armed with two chemical knives, aspartates, that reliably make cuts on peptides, the subunits that make up proteins. And a second new study by the same researchers illuminated how the cleaving works.

"Presenilin can trim peptides into building blocks helpful to its own cells, or whittle bad peptide chunks that end up in amyloid-beta plaque, a suspect in Alzheimer's disease. Or presenilin can aid and abate hepatitis C viruses by carving components it needs to reproduce.

***

"Presenilin and other intramembrane proteins warrant such proverbial desperate measures. They live in a lipid environment and hate water about the way cats do, and that's a problem for researchers studying them.

"'When you have proteins that are not soluble in water, you're in trouble," Lieberman said. "The usual techniques to analyze them become very, very difficult, if not impossible. And when you chemically bootstrap these proteins to be able use these water-soluble methods, you have really poor chances of seeing the protein's actual structure that performs its function.'"

Comment: Another addition to cell complexity. Enzymes are giant molecules. A chance mechanism of evolution could never design a hydrophobic molecule of this size and complexity. It has to do its work inside the lipids of the cell membrane walls, where water is not used as a solute, while most of life is very wet with water. Our bodies are about 90% water.

Biological complexity: cell protein transport more defined

by David Turell @, Sunday, February 11, 2018, 20:27 (2238 days ago) @ David Turell

Cells transport proteins along actin microtubules tubules with walking molecules that are much more complex than thought and can carry more cargo:

https://phys.org/news/2018-02-microscopic-chariots-molecules-cells.html

"On the cellular highway, motor proteins called dyneins rule the road. Dyneins "walk" along structures called microtubules to deliver cellular cargo, such as signaling molecules and organelles, to different parts of a cell. Without dynein on the job, cells cannot divide and people can develop neurological diseases.

"Now a new study, which appears in the journal Nature Structural & Molecular Biology, provides the first three-dimensional (3D) visualization of the dynein-dynactin complex bound to microtubules. The study leaders from The Scripps Research Institute (TSRI) report that a protein called dynactin hitches two dyneins together, like a yoke locking together a pair of draft horses.

***

"With their new, detailed structure, the researchers noticed a surprising feature: the complex has two dynein molecules where they expected to only see one. This means because each dynein has two motor domains, the dynein-dynactin complex has four motor domains total.

"'This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books," says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

"'There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule," Lander adds.

"The researchers could also see where dynactin fit in. They found that the molecule provides a stable scaffold, hitching together the team of motor domains and activating their ability to move along microtubules. This discovery helps explain how dynein can haul large loads, such as organelles that are much bigger than themselves, over long distances in a crowded cellular environment.

"The image processing approach used in this study has the potential to be extremely useful for solving the structures of other large, flexible proteins.

"'We're now able to move past cartoon models and visualize the fine details of many dynamic macromolecular complexes," says Grotjahn. "As we learn more about the 3D organization and architecture of these molecular machines, we will be better equipped to understand how they malfunction in disease.'"

Comment: cells have specific duties in multicellular organisms. Current evolutionary theory offers no suggestion as to how this might have developed stepwise. I suggest it was designed all at once. The complexity of living biology demands a designer

Biological complexity: cell protein products are addressed

by David Turell @, Tuesday, February 20, 2018, 16:49 (2229 days ago) @ David Turell

They carry a code indicating destination:

https://www.nytimes.com/2018/02/19/obituaries/gunter-blobel-nobel-laureate-who-found-ce...

"In 1971, Dr. Blobel and a colleague, Dr. David D. Sabatini, who later headed cell biology studies at the New York University School of Medicine, proposed a bold idea known as the “signal hypothesis.” It suggested that each protein carries in its structure a sequence of signals comparable to address tags on airport luggage or ZIP codes on mail to ensure that it all arrives safely.

"The signals, Dr. Blobel found, are chains of amino acids created by protein-making machines that read distinctive RNA codes and then fix them on each new batch.

"Like transmitters, these signals order receptors in membranes to open up watery holes so that proteins can pass through. They then act as GPS devices to cross the crowded terrain of a cell or a human body and, like finding a mailbox across the universe, penetrate precisely the right worksite organelle for each protein’s assigned task.

***

"Despite proteins’ variety and complexity, however, Dr. Blobel demonstrated that their signaling system for getting through barriers and finding their worksites is universal, operating similarly in all animals, plants and even common yeasts.

"Moreover, he found, this signaling system has evidently been working quite smoothly for millions of years, since the evolution of the first cell. Mistakes can be catastrophic to an organism, but they are relatively rare.

“'Günter Blobel’s discovery has had an immense impact on modern cell biological research,” the Nobel Assembly at the Karolinska Institute in Stockholm said in announcing the prize on Oct. 11, 1999. “Furthermore, knowledge about the topogenic signals has increased our understanding of many medically important mechanisms.'”

Comment: There is no way this highly complex and purposeful living address system for cell protein products could have developed except by design by God.

Biological complexity: nucleolus 'glue'

by David Turell @, Monday, February 26, 2018, 20:22 (2223 days ago) @ David Turell

The nucleolus is a membraneless blob in the nucleus and is held together by a protein within it:

https://phys.org/news/2018-02-reveals-key-mechanism-cell-smart.html

"The protein, nucleophosmin, is a kind of "smart glue" in a structure called the nucleolus inside the cell's nucleus. In the nucleolus, nucleophosmin helps organize and regulate the construction of ribosomes—the biological machines that assemble proteins using their RNA genetic code as a guide.

"Nucleophosmin is critical to the liquid-like structure of the nucleolus called a membrane-less organelle. That is because unlike cell structures like the nucleus, the nucleolus is not enclosed in membranes. Instead, the nucleolus and other such organelles are something like the colorful undulating blobs in lava lamps—dynamically forming, shifting and fusing.

***

"In earlier studies, Kriwacki and colleagues had discovered how nucleophosmin binds to proteins and RNA to foster phase separation, as well as ribosomes' assembly. However, their studies of nucleophosmin were yielding results hinting that its "heterotypic" reactions—those with proteins other than itself and RNA—did not fully explain how part of the molecule called the intrinsically disordered region functioned.

***

"The experiments point to how the intrinsically disordered region undergoes changes as ribosomes are assembled and the makeup of the nucleolus changes. The changes were to increase homotypic interactions, or within the nucleophosmin molecule itself. The research also revealed how nucleophosmin interacts with another protein called SURF6. Scientists discovered SURF6 acts as a partner to nucleophosmin in creating and maintaining the loose scaffolding that holds the fluid nucleolus together.

***

"The experiments revealed important new details of the mechanism by which the smart glue nucleophosmin changes its internal conformation as the liquid-like nucleolus facilitates ribosome assembly. At an early stage of the process, its primary job is to shepherd RNA and proteins to assemble ribosomes. But as the glue molecule hands off its cargo as ribosomes form, the glue molecule adjusts itself homotypically to interact with other glue molecules.
This cross-linking of nucleophosmin proteins constitutes a kind of buffering, in which nucleophosmin helps maintain the liquid consistency of the nucleolus. In this buffering, the homotypic mechanism competes with nucleophosmin's heterotypic mechanisms by which it attaches to RNA and proteins in helping assemble ribosomes."

Comment: Just more evidence of the complexity of cell function. Requires design, not chance. Ribosomes are an integral part of the RNA messenger system, vital to life's functions and continual existence.

Biological complexity: mitochondrial cell differentiation

by David Turell @, Sunday, March 24, 2019, 00:23 (1832 days ago) @ David Turell

Mitochondria actually have control over several types of cell differentiation:

https://www.quantamagazine.org/shape-shifting-mitochondria-direct-stem-cells-fate-20190...

"One crucial role that has emerged is in promoting the differentiation of various types of stem cell, including those for blood and fat cells — and, most recently, for neurons.

***

"In 2016, Slack, Khacho and their colleagues reported the first evidence that mitochondrial shape-shifting is a key regulator of neural stem cell fate, the decision to self-renew or differentiate. By deleting genes that encoded key proteins for the fusion and fission machinery in mice, they discovered that a deficiency in fusion proteins reduced neural stem cells’ capacity to replenish themselves and encouraged the cells to become neurons. A loss of fission proteins, on the other hand, stimulated the stem cells to self-renew.

"Their work showed that changes in the shape and architecture of mitochondria are among the earliest, most “upstream” signals to determine which way neural stem cells will go.

***

"The real significance of Slack and Khacho’s work in neural stem cells might be that the mitochondria’s role in neurogenesis relates to something more dynamic than shape alone. According to Khacho, it’s likely that what matters isn’t the organelles’ form in a cell at a given moment, but rather their ability to morph through fission and fusion. Fission and fusion are happening all the time, and so far, scientists have only been looking at snapshots of this process. “Perhaps it’s the plasticity, the ability to change,” Khacho said. “That’s the important thing.”

***

"Findings from Slack, Khacho and their colleagues suggest that changes in mitochondrial structure could modify the amount of ROS in cells. They’ve shown that fission and fusion can control levels of ROS, [reactive oxygen species] which can in turn regulate the decisions of stem cells to proliferate or differentiate.

“'What they found is something interesting,” Chandel said. “The same ROS signaling that we’ve been talking about for 20 years happens in neurons, and mitochondrial dynamics can control that.”

"But ROS is probably only part of the answer. Mitochondria can communicate with the cell in many ways, such as through the generation of other metabolites, the release and uptake of calcium, and changes in membrane potential. “Any signaling molecules that result from metabolic changes — and there are many, many molecules — could be important,” Slack said.

"Moreover, it’s unlikely that the same mitochondrial signals control the fate of different stem cell types. “We know that [mitochondria] participate in a number of differentiation processes,” said Luca Scorrano, a biochemist at the University of Padua in Italy. But “as soon as we look into the specificity of the mitochondrial participation … we see that the signaling cascades which are regulated by mitochondrial dynamics are not necessarily the same.'”

Comment: Mitochondria do much more than produce energy. More complex than realized as each layer of the onion is peeled away.

Biological complexity: mitochondrial cell differentiation

by dhw, Sunday, March 24, 2019, 11:02 (1832 days ago) @ David Turell

DAVID: Mitochondria actually have control over several types of cell differentiation:

https://www.quantamagazine.org/shape-shifting-mitochondria-direct-stem-cells-fate-20190...

QUOTE: In 2016, Slack, Khacho and their colleagues reported the first evidence that mitochondrial shape-shifting is a key regulator of neural stem cell fate, the decision to self-renew or differentiate.

QUOTE: The real significance of Slack and Khacho’s work in neural stem cells might be that the mitochondria’s role in neurogenesis relates to something more dynamic than shape alone. According to Khacho, it’s likely that what matters isn’t the organelles’ form in a cell at a given moment, but rather their ability to morph through fission and fusion. Fission and fusion are happening all the time, and so far, scientists have only been looking at snapshots of this process. “Perhaps it’s the plasticity, the ability to change,” Khacho said. “That’s the important thing.”

Thank you for a whole raft of interesting articles. I found this one particularly stimulating, although as always I have difficulty coping with the technical details. The quotes once again highlight the importance of stem cells in the whole process of evolution, and perhaps the key question is what actually makes the “decision to self-renew or differentiate”.

Biological complexity: mitochondrial cell differentiation

by David Turell @, Sunday, March 24, 2019, 18:50 (1832 days ago) @ dhw

DAVID: Mitochondria actually have control over several types of cell differentiation:

https://www.quantamagazine.org/shape-shifting-mitochondria-direct-stem-cells-fate-20190...

QUOTE: In 2016, Slack, Khacho and their colleagues reported the first evidence that mitochondrial shape-shifting is a key regulator of neural stem cell fate, the decision to self-renew or differentiate.

QUOTE: The real significance of Slack and Khacho’s work in neural stem cells might be that the mitochondria’s role in neurogenesis relates to something more dynamic than shape alone. According to Khacho, it’s likely that what matters isn’t the organelles’ form in a cell at a given moment, but rather their ability to morph through fission and fusion. Fission and fusion are happening all the time, and so far, scientists have only been looking at snapshots of this process. “Perhaps it’s the plasticity, the ability to change,” Khacho said. “That’s the important thing.”

dhw: Thank you for a whole raft of interesting articles. I found this one particularly stimulating, although as always I have difficulty coping with the technical details. The quotes once again highlight the importance of stem cells in the whole process of evolution, and perhaps the key question is what actually makes the “decision to self-renew or differentiate”.

And my answer is the same as always. The genome contains the proper information to help with the choices. The information is carried by instructive molecules, whose shape delivers the info, or in a series of molecular reactions to dictate an outcome.

Biological complexity: homeostasis from feedback loops

by David Turell @, Friday, March 02, 2018, 15:47 (2219 days ago) @ David Turell

I have mentioned feedback loops over and over as a explanation of automaticity in life. They are a requirement for automatic homeostasis:

https://aeon.co/essays/the-feedback-loop-is-a-better-symbol-of-life-than-the-helix?utm_...

"The union of genetics with molecular biology has undoubtedly created a powerful new science. By unpicking the molecular interactions inside cells, we’ve been able to develop drugs to mimic or interfere with specific processes. The discovery of enzymes that synthesise and edit DNA laid the foundations for genetic engineering, which is usually discussed in terms of its commercial applications, but whose most common use has always been in pure research. In this way, advances in knowledge create the tools to advance knowledge, in a virtuous circle. Nevertheless, we appear to have come to a threshold. The more we know about the molecular processes, the less sense the gene-centric perspective makes.

***

"Schooling and flocking behaviours are, of course, restricted to large groups of individuals from a single species. Might self-organising properties operate even at the level of multi-species ecosystems? There’s reason to think that they do. Vegetation on arid soils will, for example, arrange itself into groups with plain soil between them: the plants in the groups all benefit from their mutual ability to help rare rainfall penetrate the ground. And in simple experimental microbial communities (not, in fact, different species, but yeasts genetically engineered to have different metabolisms that can co-operate to use environmental nutrients), the different types of individual self-organise into mixed clusters that bring co‑operators together. Many ecologists believe that large-scale ecosystems of co‑operating organisms, for example trees and fungi, show similar self‑organising behaviour.

"All of these examples, and many more like them, turn out to have something in common when analysed at the mechanistic level: in each case, what has been achieved so far by the system is used to control its current behaviour. This type of control is called feedback, and is represented by a loop feeding information from the output of a process back to its input.

"In the case of the cytoskeleton, the stability of a filament depended on whether it was carrying a mechanical force, which in turn depended on whether it was in the right place to connect to cell junctions. The achievement of a filament (to be in a useful place or not) is therefore fed back to decide what it will do next (survive, or be disassembled). In the case of the blood capillaries, the extent to which present growth has been adequate to bring enough oxygen into the tissues is fed back, via VEGF, to control whether the capillaries continue to grow or remain as they are. And the same principle seemed to explain the schooling of fish: any error in an individual fish’s relative positions and direction compared to its neighbours is used to modify its swimming, to make the error smaller. Seen from the abstract perspective of feedback loops, adaptive self-organisation looks more or less the same across all scales of life, from the architecture of subcellular assemblies to the arrangements of co-operating species in ecosystems.

"In this sense, the loop is a near-universal symbol of living processes.

***

"The DNA helix is important, of course. But the most important thing it does is make proteins that can operate in regulatory loops. These loops can also operate at the molecular level: genes make proteins, but these proteins determine which genes are ‘off’ and which are ‘on’ (as HIF1A does), making a control loop at even the molecular level. Unlike the helix, loops also operate at scales far above the molecular, covering a range of sizes from bacterial colonies to the vast ecosystems of the rainforest – perhaps to the ecosystem of the entire Earth. Beyond Earth, life without DNA is just about thinkable (one can imagine alternative strategies for storing information). Life without feedback loops, though? I have never met any biologist who can imagine that."

Comment: You may think my brain is rigid, but in medical school I was raised on feedback loops. That is how life works, and it creates reactions and responses that are automatic even as environmental challenges change. 'A' responds to a stimulus by triggering 'B', which nudges 'C', which tells 'D' which informs 'E' which comes back to 'A' to change its output. All the letters are complex protein molecules, and some of them are giant enzymes. Each step is a modulation of response. DNA simply codes the manufacture of the proteins. But the entire structure is designed to work harmoniously by God. I've skipped the author's long examples. The whole essay is worth reading.

Biological complexity: homeostasis from feedback loops

by Balance_Maintained @, U.S.A., Saturday, March 03, 2018, 08:38 (2218 days ago) @ David Turell

Sounds a lot like game design to me. The field of biology has benefitted tremendously from the inclusion of engineering as a discipline, I suspect the same would be true of game designers. After all, who better to deconstuct engineering and design than
engineers and designers? Besides, those who already view life as being engineered and designed don't have to wade through all the mental hurdles needed to rationalize Darwinism.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: homeostasis from feedback loops

by David Turell @, Saturday, March 03, 2018, 14:37 (2218 days ago) @ Balance_Maintained

Tony: Sounds a lot like game design to me. The field of biology has benefitted tremendously from the inclusion of engineering as a discipline, I suspect the same would be true of game designers. After all, who better to deconstuct engineering and design than
engineers and designers? Besides, those who already view life as being engineered and designed don't have to wade through all the mental hurdles needed to rationalize Darwinism.

Thanks for the response. The article leaves no room for denying design or the need for a designer.

Biological complexity: nuclear pore architectural complexity

by David Turell @, Thursday, March 15, 2018, 20:44 (2206 days ago) @ David Turell

The nucleus has a double membrane and complex pores to allows molecules in and out under tight control:

https://www.sciencedaily.com/releases/2018/03/180315130704.htm

"Like an island nation, the nucleus of a cell has a transportation problem. Evolution has enclosed it with a double membrane, the nuclear envelope, which protects DNA but also cuts it off from the rest of the cell. Nature's solution is a massive -- by molecular standards -- cylindrical configuration known as the nuclear pore complex, through which imports and exports travel, connecting the bulk of the cell with its headquarters.

***

"The pore complex contains 552 component proteins, called nucleoporins, and scientists hadn't previously known how they all fit together. It took a combination of approaches to assemble a comprehensive map of these pieces.

"The pore complex first emerged when single-celled organisms -- the only living things at the time -- acquired special compartments containing organ-like structures, including the nucleus, which houses the cell's genetic code.

"It serves not only as a conduit to and from the nucleus, but also as a checkpoint regulating what passes in and out. Genetic instructions transcribed into RNA are allowed to exit, for example, while proteins needed inside the nucleus may enter. Other things, such as viruses bent on taking over the cell, are kept at bay.

***

"They uncovered a complicated ringed structure containing rigid, diagonal columns and flexible connectors that evoke the towers and cables of human-made structures like the Golden Gate Bridge."

Comment: When the nucleus appeared, this control mechanism had to be in place. This means 552 proteins had to be found to construct this extraordinary structure all at once. It is designed, and not by chance.

Biological complexity: nuclear pore architectural complexity

by David Turell @, Thursday, March 15, 2018, 22:58 (2206 days ago) @ David Turell

A drawing of the nuclear pore showing its complexity in animation:

https://3c1703fe8d.site.internapcdn.net/newman/gfx/news/2018/scientistsma.gif

Comment: It is amazing. Not by chance. It has to be designed, which means there must be designer.

Biological complexity: how a molecular machine is assembled

by David Turell @, Wednesday, March 21, 2018, 22:08 (2200 days ago) @ David Turell

It is irreducibly complex and must be designed:

https://evolutionnews.org/2018/03/irreducible-complexity-in-molecular-machine-assembly/

"We know that many molecular machines are irreducibly complex (IC) in their operation. Even more IC is the process of assembling them in the cell. A good example of this is the process of building our good old standby machine, ATP synthase.

***
"In a companion Commentary on PNAS, three scientists (Song, Pfanner and Becker) put it bluntly: “The assembly of the mitochondrial ATP synthase is a complicated process that involves the coordinated association of mitochondrially and nuclear encoded subunits.”

***

"Whether or not you can follow the jargon is not as important as what they witnessed: an “elegant” process that requires precise timing and coordination. Different machine parts must arrive on schedule, and assemble into intermediate (vestigial) forms that are nonfunctional alone. An inhibitor protein makes sure the machine doesn’t switch on ahead of schedule. The proton-conducting channel has to form just right so that it doesn’t “leak” protons. Only when all the parts are ready does the machine begin to rotate, but even then, the work isn’t complete. Another player is “added to the assembly line” to position the machines on the folds of the mitochondrial membrane (called cristae) at precise angles and spacings for optimum productivity.

"The parts must arrive at the construction site on time. Some of them come from the nucleus, which must seem like many miles away at the scale of the machine. Some are built locally by genes within the mitochondrial genome. Interestingly, there are differences between yeast and humans regarding which genes are encoded where, and in what order they are assembled. But the proof of the pudding is in the respiration after eating: both versions of the machine work efficiently for their respective organisms.

"The intermediate structure, somewhat like a scaffold on which the machine will be built, is also irreducibly complex:We have shown that the assembly of human ATP synthase in the inner organellar membrane involves the formation of a monomeric intermediate made from 25 nuclear-encoded proteins into which the two mitochondrially encoded subunits are inserted and then sealed by association of another nuclear-encoded protein, thereby dimerizing the complex. Association of a final nuclear protein oligomerizes the dimers back-to-face along the cristae edges.

"Notice that parts from the different genomes have to work tightly together. It’s like a manufacturing plant receiving parts locally and from India that have to meet agreed-on specifications to match. There are also rules for import, just like for parts arriving from a far country. The nuclear-encoded parts have to pass through two distinct checkpoints (the inner and outer membranes of the mitochondrion), which each have their robotic security personnel to validate them and facilitate their transport to the inside.

"Previous work has shown how the completed “factory” of machines is organized within the mitochondrion. A specific nuclear protein seals them in two’s (dimers) at an angle, such that the rotating F0 proton pumps can maximize the intake of proton fuel, while the F1 parts, where ATP synthesis occurs, are farther apart to not crowd the output molecules. A “final nuclear protein” joins the dimers together (oligomerizes them) along the membrane edges. The longitudinal spacing is also tightly controlled, so that they don’t crowd each other. Every point of the assembly is programmatically directed. When everything is completed, rows of ATP synthase motors are arranged like turbines in a hydroelectric plant, feeding off a flow of protons produced by upstream machines in the respiration transport chain."

Comment: I have not reproduced the actual quotes from the actual paper, but these simple explanations. All of this is taking place in the mitochondrion where respiration and energy use is handled. This cannot be assembled by chance. It is a complex design and the assembly has to be choreographed by forces that shepherd the construction, and those forces must also be designed. Only God can do this.

Biological complexity: cell division complexity

by David Turell @, Saturday, March 24, 2018, 18:25 (2197 days ago) @ David Turell

This article shows how complex:

https://www.sciencedaily.com/releases/2018/03/180323104819.htm

"Cell division is the basis of all life. Even the smallest errors in this complex process can lead to grave diseases like cancer. Certain proteins have to be switched on or off at certain times for everything to go according to plan. Biophysicists and medical biochemists at Martin Luther University Halle-Wittenberg (MLU) have managed to describe the underlying mechanism of this process. They have figured out how different signaling pathways in the cell change the structure of proteins, thereby driving the cell division cycle in the right direction at the right time.

"The cell cycle is an extremely complex and precisely defined process. "The parent cell has to double its existing components and then divide into to daughter cells. In order to do this, numerous genes have to be switched on and off at very specific times," says biophysicist Professor Jochen Balbach from MLU. The cell cycle is sub-divided into various phases. These are controlled by what are known as inhibitors proteins, also called CDK inhibitors. Like a red traffic light, these proteins block transition to the next phase until the cell gives the relevant start signal. The signal to start the next phase of the cell cycle comes from a special enzyme group, the kinases. "Previously we only knew that the kinases passed on the signal by adding a phosphate group onto the CDK inhibitors. There was no knowledge, however, of which kinases do this and the underlying molecular mechanism for this," continues Balbach. (my bold)

"Together with the working group led by Professor Mechthild Hatzfeld from the Pathobiochemistry Section of the Medical Faculty of MLU, the researchers have now been able to describe this signaling pathway for the first time. They combined high-resolution magnetic resonance spectroscopy data with methods from cell biology. This meant that the researchers were able to explain the mechanism first in test tubes and then directly in cells. The researchers found that the kinases change the structure of the inhibitor proteins by unfolding them. This process disables the original function of the inhibitor proteins and releases a further blocked kinase that gives the signal for the cell cycle to continue. This local unfolding also triggers the degradation of the inhibitor in the cell, determining the direction in which the progression occurs. The researchers from Halle assume that this mechanism preserved by evolution is the basis of many cellular signal pathways." (my bold)

Comment: This again illustrates feedback loop controls. Since bacteria were present at the start of organismal life, this process was present at that first point of origin. It's complexity can only be explained by design, since all the parts had to work together from the very beginning. Further kinases are giant enzyme molecules that chance evolution is extremely unlikely to discover. Complete evidence for God.

Biological complexity: no life if no enzymes

by David Turell @, Tuesday, April 17, 2018, 22:53 (2173 days ago) @ David Turell
edited by David Turell, Tuesday, April 17, 2018, 23:09

Enzymes manage all reactions in life. They are giant complex molecules that force the completion of biochemical reactions: An other enzyme structure is described:

https://www.sciencedaily.com/releases/2018/04/180417130122.htm

"Without enzymes, nature would come to a standstill. These tiny molecules accelerate biochemical reactions or make them possible in the first place. But how does this happen on a molecular level? "Understanding the exact function of enzymes is one of the greatest challenges of modern biochemistry," says Ville Kaila, Professor of Computational Biocatalysis at the Technical University of Munich.

"The research team led by Ville Kaila and Michael Groll, Professor of Biochemistry at the Technical University of Munich, have, for the first time, deciphered the mechanism of the enzyme aspoquinolone J (AsqJ), a dioxygenase that activates carbon bonds with oxygen.

"The enzyme AsqJ is particularly exciting as it catalyzes a cascade of chemical reactions that ultimately lead to the formation of antibacterial compounds. It was discovered only a few years ago in the Aspergillus nidulans fungus.

***

"'Our calculations illustrate how the enzyme catalyzes the formation of quinolone alkaloid," reports Kaila. "Tiny details have amazing effects: A slight change in the substrate, like the removal of a small chemical group, is sufficient to practically stop the reaction."

"Next, the team computationally designed a new variant of the enzyme that catalyzes the formation of quinolone alkaloids with the modified substrate. This new enzyme was experimentally produced in bacteria and tested for its functionality. "The results were impressive: the expected reaction took place after only a few seconds," recalls Bräuer."

Comment: The change in one amino acid in this giant molecule changed the way it controlled reactions, showing how precise each enzyme has to be to perform its proper function. These molecules must be present for life to exist with life's need for immediate results. The odds against chance evolution making such structures are enormous. Design is more logical.

Look at the illustration and the comment:

"While the difference between the natural and the modified AsqJ is only one amino acid, the reactivity is clearly different. The natural AsqJ (left) possesses a valine at position 72 (blue). The modified form possesses an isoleucine (red) at position 72. The substrate in the active site is green-colored, alpha-ketoglutarate yellow, the iron atom gray, and two histidine chains cyan and blue." (my bold)

Further here is an article about improving an enzyme by accident:

http://bigthink.com/brandon-weber/theres-a-plastic-eating-bacteria-and-its-now-on-stero...

"A few years ago, at an Osaka, Japan recycling plant, scientists discovered a bacteria called Ideonella sakaiensis that eats one of the most common forms of plastic, known as polyethylene terephthalate or PET. That form of plastic is found in water bottles, food containers, and polyester.

"Researchers from Britain’s University of Portsmouth and the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) were trying to model the enzyme and ended up with a mutant strain of the same thing, with a crucial difference: it eats plastic even better.

"'We hoped to determine its structure to aid in protein engineering, but we ended up going a step further and accidentally engineered an enzyme with improved performance at breaking down these plastics," said NREL's lead researcher Gregg Beckham."

Comment: This was study in a lab run by designing minds, but Darwin asks us to accept that nature does this by accident all the time. I don't accept that. Only design fits.

Biological complexity: no life if no enzymes

by dhw, Wednesday, April 18, 2018, 13:17 (2172 days ago) @ David Turell

QUOTE: "'We hoped to determine its structure to aid in protein engineering, but we ended up going a step further and accidentally engineered an enzyme with improved performance at breaking down these plastics," said NREL's lead researcher Gregg Beckham."

DAVID’s comment: This was study in a lab run by designing minds, but Darwin asks us to accept that nature does this by accident all the time. I don't accept that. Only design fits.

The papers have been full of this discovery, as a possible method of solving the enormous problems plastic has created. I read one comment to the effect that evolution would probably have created the same improvement, but it would have taken far longer. I agree with you that this is no accident. It is living proof of the manner in which bacteria adjust themselves to new environments and new opportunities. I do not believe that 3.8 billion years ago they were preprogrammed to eat plastic, or that your God has come along to teach them. Do you?

Biological complexity: no life if no enzymes

by David Turell @, Wednesday, April 18, 2018, 15:01 (2172 days ago) @ dhw

QUOTE: "'We hoped to determine its structure to aid in protein engineering, but we ended up going a step further and accidentally engineered an enzyme with improved performance at breaking down these plastics," said NREL's lead researcher Gregg Beckham."

DAVID’s comment: This was study in a lab run by designing minds, but Darwin asks us to accept that nature does this by accident all the time. I don't accept that. Only design fits.

dhw: The papers have been full of this discovery, as a possible method of solving the enormous problems plastic has created. I read one comment to the effect that evolution would probably have created the same improvement, but it would have taken far longer. I agree with you that this is no accident. It is living proof of the manner in which bacteria adjust themselves to new environments and new opportunities. I do not believe that 3.8 billion years ago they were preprogrammed to eat plastic, or that your God has come along to teach them. Do you?

No I don't. A shift in one amino acid does the trick. Bacteria have thousands of enzymes in which this could happen. Nylonase is one recent example.

Biological complexity: 3 plant enzymes produce lignin

by David Turell @, Tuesday, May 01, 2018, 01:19 (2159 days ago) @ David Turell

The complex process is now understood:

https://phys.org/news/2018-04-molecular-machinery-cell-wall-components.html

"Plants are among the most effective energy convertors on Earth. They capture solar energy and convert it to carbon-based compounds that are used for energy and also to build up essential plant components, including the cell walls that surround every single plant cell. In a new biochemical genetics study at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory, scientists reveal new details of the molecular machinery that helps channel carbon into a key cell-wall component.

***

"The study, published in Nature Plants, reports how two proteins embedded on membranes within plant cells serve as a scaffold to organize three key enzymes that specifically channel carbon into the synthesis of a cell-wall polymer called lignin.

***

"The three enzymes establish the structural characteristics of biochemical building blocks known as monolignols, which link up to form lignin. Scientists previously thought that these enzymes were associated with one another and served as the anchor sites for organizing monolignol synthesis.

"'We started this project to study the interactions of these three enzymes in detail," said Brookhaven biochemist and project leader Chang-Jun Liu. "We discovered that even though the three enzymes are located near one another on a membrane known as the endoplasmic reticulum, they don't interact directly. Instead, two separate proteins interact with all three enzymes."

"The separate proteins are "membrane steroid binding proteins" (MSBPs) embedded in the endoplasmic reticulum—a cell's interior "highway" of membranes lined with the molecular machines that make proteins and transport those products within or out of cells.

"'These membrane-bound proteins serve as a scaffold to organize and stabilize the three enzymes into a type of molecular machinery that controls the metabolic pathway channeling carbon specifically into building lignin precursors," Liu said.

***

"'Those observations strongly suggested that the MSBPs organize the monolignol biosynthesis enzymes into a multimeric protein complex or enzymatic cluster," Liu said.
"With that type of organization, the three enzymes could be located close to one another without necessarily having direct interactions," he added. Such an arrangement would help drive lignin synthesis by keeping the enzymes and their common cofactor near one another at high enough concentrations to effectively transfer the carbon substrates and electrons needed for efficient chemical reactions to take place.

"To test the role of the MSBPs, the scientists created plant lines in which the genes for these proteins were suppressed. While those plants could still make the three monolignol synthesis enzymes, they ended up with significantly less lignin.

"In addition, such suppression did not affect the formation of another closely related class of chemicals whose synthesis requires one of the three monolignol synthesis enzymes.
These data convinced the scientists that MSBP-mediated enzyme organization specifically facilitates lignin formation. "

Comment: Lignin gives plants strength to stand tall like trees. The efficiency of this arrangement reeks of design, and the combination of three giant complex enzymes cannot have happened by chance. Each enzyme has a specific function so this mimics a factory production line, which, of course, is designed.

Biological complexity: plants signal overcrowding

by David Turell @, Friday, May 04, 2018, 16:11 (2156 days ago) @ David Turell

Plants tell each other through the roots that things are too crowded:

https://cosmosmagazine.com/biology/plants-warn-neighbours-of-overcrowding

"Plants actively participate in social interactions with their neighbours, and respond to signals generated by roots that inform them about crowded conditions above-ground.

"That’s the conclusion reached by a group of researchers studying maize plants – and one that carries implications not just for agriculturalists, but also for other researchers. The mere act of brushing the leaves of one plant, it turns out, can significantly change the shape and growth direction of another.

***

"A 2012 study, for instance, found that some plants will allocate more biomass to root development and less to fruits if the plants next to them are siblings. Relationships are identified by means of chemicals secreted by the roots.

"A 2006 study showed that trees called lodgepole pines stopped expanding their crowns when the outermost leaves brush against those of a neighbouring tree.

"Elhakeem and colleagues wondered whether two neighbouring maize plants coming into contact with each other would then signal their close proximity to other, nearby plants, and if so what would happen.

"To discover this, they germinated a number of plants in hydroponic containers, some as pairs and some on their own. One plant from each pair was then lightly touched, simulating the pressure of an adjacent leaf brushing up against it.

"In the paired containers, the roots of the untouched plants grew significantly more away from the roots of the touched one. New plants put into hydroponic containers that had previously contained a touched plant grew smaller root systems and larger above-ground structures.

"Elhakeem’s team found that touched plants exuded a particular mix of chemicals from their roots, which influenced the growth, above and below ground, of their neighbours.

"The scientists conclude that the results reveal “a new level of complexity in below-ground plant-plant interactions showing that the direction and extent of plant root responses to neighbours can be affected by the above-ground physical stress to which neighbours are exposed'”.

Comment: As usual we find that chemical reactions are clear signals of information being transmitted. Life runs on information, which cannot be developed by chance.

Biological complexity: cells exchange information

by David Turell @, Friday, May 04, 2018, 20:38 (2156 days ago) @ David Turell
edited by David Turell, Friday, May 04, 2018, 20:51

They use vesicle packages to transmit information in the form of molecules:

https://www.quantamagazine.org/cells-talk-in-a-language-that-looks-like-viruses-20180502

"scientists discovered that cells could package their molecular information in what are known as extracellular vesicles. Like notes passed by children in class, the information packaged in an extracellular vesicle is folded and delivered to the recipient.

***

"As scientists uncovered the secrets about how the vesicles are made, how they package their information and how they’re released, it became clear that there are powerful similarities between vesicles and viruses.

***

"Extracellular vesicles and viruses, Margolis argues, are part of a continuum of membranous particles produced by cells. Between these two extremes are lipid-lined sacs filled with a variety of genetic material and proteins — some from hosts, some from viruses — that cells can use to send messages to one another.

***

"Sending information in extracellular vesicles must have first appeared billions of years ago because even bacteria do it. “This idea of using a membrane-bound sac of information to transport between cells has been around a long time,”

***

"One of the most striking pieces of evidence supporting Margolis and Gallo’s hypothesis is the recent discovery, widely reported in January, that a mammalian protein called Arc, which is implicated in learning and memory, is actually a repurposed retroviral protein. More important, Arc appears to be secreted from the synapses of neurons in extracellular vesicles. “These vesicles may be acting like a viral envelope,”

***

"The field took off in 2006–2007 when a Swedish team and a joint American-European group independently discovered that exosomes and extracellular vesicles could carry several types of RNA. These included the messenger RNAs (mRNAs) that are intermediaries in the translation of DNA into proteins, as well as the small molecules called microRNAs that affect gene expression.

***

“'Cell-cell communication is one of the most ancient mechanisms that makes us who we are,” Margolis said. “Since vesicles resemble viruses, the question of course is whether the first extracellular vesicles were primitive viruses and the viruses learned from extracellular vesicles or vice versa.”

***

"What researchers have come to realize is that sometime millions of years ago, part of a retrovirus genome inserted itself into its host’s DNA, and that sequence was then passed on to countless generations of offspring. Around 8 percent of the human genome is ultimately derived from viruses. Although some of this DNA is, in fact, “junk,” scientists are learning that much of it plays a role in our biology.

***

“'Although these viruses aren’t good for individuals, they provide the raw materials for new genes,” Shepherd says. “They’re a potential gold mine.”

In the case of Arc, the Gag-derived viral gene gave mammals a ready-made delivery device that could be packaged in an extracellular vesicle. A retrovirus packages RNA and moves it out of the cell, Feschotte said. “Arc has preserved many of these same functions.”

***

"Because extracellular vesicles and exosomes can pass information between cells, scientists have begun to implicate them in everything from cancer to viral infections to basic neural functioning. To Lynne Maquat, an expert on retrotransposons at the University of Rochester, this process shows how parts of the genome we used to think of as junk actually have important functions.

***

"Although it’s now clear that extracellular vesicles are far from simple cellular debris, and the viral genes littering our DNA aren’t exactly junk, researchers have only just begun to crack the mystery of what they can do."

Comment: Life runs on transmitting information. We are learning how. Too complex for chance development. Only design can do this.

Biological complexity: the dance of enzymes

by David Turell @, Saturday, May 05, 2018, 00:21 (2155 days ago) @ David Turell
edited by David Turell, Saturday, May 05, 2018, 00:28

They shift their shapes to do their job changing shapes by using charged ions in their structure, but are they thinking or automatically following instructions or reacting to changes they sense by electrical signals; it is not clear but fascinating to study:

https://phys.org/news/2018-05-molecular-phospholipid-synthesis.html

"The most abundant molecule in cell membranes is the lipid phosphatidylcholine (PC, commonly known as lecithin); accordingly, the enzymes responsible for synthesizing it are essential.

***

"When bound to membranes, the CCT enzyme changes shape in a way that allows it to carry out the key rate-limiting step in PC synthesis. When the amount of PC making up the membrane increases, the CCT falls off the membrane, and PC production ceases.

"'The membrane is this big macromolecular array with lots of different molecules in it," Cornell said. "How does this enzyme recognize that 'Oh, I should slow down because the PC content of the membrane is getting too high?

***

"'What it looks like (when you visualize the output) is your big molecule dancing in front of your eyes," Cornell said. "We set up the molecular dynamics simulation not once, not twice, but 40 different (times). It took months and months just to do the computational parts and even more months trying to analyze the data afterward. We actually spent a lot of time once we got the data just looking on the screen at these dancing molecules."

"The simulated dance of the CCT molecule showed that when the M-domain, the section of the enzyme that typically binds to the membrane, detaches from a membrane, it snags the active site of the enzyme, preventing it from carrying out its reaction. When the snagging segment was removed from the simulation, the team saw a dramatic bending motion in the docking site for the snagging element, and speculated that this bending would create a better enzyme active site for catalyzing the reaction when attached to a membrane. The team confirmed these mechanisms using biochemical laboratory experiments."

Comment: In any live process of production, that process must have limits. These processes normally are controlled by feedback loops. In this case the enzyme seems to control its own activity, but there may be unknown restrictions at work. In any case this is a giant molecule that could not have been found in any evolutionary process by chance. Only design is capable to achieving this result.

Biological complexity: the dance of enzymes

by dhw, Saturday, May 05, 2018, 12:34 (2155 days ago) @ David Turell

DAVID: They shift their shapes to do their job changing shapes by using charged ions in their structure, but are they thinking or automatically following instructions or reacting to changes they sense by electrical signals; it is not clear but fascinating to study:

https://phys.org/news/2018-05-molecular-phospholipid-synthesis.html

Thank you for asking that question in such a fair-minded, even-handed manner.

Biological complexity: the dance of enzymes

by David Turell @, Saturday, May 05, 2018, 14:49 (2155 days ago) @ dhw

DAVID: They shift their shapes to do their job changing shapes by using charged ions in their structure, but are they thinking or automatically following instructions or reacting to changes they sense by electrical signals; it is not clear but fascinating to study:

https://phys.org/news/2018-05-molecular-phospholipid-synthesis.html

dhw: Thank you for asking that question in such a fair-minded, even-handed manner.

Thank you. But of course the articles presented in this stream pointedly show that such complexity cannot be a result of the Darwin theory proposals.

Biological complexity: potassium ion channel controls

by David Turell @, Thursday, June 21, 2018, 18:30 (2108 days ago) @ David Turell

Ions must be controlled as they cross cell membranes. This article describes potassium control by a special amino acid and how to reverse it:

https://phys.org/news/2018-06-team-reverse-potassium-channels-bacteria.html

"For the first time ever, researchers at the Texas Tech University Health Sciences Center (TTUHSC) have identified a specific amino acid residue that is responsible for inverting the communication between the opening of the activation gate and the inactivation of a potassium channel's selectivity filter.

***

"'Normally, a potassium channel opens the activation gate and manages ion conduction for hundreds of milliseconds, then because the activation gate and the filter cross-talk, the filter undergoes a change in its conformation that yielded its collapse, which ceases ion conduction, inactivating the channel," Cuello said.

"Potassium channels are extremely specialized proteins that are embedded in a membrane that is surrounding any living cell. By closing and opening a narrow constriction known as the activation gate, they control the transport of potassium ions in and out of the cell. The selectivity filter of potassium channels is the region within the protein structure in charge of the selective discrimination between potassium and sodium ions, which are about the same size. Cuello said this area of the protein procures a passage that perfectly fits potassium ions but is incapable to accommodate sodium ions, which makes it "selective" for potassium ions. The filter also can act as a secondary gate in series to the activation gate.

"'The opening of the activation gate induces the collapsing of the selectivity filter which preclude the flow of ions through it despite having the activation gate open. The collapsing of a potassium channel is the underlying cause for a process known as C-type inactivation, which makes the selectivity filter the C-type inactivation gate."

"Potassium channels are proteins that are made of amino acid residues. A THREONINE is one of the 20 different amino acid residues that a cell uses to build a protein molecule. Cuello's lab identified a Threonine residue (Threonine 75) as a crucial player that communicates the opening of the activation to the channel selectivity filter.

***

"Cuello's research found a way to reverse this process in a mutant channel, the threonine to alanine mutation in channels from bacteria all the way up to humans reverts the process. These mutant channels have a selectivity inactive filter when the activation gate is closed and resets to a conductive conformation when the activation gate is open."

Comment: this lab work found a specific amino acid change by design. It had to develop in nature by design. In fact the whole channel is so complex, it had to be designed.

Biological complexity: nuclear membrane pore controls

by David Turell @, Wednesday, June 27, 2018, 23:37 (2102 days ago) @ David Turell

These pores are highly complex:

https://evolutionnews.org/2018/06/how-the-nucleus-guards-its-gates/

"The nuclear pore complex (NPC), which we mentioned briefly here and here, has been a prime target of research for years now, ever since biochemists realized how large it is and the vital role it plays guarding what moves in and out of the nucleus. The NPC has to validate cargo large and small through its hoop-like opening with dangling ends that resemble a basketball net.

"Standing guard between a cell’s nucleus and its main chamber, called the cytoplasm, are thousands of behemoth protein structures called nuclear pore complexes, or NPCs. NPCs are like the bouncers of a cell’s nucleus, tightly guarding exactly what goes in and out. Each structure contains about 1,000 protein molecules, making NPCs some of the biggest protein complexes in our bodies. One of the most notable clients of NPCs is a class of molecules known as messenger RNAs, or mRNAs. These are the messengers that carry genetic instructions from the nucleus to the cytoplasm, where they are then translated into proteins.

"Moreover, the article goes on to say, mRNAs, though being one of the largest cargoes ferried through the NPC, make it through the whole process in a fraction of a second.

***

"The NPC has tags of its own. A molecule can’t get through without a ticket.

"In a new study in the June 13 issue of Nature Communications, Hoelz and his group… report the first atomic-scale look at the specific components of human NPCs responsible for dropping mRNAs off in the cytoplasm. For an mRNA to be transported through an NPC, it must be tagged with a nuclear export factor, a type of small protein. That tag is like a ticket that allows the mRNA to enter the central transport channel of the NPC. Once the mRNA reaches the cytoplasmic side, it must surrender the ticket — otherwise, the mRNA could travel back into the nucleus, and the proteins it encodes wouldn’t get made.

"It was enough of a challenge to figure out that one step, how the ticket is surrendered. To study it, they had to figure out the crystal structure of human Gle1, an essential component of the NPC validation system. Unlike its counterpart in yeast, Gle1 was found to be stabilized by Nup42, one of dozens of “nucleoporin” (Nup) proteins. Another protein named DDX19 un-tags the molecule as it exits.

"The scientists marveled that yeast Gle1 was almost identical to human Gle1. Caltech offers rotating images of the proteins. They’re hard to tell apart.

***

"Strikingly, the Gle1CTD•Nup42GBM interaction mechanism is virtually identical in species separated by more than a billion years of evolution.

***

"The flow of genetic information requires newly transcribed and processed mRNAs to be exported from the nucleus to the cytoplasm through nuclear pore complexes (NPCs). NPCs are massive macromolecular machines perforating the nuclear envelope, each composed of ~1000 protein subunits (collectively termed nucleoporins) totaling to a molecular mass of ~120 MDa in humans. By fusing the inner and outer nuclear membranes, NPCs create pores through the nuclear envelope and simultaneously generate a passive diffusion barrier composed of disordered protein sequences enriched in phenylalanine-glycine (FG) repeats. Each NPC is composed of a ~60 MDa symmetric core that is decorated by different proteins on its nuclear and cytoplasmic faces, which are referred to as the nuclear basket and cytoplasmic filament nucleoporins, respectively.


"Preparation of mRNAs for nuclear export is a highly coordinated process that begins co-transcriptionally and results in the addition and removal of mRNA-binding proteins during transcription and nuclear processing until an export-competent messenger ribonucleoprotein particle (mRNP) is formed.

***

"Multiple levels of quality control can be seen in action here. The ticketing process begins as the gene is transcribed. It is re-checked by “nuclear processing” inside the nucleus. Only when the mRNA is “export competent” can it pass the NPC. As it passes through, its ticket is removed, so that it cannot return. “This spatial regulation of activity prevents re-import of mRNPs into the nucleus, and thus ensures the directionality of mRNA export.” The NPC has all the marks of a programmed system with built-in quality control. It is very rapid, working in just fractions of a second. It’s even environmentally friendly; all the parts are recycled. And there are thousands of these little factories in each nuclear envelope. Then there’s this minor miracle of coordination: at cell division, the entire nuclear envelope, with all its NPCs, is torn down and reconstructed.

Comment: Try to deny this system is not designed. Look at the article to see the NPC diagram.

Biological complexity:mitochondria helps nucleus in distress

by David Turell @, Thursday, July 05, 2018, 22:39 (2094 days ago) @ David Turell

New research shows the mitochondria release proteins to help the nucleus during cell stress:

https://www.sciencedaily.com/releases/2018/07/180705114047.htm

"Research conducted by scientists at the USC Leonard Davis School of Gerontology is the first to show that the mitochondrial and nuclear genomes co-evolved to independently cross-regulate each other. Understanding how intracellular DNA communication is hardwired into the cell will lead more researchers to appreciate the coordination of genes encoded in both genomes and their role in aging and disease.

***

"Mitochondria have their own DNA that presumably comes from ancient bacteria that joined our cells a long time ago. We didn't know that our mitochondrial DNA encoded messages to control the nucleus. In fact, the nucleus has been long thought to hold all our genetic blueprint for building and operating a cell," Lee said. "This is a fundamental discovery that integrates our two genomes as a co-evolved genetic system and may have a lasting impact for a broad range of scientific and medical fields."

***

"USC researchers focused on the two parts of the cell that carry DNA: the nucleus and the mitochondria. Most genetic material resides in the nucleus, which is the largest component of the cell. Its DNA sends coded templates telling the cell what to do. Smaller mitochondria function as energy-producing factories, turning food into fuel to power the cell. But size can be misleading. The mitochondria also contain DNA, all of it inherited from the mother, and as the new study shows, they are not just taking orders from the nucleus.

"Working with human cells, the scientists discovered that when a cell is under stress and starved for nutrients, MOTS-c, a small protein encoded in the mitochondria DNA, moves into the nucleus to control genes and turn on a defensive system, including an antioxidant response."

Comment: This is only part of the obvious complexity. The mechanism of how the mitochondria recognize the cell stress is still awaiting research. It is only a tiny part of the mechanism of life remaining in equilibrium.

Biological complexity:new enzyme controlling cell division

by David Turell @, Thursday, July 12, 2018, 22:19 (2087 days ago) @ David Turell

It creates liquid bubbles in the cell to help with separation of organelles

https://phys.org/news/2018-07-cell-division.html

"When a cell divides, its constituents are usually evenly distributed among the daughter cells. University of Zurich researchers have now identified an enzyme that guarantees that cell constituents that are concentrated in organelles without a membrane are properly distributed.

***

:In physical terms, this constitutes the formation of two phases in the liquid. Phase separation of molecules also takes place inside cells. Here, liquid drops form in the cell plasma.

"Researchers.. have now discovered that a class of enzymes – which are dual specificity kinases – actively control this process in cells. When a cell divides, the enzyme DYRK3 promotes the mixing of the phases. This guarantees that the cells can correctly build the machinery for separating the chromosomes and dividing the cell content. After division, the enzyme is broken down and the individual phases start to form again. If everything goes according to plan, the genetic material, organelles and cell contents are correctly distributed among the daughter cells. "These fundamental findings give us completely new insights into cell division: as a process in which the cell contents mix together and then separate again," says Lucas Pelkmans."

Comment: Every piece of research adds to the known complexity of cell division. Since cell division must be accurate, the entire process had to be designed all at once.

Biological complexity: reusing dead cell debris proteins

by David Turell @, Tuesday, August 14, 2018, 22:28 (2054 days ago) @ David Turell

Involves containment in vacuoles and autophagosomes using several special molecules:

https://www.sciencedaily.com/releases/2018/08/180814101444.htm

"Cells collect, decompose and recycle surplus or damaged cell material. This process, known as autophagy, is important, because cellular waste can be harmful to the entire organism if it accumulates in the cells. Like the treatment of household waste, autophagy requires certain mechanisms and elements. A team led by Prof. Dr. Claudine Kraft from the Institute of Biochemistry and Molecular Biology at the University of Freiburg and Levent Bas from the Institute of Biochemistry and Cellular Biology at the University of Vienna in Austria has made new findings on the role of proteins in the amalgamation of autophagosomes and vacuoles.

***

"During the process of autophagy, damaged cellular components, unused proteins and other cellular waste are incorporated into a vesicle, called the autophagosome, rather like how domestic waste is packed up in bin bags. In mammals the vesicles are transported to a lysosome, or in yeasts and plants to vacuoles, the cell organelles. These organelles have a similar function to a recycling plant: they decompose the materials included with the autophagosomes, so that the individual components can be reused. Numerous proteins initiate and regulate the process in the cells: more than 40 different types have already been identified. However their molecular functions are still largely unknown. Also, until now it has not been understood how the autophagosomes fuse with vacuoles so that the cellular waste can be recycled.

"In her latest publication the Freiburg biochemist offers a possible explanation: in order to understand what is needed for the fusion of the autophagosomes and vacuoles, Kraft and Bas and their team have traced the process in the laboratory. They segregated vacuoles, autophagosomes and intracellular liquid from yeast cells and created an environment in which the fusion could be observed in vitro, that is, outside a living organism.

"In general, membrane fusions require four bundled proteins known as SNARE proteins. Kraft and her colleagues have now managed to confirm that the fusion of the autophagosomes and vacuoles is also a process driven by SNARE proteins and that three already-known SNAREs are operative in the fusion process. They also discovered the fourth necessary SNARE, now called Ykt6. These results help to understand autophagy and its underlying molecular processes better. And thanks to their newly-developed in-vitro approach, in future it will be possible to identify other proteins that operate in the fusion process."

Comment: This process had to present from the beginning of life or life would not have survived. Designed.

Biological complexity: controlling cell volume

by David Turell @, Friday, August 17, 2018, 18:13 (2051 days ago) @ David Turell

A very complex molecular machine is unraveled:

https://www.sciencedaily.com/releases/2018/08/180816153144.htm

"Scientists at Scripps Research have solved the structure of a key protein that senses when our cells swell. This protein, called SWELL1 (or LRRC8A), works as an "ion channel" on the cell membrane to relieve pressure inside cells.

***

"SWELL1 was discovered in 2014 in the lab of Ardem Patapoutian, PhD, professor at Scripps Research and investigator with the Howard Hughes Medical Institute. The discovery opened the door to crucial studies into how the protein functions.

"The next important step was to shed light on SWELL1's molecular structure. The scientists aimed to understand the basics of how this ion channel senses changes in volume. To do this, they needed to take a look at the channel's molecular machinery.

***

"This new look at the ion channel suggests that interacting parts of the tendrils-sites that have a positive or a negative charge-sense a change in ionic strength in the cell (a dilution of the cell's salt contents as it absorbs water). The charged residues could send a signal up to the pore of the channel, telling the channel to release chloride ions from the cell and relieve the pressure.

***

"Next, the researchers took a closer look at how the different parts of the SWELL1 structure affect channel function. They found that mutating the protein at either of two sites keeps the structure from properly controlling traffic through the ion channel.

"The new study shows bundles of the SWELL1 subunit alone-and scientists know that SWELL1 has to be there for a functional channel. But up to four other subunits can swap into the structure at different sites. Kefauver says the next step is to determine how different combinations of SWELL1 subunits come together to form ion channels with different activities."

Comment: be sure to look at the illustration to see the complexity of the molecular arrangement. The importance of volume maintenance cannot be underestimated, as cellular function can be damaged or destroyed under too much pressure. This mechanism had to be present in the first cells of life.

Biological complexity: plant growth complex protein control

by David Turell @, Tuesday, August 21, 2018, 18:01 (2047 days ago) @ David Turell

A new complex mechanism is found:

https://www.sciencedaily.com/releases/2018/08/180821111952.htm

"A little-studied plant cellular complex plays an essential role in a biological process -- vacuole fusion -- critical to plant growth and development, according to new research from North Carolina State University. The findings shed light on complex and important plant processes as well as on how plants may have adapted to respond to environmental signals.

"Vacuoles are critical plant cell units that comprise some 80 to 95 percent of most plant cells. Plants die if vacuoles fail to develop properly. Believed to be a kind of plant garbage dump, with multiple roles in storage and recycling, vacuoles are also critical for pollen development, with sterility the consequence if the process goes awry.

***

"vacuoles control the opening and closing of stomata -- plant "pores" that must be regulated to balance carbon dioxide intake and the release of oxygen via water vapor.

"'Vacuoles fuse together when stomata open as they are exposed to light, and then they come apart or fragment to close the stomata when it is dark," Rojas-Pierce, associate professor of plant and microbial biology at NC State and the corresponding author of a paper describing the research, said. "But this beautiful and elaborate system must be tightly regulated to properly ensure the plant's response to the environment."

"Rojas-Pierce and colleagues examined the homotypic fusion and vascular protein sorting, or HOPS, complex of proteins. First identified as important in vacuole fusion in yeast, HOPS works with another group of proteins, the soluble NSF attachment protein receptors, or SNAREs, to promote vacuole fusion.

"'SNARE proteins actually do the job of vacuole fusion, but our study showed that the HOPS protein VPS41 may be a key player in the process, while HOPS protein VPS33 may act as a chaperone to guide vacuole fusion," Rojas-Pierce said.

"She added that this system is similar in other eukaryotes, or organisms with a cell nucleus.

"The study also revealed some surprising findings. In yeast, the presence of certain lipids is required for vacuolar fusion to take place. This and a previous study found, instead, that these regulatory lipids inhibited vacuole fusion in plants. The current study also showed that the curvature of the vacuolar membranes may play an important role in their fusion in plants.

"'This study showed both highly conserved and specific mechanisms for HOPS and its role in vacuolar fusion," Rojas-Pierce said."

Comment: Living organisms must maintain tight controls over all aspect of their living chemistry, generally using feedback loops, which means they can only be present in life by design. These loops defy chance stepwise development.

Biological complexity: protein hearing controls

by David Turell @, Wednesday, August 22, 2018, 23:25 (2046 days ago) @ David Turell

It takes a specific protein to handle hearing an d balance:

https://www.sciencedaily.com/releases/2018/08/180822130959.htm

"Scientists at Harvard Medical School say they have ended a 40-year-quest for the elusive identity of the sensor protein responsible for hearing and balance.

"The results of their research, reported Aug. 22 in Neuron, reveal that TMC1, a protein discovered in 2002, forms a sound- and motion-activated pore that allows the conversion of sound and head movement into nerve signals that travel to the brain -- a signaling cascade that enables hearing and balance.

***

"'We believe our findings settle that issue for good and yield definitive proof that TMC1 is the critical molecular sensor that converts sound and motion into electrical signals the brain can understand," said co-senior author Jeffrey Holt, Harvard Medical School professor of otolaryngology and of neurology at Boston Children's Hospital. "It is, indeed, the gatekeeper of hearing."

***

"In an initial set of experiments, the research team found that TMC1 proteins assemble in pairs to form sound-activated pores, or ion channels. Given that most ion-channel proteins form clusters of three to seven units, TMC1's minimalistic pairing was a surprise. It also offered a helpful clue into its structure.

"Next, to map out the molecular architecture of the TMC1 protein, the scientists turned to computer predictive modeling. Such models work by predicting the most probable arrangement of a protein's building blocks based on the configuration of a close relative with a known structure. The algorithm revealed that TMC1's closest relative with known structure was a protein known as TMEM16.

"Each protein's function is determined by its structure -- the specific sequence and arrangement of amino acids, the building blocks of proteins. TMEM16's amino acid arrangement yielded a possible amino acid model for TMC1. (my bold)

***

"Substituting 17 amino acids -- one at a time -- the researchers gauged whether and how each single substitution altered the cells' ability to respond to sound and allow the flow of ions.

"Of the 17 amino acid substitutions, 11 altered the influx of ions, and five did so dramatically, reducing ion flow by up to 80 percent, compared with nonmodified cells. One particular substitution blocked calcium influx completely, a finding that confirmed the precise location of the pore that normally allows calcium and potassium influx to initiate signal transmission.

***

"The ability to hear a sound and distinguish its meaning as a threat or a mere nuisance, for example, is crucial for biologic survival -- think hearing the sound of a bear approaching in the woods. But among many higher species, hearing is also important for social bonding and interaction -- think recognizing different voices or changes in voice patterns and intonation. The exquisitely complex ability to detect changes in intonation begins with the opening of a tiny molecular gate in TMC1.

"'We now know that TMC1 forms the pore that enables sound detection in animals ranging from fish to birds to humans," Corey said. "It is truly the protein that lets us hear.'"

Comment: Once again a specific protein fits the bill. Only design can achieve this result. Note my bold about the specificity of a protein's structural design and its action.

Biological complexity: protein hearing controls

by Balance_Maintained @, U.S.A., Thursday, August 23, 2018, 05:45 (2045 days ago) @ David Turell

It takes a specific protein to handle hearing an d balance:

https://www.sciencedaily.com/releases/2018/08/180822130959.htm

"Scientists at Harvard Medical School say they have ended a 40-year-quest for the elusive identity of the sensor protein responsible for hearing and balance.

"The results of their research, reported Aug. 22 in Neuron, reveal that TMC1, a protein discovered in 2002, forms a sound- and motion-activated pore that allows the conversion of sound and head movement into nerve signals that travel to the brain -- a signaling cascade that enables hearing and balance.

***

"'We believe our findings settle that issue for good and yield definitive proof that TMC1 is the critical molecular sensor that converts sound and motion into electrical signals the brain can understand," said co-senior author Jeffrey Holt, Harvard Medical School professor of otolaryngology and of neurology at Boston Children's Hospital. "It is, indeed, the gatekeeper of hearing."

***

"In an initial set of experiments, the research team found that TMC1 proteins assemble in pairs to form sound-activated pores, or ion channels. Given that most ion-channel proteins form clusters of three to seven units, TMC1's minimalistic pairing was a surprise. It also offered a helpful clue into its structure.

"Next, to map out the molecular architecture of the TMC1 protein, the scientists turned to computer predictive modeling. Such models work by predicting the most probable arrangement of a protein's building blocks based on the configuration of a close relative with a known structure. The algorithm revealed that TMC1's closest relative with known structure was a protein known as TMEM16.

"Each protein's function is determined by its structure -- the specific sequence and arrangement of amino acids, the building blocks of proteins. TMEM16's amino acid arrangement yielded a possible amino acid model for TMC1. (my bold)

***

"Substituting 17 amino acids -- one at a time -- the researchers gauged whether and how each single substitution altered the cells' ability to respond to sound and allow the flow of ions.

"Of the 17 amino acid substitutions, 11 altered the influx of ions, and five did so dramatically, reducing ion flow by up to 80 percent, compared with nonmodified cells. One particular substitution blocked calcium influx completely, a finding that confirmed the precise location of the pore that normally allows calcium and potassium influx to initiate signal transmission.

***

"The ability to hear a sound and distinguish its meaning as a threat or a mere nuisance, for example, is crucial for biologic survival -- think hearing the sound of a bear approaching in the woods. But among many higher species, hearing is also important for social bonding and interaction -- think recognizing different voices or changes in voice patterns and intonation. The exquisitely complex ability to detect changes in intonation begins with the opening of a tiny molecular gate in TMC1.

"'We now know that TMC1 forms the pore that enables sound detection in animals ranging from fish to birds to humans," Corey said. "It is truly the protein that lets us hear.'"

Comment: Once again a specific protein fits the bill. Only design can achieve this result. Note my bold about the specificity of a protein's structural design and its action.

And that specific protein is used across a wide range of species, as predicted.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: protein hearing controls

by David Turell @, Thursday, August 23, 2018, 15:31 (2045 days ago) @ Balance_Maintained

DAvid: It takes a specific protein to handle hearing an d balance:

https://www.sciencedaily.com/releases/2018/08/180822130959.htm

"Scientists at Harvard Medical School say they have ended a 40-year-quest for the elusive identity of the sensor protein responsible for hearing and balance.

"The results of their research, reported Aug. 22 in Neuron, reveal that TMC1, a protein discovered in 2002, forms a sound- and motion-activated pore that allows the conversion of sound and head movement into nerve signals that travel to the brain -- a signaling cascade that enables hearing and balance.

***

"'We believe our findings settle that issue for good and yield definitive proof that TMC1 is the critical molecular sensor that converts sound and motion into electrical signals the brain can understand," said co-senior author Jeffrey Holt, Harvard Medical School professor of otolaryngology and of neurology at Boston Children's Hospital. "It is, indeed, the gatekeeper of hearing."

***

"In an initial set of experiments, the research team found that TMC1 proteins assemble in pairs to form sound-activated pores, or ion channels. Given that most ion-channel proteins form clusters of three to seven units, TMC1's minimalistic pairing was a surprise. It also offered a helpful clue into its structure.

"Next, to map out the molecular architecture of the TMC1 protein, the scientists turned to computer predictive modeling. Such models work by predicting the most probable arrangement of a protein's building blocks based on the configuration of a close relative with a known structure. The algorithm revealed that TMC1's closest relative with known structure was a protein known as TMEM16.

"Each protein's function is determined by its structure -- the specific sequence and arrangement of amino acids, the building blocks of proteins. TMEM16's amino acid arrangement yielded a possible amino acid model for TMC1. (my bold)

***

"Substituting 17 amino acids -- one at a time -- the researchers gauged whether and how each single substitution altered the cells' ability to respond to sound and allow the flow of ions.

"Of the 17 amino acid substitutions, 11 altered the influx of ions, and five did so dramatically, reducing ion flow by up to 80 percent, compared with nonmodified cells. One particular substitution blocked calcium influx completely, a finding that confirmed the precise location of the pore that normally allows calcium and potassium influx to initiate signal transmission.

***

"The ability to hear a sound and distinguish its meaning as a threat or a mere nuisance, for example, is crucial for biologic survival -- think hearing the sound of a bear approaching in the woods. But among many higher species, hearing is also important for social bonding and interaction -- think recognizing different voices or changes in voice patterns and intonation. The exquisitely complex ability to detect changes in intonation begins with the opening of a tiny molecular gate in TMC1.

"'We now know that TMC1 forms the pore that enables sound detection in animals ranging from fish to birds to humans," Corey said. "It is truly the protein that lets us hear.'"

Comment: Once again a specific protein fits the bill. Only design can achieve this result. Note my bold about the specificity of a protein's structural design and its action.


Tony: And that specific protein is used across a wide range of species, as predicted.

Design from the ground up using each development as it comes along.

Biological complexity: how plants control growth

by David Turell @, Friday, August 24, 2018, 00:58 (2044 days ago) @ David Turell

The molecules are shown to be, of course, a negative feedback loop, a prime control mechanism in all life:

https://phys.org/news/2018-08-secrets.html


"University of British Columbia researchers have discovered an internal messaging system that plants use to manage the growth and division of their cells. These growth-management processes are critical for all organisms, because without them, cells can proliferate out of control—as they do in cancers and bacterial infections.

"Plants use this messaging system to survive under harsh conditions or to compete successfully when conditions are favourable. It tells them when to grow, when to stagnate, when to flower, and when to store resources—all based on the prevailing conditions. Understanding how it all works could enable innovations in agriculture, forestry and conservation as climate change takes hold.

"Plants use this messaging system to survive under harsh conditions or to compete successfully when conditions are favourable. It tells them when to grow, when to stagnate, when to flower, and when to store resources—all based on the prevailing conditions. Understanding how it all works could enable innovations in agriculture, forestry and conservation as climate change takes hold.

"UBC botany professor Geoffrey Wasteneys and his colleagues discovered that the system is driven by a protein called CLASP. The protein, found in plants, animals and fungi, plays an essential role in cell growth and division by coordinating the assembly of filaments within cells. Its gene in plants was first identified by Wasteneys in 2007.

"Their study published today in Current Biology reveals that production of CLASP is reduced by a plant-growth hormone called brassinosteroid. The researchers established this by exposing thale cress—a small flowering plant native to Eurasia and Africa—to brassinosteroid. This exposure stunted the plants in a way that closely resembled mutant versions of the plant that lacked the CLASP protein altogether. This observation led the team to conduct experiments that proved CLASP is indeed a direct target of brassinosteroid.

"However, the researchers were puzzled because limiting growth through exposure to brassinosteroid is a one-way process that merely shuts down cell division. In a surprise twist, the researchers discovered that CLASP prevents the degradation of brassinosteroid receptors, so when CLASP is scarce, brassinosteroid becomes less effective, which results in CLASP levels rising again. Essentially, the protein and the hormone affect each other in a negative-feedback loop.

"'You can liken it to the predator-prey feedback loop," said Wasteneys. "We know that fox populations plummet if they over-consume rabbits. In the absence of foxes, rabbit populations explode, causing the eventual collapse of their ecosystem.

"'These findings are unique because they show, for the first time, that CLASP is governing its own destiny by directly sustaining the hormone pathway that regulates its expression.'"

Comment: A standard system that can only exist if designed.

Biological complexity: repair of nerves

by David Turell @, Saturday, August 25, 2018, 19:08 (2043 days ago) @ David Turell

When neurons appeared in evolution and created nerve networks, a repair mechanism had to appear at the same time. The mechanism:

https://medicalxpress.com/news/2018-08-cascade-nerve-cells-characterized.html

"Through a study of roundworm nerve cells with severed axons, researchers at Nagoya University showed that a signaling cascade that normally functions in promoting the phagocytosis of apoptotic cells also acts in inducing axon regeneration. The findings shed light on a fundamental feature of nerve repair, which is limited in the central nervous system in humans, and thus could pave the way towards treatments for brain and spinal cord injuries.

"Researchers have identified the series of molecules involved in the regeneration of damaged nerves in roundworm, showing that it largely overlaps with the signals used by the intrinsic removal system to take up and process dying cells.

"The branches of nerve cells called axons are particularly susceptible to damage due to the long distances they extend to communicate with each other. In humans,such damage in peripheral regions of the body can be relatively well repaired,but this repair is less effective in the brain and the spinal cord, which helps to explain why conditions such as brain and spinal cord injuries are so debilitating.

***

"The team used a laser to cut roundworm axons and then analyzed the subsequent series of molecular reactions that occurred. They found that this damage resulted in the movement of a lipid called phosphatidylserine (PS) from the inside of cells to their outside,which was mediated by a protein called an ABC transporter. This externalized PS was then recognized by another molecule, triggering a series of reactions that eventually led to repair of the axon. Interestingly, PS is better known as an "eat me" signal that helps the phagocytosis of a dying cell by its neighbors.

"'We were able to dissect the complex range of molecules involved in axon repair by using fluorescent labels in and around the severed axon and knocking down the individual components suspected of being involved,"says corresponding author Kunihiro Matsumoto."Although many of these molecules are also active in promoting phagocytosis of apoptotic cells,in axon repair that creates a "save me" signal rather than an "eat me" one,which enables the axons to regenerate."

"The team explains that for the repair of damaged nerves,the PS labeling appears only at the severed sites and exists for only a short time(~1 hr),which is in contrast to the labeling in eliminating dying cells that remains for a long time until the cells are eliminated. The researchers now guess that this difference in signal timing may be one way for the cells to distinguish the meaning of the PS signal -"eat me" vs. "save me.'"

Comment: It seems reasonable to assume that this repair system was designed when nerve networks also appeared becasue such protection s were needed from the beginning.

Biological complexity: mechanism of Big Potassium ion pore

by David Turell @, Saturday, August 25, 2018, 20:26 (2043 days ago) @ David Turell

This is the way electricity is able to move quickly in an out of the neuron body:

https://www.sciencedaily.com/releases/2018/08/180824090613.htm

"Chen says, "The main way for the nervous system to send electrical signals is by opening and closing potassium and other ion channels that help regulate neuronal firing and neurotransmitter release. These Big Potassium channels are central for coupling electrical signaling to calcium-mediated events such as muscle contraction and neural excitation," and how blood pressure is regulated, for example.

"'These BK channels contain extra-large pores, so they can sustain very large current, which lets the cell respond faster," he adds. BK channels play an important role in many health conditions such as hypertension, epilepsy, autism and mental retardation.

***

"The gate mechanism in BK channels they have been studying is "drastically different from what has been observed in other ion channels," the authors point out. "We believe that this work represents a paradigm shift in our thinking of regulation and gating of BK channels," and is "one of the first few examples of a true 'hydrophobic gate,' where the barrier to ion permeation arises directly from dewetting transitions."

"Hydrophobic dewetting refers to a phenomenon similar to the way water placed on an oily surface beads to form droplets. Initiation of dewetting transitions in BK channels requires changes in the pore shape and surface hydrophobicity driven by calcium binding. When the BK pore is oily, the water forms a vapor phase that acts like a barrier and prevents all ions from entering, Chen says. "Nothing gets through."

***

"He says, "If you think about why nature might want to use a vapor barrier where there is a big pore that has to carry a lot of electrical current, to apply a physical barrier you would need a protein structural re-arrangement which would probably be either too big or too slow, or both. In a way, nature is really clever in using this hydrophobic dewetting phenomenon to create a sensitive and fast gate. We were actually really surprised to see that the changes in pore shape and surface properties are relatively small and subtle, but they have big consequences on its hydration properties."

"Further, Chen says, "In terms of understanding how the channel is gated, now we know more and it gives us a strong basis to see how other domains of BK channels talk to the pore and how the membrane voltage, calcium gradient, and a few other chemical signals control the state of the pore. In principle, that knowledge should be useful in developing new therapies and strategies in targeting the channel.'"

Comment: Here is another highly complex mechanism that requires design all at once to create controls over the speed of ions moving. Think about how quickly you move when mistakenly touching a hot stove. Pore size will always be controlled by feedback loops which also have to be designed for they involve several steps.

Biological complexity: red cell shape mechanics

by David Turell @, Monday, September 10, 2018, 21:01 (2027 days ago) @ David Turell

The red cell has no nucleus, is doughnut shaped but the center is filled with a slim area of the cell. The cell has to change shape to twist its way through tiny capillaries. This shape gives the greatest surface area for gas exchange. The cell handles both oxygen and CO2:

https://www.the-scientist.com/the-literature/how-red-blood-cells-get-their-dimples-6468...

"Back in the 1980s, when Fowler started working with red blood cells, it wasn’t clear whether they even contained myosin. She suspected they might, because the protein appeared to play a role in giving other cells their shapes. After painstaking experiments, Fowler finally showed that red blood cells do carry the protein, but exactly how it influenced erythrocytes’ shape remained a mystery. “We didn’t have the tools to do those experiments then,” she says. The myosin filaments in red blood cells are tiny, only around 200 to 450 nanometers long, making them extremely challenging to image. And the first inhibitor of myosin IIA—the specific protein found in red blood cells—wasn’t developed until the early 2000s, so scientists couldn’t see what happened when the protein wasn’t functioning in the cells.

***

"When myosin and actin interact and myosin contracts, the cell membrane stiffens, giving the cell a dimple at its center. Inhibiting the motor activity of the protein causes the myosin filaments to expand so they no longer tug on spectrin and actin. That leads to less tension in the membrane and, ultimately, the disappearance of the dimple.

"By expanding and contracting, the myosin filaments likely make it possible for red blood cells to shape-shift as they tumble in the bloodstream’s shear flow and squeeze through microvessels such as capillaries, then pop back into their dimpled form, Fowler says.

"This discovery could also give clues to how myosin works in other types of cells, Vann Bennett, a biochemist at Duke University who was not involved in the new study, tells The Scientist. “Red blood cells are a true experiment of nature,” he says. “They’ve gotten rid of the cell nucleus, mitochondria, and all cytoskeletal proteins.” These simplified cells “have been a powerhouse for generating concepts about how [plasma] membranes are organized in other cell types,” Bennett explains. Understanding the importance of myosin’s contraction in shaping red blood cells, he says, may help in teasing out its functions in other cell types.

"Another recent study supports myosin’s widespread importance in maintaining cell structure: the research showed the protein is critical for axons to grow and shape themselves, suggesting it could be involved in brain plasticity."

Comment: A supreme design well beyond the capacity of a chance evolutionary mechanism. Since the cell does not have a nucleus it must be programmed to feel blood vessel pressure and respond by altering the myosin's actions. This is an example of automaticity such as I believe bacteria are capable of performing.

Biological complexity: red cell shape mechanics

by Balance_Maintained @, U.S.A., Monday, September 10, 2018, 23:47 (2027 days ago) @ David Turell

The red cell has no nucleus, is doughnut shaped but the center is filled with a slim area of the cell. The cell has to change shape to twist its way through tiny capillaries. This shape gives the greatest surface area for gas exchange. The cell handles both oxygen and CO2:

https://www.the-scientist.com/the-literature/how-red-blood-cells-get-their-dimples-6468...

"Back in the 1980s, when Fowler started working with red blood cells, it wasn’t clear whether they even contained myosin. She suspected they might, because the protein appeared to play a role in giving other cells their shapes. After painstaking experiments, Fowler finally showed that red blood cells do carry the protein, but exactly how it influenced erythrocytes’ shape remained a mystery. “We didn’t have the tools to do those experiments then,” she says. The myosin filaments in red blood cells are tiny, only around 200 to 450 nanometers long, making them extremely challenging to image. And the first inhibitor of myosin IIA—the specific protein found in red blood cells—wasn’t developed until the early 2000s, so scientists couldn’t see what happened when the protein wasn’t functioning in the cells.

***

"When myosin and actin interact and myosin contracts, the cell membrane stiffens, giving the cell a dimple at its center. Inhibiting the motor activity of the protein causes the myosin filaments to expand so they no longer tug on spectrin and actin. That leads to less tension in the membrane and, ultimately, the disappearance of the dimple.

"By expanding and contracting, the myosin filaments likely make it possible for red blood cells to shape-shift as they tumble in the bloodstream’s shear flow and squeeze through microvessels such as capillaries, then pop back into their dimpled form, Fowler says.

"This discovery could also give clues to how myosin works in other types of cells, Vann Bennett, a biochemist at Duke University who was not involved in the new study, tells The Scientist. “Red blood cells are a true experiment of nature,” he says. “They’ve gotten rid of the cell nucleus, mitochondria, and all cytoskeletal proteins.” These simplified cells “have been a powerhouse for generating concepts about how [plasma] membranes are organized in other cell types,” Bennett explains. Understanding the importance of myosin’s contraction in shaping red blood cells, he says, may help in teasing out its functions in other cell types.

"Another recent study supports myosin’s widespread importance in maintaining cell structure: the research showed the protein is critical for axons to grow and shape themselves, suggesting it could be involved in brain plasticity."

Comment: A supreme design well beyond the capacity of a chance evolutionary mechanism. Since the cell does not have a nucleus it must be programmed to feel blood vessel pressure and respond by altering the myosin's actions. This is an example of automaticity such as I believe bacteria are capable of performing.

And the mechanism to make that happen would have needed to precede the necessity of them, or it would mean death. Darwinism would break down because premature death would prevent this becoming a dominant trait.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: red cell shape mechanics

by David Turell @, Tuesday, September 11, 2018, 01:35 (2026 days ago) @ Balance_Maintained

The red cell has no nucleus, is doughnut shaped but the center is filled with a slim area of the cell. The cell has to change shape to twist its way through tiny capillaries. This shape gives the greatest surface area for gas exchange. The cell handles both oxygen and CO2:

https://www.the-scientist.com/the-literature/how-red-blood-cells-get-their-dimples-6468...

"Back in the 1980s, when Fowler started working with red blood cells, it wasn’t clear whether they even contained myosin. She suspected they might, because the protein appeared to play a role in giving other cells their shapes. After painstaking experiments, Fowler finally showed that red blood cells do carry the protein, but exactly how it influenced erythrocytes’ shape remained a mystery. “We didn’t have the tools to do those experiments then,” she says. The myosin filaments in red blood cells are tiny, only around 200 to 450 nanometers long, making them extremely challenging to image. And the first inhibitor of myosin IIA—the specific protein found in red blood cells—wasn’t developed until the early 2000s, so scientists couldn’t see what happened when the protein wasn’t functioning in the cells.

***

"When myosin and actin interact and myosin contracts, the cell membrane stiffens, giving the cell a dimple at its center. Inhibiting the motor activity of the protein causes the myosin filaments to expand so they no longer tug on spectrin and actin. That leads to less tension in the membrane and, ultimately, the disappearance of the dimple.

"By expanding and contracting, the myosin filaments likely make it possible for red blood cells to shape-shift as they tumble in the bloodstream’s shear flow and squeeze through microvessels such as capillaries, then pop back into their dimpled form, Fowler says.

"This discovery could also give clues to how myosin works in other types of cells, Vann Bennett, a biochemist at Duke University who was not involved in the new study, tells The Scientist. “Red blood cells are a true experiment of nature,” he says. “They’ve gotten rid of the cell nucleus, mitochondria, and all cytoskeletal proteins.” These simplified cells “have been a powerhouse for generating concepts about how [plasma] membranes are organized in other cell types,” Bennett explains. Understanding the importance of myosin’s contraction in shaping red blood cells, he says, may help in teasing out its functions in other cell types.

"Another recent study supports myosin’s widespread importance in maintaining cell structure: the research showed the protein is critical for axons to grow and shape themselves, suggesting it could be involved in brain plasticity."

Comment: A supreme design well beyond the capacity of a chance evolutionary mechanism. Since the cell does not have a nucleus it must be programmed to feel blood vessel pressure and respond by altering the myosin's actions. This is an example of automaticity such as I believe bacteria are capable of performing.


Tony: And the mechanism to make that happen would have needed to precede the necessity of them, or it would mean death. Darwinism would break down because premature death would prevent this becoming a dominant trait.

The circulatory system in red-blooded animals had to have this type of cell to handle the fine capillaries that are in all muscle tissues and organs, but less in bone. The hemoglobin molecule that fills these cells does two way duty. Delivering oxygen and taking out CO2, exchanging those gases at the lungs in a beautifully designed system. Not by Darwin.

Biological complexity: a muscle peptide can burn fat

by David Turell @, Tuesday, September 11, 2018, 16:48 (2026 days ago) @ David Turell

One specific small peptide, found only in muscle, can causer an increase in energy use and burn fat:

https://medicalxpress.com/news/2018-09-sarcolipin-muscle-cells-energy-fat.html

"Ever wonder why you burn fat and heat up when you exercise or shiver? Now, researchers at Sanford Burnham Prebys Medical Discovery Institute (SBP) have shown that sarcolipin, a small peptide only found in muscles, increases muscle energy expenditure and fat oxidization. The study was published today in the journal Cell Reports.

"The scientists found sarcolipin forces muscle to use more energy to move calcium by interacting with calcium ion transporter SERCA and making it less efficient. This drives mitochondrial power plants to produce extra energy by burning more fat.

"'This study shows a direct relationship between sarcolipin and energy metabolism," says Muthu Periasamy, Ph.D., senior author of the paper and professor at SBP Lake Nona. "This mechanism is intrinsic to muscle and generates heat at the expense of fat burning."

"Two factors increase energy expenditure in muscle—exercise and cold. When either happens, muscle cells intensify calcium cycling and recruit SERCA to move calcium ions into the sarcoplasmic reticulum, a structure within muscle cells that balances calcium levels. This process uses a lot of (ATP) energy because SERCA relies on ATP to move calcium. When sarcolipin binds to SERCA, it uncouples SERCA activity. As a result, it allows ATP consumption but not efficient calcium transport, which causes more energy consumption. The net result is more heat and fat burning.

"'When you exercise, your muscle makes more mitochondria and oxidizes more fat," says Periasamy. "Sarcolipin is the missing link. It's recruited during exercise or cold exposure and alters calcium cycling to increase mitochondria biogenesis and fat burning."

"In the study, the team found that animals without sarcolipin had fewer mitochondria and had trouble burning fat, accumulating more in their muscle (called lipotoxicity), which is a common cause of insulin resistance. However, those with more sarcolipin boosted their concentration of mitochondria and showed increased fat oxidation.

"'When we feed mice with more sarcolipin a high-fat diet, they don't accumulate any fat in their muscle, and they don't develop insulin resistance and type 2 diabetes," says Santosh Maurya, Ph.D., first author of the paper and staff scientist at SBP Lake Nona."

Comment: One can wonder how chance evolution found this particular protein molecule to perfor, this function. Not by chance

Biological complexity: how the liver can regenerate

by David Turell @, Wednesday, September 26, 2018, 20:36 (2011 days ago) @ David Turell

The liver is as vital an organ as the heart for maintaining life. it detoxifies just as the kidney does, it produces bile to digest fat, and it produces modifications of necessary metabolic functions:

https://phys.org/news/2018-09-liver-cells-reprogramming-regenerate.html


"New research conducted by biochemists at the University of Illinois has determined how damaged liver cells repair and restore themselves through a signal to return to an early stage of postnatal organ development. The findings are reported in the journal Nature Structural & Molecular Biology.

"'The liver is a resilient organ," said U. of I. biochemistry professor Auinash Kalsotra, who led the new research. "It can restore up to 70 percent of lost mass and function after just a few weeks.

"'We know that in a healthy adult liver, the cells are dormant and rarely undergo cell division," he said. "However, if the liver is damaged, the liver cells re-enter the cell cycle to divide and produce more of themselves."

"The human liver can become chronically damaged by toxins such as alcohol and even certain medicines, but still continue to function and self-repair, Kalsotra said.

"'This research looked at what is happening at the molecular level in a damaged liver that enables it to regenerate while still performing normal functions," he said.

"Using a mouse model of a liver severely damaged by toxins, the researchers compared injured adult liver cells with healthy cells present during a stage of development just after birth.

" They found that injured cells undergo a partial reprograming that returns them to a neonatal state of gene expression.

"The team discovered that fragments of messenger RNA, the molecular blueprints for proteins, are rearranged and processed in regenerating liver cells in a manner reminiscent of the neonatal period of development. This phenomenon is regulated through alternative splicing, a process wherein exons (expressed regions of genes) are cut from introns (intervening regions) and stitched together in various combinations to direct the synthesis of many different proteins from a single gene. These proteins can have different cellular functions or properties.

"'We found that the liver cells after birth use a specific RNA-binding protein called ESRP2 to generate the right assortment of alternatively spliced RNAs that can produce the protein products necessary for meeting the functional demands of the adult liver," said graduate student Sushant Bangru, the lead author of the study. "When damaged, the liver cells lower the quantity of ESRP2 protein. This reactivates fetal RNA splicing in what is called the 'Hippo signaling pathway,' giving it instructions about how to restore and repopulate the liver with new and healthy cells.'"

Comment: The liver is so vital, it had to be designed from the beginning to have this regeneration mechanism. It didn't just evolve by chance.

Biological complexity: deciding red or white cell production

by David Turell @, Wednesday, September 26, 2018, 20:51 (2011 days ago) @ David Turell

A new study has found the controls which help make the decisions:

https://medicalxpress.com/news/2018-09-white-blood-cell.html

"Using a genetic technique known as double knock-out (DKO), which represses two genes, rendering them non-functional, the scientists targeted Bach1 and Bach2 transcription factor proteins in mice. Transcription factors are proteins that control gene expression in cells by turning genes on or off according to certain stimuli. They found that red blood cell production was ineffective in the DKO mice, leading them to conclude that infection stimulates a reduced expression of Bach factors, which may contribute to the development of anemia of infection/inflammation.

***

"According to lead author Hiroki Kato, a researcher in the Department of Biochemistry and the Department of Hematology and Rheumatology at Tohoku University Graduate School of Medicine in Sendai, Japan, transcription factors Bach1 and Bach2 support the formation of red blood cells by repressing white blood cell formation at the normal (healthy) state. Repressing Bach1 and Bach2 in the DKO mice induced the formation of white myeloid blood cells at the expense of producing red blood cells and another type of white blood cells called lymphoid cells.

***

"The results of this study and previous research show that Bach factors play multiple roles in the formation of blood, such as supporting the formation of red blood cells and lymphoid cells from immature blood cells and the development and response of immune cells at mature cell levels, said Kato.

"'These facts suggest that Bach factors work as a 'switch' controlling the steady state as well as the emergency state of blood cell formation," Kato explained. "We would like to reveal the fundamental mechanism of the switching system."

"According to co-author Kazuhiko Igarashi, a scientist in the Department of Biochemistry and the Center for Regulatory Epigenome and Diseases at Tohoku University, the principle of blood cell formation: to be or not to be white myeloid cells, is regulated by a network of transcription factors—proteins that control the rate of transcription of genetic information from DNA to messenger RNA by binding to a specific DNA sequence.

"'Cells appear to stabilize their state of gene expression and thus identities by non-genetic modifications of chromatin," said Igarashi."

Comment: Once again we see the genomic system being manipulated by response to various stimuli. This is a built-in response by design because survival depends upon these quick responses

Biological complexity: how cells make proteins

by David Turell @, Monday, October 08, 2018, 15:32 (1999 days ago) @ David Turell

It is a complex highly organized process in the ribosome:

https://www.nature.com/articles/s41586-018-0462-y

"Abstract:

The folding of newly synthesized proteins to the native state is a major challenge within the crowded cellular environment, as non-productive interactions can lead to misfolding, aggregation and degradation1. Cells cope with this challenge by coupling synthesis with polypeptide folding and by using molecular chaperones to safeguard folding cotranslationally2. However, although most of the cellular proteome forms oligomeric assemblies3, little is known about the final step of folding: the assembly of polypeptides into complexes. In prokaryotes, a proof-of-concept study showed that the assembly of heterodimeric luciferase is an organized cotranslational process that is facilitated by spatially confined translation of the subunits encoded on a polycistronic mRNA4. In eukaryotes, however, fundamental differences—such as the rarity of polycistronic mRNAs and different chaperone constellations—raise the question of whether assembly is also coordinated with translation. Here we provide a systematic and mechanistic analysis of the assembly of protein complexes in eukaryotes using ribosome profiling. We determined the in vivo interactions of the nascent subunits from twelve hetero-oligomeric protein complexes of Saccharomyces cerevisiae at near-residue resolution. We find nine complexes assemble cotranslationally; the three complexes that do not show cotranslational interactions are regulated by dedicated assembly chaperones. Cotranslational assembly often occurs uni-directionally, with one fully synthesized subunit engaging its nascent partner subunit, thereby counteracting its propensity for aggregation. The onset of cotranslational subunit association coincides directly with the full exposure of the nascent interaction domain at the ribosomal tunnel exit. The action of the ribosome-associated Hsp70 chaperone Ssb8 is coordinated with assembly. Ssb transiently engages partially synthesized interaction domains and then dissociates before the onset of partner subunit association, presumably to prevent premature assembly interactions. Our study shows that cotranslational subunit association is a prevalent mechanism for the assembly of hetero-oligomers in yeast and indicates that translation, folding and the assembly of protein complexes are integrated processes in eukaryotes.

Very simply the ribosome is a highly complex factory of proteins making product proteins. It is irreducibly complex and cannot have originated by chance mutations. For cells to survive in the beginning of life, this organelle, the ribosome, had to be present.

Biological complexity: plant growth complex protein control

by David Turell @, Wednesday, January 09, 2019, 22:02 (1906 days ago) @ David Turell

New study on rooted plants show automatic controls with feedback loop controls:

https://www.sciencedaily.com/releases/2019/01/190109142645.htm

" Radial growth provides physical support to plants, yields everyday items like wood and cork, and plays a major role in converting atmospheric carbon into plant biomass.

"Radial growth also produces specialised vascular tissues that transport water and nutrients around plants and is visible as concentric patterns known as annual growth rings in tree trunk cross-sections. In many cases, plants and trees continue this outwards growth for their entire lifetime. Radial growth is also responsible for producing our root and tuber vegetables such as turnips, carrots, sugar beet and potatoes.

***

"Professor Ykä Helariutta's team at the Sainsbury Laboratory Cambridge University (SLCU) focused on the early (primary) stage of vascular development. They showed that in contrast to the late stage, during this early stage young phloem cells (protophloem) are initiating and organising the primary (procambial) stage of radial growth. They also described an underlying gene regulatory network and an integrating role for a newly identified group of mobile transcription factors.

"Together, their findings reveal some of the regulatory mechanisms that enable plants to continue to radially grow in a highly organised fashion, resulting in the concentric patterns seen in cross-sections of stems and roots. The key is the positioning of cells and a complex network of feedback signalling.

"Dr Mähönen's team combined individual cell lineage tracing and molecular genetics to show early-stage xylem cells, which had not yet differentiated, take over as the organiser and direct adjacent vascular cells to divide and function as stem cells: "We showed that this secondary development is a tightly controlled process and revealed a dynamic nature of the organiser. Differentiation of the organiser into a xylem vessel leads to formation of a new organiser in the adjacent cambial stem cell, thus ensuring the maintenance of the vascular cambium. We also identified a molecular mechanism that defines the stem cell organiser."

***

"'Very early-stage phloem tissues (protophloem) are helping to guide the behaviour of cells and establish patterns of developmental potential that impact on future radial growth," says Professor Helariutta. "This is established through a group of mobile transcription factors that move from the protophloem sieve element (PSE) to the neighbouring cells, to promote cell division, and to develop their own identity. The activity of these mobile transcription factors is regulated by a set of signals of various chemical nature, such as plant hormones, other transcription factors and mobile microRNA species.'"

Comment: Automaticity in growth by feedback loops to control transcription factors, hormones and microRNA. This is h ow cells work in everyday projects.

Biological complexity: plant root branching controls

by David Turell @, Saturday, January 19, 2019, 20:24 (1896 days ago) @ David Turell

A series of molecular reactions:

https://www.sciencedaily.com/releases/2019/01/190118095938.htm

"Plant root systems are mainly shaped by the lateral roots that grow from tissue inside the existing roots. These roots form from "lateral root founder cells" that are positioned at regularly-spaced intervals at a distance from the meristem tissue (tissue responsible for growth). Previous studies using Arabidopsis plants showed that lateral root founder cells are made from sites where there is high response to the chemical auxin, and indicated that transcription factor LBD16 induced by auxin may inhibit the cells near lateral root founder cells from forming roots.

"This time a joint research team, using plant model Arabidopsis, searched for the gene that is activated by transcription factor LBD16 and successfully identified the TOLS2 gene. The TOLS2 gene is mainly expressed in lateral root founder cells and root germs. In Arabidopsis plants that overexpress TOLS2, the number of lateral roots decreases, indicating that the TOLS2 gene can inhibit the formation of lateral root founder cells. The team analyzed secretions from plants with overexpression of TOLS2 and revealed that the mature TOLS2 peptide is formed from 11 amino acids. When they artificially created mature TOLS2 peptide and added it to a wild-type Arabidopsis, the number of lateral root founder cells and lateral roots decreased. (my bold)

"Based on further investigation, the research team identified the receptor for TOLS2 as RLK7. RLK7 proteins express in the inner sheath of the roots (where the lateral root founder cells are located), the endodermis and the dermal layer, but RLK7 expression could not be found in the lateral root founder cells. It is likely that these proteins suppress the formation of lateral roots in cells adjacent to lateral root founder cells.

***

"Their results confirmed that the TOLS2 peptide and the RLK7 receptor are necessary to preserve the correct spacing between lateral root founder cells. From this analysis the research team proposed that Arabidopsis, by responding to auxin and inducing TOLS2 peptide in lateral root founder cells, through RLK7 receptors inhibits nearby lateral root founder cells in a non-cell-autonomous manner."

Comment: Note my bold. Life' s processes always require specifically design protein molecules. I have previously entered research on root receptors that guide where to grow for water and nutrients. Always a series of protein molecules reacting automatically in in a standardized progression.

Biological complexity: plant root growth stimulation

by David Turell @, Saturday, June 08, 2019, 19:01 (1756 days ago) @ David Turell

In low nitrogen situations plant root growth is stimulated by specialized hormones:

https://www.sciencedaily.com/releases/2019/06/190607110518.htm

"As sessile organisms, plants rely on their ability to adapt the development and growth of their roots in response to changing nutrient conditions. One such response, known to be displayed by plants grown in low nitrogen conditions, is the elongation of primary and lateral roots to explore the surrounding soil.

***

" As soon as plants run into nitrogen deficiency, they immediately induce a foraging response, in which roots elongate to explore a larger soil volume. The regulatory mechanisms underlying this nitrogen-dependent root response were previously unknown. Researchers from the IPK in Gatersleben have now discovered that a class of steroid hormones modulate root foraging under low nitrogen conditions and thereby determine the extent of this response.

***

"the researchers were able to show that BSK3, a brassinosteroid signaling kinase, is modulating the extent of root elongation under low nitrogen. Further, they demonstrated that mild nitrogen deficiency activates brassinosteroid signaling by upregulating the transcript levels of the brassinosteroid co-receptor BAK1 that enhances the sensitivity of root cells to brassinosteroids. (my bold)

"The results reveal a previously unknown role of brassinosteroid-type plant hormones in shaping root systems in response to nutrient deficiencies. This novel insight allows a deeper understanding of the regulation behind adaptive responses of plants to changes in nitrogen availability, but also provides a perspective for practical application in agriculture."

Comment: This finding presents the usual problem for Darwin-style evolutionary theory. The bolded molecule is a giant enzyme, with exact structure to provide the necessary result in action. Of all the possible structures to chose from, how did unguided evolution find such a molecule? Since this is an issue of survival, this mechanism had to be part of the original design of the plant.

Biological complexity:mitochondria repair membranes

by David Turell @, Saturday, May 16, 2020, 14:43 (1413 days ago) @ David Turell

An other function is found in cell culture techniques:

https://science.sciencemag.org/content/368/6492/727.2

When the plasma membrane is disrupted, lethal consequences can ensue. However, some cells can mount a plasma membrane repair response specifically targeted to the wound site. Horn et al. studied the role of mitochondria in plasma membrane repair in cultured mammalian cells. Mitochondria form a distributed interconnected network throughout the cytoplasm. When the plasma membrane is breached, a local influx of calcium promotes a localized wave of rapid mitochondrial fission. The fission process is mediated by the mitochondrial fission protein Drp1. At the injury site, the locally fragmented mitochondria help to clear the influx of calcium from the cytosol and generate a localized redox signal that promotes membrane repair. In cells lacking Drp1 or its adaptor protein, the mitochondria do not fragment and fail to repair plasma membrane damage.

Comment: Cell damage can kill. Membranes must stay intact. this mechanism had to be present when multicellular organisms appeared. Design required.

Biological complexity:mitochondria energy control

by David Turell @, Wednesday, June 24, 2020, 19:42 (1374 days ago) @ David Turell

Mitochondria are energy production machines for cells. The levels of production are controlled to increase when necessary:

https://phys.org/news/2020-06-scientists-mechanism-mitochondrial-energy-production.html

"The study shows that mitochondria adjust the efficiency of the electron transport chain (ETC) to meet the body's needs by regulating the associations between its component macromolecular structures. The researchers found that the protein SCAF1, discovered by the same team in 2016, plays a key role in this metabolic regulation by optimizing mitochondrial energy efficiency in response to high energy demand.

"Mitochondria, which house the mitochondrial ETC, generate most of the cell's energy supply and adjust their function to meet the body's metabolic needs. "The electron transport chain generates energy from nutrient molecules, such as glucose and fatty acids, and also has an important role in the synthesis of molecules needed to maintain cellular and bodily health," explained Dr. José Antonio Enríquez.

***

"The ETC is composed of four large multiprotein complexes: CI, CII, CIII, and CIV. These complexes can alter their structural organization to carry out different functions and adapt to local conditions.

"""

"Using this technology, "We show that, in the absence of SCAF1, the ETC complexes adopt a suboptimal configuration that reduces the efficiency of energy production," said Pablo Hernansanz-Agustín.

"The study also shows that the lack of SCAF1 reduces the capacity of mice for intense physical activity. "The physical output of these mice is 30% below that of unmodified mice," explained Sara Cogliati.

***

"The research team conclude that SCAF1-mediated physical interaction between CIII and CIV is essential for optimal mitochondrial energy production. Marta Loureiro-López explained that "SCAF1 is a regulatory factor that allows mitochondria to adapt to the available nutrient sources of sugars, fats, or proteins. This capacity for metabolic adaptation also explains the ability of mitochondria to adapt to stress situations, for example during intense physical exercise.'"

Comment: A precisely designed mechanism to see that the energy levels for cells care always appropriate to the needs. Not by chance.

Biological complexity: plants intelligent 'responses'

by David Turell @, Saturday, December 01, 2018, 01:58 (1945 days ago) @ David Turell

Plants make some amazing responses without a brain:

https://mindmatters.ai/2018/11/can-plants-be-as-smart-as-animals/

"Unlike even insects, whose brains “are far too complex to be fully understood in the near future” (Scientific American, 2013), plants do not have a brain. How then could they communicate or learn?

"One science writer, while ridiculing mystical claims about plant intelligence, admits,
There’s no doubt that plants do some amazing things. When being eaten by caterpillars, cotton plants release signals that attract insect-eating parasitic wasps to attack the caterpillars. Bean plants in close proximity to each other seem to communicate if one is under attack. Bean plants connected by symbiotic fungus will raise their chemical defenses if a compatriot is besieged by aphids. Mimosa plants even seem to have a basic memory. While the sensitive plants usually curl up when touched or dropped, scientist Monica Gagliano got them to ditch their regular response by repeatedly exposing them to a harmless six-inch fall to a cushioned surface.

"Because plants are chemical factories, among other things, they can mimic the senses an animal has by using electrical or chemical signals. In a study published in Nature Communications, researchers report that plants can “evaluate the competitive ability of their neighbors and optimally match their responses to them.” Some plants, for example, use flashes of fluorescent light to warn leaves against insects.

"From a 2014 report on a study of plants releasing chemicals against aphids that were picked up as signals by other plants:

"Researchers are unearthing evidence that, far from being unresponsive and uncommunicative organisms, plants engage in regular conversation. In addition to warning neighbors of herbivore attacks, they alert each other to threatening pathogens and impending droughts, and even recognize kin, continually adapting to the information they receive from plants growing around them. Moreover, plants can “talk” in several different ways: via airborne chemicals, soluble compounds exchanged by roots and networks of threadlike fungi, and perhaps even ultrasonic sounds. Plants, it seems, have a social life that scientists are just beginning to understand.

"Actually, none of the plants’ extensive “social life” requires reason, emotion, value systems, mind, consciousness, or a sense of self. It requires only that the plant, like an animal, seek to continue its highly organized existence. Plants’ ability to process information for that purpose gives pause for thought.

"The sheer complexity of the communications systems plants demonstrate astonishes us to the point that scientists have refused to believe the evidence. In 1983, plant scientists Jack Schultz and Ian Baldwin reported that maple saplings that were exposed to maples damaged by herbivores increased their own defenses. They attributed the increase to the chemical signals released by the injured trees, signals to which the saplings responded.

"But, as Cossins recounts, many researchers would not accept that plants could behave so as to benefit neighboring plants but not themselves. Such behavior contradicted evolution theory; it would not be “evolutionarily stable.” However, by 2000, the behavior was demonstrated in a number of species, with the signals being picked up by both members of the sending plant’s own species and by other species as well.

"Plants show the extent to which communication is possible without any of the qualities we associate with individual intelligence, provided the entity seeks to thrive and grow. Time will tell if an artificial entity that is not and never has been alive can be enabled to “seek” the same things."

Comment: dhw and I will commence to go back and forth whether this is automatic responses to stimuli or the plants can think. My view, if plants can't move to avoid problems, they are programmed to respond appropriately for self-protection, and to help other plants. This is not altruism in the Darwinian sense.

Biological complexity: plants intelligent 'responses'

by dhw, Saturday, December 01, 2018, 14:34 (1945 days ago) @ David Turell

QUOTE: "Plants show the extent to which communication is possible without any of the qualities we associate with individual intelligence, provided the entity seeks to thrive and grow."

DAVID: dhw and I will commence to go back and forth whether this is automatic responses to stimuli or the plants can think. My view, if plants can't move to avoid problems, they are programmed to respond appropriately for self-protection, and to help other plants. This is not altruism in the Darwinian sense.

Thank you for this amazing article. Clearly the authors, like you, recognize all the signs of a directing intelligence but refuse to believe them. But we needn’t go over it all again. As you said under “Bacterial immunity”: “That directive process can also be automatic or shown to be an independent control. At some point as layers are plied off the answer will appear.

Biological complexity: plants intelligent 'responses'

by David Turell @, Saturday, December 01, 2018, 19:26 (1945 days ago) @ dhw

QUOTE: "Plants show the extent to which communication is possible without any of the qualities we associate with individual intelligence, provided the entity seeks to thrive and grow."

DAVID: dhw and I will commence to go back and forth whether this is automatic responses to stimuli or the plants can think. My view, if plants can't move to avoid problems, they are programmed to respond appropriately for self-protection, and to help other plants. This is not altruism in the Darwinian sense.

dhw: Thank you for this amazing article. Clearly the authors, like you, recognize all the signs of a directing intelligence but refuse to believe them. But we needn’t go over it all again. As you said under “Bacterial immunity”: “That directive process can also be automatic or shown to be an independent control. At some point as layers are plied off the answer will appear.

Yes, at some point.

Biological complexity: plants can smell

by David Turell @, Wednesday, January 23, 2019, 21:18 (1892 days ago) @ David Turell

Odor molecules can affect their genes:

https://www.sciencedaily.com/releases/2019/01/190123105827.htm

"Plants detect a class of odor molecules known as volatile organic compounds, which are essential for many plant survival strategies, including attracting birds and bees, deterring pests, and reacting to disease in nearby plants. These compounds also give essential oils their distinctive scents.

"Touhara's team exposed tobacco cells and 4-week-old tobacco plants to different volatile organic compounds. They discovered that odor molecules change gene expression by binding to other molecules called transcriptional co-repressors that can turn genes on or off.

"In plants, the odor molecules must move into the cell and accumulate before they affect plant behavior. In animals, odor molecules are recognized by receptors on the outside of cells in the nose and immediately trigger a signaling pathway to recognize the odor and change behavior.

***

"'Humans have about 400 odor receptors. Elephants have about 2,000, the largest number in animals. But based on how many transcription factor genes are in plants, plants may be able to detect many more odors than animals," said Touhara."

Comment: Not surprising since plant already use volatile organic compounds in other ways.

Biological complexity: homeostasis

by David Turell @, Tuesday, October 16, 2018, 19:04 (1991 days ago) @ David Turell

Another study tries to define the concept and find life obviously keeps in critical balance:

https://www.sciencedaily.com/releases/2018/10/181005111502.htm

"Biologists know a lot about how life works, but they are still figuring out the big questions of why life exists, why it takes various shapes and sizes, and how life is able to amazingly adapt to fill every nook and cranny on Earth. An interdisciplinary team of researchers has discovered that the answers to these questions may lie in the ability of life to find a middle ground, balancing between robustness and adaptability.

"To perform their study, they examined data from the Cell Collective database. This rich resource represents biological processes across life -- encapsulating a wide range of biological processes from humans to animals, plants, bacteria and viruses. The number of components in these networks ranged from five nodes to 321 nodes, encompassing 6500 different biological interactions.

"And these nodes include many of life's key building blocks -- genes and proteins that act as master switches controlling cell division, growth and death, and communication.

***

"'In a stable system, organisms will always come back to their original state," explains Daniels. "In an unstable system, the effect of a small change will grow and cause the whole system to behave differently."

"Through rigorous testing of the 67 networks, the team found that all of the networks shared a special property: They existed in between two extremes, neither too stable nor unstable.
As such, the team found that sensitivity, which is a measure of stability, was near a special point that biologists call "criticality," suggesting that the networks may be evolutionarily adapted to an optimal tradeoff between stability and instability.

"Previous studies have shown that a handful of biological systems, from neurons to ant colonies, lie in this middle ground of criticality and this new research expands the list of living systems in this state.

***

"'We still don't really understand what life is," says Walker, "and determining what quantitative properties, such as criticality, best distinguish life from non-life is an important step toward building that understanding at a fundamental level so that we may recognize life on other worlds or in our experiments on Earth, even if it looks very different than us."

"The findings also advance the field of quantitative biology by showing that, from the basic building blocks of life, scientists can identify a critical sensitivity that is common across a large swath of biology. And it promises to advance synthetic biology by allowing scientists to use life's building blocks to more accurately construct biochemical networks that are similar to living systems.

"'Each biological system has distinctive features, from its components and its size to its function and its interactions with the surrounding environment," explains co-author Hyunju Kim of the School of Earth and Space Exploration and the Beyond Center. "In this research, for the first time, we are able to make connections between the theoretical hypothesis on biological systems' universal tendency to retain the balance at the medium degree of stability and 67 biological models with various characteristics built on actual experiment data.'"

Comment: As far as I am concerned they are simply describing the obvious to any biologist, the fact that life must constantly exist in homeostasis.

Biological complexity: homeostasis and cell function

by David Turell @, Tuesday, October 16, 2018, 19:14 (1991 days ago) @ David Turell
edited by David Turell, Tuesday, October 16, 2018, 19:22

Cells are busy factories under tight controls:

https://www.sciencedaily.com/releases/2018/10/181015084553.htm

"Proteins in a cell are like cars in a city. The cell has different means to fix broken proteins, sometimes choosing less obvious paths.

"The steps cells take in response to challenges are more complex than previously thought, finds new research published in the journal eLIFE.

***

"Surprisingly, cells often take an approach that seems quite inefficient," explains Christine Vogel, an associate professor at New York University's Department of Biology and the study's lead author.

***

Each cell in the human body produces as many as 1.5 million protein molecules every minute -- and folding the proteins into their right shape is a vital and enormous task. If too many proteins misfold and accumulate, cellular health is in immediate danger and may eventually cause the cell to die. (my bold)

"For that reason, the "cellular stress response" is central to many human diseases. Misfolded proteins occur in rapidly dividing cancer cells that produce many more protein molecules than normal -- or in virus infected cells where the virus hijacks the host's protein manufacturing machinery.

"Therefore, cells develop multiple mechanisms to fight the accumulation of misfolded proteins, to stop the synthesis of proteins, and refold existing ones properly.

***

What the scientists discovered was contrary to their expectations."The normal process to make proteins from genes consists of two major steps, called transcription and translation," explains Vogel. "If you have misfolded proteins accumulating in the cell, you would think that the first and easiest response should be to shut down these two steps in order to avoid producing even more proteins. And indeed, we observe many genes for which translation stops in response to misfolded molecules in the cell."

"However, the researchers also found a surprising number of very different responses. For example, many genes did not participate in the global translation shutdown, but rather increased the second synthesis step, producing even more protein molecules from these genes.

"Others did decrease their translation according to the standard model, but, conversely, increased the first step -- transcription -- rendering a seemingly uneconomical process.
Why the easiest route is often not taken is still subject to speculation, the researchers note.

"'The cells are much smarter than just turning everything off under stress, and we have some ideas as to why," Vogel says. "For some genes, the cells want to be particularly fast in ramping up synthesis when misfolded proteins occur -- to support the refolding machinery, for example. To save time, the cell then always conducts the first step for these genes in a somewhat wasteful manner, so that only the second step is left to do when the proteins are needed. For others, the cell activates the genes' protein production halfway through 'just in case' they are needed -- and therefore prepares for all eventualities.'"

Comment: We are looking at cells through human eyes and only partially, at this point, understand fully why cells are acting in ways like they are. Remember the human retina: it looks like it is designed wrong, but research shows that strange design gives us special sight properties we might otherwise not have. At some point in research we will understand cells actions as well designed and reasonable. Note my bold which shows just how busy cells are. There must be tight feedback controls. Not by chance.

Biological complexity: how cells handle glucose

by David Turell @, Wednesday, October 17, 2018, 18:02 (1990 days ago) @ David Turell

Glucose is the primary food of life. This study shows how a series of actions by the cell controls glucose :

https://phys.org/news/2018-10-cellular-clean-up-crews-linked-body.html

" How our bodies handle glucose—the simple sugar that provides energy from the food we eat—appears to be intertwined with how cells keep themselves functioning normally, according to new University of Chicago research.

"The study, published with Scripps Research Institute scientists on Oct. 15 in Nature, found a link between the process that handles glucose in cells and the one that regulates detoxification. This suggests a new understanding of a fundamental function in our bodies, and one that may provide new insights into disorders from cancer to diabetes.

"Raymond Moellering, assistant professor in the Department of Chemistry at UChicago, was trying to tease out the role of a particular molecule involved in the pathway that triggers a cell's detoxification process—a sort of cleaning crew to remove toxins and buildups when something goes awry in the cell.

***

"It appeared that the key protein to trigger this pathway, KEAP1, was being activated by a new small molecule discovered in the lab—but it didn't appear to be using any of the normal mechanisms known to scientists.

"By tracking down the pathways being affected by this molecule, Moellering's team found that it involved anotherpathway besides detoxification: the pathway that the body uses to process glucose. "Nobody knew those were directly connected," Moellering said.

***

"Using a combination of techniques, they found that KEAP1 is actually triggered to action by a buildup of glucose in the cell. "It looks very clearly like KEAP1 is listening to glucose metabolism, and turning on detox mechanisms as a result," Moellering said.

"The strange part was how this happens. Researchers showed that when KEAP1 is exposed to a molecule that is produced during the breakdown of glucose, individual KEAP1 proteins join up in pairs, which then triggers a waterfall of other signals in the cell to begin detoxification mechanisms.

***

"Additionally, the work shows that the cell protects itself from damage by triggering detoxification via glucose metabolism, but pushing this signal too far—as may happen in diseases like diabetes—could lead to damage that exceeds the capacity of the clean-up crew.

***

"On another level, this discovery appears to establish a new category of how proteins are controlled in the body. In their quest to understand what happens every day in human cells, scientists know two major ways for proteins to go about their business. One way is for enzymes to place chemical marks on proteins, turning them off and on. The other way is for free-floating molecules in the cell to reversibly interact with proteins to control their functions. This study appears to establish a third way, which is a hybrid of the two—where these free-floating molecules directly form chemical marks on the proteins they interact with, causing specific and longer-lived effects. "Finding this kind of regulation with KEAP1 suggests it is a widespread way to control protein function," Moellering said."

Comment: Once again cellular research shows that cells function by a series of automatic reactions between special proteins, no thought processes involved. Feedback loops are always involved to control reaction limits and levels.

Biological complexity: single-celled decision making

by David Turell @, Wednesday, October 17, 2018, 18:35 (1990 days ago) @ David Turell

Diatoms divide to reproduce but under circumstances of poor food supply they turn to sexual reproduction. They can make decisions:

https://www.sciencedaily.com/releases/2018/10/181016154241.htm


"Unicellular diatoms are able to adapt their behavior to different external stimuli based on an evaluation of their own needs. In experiments, Seminavis robusta diatoms directed their orientation either towards nutrient sources or mating partners, depending on the degree of starvation and the need to mate.

"Unicellular diatoms are able to adapt their behavior to different external stimuli based on an evaluation of their own needs. This was discovered by scientists. The algae depend on nutrients in order to reproduce. However, they also need sexual mates which they find when they follow pheromone traces. In experiments, Seminavis robusta diatoms directed their orientation either towards nutrient sources or mating partners, depending on the degree of starvation and the need to mate. The tiny organisms demonstrated in fact a primitive form of behavioral biology.

"Diatoms are unicellular microalgae. They dominate marine phytoplankton, which is ubiquitous in our oceans. On shores and beaches, these algae can be observed as biofilms on rocks and other surfaces. Diatoms are not only the food source for many marine animals, but also responsible for an extremely important ecosystem service: They contribute significantly to global photosynthesis and thus to the production of oxygen on our planet. Moreover, they are discussed as possible produces of biofuels.

"The diatom Seminavis robusta is an ideal model organism for behavioral studies in the lab: The cells respond to different environmental conditions and their sexuality can be controlled. The research group ...wanted to know whether the tiny organisms are able to make decisions about what they needed more urgently: food or sexual mates.

"In order to find out, the scientists cultivated cells under different conditions. In particular, the cells were confronted with different amounts of nutrients and sex pheromones. Since diatoms primarily reproduce asexually by cell division, sexual reproduction may become necessary for their survival if the cells become smaller and smaller after continuous division. After all, the cells die if they become too small and fall below a minimum size. Diatoms also search actively for nutrients they need for the formation of their cell walls.
They can trace silicate minerals in their environment and move actively towards this food source. A recent study showed that they are attracted by the odor of the minerals.

"'It is striking that even unicellular organisms that obviously lack a nervous system can process different stimuli and even evaluate their individual needs. Our study showed that diatoms can adapt their behavior flexibly to environmental changes. They also responded differently depending on their need to sexually mate.

***

"The scientist would now like to find out how the single-cell organisms perceive, process and evaluate chemical signals. "Our goal is to identify the corresponding receptors and signal processing pathways, but this will be a very complex endeavor given the fact that we know so little about these important micoralagae," says Georg Pohnert." ( my bold)

Comment: Note my bold. These scientists are looking to receptors and pathways, which in my opinion will be automatic, to explain the decision making.

Biological complexity: homeostasis

by Balance_Maintained @, U.S.A., Friday, October 19, 2018, 04:25 (1988 days ago) @ David Turell

An interdisciplinary team of researchers has discovered that the answers to these questions may lie in the ability of life to find a middle ground, balancing between robustness and adaptability.

"And these nodes include many of life's key building blocks -- genes and proteins that act as master switches controlling cell division, growth and death, and communication.

***

"'In a stable system, organisms will always come back to their original state," explains Daniels. "In an unstable system, the effect of a small change will grow and cause the whole system to behave differently."

"Through rigorous testing of the 67 networks, the team found that all of the networks shared a special property: They existed in between two extremes, neither too stable nor unstable.
As such, the team found that sensitivity, which is a measure of stability, was near a special point that biologists call "criticality," suggesting that the networks may be evolutionarily adapted to an optimal tradeoff between stability and instability.

I think this touches on one of those fundamental truths that is present among most world religions and philosophies. It is this idea of conflict between order and chaos. If there is too much order, things become stagnant, and then actually regress. If there is too much chaos, the organism can not cope and dies. So, the introduction of chaos in the form of'time and unforeseen circumstances' becomes critical to growth by presenting us with challenges to overcome by which we can grow. And here we see that all life is fine tuned to thrive at this edge, most likely oscillating like a wave between periods of chaos where we take on new information and have our foundations shaken, and order where life reaches new equilibrium.

However, I have been thinking about this a lot, and I think homeostasis is wrong. I think it is the wrong way to look at the problem, because it is by definition static, and I see no real evidence to support that if we look across the long reaches of time, integrating all that we know from a multitudes of sciences from biology to geology. There is definitely some form of forward progress, an epoch moving forward with some underlying current of intentionality. I do not find the concept of macro-evolution to be solid enough, either in terms of evidence or explanatory power, to couple biological life's unique interaction with its host planet to transform the planet from a molten, gaseous, barren planetoid into a rich, varied, habitable, thriving ecosystem. It is as if every single living thing that ever existed, whether it realized it or not, whether it intended to or not, contributed to the development of the world as a whole. Humanity differs in that we possess the ability to look into the future and delay our gratification in order to reach ever higher. Call it a sacrifice.

I've been listening to a series of lectures by Jordan Peterson on a Psychological Significance of the Bible, which I highly recommend. I find it gratifying to see the physical and structural evidence of reality noted in these experiments matches with psychological and spiritual truths espoused in the texts. If something is true, or perhaps sound if the word true disturbs you, historically, scientifically, psychologically, spiritually, and philosophically, isn't that about as close as you can get to divine revelation?

I mean, without putting too fine a point on it, this contrast between chaos and order, the constant required cycle of death and rebirth, sacrifice, stripping off the old personality in order to confront the chaos, then confronting it like a battle with a dragon followed by the return home to where you start the cycle over again by rectifying your previous model to incorporate and account for your new experiences. You can't escape the chaos. It's fundamental. Perhaps more importantly though is the question "If I could avoid the chaos, should I?"

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: homeostasis

by David Turell @, Friday, October 19, 2018, 18:54 (1988 days ago) @ Balance_Maintained

David: An interdisciplinary team of researchers has discovered that the answers to these questions may lie in the ability of life to find a middle ground, balancing between robustness and adaptability.

"And these nodes include many of life's key building blocks -- genes and proteins that act as master switches controlling cell division, growth and death, and communication.

***

"'In a stable system, organisms will always come back to their original state," explains Daniels. "In an unstable system, the effect of a small change will grow and cause the whole system to behave differently."

"Through rigorous testing of the 67 networks, the team found that all of the networks shared a special property: They existed in between two extremes, neither too stable nor unstable.
As such, the team found that sensitivity, which is a measure of stability, was near a special point that biologists call "criticality," suggesting that the networks may be evolutionarily adapted to an optimal tradeoff between stability and instability.


Tony: I think this touches on one of those fundamental truths that is present among most world religions and philosophies. It is this idea of conflict between order and chaos. If there is too much order, things become stagnant, and then actually regress. If there is too much chaos, the organism can not cope and dies. So, the introduction of chaos in the form of'time and unforeseen circumstances' becomes critical to growth by presenting us with challenges to overcome by which we can grow. And here we see that all life is fine tuned to thrive at this edge, most likely oscillating like a wave between periods of chaos where we take on new information and have our foundations shaken, and order where life reaches new equilibrium.

Tony: However, I have been thinking about this a lot, and I think homeostasis is wrong. I think it is the wrong way to look at the problem, because it is by definition static, and I see no real evidence to support that if we look across the long reaches of time, integrating all that we know from a multitudes of sciences from biology to geology. There is definitely some form of forward progress, an epoch moving forward with some underlying current of intentionality. I do not find the concept of macro-evolution to be solid enough, either in terms of evidence or explanatory power, to couple biological life's unique interaction with its host planet to transform the planet from a molten, gaseous, barren planetoid into a rich, varied, habitable, thriving ecosystem. It is as if every single living thing that ever existed, whether it realized it or not, whether it intended to or not, contributed to the development of the world as a whole. Humanity differs in that we possess the ability to look into the future and delay our gratification in order to reach ever higher. Call it a sacrifice.

Homeostasis in biologic science simply means sustaining the current status of the organism. You are carrying the idea beyond its original meaning and I agree that the arrival of living organisms on the Earth transformed the planet while creating a balance of nature which is critical for living organisms to continue. And life's diversity must be present to maintain the balance.


Tony: I've been listening to a series of lectures by Jordan Peterson on a Psychological Significance of the Bible, which I highly recommend. I find it gratifying to see the physical and structural evidence of reality noted in these experiments matches with psychological and spiritual truths espoused in the texts. If something is true, or perhaps sound if the word true disturbs you, historically, scientifically, psychologically, spiritually, and philosophically, isn't that about as close as you can get to divine revelation?

Is there an on-line reference?


Tony: I mean, without putting too fine a point on it, this contrast between chaos and order, the constant required cycle of death and rebirth, sacrifice, stripping off the old personality in order to confront the chaos, then confronting it like a battle with a dragon followed by the return home to where you start the cycle over again by rectifying your previous model to incorporate and account for your new experiences. You can't escape the chaos. It's fundamental. Perhaps more importantly though is the question "If I could avoid the chaos, should I?"

Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, wich I think demonstrates God's work.

Biological complexity: homeostasis

by Balance_Maintained @, U.S.A., Saturday, October 20, 2018, 00:26 (1987 days ago) @ David Turell


Tony: I've been listening to a series of lectures by Jordan Peterson on a Psychological Significance of the Bible, which I highly recommend. I find it gratifying to see the physical and structural evidence of reality noted in these experiments matches with psychological and spiritual truths espoused in the texts. If something is true, or perhaps sound if the word true disturbs you, historically, scientifically, psychologically, spiritually, and philosophically, isn't that about as close as you can get to divine revelation?


Is there an on-line reference?


Here is a link to the podcasts. They can also be found on youtube. There are numerous online references for the bible. wol.jw.org is a great one. Whatever their bias, their research is impeccable.


Tony: I mean, without putting too fine a point on it, this contrast between chaos and order, the constant required cycle of death and rebirth, sacrifice, stripping off the old personality in order to confront the chaos, then confronting it like a battle with a dragon followed by the return home to where you start the cycle over again by rectifying your previous model to incorporate and account for your new experiences. You can't escape the chaos. It's fundamental. Perhaps more importantly though is the question "If I could avoid the chaos, should I?"


David: Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, wich I think demonstrates God's work.

I think that much of 'chaos' is simply order that we don't understand yet. But I still can't help thinking that some chaos is introduced and is necessary for life.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: homeostasis

by David Turell @, Saturday, October 20, 2018, 16:06 (1987 days ago) @ Balance_Maintained


Tony: I've been listening to a series of lectures by Jordan Peterson on a Psychological Significance of the Bible, which I highly recommend. I find it gratifying to see the physical and structural evidence of reality noted in these experiments matches with psychological and spiritual truths espoused in the texts. If something is true, or perhaps sound if the word true disturbs you, historically, scientifically, psychologically, spiritually, and philosophically, isn't that about as close as you can get to divine revelation?


Is there an on-line reference?

Tony: Here is a link to the podcasts. They can also be found on youtube. There are numerous online references for the bible. wol.jw.org is a great one. Whatever their bias, their research is impeccable.

Thanks for the links.


Tony: I mean, without putting too fine a point on it, this contrast between chaos and order, the constant required cycle of death and rebirth, sacrifice, stripping off the old personality in order to confront the chaos, then confronting it like a battle with a dragon followed by the return home to where you start the cycle over again by rectifying your previous model to incorporate and account for your new experiences. You can't escape the chaos. It's fundamental. Perhaps more importantly though is the question "If I could avoid the chaos, should I?"


David: Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, which I think demonstrates God's work.


Tony: I think that much of 'chaos' is simply order that we don't understand yet. But I still can't help thinking that some chaos is introduced and is necessary for life.

Chaos is part of reality.

Biological complexity: homeostasis

by dhw, Tuesday, October 23, 2018, 12:19 (1984 days ago) @ Balance_Maintained

DAVID’s comment (under “animals eat fruit”): Fascinating interdependence in the balance of nature, which is beautifully illustrated in this article. Note 'red in tooth and claw' is not involved. Lots of balance in nature is not competitive killing.

dhw: It’s about time you caught up with Lynn Margulis, who pointed out 50 years ago that cooperation was just as important as competition.

DAVID: I been touting balance of nature all along, and you've down played it!

It is interdependence or cooperation between organisms that is highlighted, as opposed to competition. As I keep pointing out, your “balance of nature” changes with every success and every failure. I really don’t know why you are so desperate to tout it.

TONY: I think homeostasis is wrong. I think it is the wrong way to look at the problem, because it is by definition static, and I see no real evidence to support that if we look across the long reaches of time, integrating all that we know from a multitudes of sciences from biology to geology.

I agree. There may be long periods of stasis, but then the balance shifts and new forms take over. You talk later of intentionality and of chaos versus order. On the micro level, every organism is balanced or ordered until it becomes unbalanced and disordered (e.g. through disease and death). On the macro level, every ecosystem and solar system is balanced and ordered until for whatever reason it becomes unbalanced and disordered. The theist sees the order and says: “Look at the design”, and the atheist sees the mixture of order and disorder and says: “That’s how Nature works.”

TONY: There is definitely some form of forward progress, an epoch moving forward with some underlying current of intentionality. I do not find the concept of macro-evolution to be solid enough, either in terms of evidence or explanatory power, to couple biological life's unique interaction with its host planet to transform the planet from a molten, gaseous, barren planetoid into a rich, varied, habitable, thriving ecosystem. It is as if every single living thing that ever existed, whether it realized it or not, whether it intended to or not, contributed to the development of the world as a whole. Humanity differs in that we possess the ability to look into the future and delay our gratification in order to reach ever higher. Call it a sacrifice.

I agree that we can talk of forward progress in terms of barren gases to ecosystems, from single cells to multicellularity, from invertebrates to vertebrates, from apes to humans. That’s what some of us would call evolution, both micro and macro. You see intentionality behind everything because you believe in a designing God. An atheist sees a natural progression without intentionality. Humanity differs in far more ways than our ability to delay gratification, but I don’t know why you suddenly switch from the whole world to humans.

David: Homeostasis in biologic science simply means sustaining the current status of the organism. You are carrying the idea beyond its original meaning and I agree that the arrival of living organisms on the Earth transformed the planet while creating a balance of nature which is critical for living organisms to continue. And life's diversity must be present to maintain the balance.

What “balance” does life maintain? As above, the diversity, linked to constantly changing conditions, is what keeps CHANGING the balance!

DAVID: Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, wich I think demonstrates God's work.

TONY: I think that much of 'chaos' is simply order that we don't understand yet. But I still can't help thinking that some chaos is introduced and is necessary for life.

I also see a drive to complexity and improvement, though simplicity survives without improvement in the form of bacteria. And I agree that some “chaos” (e.g. environmental change) is necessary for evolution, since the alternative would be stasis. If there is a God, one might regard the chaos as integral to the interest of the great spectacle (how boring it would be if everything was predictable). If there is no God, order and chaos are the natural outcome of first cause energy and matter constantly forming and re-forming themselves.

Biological complexity: homeostasis

by David Turell @, Tuesday, October 23, 2018, 15:04 (1984 days ago) @ dhw

DAVID’s comment (under “animals eat fruit”): Fascinating interdependence in the balance of nature, which is beautifully illustrated in this article. Note 'red in tooth and claw' is not involved. Lots of balance in nature is not competitive killing.

dhw: It’s about time you caught up with Lynn Margulis, who pointed out 50 years ago that cooperation was just as important as competition.

DAVID: I been touting balance of nature all along, and you've down played it!

dhw: It is interdependence or cooperation between organisms that is highlighted, as opposed to competition. As I keep pointing out, your “balance of nature” changes with every success and every failure. I really don’t know why you are so desperate to tout it.

Not desperate, but insistent to reverse each time you downplay as again here. Each econiche is carefully balanced naturally as long as as top predator is not displaced. It isa form of natural homeostasis.


TONY: I think homeostasis is wrong. I think it is the wrong way to look at the problem, because it is by definition static, and I see no real evidence to support that if we look across the long reaches of time, integrating all that we know from a multitudes of sciences from biology to geology.

dhw: I agree. There may be long periods of stasis, but then the balance shifts and new forms take over. You talk later of intentionality and of chaos versus order. On the micro level, every organism is balanced or ordered until it becomes unbalanced and disordered (e.g. through disease and death). On the macro level, every ecosystem and solar system is balanced and ordered until for whatever reason it becomes unbalanced and disordered. The theist sees the order and says: “Look at the design”, and the atheist sees the mixture of order and disorder and says: “That’s how Nature works.”

TONY: There is definitely some form of forward progress, an epoch moving forward with some underlying current of intentionality. I do not find the concept of macro-evolution to be solid enough, either in terms of evidence or explanatory power, to couple biological life's unique interaction with its host planet to transform the planet from a molten, gaseous, barren planetoid into a rich, varied, habitable, thriving ecosystem. It is as if every single living thing that ever existed, whether it realized it or not, whether it intended to or not, contributed to the development of the world as a whole. Humanity differs in that we possess the ability to look into the future and delay our gratification in order to reach ever higher. Call it a sacrifice.

dhw: I agree that we can talk of forward progress in terms of barren gases to ecosystems, from single cells to multicellularity, from invertebrates to vertebrates, from apes to humans. That’s what some of us would call evolution, both micro and macro. You see intentionality behind everything because you believe in a designing God. An atheist sees a natural progression without intentionality. Humanity differs in far more ways than our ability to delay gratification, but I don’t know why you suddenly switch from the whole world to humans.

David: Homeostasis in biologic science simply means sustaining the current status of the organism. You are carrying the idea beyond its original meaning and I agree that the arrival of living organisms on the Earth transformed the planet while creating a balance of nature which is critical for living organisms to continue. And life's diversity must be present to maintain the balance.

dhw: What “balance” does life maintain? As above, the diversity, linked to constantly changing conditions, is what keeps CHANGING the balance!

Maintaining any living organism requires a balance of a large variety of living mechanisms in th at organism.


DAVID: Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, wich I think demonstrates God's work.

TONY: I think that much of 'chaos' is simply order that we don't understand yet. But I still can't help thinking that some chaos is introduced and is necessary for life.

dhw: I also see a drive to complexity and improvement, though simplicity survives without improvement in the form of bacteria. And I agree that some “chaos” (e.g. environmental change) is necessary for evolution, since the alternative would be stasis. If there is a God, one might regard the chaos as integral to the interest of the great spectacle (how boring it would be if everything was predictable). If there is no God, order and chaos are the natural outcome of first cause energy and matter constantly forming and re-forming themselves.

Back to humanizing God as being bored.

Biological complexity: homeostasis

by dhw, Wednesday, October 24, 2018, 11:18 (1983 days ago) @ David Turell

DAVID’s comment (under “animals eat fruit”): Fascinating interdependence in the balance of nature, which is beautifully illustrated in this article. Note 'red in tooth and claw' is not involved. Lots of balance in nature is not competitive killing.

dhw: It’s about time you caught up with Lynn Margulis, who pointed out 50 years ago that cooperation was just as important as competition.

DAVID: I been touting balance of nature all along, and you've down played it!

dhw: It is interdependence or cooperation between organisms that is highlighted, as opposed to competition. As I keep pointing out, your “balance of nature” changes with every success and every failure. I really don’t know why you are so desperate to tout it.

DAVID: Not desperate, but insistent to reverse each time you downplay as again here. Each econiche is carefully balanced naturally as long as as top predator is not displaced. It is a form of natural homeostasis.

Yes, each econiche is balanced so long as it is balanced, and when it is not balanced it is replaced by another econiche. And the new econiche is balanced until it is not balanced...And you moan about the tautology of “natural selection”!

DAVID: …And life’s diversity must be present to maintain the balance.

dhw: What “balance” does life maintain? As above, the diversity, linked to constantly changing conditions, is what keeps CHANGING the balance!

DAVID: Maintaining any living organism requires a balance of a large variety of living mechanisms in that organism.

Obviously. And when the balance is disturbed, the organism falls ill and/or dies. What is your point? You have not answered my question “what balance”? There is no such thing as THE balance which life maintains. Balance changes as conditions change, and diversity results from change – it does not “maintain THE balance”.

DAVID: Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, wich I think demonstrates God's work.

TONY: I think that much of 'chaos' is simply order that we don't understand yet. But I still can't help thinking that some chaos is introduced and is necessary for life.

dhw: I also see a drive to complexity and improvement, though simplicity survives without improvement in the form of bacteria. And I agree that some “chaos” (e.g. environmental change) is necessary for evolution, since the alternative would be stasis. If there is a God, one might regard the chaos as integral to the interest of the great spectacle (how boring it would be if everything was predictable). If there is no God, order and chaos are the natural outcome of first cause energy and matter constantly forming and re-forming themselves.

DAVID: Back to humanizing God as being bored.

Back to your purposeful God whose possible purpose we mustn’t discuss, although he is like us but is not like us.

Biological complexity: homeostasis

by David Turell @, Wednesday, October 24, 2018, 18:04 (1983 days ago) @ dhw

DAVID: Not desperate, but insistent to reverse each time you downplay as again here. Each econiche is carefully balanced naturally as long as as top predator is not displaced. It is a form of natural homeostasis.

dhw: Yes, each econiche is balanced so long as it is balanced, and when it is not balanced it is replaced by another econiche. And the new econiche is balanced until it is not balanced...And you moan about the tautology of “natural selection”!

Not a tautology, but a continuum of balance as you have stated.


DAVID: …And life’s diversity must be present to maintain the balance.

dhw: What “balance” does life maintain? As above, the diversity, linked to constantly changing conditions, is what keeps CHANGING the balance!

DAVID: Maintaining any living organism requires a balance of a large variety of living mechanisms in that organism.

dhw: Obviously. And when the balance is disturbed, the organism falls ill and/or dies. What is your point? You have not answered my question “what balance”? There is no such thing as THE balance which life maintains. Balance changes as conditions change, and diversity results from change – it does not “maintain THE balance”.

Obvious as you state above: as long as every living system is in balance the organism stays alive. It requires constant work.


DAVID: Gleick's book,Chaos, 1987, points out how much order is really hidden in chaos. I have no disagreement with your points. What I see built-in into the history of the Earth is a drive to complexity and improvement of conditions, wich I think demonstrates God's work.

TONY: I think that much of 'chaos' is simply order that we don't understand yet. But I still can't help thinking that some chaos is introduced and is necessary for life.

dhw: I also see a drive to complexity and improvement, though simplicity survives without improvement in the form of bacteria. And I agree that some “chaos” (e.g. environmental change) is necessary for evolution, since the alternative would be stasis. If there is a God, one might regard the chaos as integral to the interest of the great spectacle (how boring it would be if everything was predictable). If there is no God, order and chaos are the natural outcome of first cause energy and matter constantly forming and re-forming themselves.

DAVID: Back to humanizing God as being bored.

dhw: Back to your purposeful God whose possible purpose we mustn’t discuss, although he is like us but is not like us.

The problem is He is not as human as you would like to propose.

Biological complexity: homeostasis

by dhw, Thursday, October 25, 2018, 11:13 (1982 days ago) @ David Turell

DAVID: Not desperate, but insistent to reverse each time you downplay as again here. Each econiche is carefully balanced naturally as long as as top predator is not displaced. It is a form of natural homeostasis.

dhw: Yes, each econiche is balanced so long as it is balanced, and when it is not balanced it is replaced by another econiche. And the new econiche is balanced until it is not balanced...And you moan about the tautology of “natural selection”!

DAVID: Not a tautology, but a continuum of balance as you have stated.

It is NOT a continuum. It constantly changes!

DAVID: Maintaining any living organism requires a balance of a large variety of living mechanisms in that organism.

dhw: Obviously. And when the balance is disturbed, the organism falls ill and/or dies. What is your point? You have not answered my question “what balance”? There is no such thing as THE balance which life maintains. Balance changes as conditions change, and diversity results from change – it does not “maintain THE balance”.

DAVID: Obvious as you state above: as long as every living system is in balance the organism stays alive. It requires constant work.

Yes, you might as well say that every organism is alive until it’s dead. And you still haven't answered my question "what balance"?

DAVID: Back to humanizing God as being bored.

dhw: Back to your purposeful God whose possible purpose we mustn’t discuss, although he is like us but is not like us.

DAVID: The problem is He is not as human as you would like to propose.

And may I ask how you know this?

Biological complexity: homeostasis

by David Turell @, Thursday, October 25, 2018, 15:23 (1982 days ago) @ dhw

DAVID: Not desperate, but insistent to reverse each time you downplay as again here. Each econiche is carefully balanced naturally as long as as top predator is not displaced. It is a form of natural homeostasis.

dhw: Yes, each econiche is balanced so long as it is balanced, and when it is not balanced it is replaced by another econiche. And the new econiche is balanced until it is not balanced...And you moan about the tautology of “natural selection”!

DAVID: Not a tautology, but a continuum of balance as you have stated.

dhw: It is NOT a continuum. It constantly changes!

The concept is the requirement for balance is the constant continuum, not the individual parts of each balanced system .


DAVID: Maintaining any living organism requires a balance of a large variety of living mechanisms in that organism.

dhw: Obviously. And when the balance is disturbed, the organism falls ill and/or dies. What is your point? You have not answered my question “what balance”? There is no such thing as THE balance which life maintains. Balance changes as conditions change, and diversity results from change – it does not “maintain THE balance”.

DAVID: Obvious as you state above: as long as every living system is in balance the organism stays alive. It requires constant work.

dhw: Yes, you might as well say that every organism is alive until it’s dead. And you still haven't answered my question "what balance"?

A recent study I did not present roughly described the maintenance of life as on a critical edge of stability and chaos. I didn't post it because it was a poor attempt to describe life, which is in constant production of balancing proteins requiring a constant input of energy.


DAVID: Back to humanizing God as being bored.

dhw: Back to your purposeful God whose possible purpose we mustn’t discuss, although he is like us but is not like us.

DAVID: The problem is He is not as human as you would like to propose.

dhw: And may I ask how you know this?

I could ask you the same question: how do you know God has a human side?

Biological complexity: homeostasis

by Balance_Maintained @, U.S.A., Thursday, October 25, 2018, 00:47 (1982 days ago) @ dhw

By Odin's hoary beard....sometimes the conversations here are enough to drive me to distraction.

It's pretty darn simple, all three of us seem to agree that blind chance doesn't really stand a chance. Yay! Which means that, unless otherwise necessary, we don't really have to keep kicking that dead horse.

That leaves purposeful design, from SOME source or another. DHW favors panpsychism, where each organism has some form of undetected(undetectable) degree of extreme intelligence, foresight, and community that allows it to dictate its own design. Or, at least, that is how it comes across. As an agnostic, getting him to commit to something is damn difficult which, by nature, makes conversations frustrating. No biggie.

David and I both agree with a theistic approach, but we differ in our speculations about the unknowable. Fair enough. We CAN'T know. Yay! We can stop kicking that dead horse too. We can still talk about it, but the constant commentary about what we can't know does not seem very productive. After all, it should be understood at that point that, if no evidence can be had, whatever we are discussing is a matter of belief or, hopefully, faith based on reason.

DHW and David both seem to flavor some form of evolution, though, I can't really see how except in the most vague sense of the term: everything changes over time, oh, and somehow common descent works even though every bit of evidence suggest strongly that it doesn't actually work.

Some topics are continuously trivialized in terms of importance, which I find both peculiar and frustrating. David links a great many articles about complexity, and yet, that complexity is delved into very little except to kick the aforementioned dead horses.

So lets take one box and label it "Things we think we understand", another labeled "Things we don't understand", and a third called "Things we can't understand". The things we do understand, let's just leave them be for a bit, unless the things we don't understand cause conflict with our supposed understanding of the things we think we understand. We can also ignore that which we can't understand, except for the occasional review just to see if new information has shed any new light.

That means we can focus on that which it is possible to understand, but which we do not understand yet. Then try to find a road map to get from ignorance to understanding. Given that we all seem to agree that 'random chance' is right out, we can examine each individual organism under a lens of 'individual purpose', or 'environmental role' if the word purpose makes your eyes twitch. And just in case you aren't sure there is one, just ask the basic question of "What would the host environment be like if <insert organism> did not exist and reproduce, or consume, produce, and/or convert materials?"

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Biological complexity: homeostasis

by David Turell @, Thursday, October 25, 2018, 04:57 (1982 days ago) @ Balance_Maintained

Tony: By Odin's hoary beard....sometimes the conversations here are enough to drive me to distraction.

It's pretty darn simple, all three of us seem to agree that blind chance doesn't really stand a chance. Yay! Which means that, unless otherwise necessary, we don't really have to keep kicking that dead horse.

That leaves purposeful design, from SOME source or another. DHW favors panpsychism, where each organism has some form of undetected(undetectable) degree of extreme intelligence, foresight, and community that allows it to dictate its own design. Or, at least, that is how it comes across. As an agnostic, getting him to commit to something is damn difficult which, by nature, makes conversations frustrating. No biggie.

David and I both agree with a theistic approach, but we differ in our speculations about the unknowable. Fair enough. We CAN'T know. Yay! We can stop kicking that dead horse too. We can still talk about it, but the constant commentary about what we can't know does not seem very productive. After all, it should be understood at that point that, if no evidence can be had, whatever we are discussing is a matter of belief or, hopefully, faith based on reason.

DHW and David both seem to flavor some form of evolution, though, I can't really see how except in the most vague sense of the term: everything changes over time, oh, and somehow common descent works even though every bit of evidence suggest strongly that it doesn't actually work.

By common descent I mean that I can see a single-celled beginning of live, a nd at the end of the process humans like us are here. The issue is what happened in between. I am with the concept that God guided a process in which less complex evolved into more complex. Did God make each creation separately or simple guide an evolutionary process is not clear to me.


Tony: Some topics are continuously trivialized in terms of importance, which I find both peculiar and frustrating. David links a great many articles about complexity, and yet, that complexity is delved into very little except to kick the aforementioned dead horses.

I'm not sure of your point about complexity. Complexity points to the necessity for a designing mind. I can give you a more in depth exposition of the biochemistry of the reactions, but that would involve lots of time and not make the points any better than what I do present. We can agree that the complexity demands a designing mind, but that won't budge dhw whose thinking is stuck in mid-air..


Tony: So lets take one box and label it "Things we think we understand", another labeled "Things we don't understand", and a third called "Things we can't understand". The things we do understand, let's just leave them be for a bit, unless the things we don't understand cause conflict with our supposed understanding of the things we think we understand. We can also ignore that which we can't understand, except for the occasional review just to see if new information has shed any new light.

That means we can focus on that which it is possible to understand, but which we do not understand yet. Then try to find a road map to get from ignorance to understanding. Given that we all seem to agree that 'random chance' is right out, we can examine each individual organism under a lens of 'individual purpose', or 'environmental role' if the word purpose makes your eyes twitch. And just in case you aren't sure there is one, just ask the basic question of "What would the host environment be like if <insert organism> did not exist and reproduce, or consume, produce, and/or convert materials?"

I'll agree that life changed the Earth with its presence.

Biological complexity: homeostasis

by dhw, Thursday, October 25, 2018, 11:33 (1982 days ago) @ Balance_Maintained

TONY: It's pretty darn simple, all three of us seem to agree that blind chance doesn't really stand a chance. Yay! Which means that, unless otherwise necessary, we don't really have to keep kicking that dead horse.
That leaves purposeful design, from SOME source or another. DHW favors panpsychism, where each organism has some form of undetected(undetectable) degree of extreme intelligence, foresight, and community that allows it to dictate its own design. Or, at least, that is how it comes across. As an agnostic, getting him to commit to something is damn difficult which, by nature, makes conversations frustrating. No biggie.

It is indeed damn difficult to get me to commit to believe explanations that defy reason. And of course it makes conversations frustrating, because the whole damn universe and the whole damn history of life is one frustratingly insoluble mystery! But I appreciate that it is doubly frustrating for people like you and David who think they know the answers. No, I do not favour panpsychism. I offer it as a bottom-up alternative to your concept of a single top-down mind, but it throws up as many unanswerable questions as your God theory.

As for the intelligence of organisms, however, it is hardly undetected or undetectable, since David’s thread of “natural wonders” lists vast numbers of examples. You and David appear to regard these organisms as automatons, merely obeying the instructions your God has planted in them. I see no reason to assume that their intelligent actions are not the product of their own intelligence, and I see no reason why a theist should not believe it possible that his God invented the mechanisms that provided them with the ability to do their own designing. Presumably you believe that is precisely what he did for humans. That does not, of course, mean their intelligences are the same as ours. But in my view it is sheer arrogance for humans to assume that other organisms are not intelligent. However…(yes, there is always a “however”)…like everyone else, I am mystified by speciation, and I am not convinced that the intelligence of the cell communities of which all organisms are composed is powerful enough to invent the innovations that have driven evolution from the single cell to the vast complexities of us humans. That is why for me it remains a hypothesis. If I were an atheist, though, I would consider it far more convincing than random chance.

TONY: So lets take one box and label it "Things we think we understand", another labeled "Things we don't understand", and a third called "Things we can't understand". [...]
That means we can focus on that which it is possible to understand, but which we do not understand yet. Then try to find a road map to get from ignorance to understanding. Given that we all seem to agree that 'random chance' is right out, we can examine each individual organism under a lens of 'individual purpose', or 'environmental role' if the word purpose makes your eyes twitch. And just in case you aren't sure there is one, just ask the basic question of "What would the host environment be like if <insert organism> did not exist and reproduce, or consume, produce, and/or convert materials?"

Of course this would be an endless topic of discussion, since we would have to examine the role of every organism throughout the history of life, but I doubt if we would be any the wiser at the end of it! I expect the environment with trilobites and dinosaurs was different from the environment without trilobites and dinosaurs. Our own environment without bacteria would undergo the most dramatic changes, but I doubt if it would be radically changed if the duckbilled platypus went extinct. The word "purpose" doesn't make my eyes twitch. We had a long discussion about it, if you remember, and with my theist's hat on, I proposed that your God devised a mechanism to create the vast spectacle of life as we know it, thereby perhaps relieving the tedium of everlasting isolation. You didn't like that, though.

DAVID: We can agree that the complexity demands a designing mind, but that won't budge dhw whose thinking is stuck in mid-air..

Your thinking is stuck on the concept of a single "designing mind”. I agree that the complexity demands intelligence.

Biological complexity: homeostasis

by David Turell @, Thursday, October 25, 2018, 18:51 (1982 days ago) @ dhw

TONY: It's pretty darn simple, all three of us seem to agree that blind chance doesn't really stand a chance. Yay! Which means that, unless otherwise necessary, we don't really have to keep kicking that dead horse.
That leaves purposeful design, from SOME source or another. DHW favors panpsychism, where each organism has some form of undetected(undetectable) degree of extreme intelligence, foresight, and community that allows it to dictate its own design. Or, at least, that is how it comes across. As an agnostic, getting him to commit to something is damn difficult which, by nature, makes conversations frustrating. No biggie.

dhw: It is indeed damn difficult to get me to commit to believe explanations that defy reason. And of course it makes conversations frustrating, because the whole damn universe and the whole damn history of life is one frustratingly insoluble mystery! But I appreciate that it is doubly frustrating for people like you and David who think they know the answers. No, I do not favour panpsychism. I offer it as a bottom-up alternative to your concept of a single top-down mind, but it throws up as many unanswerable questions as your God theory.

As for the intelligence of organisms, however, it is hardly undetected or undetectable, since David’s thread of “natural wonders” lists vast numbers of examples. You and David appear to regard these organisms as automatons, merely obeying the instructions your God has planted in them. I see no reason to assume that their intelligent actions are not the product of their own intelligence, and I see no reason why a theist should not believe it possible that his God invented the mechanisms that provided them with the ability to do their own designing. Presumably you believe that is precisely what he did for humans. That does not, of course, mean their intelligences are the same as ours. But in my view it is sheer arrogance for humans to assume that other organisms are not intelligent. However…(yes, there is always a “however”)…like everyone else, I am mystified by speciation, and I am not convinced that the intelligence of the cell communities of which all organisms are composed is powerful enough to invent the innovations that have driven evolution from the single cell to the vast complexities of us humans. That is why for me it remains a hypothesis. If I were an atheist, though, I would consider it far more convincing than random chance.

TONY: So lets take one box and label it "Things we think we understand", another labeled "Things we don't understand", and a third called "Things we can't understand". [...]
That means we can focus on that which it is possible to understand, but which we do not understand yet. Then try to find a road map to get from ignorance to understanding. Given that we all seem to agree that 'random chance' is right out, we can examine each individual organism under a lens of 'individual purpose', or 'environmental role' if the word purpose makes your eyes twitch. And just in case you aren't sure there is one, just ask the basic question of "What would the host environment be like if <insert organism> did not exist and reproduce, or consume, produce, and/or convert materials?"

dhw: Of course this would be an endless topic of discussion, since we would have to examine the role of every organism throughout the history of life, but I doubt if we would be any the wiser at the end of it! I expect the environment with trilobites and dinosaurs was different from the environment without trilobites and dinosaurs. Our own environment without bacteria would undergo the most dramatic changes, but I doubt if it would be radically changed if the duckbilled platypus went extinct. The word "purpose" doesn't make my eyes twitch. We had a long discussion about it, if you remember, and with my theist's hat on, I proposed that your God devised a mechanism to create the vast spectacle of life as we know it, thereby perhaps relieving the tedium of everlasting isolation. You didn't like that, though.

DAVID: We can agree that the complexity demands a designing mind, but that won't budge dhw whose thinking is stuck in mid-air..

dhw: Your thinking is stuck on the concept of a single "designing mind”. I agree that the complexity demands intelligence.

Intelligence implies the ability to plan and design, being able to view future needs theoretically. Cells can't do this, but they can be designed to act intelligently, which is exactly what we see, nothing more.

Biological complexity: homeostasis

by dhw, Friday, October 26, 2018, 11:25 (1981 days ago) @ David Turell

DAVID: We can agree that the complexity demands a designing mind, but that won't budge dhw whose thinking is stuck in mid-air..

dhw: Your thinking is stuck on the concept of a single "designing mind”. I agree that the complexity demands intelligence.

DAVID: Intelligence implies the ability to plan and design, being able to view future needs theoretically. Cells can't do this, but they can be designed to act intelligently, which is exactly what we see, nothing more.

Intelligence does NOT imply the ability to view future needs theoretically! You keep giving us examples of organisms solving problems (think of the corvids). Human intelligence – vastly superior to that of our fellow animals – can theorize about the future, but other life forms RESPOND intelligently to changing conditions. Hence adaptation, problem-solving, decision-making. You are “stuck” not only on the concept of a single designing mind, but on an astonishingly narrow view of what constitutes intelligence. But to anticipate your stock reply, I agree that we do not know whether cellular intelligence can extend so far as to innovate, which is why my hypothesis is a hypothesis.

xxxxxxxxxxxxxxx

dhw: As I keep pointing out, your "balance of nature" changes with every success and every failure. I really don't know why you are so desperate to tout it.

DAVID: Not desperate, but insistent to reverse each time you downplay as again here. Each econiche is carefully balanced naturally as long as as top predator is not displaced. It is a form of natural homeostasis.

dhw: Yes, each econiche is balanced so long as it is balanced, and when it is not balanced it is replaced by another econiche. And the new econiche is balanced until it is not balanced...And you moan about the tautology of “natural selection”!

DAVID: Not a tautology, but a continuum of balance as you have stated.

dhw: It is NOT a continuum. It constantly changes!

DAVID: The concept is the requirement for balance is the constant continuum, not the individual parts of each balanced system.

Of course life REQUIRES balance to survive, and of course econiches REQUIRE balance to survive. It’s you who stated that there IS a continuum of balance, but now that you have changed that to there being a continuous REQUIREMENT for balance if organisms and econiches are to survive, we can drop the subject once and for all. No one is going to disagree with such an obvious statement.

DAVID: Back to humanizing God as being bored.

dhw: Back to your purposeful God whose possible purpose we mustn’t discuss, although he is like us but is not like us.

DAVID: The problem is He is not as human as you would like to propose.

dhw: And may I ask how you know this?

DAVID: I could ask you the same question: how do you know God has a human side?

I don’t even know if your God exists, but since you make great play of his purposefulness, I keep asking you what that purpose might be. You have offered several “human” purposes (a relationship with us, our recognition of his work, getting us to puzzle out how he did it, and even the pleasure of creation), and you have acknowledged many times that he may well be like us – i.e. have a human side. However, although he may well have a human side, when I offer a different HYPOTHESIS (not a statement of knowledge) from your own, you state that “He is not as human as you propose.” How do you know the degree of his humanity?

Biological complexity: homeostasis

by David Turell @, Friday, October 26, 2018, 15:11 (1981 days ago) @ dhw

dhw: Your thinking is stuck on the concept of a single "designing mind”. I agree that the complexity demands intelligence.

DAVID: Intelligence implies the ability to plan and design, being able to view future needs theoretically. Cells can't do this, but they can be designed to act intelligently, which is exactly what we see, nothing more.

dhw: Intelligence does NOT imply the ability to view future needs theoretically! You keep giving us examples of organisms solving problems (think of the corvids). Human intelligence – vastly superior to that of our fellow animals – can theorize about the future, but other life forms RESPOND intelligently to changing conditions. Hence adaptation, problem-solving, decision-making. You are “stuck” not only on the concept of a single designing mind, but on an astonishingly narrow view of what constitutes intelligence. But to anticipate your stock reply, I agree that we do not know whether cellular intelligence can extend so far as to innovate, which is why my hypothesis is a hypothesis.

You didn't note I was responding to a single concept of intelligence, specifically the ability to foresee future needs and thus design. The remainder of your comment is fine.


xxxxxxxxxxxxxxx

DAVID: Back to humanizing God as being bored.

dhw: Back to your purposeful God whose possible purpose we mustn’t discuss, although he is like us but is not like us.

DAVID: The problem is He is not as human as you would like to propose.

dhw: And may I ask how you know this?

DAVID: I could ask you the same question: how do you know God has a human side?

dhw: I don’t even know if your God exists, but since you make great play of his purposefulness, I keep asking you what that purpose might be. You have offered several “human” purposes (a relationship with us, our recognition of his work, getting us to puzzle out how he did it, and even the pleasure of creation), and you have acknowledged many times that he may well be like us – i.e. have a human side. However, although he may well have a human side, when I offer a different HYPOTHESIS (not a statement of knowledge) from your own, you state that “He is not as human as you propose.” How do you know the degree of his humanity?

Back and forth we go: none of us can know his degree of humanity, if any. And that includes guesses at purpose. Just look at what He has created and be thankful. Dayenu. Overanalysis and sought for proofs lead to the picket fence.

Biological complexity: homeostasis

by dhw, Saturday, October 27, 2018, 09:29 (1980 days ago) @ David Turell

DAVID: Intelligence implies the ability to plan and design, being able to view future needs theoretically. Cells can't do this, but they can be designed to act intelligently, which is exactly what we see, nothing more.

dhw: Intelligence does NOT imply the ability to view future needs theoretically! You keep giving us examples of organisms solving problems (think of the corvids). Human intelligence – vastly superior to that of our fellow animals – can theorize about the future, but other life forms RESPOND intelligently to changing conditions. Hence adaptation, problem-solving, decision-making. You are “stuck” not only on the concept of a single designing mind, but on an astonishingly narrow view of what constitutes intelligence. […]

DAVID: You didn't note I was responding to a single concept of intelligence, specifically the ability to foresee future needs and thus design. The remainder of your comment is fine.

That is precisely what I noted and objected to. You have a single concept of intelligence which automatically excludes any organism which cannot foresee the future. If the rest of my comment is fine, then please don’t tell us that “intelligence implies the ability to use future needs theoretically” and therefore cells can’t be intelligent.

DAVID: …how do you know God has a human side?

dhw: I don’t even know if your God exists, but since you make great play of his purposefulness, I keep asking you what that purpose might be. You have offered several “human” purposes (a relationship with us, our recognition of his work, getting us to puzzle out how he did it, and even the pleasure of creation), and you have acknowledged many times that he may well be like us – i.e. have a human side. However, although he may well have a human side, when I offer a different HYPOTHESIS (not a statement of knowledge) from your own, you state that “He is not as human as you propose.” How do you know the degree of his humanity?

DAVID: Back and forth we go: none of us can know his degree of humanity, if any. And that includes guesses at purpose. Just look at what He has created and be thankful. Dayenu. Overanalysis and sought for proofs lead to the picket fence.

Then please don’t make authoritative statements like: “He is not as human as you would like to propose”, and please stop talking about his purposefulness if you are unwilling to discuss what that purpose might be, and please stop telling us that his prime purpose was to create the brain of Homo sapiens. On the other hand, it is perfectly possible to love life and be thankful for it without (a) believing in God, and (b) while still looking for answers to all the great questions. What you call “overanalysis” is simply analysis which questions your assumptions and offers alternatives. There can be no proofs, but I respect your faith in God just as I respect the atheist’s faith in chance, and I know that you respect my picket fence position, even if you like to make fun of it!

Biological complexity: homeostasis

by David Turell @, Saturday, October 27, 2018, 19:25 (1980 days ago) @ dhw

dhw: Intelligence does NOT imply the ability to view future needs theoretically! You keep giving us examples of organisms solving problems (think of the corvids). Human intelligence – vastly superior to that of our fellow animals – can theorize about the future, but other life forms RESPOND intelligently to changing conditions. Hence adaptation, problem-solving, decision-making. You are “stuck” not only on the concept of a single designing mind, but on an astonishingly narrow view of what constitutes intelligence. […]

DAVID: You didn't note I was responding to a single concept of intelligence, specifically the ability to foresee future needs and thus design. The remainder of your comment is fine.

dhw: That is precisely what I noted and objected to. You have a single concept of intelligence which automatically excludes any organism which cannot foresee the future. If the rest of my comment is fine, then please don’t tell us that “intelligence implies the ability to use future needs theoretically” and therefore cells can’t be intelligent.

What a weird comment. Design for the future must require intelligence that can understand the requirements for a new design. You've turned my point around backwards. Cells do not contain that type of intelligence. All that has ever been shown is simple responses to simple stimuli.


DAVID: Back and forth we go: none of us can know his degree of humanity, if any. And that includes guesses at purpose. Just look at what He has created and be thankful. Dayenu. Overanalysis and sought for proofs lead to the picket fence.

dhw: Then please don’t make authoritative statements like: “He is not as human as you would like to propose”, and please stop talking about his purposefulness if you are unwilling to discuss what that purpose might be, and please stop telling us that his prime purpose was to create the brain of Homo sapiens. On the other hand, it is perfectly possible to love life and be thankful for it without (a) believing in God, and (b) while still looking for answers to all the great questions. What you call “overanalysis” is simply analysis which questions your assumptions and offers alternatives. There can be no proofs, but I respect your faith in God just as I respect the atheist’s faith in chance, and I know that you respect my picket fence position, even if you like to make fun of it!

Yes I do! My statements as to his purposes or personality are responses to your questions. They are only prompted guesses that I wouldn't otherwise think about.

Biological complexity: homeostasis

by dhw, Sunday, October 28, 2018, 11:14 (1979 days ago) @ David Turell

DAVID: You didn't note I was responding to a single concept of intelligence, specifically the ability to foresee future needs and thus design. The remainder of your comment is fine.

dhw: That is precisely what I noted and objected to. You have a single concept of intelligence which automatically excludes any organism which cannot foresee the future. If the rest of my comment is fine, then please don’t tell us that “intelligence implies the ability to use future needs theoretically” and therefore cells can’t be intelligent.

DAVID: What a weird comment. Design for the future must require intelligence that can understand the requirements for a new design. You've turned my point around backwards. Cells do not contain that type of intelligence. All that has ever been shown is simple responses to simple stimuli.

The reversals are yours. Firstly you wrote that “intelligence implies the ability to plan and design, being able to view future needs theoretically.” No, it doesn’t. That is one particular form of intelligence. I then pointed out that adaptation, problem-solving and decision-making were examples of the way in which “other life forms RESPOND intelligently to changing conditions”, and you agreed. These are forms of intelligence which have been demonstrated by cells, and so the inability to theorize about the future is irrelevant to the question of whether, as Shapiro & Co claim, cells are intelligent. Thirdly, you ignored my final point: “But to anticipate your stock reply, I agree that we do not know whether cellular intelligence can extend so far as to innovate, which is why my hypothesis is a hypothesis.” And lastly, as I keep repeating ad nauseam, I propose that evolution advances not through planning for a future which organisms know nothing about, but through their responses to the requirements and opportunities that arise out of the changing conditions in which they live at the time.

Biological complexity: homeostasis

by David Turell @, Sunday, October 28, 2018, 18:28 (1979 days ago) @ dhw

DAVID: You didn't note I was responding to a single concept of intelligence, specifically the ability to foresee future needs and thus design. The remainder of your comment is fine.

dhw: That is precisely what I noted and objected to. You have a single concept of intelligence which automatically excludes any organism which cannot foresee the future. If the rest of my comment is fine, then please don’t tell us that “intelligence implies the ability to use future needs theoretically” and therefore cells can’t be intelligent.

DAVID: What a weird comment. Design for the future must require intelligence that can understand the requirements for a new design. You've turned my point around backwards. Cells do not contain that type of intelligence. All that has ever been shown is simple responses to simple stimuli.

dhw: The reversals are yours. Firstly you wrote that “intelligence implies the ability to plan and design, being able to view future needs theoretically.” No, it doesn’t. That is one particular form of intelligence. I then pointed out that adaptation, problem-solving and decision-making were examples of the way in which “other life forms RESPOND intelligently to changing conditions”, and you agreed. These are forms of intelligence which have been demonstrated by cells, and so the inability to theorize about the future is irrelevant to the question of whether, as Shapiro & Co claim, cells are intelligent. Thirdly, you ignored my final point: “But to anticipate your stock reply, I agree that we do not know whether cellular intelligence can extend so far as to innovate, which is why my hypothesis is a hypothesis.” And lastly, as I keep repeating ad nauseam, I propose that evolution advances not through planning for a future which organisms know nothing about, but through their responses to the requirements and opportunities that arise out of the changing conditions in which they live at the time.

I glad we agree that one form of intelligence can foresee the future and design for it. What I have bolded is the worn out Darwinian tiny-step-by-tiny-step approach you have given which ignores every gap we see in evolution. Gaps imply only design works. Darwin wisely recognized the problem and got around the point by assuming the gaps would be filled. They haven't and have become worse than he imagined.

Biological complexity: homeostasis

by dhw, Monday, October 29, 2018, 12:10 (1978 days ago) @ David Turell

Dhw: I propose that evolution advances not through planning for a future which organisms know nothing about, but through their responses to the requirements and opportunities that arise out of the changing conditions in which they live at the time.

DAVID: I glad we agree that one form of intelligence can foresee the future and design for it. What I have bolded is the worn out Darwinian tiny-step-by-tiny-step approach you have given which ignores every gap we see in evolution. Gaps imply only design works. Darwin wisely recognized the problem and got around the point by assuming the gaps would be filled. They haven't and have become worse than he imagined.

Now that you have withdrawn your absurdly limited definition of intelligence, you revert to the dead horse flogging of Darwin’s gradualism, which I have already rejected a hundred times. You accept Darwin’s theory of common descent, but want to fill the gaps by means of a 3.8-billion-year-old computer programme or a divine dabble for every single innovation, lifestyle and natural wonder, with even the dabbles performed in anticipation of environmental changes, i.e. before they are needed. And all for the sake of the human brain. I suggest that the gaps may be filled by the intelligence of those organisms which can adapt to or exploit the changes as they arise. I acknowledge that like your own proposal, this is an unproven hypothesis.

Biological complexity: homeostasis

by David Turell @, Monday, October 29, 2018, 17:08 (1978 days ago) @ dhw

Dhw: I propose that evolution advances not through planning for a future which organisms know nothing about, but through their responses to the requirements and opportunities that arise out of the changing conditions in which they live at the time.

DAVID: I glad we agree that one form of intelligence can foresee the future and design for it. What I have bolded is the worn out Darwinian tiny-step-by-tiny-step approach you have given which ignores every gap we see in evolution. Gaps imply only design works. Darwin wisely recognized the problem and got around the point by assuming the gaps would be filled. They haven't and have become worse than he imagined.

dhw: Now that you have withdrawn your absurdly limited definition of intelligence, you revert to the dead horse flogging of Darwin’s gradualism, which I have already rejected a hundred times.

I can't help that you totally misinterpreted my comment about one form of intelligence. I've withdrawn nothing.

Biological complexity: homeostasis

by dhw, Tuesday, October 30, 2018, 09:11 (1977 days ago) @ David Turell

dhw: Now that you have withdrawn your absurdly limited definition of intelligence, you revert to the dead horse flogging of Darwin’s gradualism, which I have already rejected a hundred times.

David: I can't help that you totally misinterpreted my comment about one form of intelligence. I've withdrawn nothing.

Here is your comment: “Intelligence implies the ability to plan and design, being able to view future needs theoretically. Cells can't do this [...]”

Intelligence does not imply the ability to plan and design or to be able to view future needs theoretically. If it did, as far as we know, only humans could be called intelligent. You tried to use this argument to prove that cells are not intelligent and only "act intelligently". Your statement should have been the other way round. The ability to plan implies intelligence. And I join Shapiro & Co in proposing that the ability to solve problems, to cooperate and communicate with other organisms, and to make decisions also implies intelligence. Let’s move on.

Biological complexity: homeostasis

by David Turell @, Tuesday, October 30, 2018, 16:36 (1977 days ago) @ dhw

dhw: Now that you have withdrawn your absurdly limited definition of intelligence, you revert to the dead horse flogging of Darwin’s gradualism, which I have already rejected a hundred times.

David: I can't help that you totally misinterpreted my comment about one form of intelligence. I've withdrawn nothing.

Here is your comment: “Intelligence implies the ability to plan and design, being able to view future needs theoretically. Cells can't do this [...]”

dhw: Intelligence does not imply the ability to plan and design or to be able to view future needs theoretically. If it did, as far as we know, only humans could be called intelligent. You tried to use this argument to prove that cells are not intelligent and only "act intelligently". Your statement should have been the other way round. The ability to plan implies intelligence. And I join Shapiro & Co in proposing that the ability to solve problems, to cooperate and communicate with other organisms, and to make decisions also implies intelligence. Let’s move on.

You are correct. Great editing of my poorly written English. Thank you. We'll move on.

Biological complexity: magical photosynthesis

by David Turell @, Wednesday, November 07, 2018, 19:03 (1969 days ago) @ David Turell

The appearance of the photosynthesis mechanism transformed the Earth by adding oxygen to the atmosphere so life could evolve to the complex forms of today:

https://phys.org/news/2018-11-high-resolution-atomic-movie-photosynthesis-date.html

"When Earth formed about 4.5 billion years ago, the planet's landscape was almost nothing like what it is today. ....But it wasn't until one of those specks of life mutated and developed the ability to harness light from the sun and turn it into energy, releasing oxygen molecules from water in the process, that Earth started to evolve into the planet it is today. This process, oxygenic photosynthesis, is considered one of nature's crown jewels and has remained relatively unchanged in the more than 2 billion years since it emerged.

***

"Photosystem II is the workhorse responsible for using sunlight to break water down into its atomic components, unlocking hydrogen and oxygen.

***

"Previously, the researchers were able to determine the room temperature structure of two of the states at a resolution of 2.25 angstroms; one angstrom is about the diameter of a hydrogen atom. This allowed them to see the position of the heavy metal atoms, but left some questions about the exact positions of the lighter atoms, like oxygen. In this paper, they were able to improve the resolution even further, to 2 angstroms, which enabled them to start seeing the position of lighter atoms more clearly, as well as draw a more detailed map of the chemical structure of the metal catalytic center in the complex where water is split.
This center, called the oxygen-evolving complex, is a cluster of four manganese atoms and one calcium atom bridged with oxygen atoms. It cycles through the four stable oxidation states, S0-S3, when exposed to sunlight.

***

"One of the most significant aspects of this paper, Yano said, is that they were able to image two moments in between S2 and S3. In upcoming experiments, the researchers hope to use the same technique to image more of these in-between states, including the mad dash for home—the transient state, or S4, where two atoms of oxygen bond together—providing information about the chemistry of the reaction that is vital to mimicking this process in artificial systems.

"'The entire cycle takes nearly two milliseconds to complete," Kern said. "Our dream is to capture 50 microsecond steps throughout the full cycle, each of them with the highest resolution possible, to create this atomic movie of the entire process."

"Although they still have a way to go, the researchers said that these results provide a path forward, both in unveiling the mysteries of how photosynthesis works, and in offering a blueprint for artificial sources of renewable energy."

Comment: this is a biological system so complex we still don't fully know how it works, and it requires the invention of very advanced study tools that still do not exist to complete the job. We might ask the obvious question. How dos life invent a process like this by chance? Not likely, is it? The picket fence should be shaking.

Biological complexity: magical photosynthesis bacteria

by David Turell @, Wednesday, November 07, 2018, 19:28 (1969 days ago) @ David Turell

Cyanobacteria, which are responsible for much of the photosynthesis from 2.5 billion years ago, are designed with tricks to overcome low life conditions:

https://phys.org/news/2018-11-bacteria-strategies-survive-stress.html

"A new study by scientists from the University of Chicago shows how cyanobacteria (bacteria that produce energy through photosynthesis like plants) change the way they grow and divide in response to different levels of light. With typical light conditions, the cells remain relatively short and divide symmetrically. But as light dims, the cells grow longer and divide unevenly, resulting in two daughter cells of different lengths. The researchers believe this may be a survival strategy that evolved to help these bacteria survive in less than ideal conditions.

***

"In the new study, a postdoctoral researcher in his lab, used time-lapse imaging to track cell division in Synechococcus elongatus, a rod-shaped cyanobacterium. The researchers saw that under dim light conditions, which cause stress for cells by limiting their energy source, the S. elongatuscells grow longer than usual. When the lights are turned back up, cells shorter than eight micrometers still divide symmetrically, but above this length the divisions become uneven, typically producing one short daughter (about three micrometers) and a longer one.

"In many bacteria, the position where a mother cell splits into two is controlled by something called the Min system, a group of proteins that moves around inside the cell. In a typical short cell, one of the proteins, MinC, pools in one end and then every few minutes moves to the opposite end. As they bounce back and forth, the MinC proteins spend more time at the ends and less at mid-cell, like squeezing a water balloon in the middle and wiggling it back and forth. Since MinC inhibits cell division, this oscillation creates a sort of weak point in the middle where the cell can divide.

***

"They found that the Min system exhibits different patterns depending on the cell length. The proteins kept up a characteristic, back-and-forth oscillatory pattern in short cells, but they formed a variety of dynamic patterns in longer cells, including multi-band oscillations, traveling waves, and other more complex patterns. In all of these patterns in long cells, a region without MinC was always seen about three micrometers from the end of the cell, allowing cells to divide off-center and make a short daughter of a specific size.

"'We think the patterns change because it's geometrically sensitive, so it can adapt to a changing cell size," Liao said. "The ability to form these different patterns allows both shorter cells to divide symmetrically and longer cells to produce short daughter cells."

"Rust and Liao said they aren't sure why bacteria divide into different lengths under stressful conditions or whether one length provides an advantage over another. It could be that smaller cells are able to maneuver better to find resources. Elongating themselves could give the cell more surface area to absorb light in dim conditions. There is even evidence that length is a defense mechanism for pathogens, because it's harder for an immune cell to engulf a really long bacterial cell."

Comment: These bacteria, which were so important in creating the Earth's oxygen, were given special ways to handle low light by changing size. A great design.

Biological complexity: bacteria have complex organelles

by David Turell @, Tuesday, December 25, 2018, 15:29 (1921 days ago) @ David Turell

Recent discoveries in bacteria reveal their so-called simple protoplasm is highly complex with organelles:

https://www.the-scientist.com/features/bacteria-harbor-geometric-organelles-65114

"The investigators eventually realized they weren’t purifying viruses, but tiny, iron-laden nanocompartments native to the bacteria. (They never did figure out why the holes appeared in the cultures.)

"The structures were relatively new to science, having been described for the first time just a year earlier in the bacterium Thermotoga maritima.1 At 25–66 nm across, they are typically too small to notice unless you’re looking for them, Hoiczyk explains. But in recent years, thanks to modern genomics and bioinformatics, scientists have found nanocompartments across a range of bacterial phyla.

***

"Decades earlier, scientists had first described larger structures called microcompartments—100–600 nm in diameter—that appeared in micrographs of cyanobacteria, though researchers are only building a detailed understanding of those compartments today. “It’s becoming accepted, a lot, in the last 10 or 20 years that the prokaryotic cytoplasm is highly organized,” says Cheryl Kerfeld, a structural biologist

***

"Preliminary studies suggest that nanocompartments assist with stress responses, while microcompartments often have roles in metabolism. And although the details remain murky, it’s becoming clear that these structures create a specialized microenvironment for a specific purpose, says Kerfeld: “I would define them as organelles.” A growing number of researchers are now working to understand what these organelles do. Kerfeld predicts that eventually, the population of people studying bacterial compartments “is going to be as big as any eukaryotic organelle community.”

***

"Yeates’s group took advantage of this fact to identify putative microcompartment groupings of shell and inner enzyme genes and extrapolate their potential functions. In 2013, the team delineated seven categories of microcompartments, including known carboxysomes and metabolosomes as well as novel types, such as one apparently involved in the metabolism of amino alcohols.5 Separately, Kerfeld, by now at Michigan State and Berkeley Lab, and her team used a similar approach to identify 23 different types of microcompartments spread across 23 bacterial phyla, as they reported the following year.

"Now, Kerfeld and Markus Sutter in her Berkeley lab are repeating the bioinformatic analysis and incorporating more genomes, including those from uncultivated species. They’ve already found more microcompartments, Kerfeld says. “The proportion of bacteria that seem to make these is rising.” A couple of species possess genes for six different kinds of microcompartments, potentially giving them access to a complex metabolism.
Why house certain reactions in tiny containers? Computer modeling indicates that microcompartments should maximize the turnover of metabolites by keeping reaction intermediates close and interfering chemicals at a distance.

***

"Why house certain reactions in tiny containers? Computer modeling indicates that microcompartments should maximize the turnover of metabolites by keeping reaction intermediates close and interfering chemicals at a distance.7 For instance, concentrating the carbon-fixing enzymes RuBisCO and carbonic anhydrase in a carboxysome makes the processing of carbon dioxide more efficient.8 And cordoning off toxic reactions, such as those that produce aldehyde intermediates—a hypothesized, though unproven, job of metabolosomes—would protect the rest of the cell’s interior.

"Not all bacteria can make nano- and microcompartments. In fact, most denizens of mammalian intestines seem to lack microcompartments, although many pathogens possess them. For example, Salmonella’s microcompartments metabolize the organic compounds propanediol and ethanolamine, which are found in processed foods and the human gut. Compartmentalizing the reactions is thought to allow the bacterium to digest nutrients that members of the human intestinal microbiome cannot, allowing the pathogen to outcompete them. Other pathogens, such as Listeria and Clostridium, also contain metabolosomes."

Comment: If the first cells of life were this complex only a designer could have created them. We know that cells in eukaryotes have compartments for different production functions. It is logical to find bacteria are the same and cellular function hasn't really changed since the beginning of life. Overall complexity is simply different functioning cells coming together to make complex organisms.

Biological complexity: giant B12 receptor

by David Turell @, Friday, January 04, 2019, 20:24 (1911 days ago) @ David Turell

Just outlined:

https://phys.org/news/2019-01-body-largest-cell-receptor.html

"A giant toadstool that swallows up vitamins and nutrients in the intestines and kidneys: This is how one receptor that absorbs B12 vitamins in the small intestine looks. For the first time, researchers from Aarhus University, Denmark, have an insight into an as-yet unknown biology which has persisted for hundreds of millions of years of evolution.

"'What we're looking at is evolution at a structural level. A receptor with a toadstool structure that stems from way back to the common ancestors of insects and humans," says Associate Professor Christian Brix Folsted Andersen

"Vitamin B12 is the vitamin that humans most often lack, even with a healthy diet, which in turn can lead to serious anaemic diseases and symptoms from the central nervous system. With his research group, Andersen has now described the body's largest cell receptor: An ancient, previously unknown construction that was created by the merger of two proteins, and which, for reasons scientists do not yet understand, is preserved as a colossal structure in molecular terms.

"In the 1960s, scientist Dorothy Hodgkin received the Nobel Prize for her scientific breakthrough in determining the structure of the B12 vitamin. Now, Andersen and colleagues report this receptor structure more than 1000 times larger, which enables B12 to be absorbed in the body.

"With the help of X-ray crystallography, we've succeeded in determining how the receptor is able to organise itself in a previously unknown way in human biology. With this new knowledge, we're finally able to explain why thousands of people around the world with specific genetic changes are unable to absorb the vitamin," explains Andersen over the phone from the University of Washington in the U.S.

"'But in my mind, the most interesting aspect is that with the help of advanced electron microscopy, which I'm learning about in detail here in Seattle, we have been able to see how the receptor as a whole looks, and thus also see how the receptor absorbs B12 vitamin in the intestines and various other substances in the kidneys. It's fantastic to have the opportunity to see this as the first person ever," he says.

"Andersen points out that in an evolutionary context, there is something very mysterious about the receptor as it does not resemble anything seen previously. "At the same time, by comparing genes, we can see that the receptor has the same structure as we find in insects and that it must have been evolved very early in evolution—many millions of years ago, and thus long before the origin of mammals," he says."

Comment: Take a look at this giant receptor molecule. That it may have appeared back during insect evolution. How did 'chance' evolution find this monster? No way. Considering the necessity for B12 it looks like good advanced planning to me.

Biological complexity: making insulin fold properly

by David Turell @, Saturday, January 26, 2019, 00:51 (1889 days ago) @ David Turell

It is not automatic an d requires shepherding by a specific protein in Beta cells:

https://www.sciencedaily.com/releases/2019/01/190125094248.htm

"Insulin is produced in the beta cells of the pancreas. The hormone is produced as a precursor called proinsulin. For proinsulin to mature into functional insulin, it needs to be folded and processed correctly to acquire the right structure with assistance from proteins that are termed chaperones. The researchers have now discovered and identified such a chaperone. A proinsulin chaperone termed glucose-regulated protein GRP94.

''Even though proinsulin has a relatively short sequence, it still needs help acquiring the right structure to become mature, functional insulin. However, several other studies have shown that proinsulin can be folded without help from proteins in artificial cell-free conditions. Yet, our study conducted in live cells shows that proinsulin is not folded correctly and does not acquire the right structure without help from GRP94,' says last author of the study, Associate Professor Michal Tomasz Marzec from the Department of Biomedical Sciences at the University of Copenhagen.

"In the study the researchers removed or inhibited the protein GRP94 in to see what happened with the proinsulin and the cells. They observed that the proinsulin was not folded correctly and the beta cells did not secrete sufficient amounts of insulin. The researchers were surprised though to learn that removal of GRP94 did not affect cell viability. Nothing happened to the cells after they had removed the protein.

''This is surprising, because one would anticipate that the beta cells would die from stress when huge amounts of misfolded proinsulin accumulate inside the cells. It is like removing the bearing beam without weakening the construction. This indicates that the GRP94 protein plays a very specialized function and that beta cells are well-prepared to mount effective responses to deal with consequences of misfolding of proinsulin. "

Comment: This process must be done in one specific way by one specific protein, and others are probably present and not yet found. Some protein molecules make folds automatically, but in this case guidance is required. Only design can create such a system.

Biological complexity: how plants transport glucose

by David Turell @, Saturday, January 26, 2019, 19:05 (1889 days ago) @ David Turell

A very complex protein structure has been discovered:

https://www.sciencedaily.com/releases/2019/01/190125094239.htm

"Sugar transport through Sugar Transport Proteins (STP) is unique to plants, and is important for the proper development of plant organs such as pollen. STPs are also used to concentrate sugars in specific tissues like fruit, and they play an important role in the plant defence against fungal attacks from e.g. rust and mildew.

"Sugar is generated in plant leaves by photosynthesis, and is transported as the disaccharide sucrose to other parts of the plant through the sieve tissue. In sink tissues such as roots, pollen and fruits, the plant can absorb the sugar either as sucrose or, after cleavage, as the monosaccharides glucose and fructose.

"Uptake of glucose and other monosaccharides is driven by STPs that move sugar through the otherwise impermeable cell membrane using an acid gradient. These proteins have some specific properties compared to similar proteins from animals or bacteria. They have an extremely high affinity for sugar; in fact, they bind 1000 times more strongly to sugars than similar proteins in humans. At the same time they maintain a very high level of activity over a broad pH spectrum compared to other acid-driven sugar transporters.

***

"With the new structure, the researchers show that the STPs overall form resemble other sugar transporters from e.g. humans. But the structure also holds surprises. Peter Aasted Paulsen highlights a new domain that has not been described before. "Over the binding pocket where sugar is located, the STPs have a novel small domain that resembles a lid that is held in place with an unusual bond, a so-called disulfide bridge. It was a completely unexpected observation that immediately sparked the imagination."

"To investigate the function of the domain, the researchers made a version of the protein in which this bond was removed. With this change, the protein loses its ability to transport sugar efficiently at certain pH values. If you compare these results with an analysis of the structure, it can be seen that the lid is held in place by means of the bond, thereby creating a favourable environment for acid binding to a specific acid binding pocket. This binding causes a portion of the protein to be pushed toward the sugar molecule, thereby creating the very high affinity for sugar."

Comment: It is obvious such an intricate mechanism is irreducibly complex and had to be designed in a complete form from the beginning, not by stepwise evolution

Biological complexity: a theory how cell division works

by David Turell @, Friday, February 01, 2019, 01:24 (1883 days ago) @ David Turell

The author is looking toward an electrical flow over the complex structure of the centrosome:

https://file.scirp.org/pdf/ABB_2015072015020110.pdf

"Abstract:
Recent development in the field of quantum biology highlights that the intracellular electromagnetic field (EMF) of microtubules plays an important role in many fundamental cellular processes such as mitosis. Here I propose an intriguing hypothesis that centrosome functions as molecular dynamo to generate electric flow over the microtubules, leading to the electric excitation of microtubule EMF that is required for spindle body microtubule self-assembly. With the help of motors proteins within the centrosome, centrosome transforms the energy from ATP into intracellular EMF in the living cell that shapes the functions of microtubules. There will be a general impact for the cell biology field to understand the mechanistic function of centrosome for the first time in correlation with its structural features. This hypothesis can be tested with technics such as superresolution live cell microscope. "

Comment: Without getting into the super-technical details look at the picture of this structure and note the obvious need for design. this is the structure that makes cells divide into two similar cells

Biological complexity: how macrophages repair nerves

by David Turell @, Thursday, February 07, 2019, 01:16 (1877 days ago) @ David Turell

They obviously follow exact patterns using precise proteins:

https://cosmosmagazine.com/biology/watching-the-macrophage-at-work

"Research led by the University of Plymouth in the UK has shed new light on the science behind peripheral nerve repair by highlighting the novel function of a cell called a macrophage.
Their paper, published in the journal Cell Reports, reveals how these cells, which are part of our immune system and found in most tissues, use a specific signalling pathway to control the processes of nerve repair following damage.

***

"When a nerve is injured, the two ends may separate and new tissue, known as a nerve bridge, forms between the two nerve stumps.

"This new tissue consists of several cell types, including migrating Schwann cells and macrophages. The interaction between Schwann cells and macrophages is vital if the new nerve projections are to reach the skin and muscle, allowing for regeneration and a full recovery of nerve function.

"The new study, conducted in mice, shows how macrophages form a collar around the outside of the nerve bridge and secrete high levels of a repulsive nerve guidance cue called Slit3. The researchers also discovered that Schwann cells inside the nerve bridge express the Slit3 interacting protein called Robo1.

"Through the interaction between Slit3 and Robo1, the macrophages keep migrating Schwann cells and the regrowing nerve projections inside the bridge area.

"This is a vital part of the repair process; without it, the nerve projections cannot correctly get to their targets and will never reconnect with skin and muscle, leaving patients with a permanent loss of nerve function."

Comment: Note how precise this mechanism is. The cells obviously don't stop and think about a plan of action. My usual question. How did chance evolution find this exact set of proteins?

Biological complexity: how molecules implant in membranes

by David Turell @, Thursday, February 14, 2019, 22:16 (1870 days ago) @ David Turell

Certain very functional proteins need a process to implant into cell membranes and intracellular membranes to provide necessary functions:

https://www.sciencedaily.com/releases/2019/02/190214100038.htm

"Nearly a third of all proteins in living beings are firmly embedded in a biomembrane -- either in a cell's outer membrane or in the boundaries of internal cellular compartments. There, these membrane proteins perform important tasks, serving, for instance, as molecular channels for transporting metabolites and nutrients through the membrane or as sensor proteins for sensing the cellular environment.

***

"In experiments with bacterial proteins, the researchers were able to clarify the role of two helper proteins -- an insertase and a translocase -- that enable the membrane proteins to embed themselves in the membrane. Insertase is a single protein, while translocase is a complex composed of multiple proteins. Both of them ensure that a pore opens up in the membrane. "In the case of insertase, we can think of this pore as a slide. The membrane protein is initially present as an unstructured peptide strand that slips down this slide into the membrane. In the membrane, this peptide strand then takes on its functional three-dimensional shape," explains ETH Professor Müller. "Once the membrane protein has successfully become three-dimensional and embedded itself in the membrane, the helper protein detaches and forms a slide at a different location in the membrane for the next protein," he continues.

"Up to now, research into how these helper proteins function was imprecise and used only short peptides or was conducted only outside of biomembranes. "We have now observed and described for the first time, step by step, how an entire protein embeds itself in a membrane and takes on a three-dimensional form," says Tetiana Serdiuk, a postdoc in ETH Professor Müller's group and the study's first author.

"The ETH researchers were also able to show the differences in how insertases and translocases work: insertases insert peptide strands into the membrane relatively quickly but clumsily. "This means they work well particularly with small proteins," says Müller. Translocases, on the other hand, insert peptide strands into the membrane section by section, making them better suited for more complex proteins."

Comment: This is a complex mechanism and only can appear through design. I would assume this present in the earliest bacteria.

Biological complexity: hormones from all parts run life

by David Turell @, Tuesday, February 19, 2019, 23:10 (1864 days ago) @ David Turell

Recent research reveals a huge variety of different parts of living organisms produce an enormous number if different hormones so every part communicates with all the other parts through the circulatory system:

https://aeon.co/essays/the-revolutionary-idea-revealing-the-bodys-hormonal-democracy?ut...

"Karsenty and others eventually confirmed that bones secrete hormones essential for an animal’s health. And with that finding, the skeleton joined a growing list of tissues shown to participate in a body-wide conversation between organs. The traditional concept of the endocrine system as a second-command system working in tandem with the nervous system – and largely directed by the brain – is being replaced with a more autonomous view of interorgan communication, one in which most, if not all, organs have a voice. Grasping the logic of a control system in which the body’s organs are both the targets of hormonal commands and the source of them is still only beginning, but the clinical implications are sure to be profound.

***

"The concept of target tissues was important. There were the endocrine organs – most of them glandular tissues, whose primary function was evidently to make and secrete things – and there were the organs on which hormones acted. Textbook depictions showed, and often still do, the endocrine system as a handful of glands plus the gonads: an archipelago of hormone-making islands dotted about the body.

"But the list of hormones never stopped growing. And neither did the list of tissues that made them. Certain hormones long known to regulate blood flow, gut absorption and blood-cell production turned out to be coming from the kidney. The liver was shown to make and dispatch hormones. And secretin became only one of a number of circulating signals emanating from the digestive system.

***

" Leptin’s ability to make mice eat less sparked massive interest in somehow harnessing its biology to create drugs that did likewise for humans – a goal that remains still, for a variety reasons, unfilled.

"But as the quest for an appetite-quenching drug gathered pace by the turn of the millennium, Karsenty was looking at other functions of leptin. The hormone, he learned, also regulated bone mass – an early confirmation that energy storage and its use were intimately linked to bone. At the same time, other researchers were making a case for skin as an endocrine organ, and gaining a fuller understanding of signalling molecules released by the heart.

***

" The breadth of tissues now known to release hormones demands that we rethink the very idea of the endocrine system itself. If it isn’t a restricted set of glandular tissues that direct the behaviour of the body’s various organs – a control system complementary to the nervous system – how should we conceptualise it instead? It appears to be something far more pervasive and democratic – a system through which all the body’s organs broadcast their status by discharging molecules into the blood and so, together, shape what the body is doing at any given time.

***

" When a new hormone is identified and shown to have a significant function, it buys itself a line on a diagram like the one Perrimon and Droujinine constructed for a 2016 review detailing their plans to characterise the ICN [interorgan communication network] in fruit flies. Starting with the recent finds in mammals, they arranged, roughly in a circle, skeletal muscle, pancreas, brain, bone, gut, testes, heart, kidney, fat tissue and liver. And then, they drew arrows to show newly identified hormonal links between tissue pairs. The result was a frantic mishmash of connections.

"The classical notion of individual negative-feedback loops – each keeping a single physiological variable in check – remains a vital concept in biology. But it’s now clear that there are many loops and that they are all interlocked.

"Perrimon and Droujinine have written that it might be as fundamental as going back to the advent of early multicellular life. As organisms became more complex, and different types of cells evolved to have specialised functions within a cellular collective, there was a need to coordinate those functions. As an example from later in evolution, when muscles began driving movement, they likely relied on fat cells for nutrients. While one can see that a nervous system signalling to both tissues could make chemical communication redundant, it’s now clear that the hormonal link – and the autonomous character of peripheral tissues – never went away. As specialised populations of cells evolved, the total organism benefitted from individual tissues broadcasting their status to modulate other organs. As Karsenty puts it, ‘no organ is an island in our body.’ (my bold)

***

"If the ICN, or the endocrine system, is an instructive set of commands, its internal chemical logic needs to be determined. Unlike the nervous system – where neurons make physical contact with the cells they influence – there is no anatomical specificity to the endocrine system."

Comment: Wow. There is no end to unearthing the real complexity of living beings. Only a designer can create this.

Biological complexity: how plants construct cells

by David Turell @, Wednesday, February 20, 2019, 22:51 (1864 days ago) @ David Turell

A molecular control of cell construction after cell division:

https://www.sciencedaily.com/releases/2019/02/190220103444.htm

"For their study, the plant researchers examined the roots of the thale cress plant, Arabidopsis thaliana. They cultivated normal plants and plants in which they artificially switched off certain enzymes that affect the composition of the membranes.

***

"For plants to develop, their cells have to divide. First, the genetic material located in the cell nucleus divides. Two whole new cell nuclei are formed from the duplicated genetic material. The other components of the cell, for example the chloroplasts and mitochondria, are distributed between the two future daughter cells. All this takes place in the parent cell.

"Only then the daughter cells will be separated by a new cell wall. The whole process can be compared to a construction site. First, a temporary scaffold made of protein fibres, the so-called phragmoplast, forms in the middle of the cell. Like railway tracks, these fibres guide the building materials needed for the cell wall. Small bubbles gradually transport new cell wall material along the rails. This is assembled together by a complex fusion machinery to form a larger structure: the cell plate. The cell plate continues to grow at its edges from the centre of the cell outwards until a cell wall disc completely separates the daughter cells from one another. "The fusion machinery has to correctly coordinate the protein fibres for everything to function properly, otherwise the freight cars will transport the cell wall material to the wrong spot or at the wrong time and cell plate formation will cease," explains Heilmann.

"For plants to develop, their cells have to divide. First, the genetic material located in the cell nucleus divides. Two whole new cell nuclei are formed from the duplicated genetic material. The other components of the cell, for example the chloroplasts and mitochondria, are distributed between the two future daughter cells. All this takes place in the parent cell.

"Only then the daughter cells will be separated by a new cell wall. The whole process can be compared to a construction site. First, a temporary scaffold made of protein fibres, the so-called phragmoplast, forms in the middle of the cell. Like railway tracks, these fibres guide the building materials needed for the cell wall. Small bubbles gradually transport new cell wall material along the rails. This is assembled together by a complex fusion machinery to form a larger structure: the cell plate. The cell plate continues to grow at its edges from the centre of the cell outwards until a cell wall disc completely separates the daughter cells from one another. "The fusion machinery has to correctly coordinate the protein fibres for everything to function properly, otherwise the freight cars will transport the cell wall material to the wrong spot or at the wrong time and cell plate formation will cease," explains Heilmann.

"The results of the research group from Halle help to better understand the dynamics of the plant's cytoskeleton of microtubules. The cytoskeleton not only determines the direction of cellular transport processes during cell division, but also directs general plant growth. "

Comment: Again a very complex system which requires very specific molecules to direct the work. Not by chance. This process is inherited from the very first bacteria of life.

Biological complexity: cell grow or die controls

by David Turell @, Saturday, February 23, 2019, 20:34 (1861 days ago) @ David Turell

Very exact automatic controls:

https://phys.org/news/2019-02-illinois-growth-factors-cells.html

Whether healthy or diseased, human cells exhibit behaviors and processes that are largely dictated by growth factor molecules, which bind to receptors on the cells. For example, growth factors tell the cells to divide, move, and when to die—a process known as apoptosis.

***

"'It is believed that cells respond to growth factors at extreme levels of sensitivity," said University of Illinois at Urbana-Champaign Bioengineering Associate Professor Andrew Smith. "For example, a single molecule will result in a major change in cell behavior."

***

"'We showed the first direct cause-and-effect relationships of growth factors in single cells," he said. "We expect the outcomes to lead to a new understanding of cell signaling, how cells respond to drugs, and why cell populations become resistant to drugs, particularly toward improved treatments for cancer."

"Smith's technology platform tags each growth factor with a single engineered (10 nanometer) infrared fluorescent quantum dot, which can then be viewed using a three-dimensional microscope. In their study, they counted how many epidermal growth factor (EGF) molecules bound to human triple-negative breast cancer cells that were pre-patterned on island-like surfaces.

"EGF molecules typically signal cell division and lead to tissue growth. Numerous cancers have mutations in their EGF receptors."

Comment: A other example of precise automatic control of cells.

Biological complexity:pest plant steals water and nurients

by David Turell @, Monday, February 25, 2019, 20:36 (1859 days ago) @ David Turell

Witchweed in Africa steals from crops with complex controls from mutations:

https://phys.org/news/2019-02-secret-witchweed-devastating-ability-nutrients.html


"Striga hermonthica is a parasitic weed mainly found in the African continent south of the Sahara desert. It leeches off the roots of major cereal crops such as sorghum, millet, sweetcorn and rice, absorbing water and nutrients from its hosts.

***

"When plants are subjected to drought stress, they synthesize a plant hormone called abscisic acid (ABA). This small molecule elicits stomata closure to suppress transpiration. Striga leaves contain a large amount of ABA, and exogenous ABA treatment did not reduce transpiration. The team concluded that the cause of Striga's high transpiration levels is a defectiveness in ABA sensitivity.

***

"ABA in plants rapidly increases in response to drought stress and binds a receptor known as PYL. The ABA-bound PYL receptor complex binds and inhibits group-A type-2 C protein phosphatases (PP2Cs), which are negative regulators for ABA signaling. Consequently, inhibition of PP2Cs enable guard cells to close stomata (Figure 3). The research group isolated relevant genes in Striga and analyzed their functions. They identified the ShPP2C1 gene, and its protein blocked the signaling of ABA constitutively, because ShPP2C1 is not controlled by PYL receptors (Figure 3). ShPP2C1 has distinct amino acid mutations not seen in other plants. When the team edited five amino acid sequences in model plant Arabidopsis to resemble ShPP2C1 (represented as AtABI15 mutation), the Arabidopsis' response to ABA decreased, and its high transpiration levels remained even under drought conditions

***

"Professor Sugimoto and Assistant Professor Okamoto comment: "Our results show that amino acid mutations changed the properties of PP2C genes in Striga, lowering its sensitivity to ABA and allowing it to maintain high transpiration rates even under drought conditions.
Terrestrial plants acquired ABA signaling in order to survive in an environment with changing water conditions. Striga probably lost these functions and acquired its own nutrient acquisition methods in the process of adapting to its parasitic lifestyle."

Comment: This study simply shows how complex adaptations can be as molecular reactions are modified to reduce defenses. Not by chance.

Biological complexity: organism have backup systems

by David Turell @, Tuesday, February 26, 2019, 19:50 (1858 days ago) @ David Turell

During evolution organisms developed backup systems to protect life's very complex machinery:

https://phys.org/news/2019-02-species-evolve-ways-life-machinery.html

"Now, a team of Stanford computer scientists and biologists has looked at evolution through a new lens, by analyzing how proteins – the biological machines produced by DNA – evolve to sustain the network of molecular interactions upon which all life depends.

"The scientists studied 1,840 species – from bacteria to primates – to understand how evolution built life forms that could survive in the face of natural adversities. What they discovered was profound yet intuitive: Every species has evolved backup plans that allow its protein machinery to find bypasses and workarounds when nature tries to gum up the works. No previous study has ever surveyed such a broad swath of species to find a survival strategy common to all life: Develop a versatile and robust molecular machinery.

"'Across our entire sample, we find that the resilience of a species is strongly correlated with having protein networks that are robust to failure and can interact in multiple ways to preserve life," said Stanford computer scientist Jure Leskovec, senior author of the paper.

"Evolutionary biologist Marcus Feldman, a co-author on the paper, said this is the most ambitious effort yet to understand what scientists call the interactome – the sum total of all the protein interactions for each species, just as genome describes the sum total of a species' DNA. "We're looking at the mechanism of evolution on an unprecedented scale, using the tools of data science to study the structure of the protein networks that make life possible," Feldman said.

"The researchers wanted to understand how protein machines deal with the unexpected. So, they ran a series of data science experiments to disrupt the protein networks that sustain life. In a computational analysis, they knocked out a certain percentage of each organisms' proteins at random. They did this systematically for all 1,840 species, constantly computing whether some sort of backup system would allow the protein networks to continue to function in a way that would support life, until at some point the disruptions caused the protein machinery to fall apart.

"Leskovec likened this analytical approach to throwing a sheet of glass against the ground and counting how many pieces it breaks into. If only some small pieces of the glass break away, this indicates a high degree of resilience. Similarly, if an organism's protein networks remain largely intact even when some proteins are removed, this suggests that the organism is resilient. The study showed that organisms stave off collapse through all manner of backup and workaround mechanisms, revealed by the ability of their protein networks to maintain system integrity.

"The researchers corroborated this notion of network resilience in a second way. They used this shattering technique to compare species over time. Based on fossil record and DNA studies, scientists know roughly the order in which various life forms in the sample appeared in evolution. If protein network resilience confers an evolutionary advantage, the researchers hypothesized, later-evolved organisms should have networks that are more shatterproof than preceding life forms. This is exactly what they found.

"Leskovec believes that by studying the genome and interactome together, data scientists can better understand how evolution works. Information about how organisms are built and improved over time is stored in the genome. But as this study shows, the interactome is important to evolution, too: DNA creates and regulates protein networks, which develop backup processes to adapt to changing circumstances. In some cases, these adaptations prove so useful to a species that its genome preserves these protein improvements so they can be inherited.

"'Genes can't explain it all,'" he said.

Comment: This study supports the article I presented about the place of DNA in the control of life's processes. it is a tiny part of the controls.

Biological complexity:removing cytotoxins from cells

by David Turell @, Sunday, March 10, 2019, 02:15 (1846 days ago) @ David Turell
edited by David Turell, Sunday, March 10, 2019, 03:03

More complexity is added a partially understood system:

https://www.sciencedaily.com/releases/2019/03/190308102126.htm

"Peroxisomes are cell organelles that carry out a number of functions, including the degradation of cytotoxins. For this purpose, they require enzymes that have to be transported into peroxisomes via complicated machinery. The team from the research group Biochemistry of Intracellular Transport Mechanisms at Ruhr-Universität Bochum (RUB) headed by Professor Harald Platta has detected an as-yet unknown transport step, thus gaining a better understanding of life-threatening diseases.

"Peroxisomes are cell organelles of vital importance. Providing an insulated reaction chamber for more than 50 enzymes, they are linked to numerous cellular processes. The main function of peroxisomes is the degradation of long-chain fatty acids and cytotoxins. "In addition, they also fulfil highly specialised functions, for example in the synthesis of penicillin in fungi, the formation of lysine in yeasts, the photorespiration of plants and the generation of plasmalogens for the white matter of the brain in animals," explains Harald Platta. Defects in the formation of functional peroxisomes lead to severe metabolic disorders in humans, which often result in infant death.

"In order for peroxisomes to fulfil their functions, they have to import the relevant enzymes inside first. Most enzymes are guided into the respective peroxisome by the import receptor Pex5p. That receptor is controlled by the protein ubiquitin (Ub) that attaches itself to the receptor temporarily.

"'To date, we have been able to break down the import mechanism into five steps," elaborates Harald Platta: "First, the binding of Pex5p to the imported enzyme in the cytoplasm. Second, the binding of the Pex5p enzyme complex with the peroxisome. Third, the enzyme being released inside the peroxisome. Fourth, Ub attaching itself to Pex5p. And fifth, the export of Ub-modified Pex5p into the cytoplasm to enable further import reactions."

"However, it had remained unclear what exactly happened to the exported Ub-modified Pex5p.

"The current study, which is based in the first place on the PhD projects of Rebecca Brinkmeier and Fouzi El Magraoui, has provided an answer to this question. By analysing systematically generated Ub and Pex5p variants, the team demonstrated that a stable Ub-Pex5p fusion causes a defect in the peroxisomal protein import. Accordingly, Ub has to be detached from Pex5p again.

"Once ubiquitin has been taken over by another enzyme, Pex5p reverts to its original status and can be reused. If this step is missing, the import receptor spins out of control. First, it careens inside the cytoplasm as a complex, until it erratically crashes back into the peroxisome where it blocks the docking complex, thus inhibiting the import of the correct Ub-modified Pex5p. "Eventually, this leads to complete loss of function in the peroxisome," concludes Platta. "Our study thus adds the necessary sixth step to the import cycle.'"

Comment: As the words state, cytotoxins are formed by metabolic reactions and must be cleared. This is a perfect example of a very complex feedback loop controlling a danger to life. There is no way this can be perfected and placed into operation other than all at once. Only a designer can create such complexity which each step fitted into the loop so it operate as a continuous loop mechanism. Chance evolution can't do it. Ir is a perfect example of the automatism in cellular activity.

Biological complexity: cellular organelles communicate

by David Turell @, Monday, March 11, 2019, 19:30 (1845 days ago) @ David Turell

There is lots of cross talk and communication between all parts of the cells:

https://www.nature.com/articles/d41586-019-00792-9?utm_source=Nature+Briefing&utm_c...

"In a 1990 paper, Vance showed that the meeting points between the ER and mitochondria were crucibles for the synthesis of lipids1. By bringing the two organelles together, these junctions could serve as portals for the transfer of newly made fats. This would answer the long-standing question of how mitochondria receive certain lipids — they are directly passed from the ER.

***

"close to three decades later, Vance’s paper is seen as a landmark — one that has come to transform scientists’ understanding of how cells maintain order and function in their crowded interiors, which buzz with various types of organelles, including mitochondria, nuclei and the ER. Researchers now recognize that interactions between organelles are ubiquitous, with almost every type coming into close conversation with every other type. Probing those connections is also leading biologists to discover proteins that are responsible for holding the organelles together and maintaining a healthy cell.

***

" Vance’s 1990 paper was seldom cited until the past decade, when the field rediscovered her work. That’s also when researchers began to pinpoint the specific proteins — called tethers — that form the contact points between organelles. Knowing their identity meant that cell biologists could artificially construct contact sites or destroy them and, in so doing, drill down into the function of the different trading exchanges.

***

"Scott Emr, a yeast biologist at Cornell University in Ithaca, New York, encountered this when he began studying contact sites between the ER and the plasma membrane. His group eventually identified six tethering components, any one of which could correctly hold the tether together4. His team could disrupt the bond only by eliminating all six proteins.

"The quest to identify tethers is also complicated by the elaborate network of interactions between organelles. At first, all interactions seemed to involve the ER. But scientists began to document other couplings. And they soon realized that cells can reroute transport when direct shipping lanes are blocked.

***

"Mitochondrial biologist Jodi Nunnari at the University of California, Davis, and her then colleague, cell biologist Laura Lackner, classified7 a super-contact zone containing at least two tethers and three organelles — the ER, mitochondria and the plasma membrane. “It really seems like this is some sort of functional hub that the cell has created,” says Lackner, now at Northwestern University in Evanston, Illinois. “It brings in a whole other layer of spatial organization.”

***

"One of the earliest functions to come to light was cargo transfer. After Vance’s initial discovery, experiments revealed that organelle contacts are almost like a gangway for exchanging goods between two ships. These sites transmit cholesterol, oily waxes and other fatty molecules that would otherwise form beads in the watery cytoplasmic sea, plugging up the cell like bacon grease in a drainpipe.

"Calcium, hydrogen peroxide and other water-soluble compounds also flow through these portals,
which helps the cell to aggregate these molecules for specific reactions.

***

"A few years later, Voeltz showed that a similar process also explains the division of organelles known as endosomes that help to sort and deliver molecular cargo10. Initially, she says, most scientists doubted that ER–endosome contacts even existed or were important. “Now it’s accepted as obvious,” Voeltz says

***

"the researchers identified dozens of proteins localized to contact sites: some served as tethers, but others were simply anchored in contact zones. “Most of them are completely unstudied,” says Schuldiner, hinting that these proteins might have other, undiscovered roles.

***

"As the evidence mounts that contact sites affect cellular function in both health and disease, some researchers have begun to talk about the need for a grand new synthesis of cellular transport. “An organelle cannot function in isolation,” Schuldiner says. And Lippincott-Schwartz sees an exciting future in cell biology: “This field of organelle–organelle communication and coupling is going to reveal really fundamental processes.”

"But there are still technical details to work out. Most research has focused on lipid or calcium shuttling between the ER and other organelles. The challenge now is to uncover the whole spectrum of signals transmitted across all contact sites."

Comment: All of this is automatic activity as the cell produces its products. A complex going factory. Huge article, hard to compress.

Biological complexity: cellular energy use efficiency

by David Turell @, Thursday, April 04, 2019, 20:34 (1821 days ago) @ David Turell

Cellular energy use is much more efficient than man-made machines:

https://www.acsh.org/news/2019/04/01/cell-most-energy-efficient-thing-earth-13923

"energy efficiency can be calculated as the useful energy output of a machine divided by the energy input it received. From the perspective of moving a vehicle forward, a car is about 12% to 30% energy efficient. The rest of the energy is needed to move various parts of the car or is lost as heat.

"What's the most energy efficient thing on Earth? A strong case can be made for the cell, the basic unit of life.

"Your body is an amazing machine. Cars can only burn gasoline, but your body can use several different fuel sources: carbohydrates (sugars, starches), proteins, and lipids (fats). Neurons are primarily powered by glucose (a sugar), so even if you insist on eating a low-carb diet, your body will convert the proteins and fats you eat into glucose, just so your brain won't starve. Blood glucose levels are tightly regulated, precisely for this reason.

"Indeed, glucose is the favored fuel not just of our brains but of our other body cells, as well. The cell's metabolic pathways are centered around the "burning" of glucose to generate energy. How do cells do it?

'They do not do what a combustion engine does: Combine fuel directly with oxygen. That would be a total waste. The reason is because combusting glucose (literally burning it) would release too much energy at once, and the cell would not be able to capture it.

"As an analogy, think of taking a shower. You might use 20 gallons of water. If all the water was dumped on your head in one second, that would not be a very useful shower. Instead, you use the water slowly over a period of about 10 minutes. Similarly, cells slowly release the energy of glucose in a controlled manner. Piece by piece, glucose is stripped of hydrogen atoms and high-energy electrons that the cell can eventually use to make ATP, its stored form of energy.

"How much energy can ATP store? Biochemists calculate that for every 686 Calories provided by glucose, ATP can capture about 262 Calories, for an energy efficiency of 38%. According to the popular textbook Human Anatomy & Physiology by Marieb and Hoehn, cells are "far more efficient than any man-made machines, which capture only 10-30% of the energy available to them."

"That's a bold claim. Is it true?

"It very well could be. It's tough to compare the energy efficiency of a cell to say, a car, because we aren't comparing the same outputs. (The output we care about for a car is miles driven, while the output measured by biochemists is a molecule called ATP.) Given the caveat that we aren't really comparing apples to apples, how does the 38% energy efficiency of a biological cell compare to other man-made things?

"As discussed above, cars are only about 12% to 30% energy efficient, with the best cars having a "tank-to-wheel" efficiency of 36%. Inside EVs, a website dedicated to promoting electric vehicles, claims an overall efficiency of 73% for battery electric vehicles, but this is sort of cheating. The electricity had to come from somewhere.

***

" For sure, it's very energy efficient. It's tough to conclude that it is the absolute best, however, because what we're measuring (the energy content of ATP) is quite different from what we measure for other machines. And, of course, when the cell uses ATP to do things (like move around), it will suffer the same sorts of energy losses and inefficiencies that man-made machines endure."

Comment: We use dangerous oxygen in this complex process with safe mechanisms. Such a complex system could not be developed by hit-and-miss chance. It had to designed intact from the beginning.

Biological complexity: electron shuttle use

by David Turell @, Tuesday, April 09, 2019, 20:39 (1816 days ago) @ David Turell

Used in plants to make lignin:

https://www.sciencedaily.com/releases/2019/04/190408183726.htm

"Scientists studying plant cell walls -- structural supports that help plants overcome the downward pull of gravity -- have discovered mechanistic details of a protein involved in the assembly of lignin, a key cell-wall component. The protein acts as a targeted "electron shuttle," delivering the "fuel" that drives the construction of one specific type of lignin building block.

***

"'Much of this previous work has directly targeted the enzymes that steer carbon into different biochemical pathways," said Brookhaven's Liu, who also holds an adjunct position at Stony Brook University.

"The new work suggests an alternative approach, targeting the shuttle proteins that deliver the electrons needed to activate the enzymes.

"'Electrons are like the fuel for the reaction," Liu explained. "For these enzymes, without this fuel, these reactions cannot happen. By targeting the electron-delivery proteins, we can selectively redirect the electron flow to change plants' lignin composition."

"The scientists identified the specificity of the electron shuttle protein through detailed studies of the biochemical pathways that lead to the synthesis of three different lignin precursors. They already knew that the synthesis of each lignin subtype -- H, G, and S -- is controlled by a different oxidative enzyme as part of a single, three-step hydroxylation process.

"'For all three, the enzyme itself is insufficient for the reaction to go forward," Liu said. Each one needs electrons, delivered by a partner protein.

***

"In addition to identifying an electron carrier already known to play a role in the lignin synthesis pathways, these "immunoprecipitation-mass spectrometry" studies revealed that a set of previously unidentified partners were also interacting with some of the enzymes.

To zero in on the role of these additional protein partners, the scientists used biochemical genetics. They used strains of experimental Arabidopsis plants that lacked the gene for each particular protein to see what effect the missing genes would have on the total amount of lignin and each type of subcomponent (H, G, and S).

"They found that deleting the gene for one of these proteins only affects the production of S lignin. They concluded that this "newly identified" electron-shuttle protein must be associated with the last step in the three-step process -- the one that produces S lignin.

"Additional biochemical studies confirmed the conclusion about the exclusive role of this alternate electron shuttle protein in the production of S lignin, and the rationale behind the strategy for targeting the shuttle proteins.

"'Plants use the sun's energy to convert carbon dioxide into sugars which when broken down release energy that flows into carrier proteins," said Liu. "Specific carrier proteins deliver this energy in the form of electrons into different reactions to drive the whole metabolic process. By controlling the flow of electrons into those various pathways, we can potentially control which products plants make, thereby controlling carbon conversion and storage processes in plants.'"

Comment: A system of this complexity must be completely designed from the beginning. It could not develop stepwise.

Biological complexity: cell division is complicated

by David Turell @, Monday, April 15, 2019, 21:49 (1810 days ago) @ David Turell

Control proteins are discovered:

https://www.sciencedaily.com/releases/2019/04/190415105038.htm

"New cells are formed during cell division by a precisely regulated partitioning of cellular content into the two daughter cells. Cell division is therefore a fundamental biological process in which the replicated chromosomes of the mother cell are distributed equally to two daughter cells. This is accomplished by the attachment of the paired chromosomes to a bipolar network of fibers known as the spindle apparatus (or mitotic spindle). Shortening of the fibers then draws the two sets of chromosomes to opposite poles of the network, and a contractile ring in the center cleaves the cell in two. The mitotic spindle is organized by organelles known as centrosomes, which act as spindle poles.

***

"The centrosome is comprised of a pair of cylindrical centrioles, which are embedded in an amorphous protein matrix called the pericentriolar material (PCM). In the mother cell the centrosome is normally found in the vicinity of the cell nucleus, and is replicated prior to the onset of cell division. Each centrosome then acts as a nucleation site for the assembly of spindle fibers, which gradually pushes the two centrosomes apart and thereby forms a bipolar spindle. The replicated chromosomes attach to spindle fiber emanating from the centrosomes, and are pulled towards the pole associated with the fibers. In order to withstand the enormous pulling and pushing forces exerted during cell division, the centrosomes themselves must be very robust. This robustness is provided by the PCM matrix proteins.

***

"...we came across a previously uncharacterized protein, which we named 'PCM-deficient-1', or PCMD-1 for short." In subsequent experiments, the LMU researchers attached a fluorescent label to the protein, which enabled them to track its position in the cell and they specifically deleted the pcmd-1 gene with the aid of the CRISPR/Cas9 system. This approach enabled them to determine that the protein is essential for the correct assembly of the centrosome. In particular, it is required for the formation of the PCM matrix, which is largely made up of the protein SPD-5, and is responsible for the integrity and robustness of the centrosomes. "Loss of PCMD-1 has a drastic effect on the coherence of the centrosome and the assembly of the bipolar spindle, which effectively prevents normal cell division," says Mikeladze-Dvali.

"These findings reveal that PCMD-1 plays an indispensable role in the control of cell division, and according to the authors, its characterization has significant implications for our understanding of how centrosome assembly is regulated. The vast majority of the proteins identified in C. elegans -including the PCM protein SPD-5 -- are also found in higher organisms, where they serve similar functions. "

Comment: All eukaryotic single-celled and multicellular organisms have cells constantly splitting and reproducing by this system. Unless it occurs perfectly sickness and death follow. It cannot have developed by chance steps: it is so complex all parts have to be designed and developed at one time. Darwin theory cannot accomplish this.

Biological complexity: plants stress controls

by David Turell @, Sunday, April 21, 2019, 17:57 (1804 days ago) @ David Turell

Using RNA alterations chloroplasts are changed in stress situations:

https://phys.org/news/2019-04-scientists-uncover-link-rna-chloroplast-to-nucleus.html

"How will plants fare in more extreme weather conditions? When experiencing stress or damage from various sources, plants use chloroplast-to-nucleus communication to regulate gene expression and help them cope.

"Now, Salk Institute researchers have found that GUN1—a gene that integrates numerous chloroplast-to-nucleus retrograde signaling pathways—also plays an important role in how proteins are made in damaged chloroplasts, which provides a new insight into how plants respond to stress.

***

"In plant cells, structures called chloroplasts convert energy from sunlight into chemical energy (photosynthesis). Normally, the nucleus of the cell transmits information to the chloroplasts to maintain steady energy production. However, in a stressful environment, chloroplasts send an alarm back to the cell nucleus using retrograde signaling (creating a chloroplast-to-nucleus communication feedback loop). This SOS prompts a response that helps regulate gene expression in the chloroplasts and the nucleus to optimize energy production from sunlight.

"Previously, the Chory lab identified a group of genes, including GUN1, that influence other genes' expression in the cell when the plant experiences stress. GUN1 accumulates under stressful conditions but the exact molecular function of GUN1 has been difficult to decipher, until now.

***

"In plants without GUN1, gene expression changed, as did RNA editing in chloroplasts. (RNA editing is a modification of the RNA that changes the identity of nucleotides, so that the information in the mature RNA differs from that defined in the genome, altering the instructions for making proteins.) Some areas of RNA had more editing and other locations had less editing—suggesting that GUN1 plays a role in regulating chloroplast RNA editing.

"After further analysis, the team unexpectedly found that GUN1 partners with another protein, MORF2 (an essential component of the plant RNA editing complex), to affect the efficiency of RNA editing during chloroplast-to-nucleus communication in damaged chloroplasts. Greater activity of MORF2 led to widespread editing changes as well as defects in chloroplast and leaf development even under normal growth conditions (see image). During periods of stress and injury, MORF2 overproduction also led to disruption of chloroplast-to-nucleus communication.

"'Taken together, these findings suggest a possible link between chloroplast-to-nucleus communication and chloroplast RNA editing, which are important regulatory functions for flowering plants, especially during stress," says Chory, Howard Hughes Medical Institute investigator."

Comment: This type of complex series of reactions cannot be developed step by step. It must be designed all at once.

Biological complexity: cell automaticity making proteins

by David Turell @, Thursday, May 16, 2019, 20:56 (1779 days ago) @ David Turell

How mRNA instructions are tightly controlled within a productive cell:

https://phys.org/news/2019-05-uncovers-key-cell-protein-production.html

"Proteins are the building blocks of life and our cells make them based on instructions from our DNA. These instructions that have to be transported from the cell nucleus, which holds the DNA, to the cytoplasm where proteins are made.

"The research, led by Professor Stuart Wilson from the University of Sheffield's Department of Molecular Biology and Biotechnology, revealed how our cells know when these instructions, known as mRNA, are ready to be transported.

"Professor Stuart Wilson, lead researcher from the University of Sheffield, explained: "If the mRNA is transported before the processing is complete, then it is a disaster for the cell, which can't make proteins and ultimately dies. Faults in this process are behind many human diseases. So it's vitally important, not just that the processing is done correctly, but the cell knows when this is complete."

"The team, from the Sheffield Institute for Nucleic Acids, found that molecules known as 'export factors' - which help transport the mRNA—also signal to the cell when the processing is complete by moving their position on the mRNA.

"Scientists have long argued over the position of export factors—whether they sit at the beginning of the mRNA or centrally, where the protein-making instructions have been spliced together.

"Professor Wilson, working with his co-researchers Dr. Nicolas Viphakone and Dr. Ian Sudbery, found that in fact, both views are correct. The export factors initially sit at the beginning of the mRNA while the processing takes place, then once it is complete, they move further in, sitting at points where splicing has taken place, to signal that transport can begin.

"'This research helps us understand a basic process that is fundamental to life, but which will enable us to develop treatments for diseases in the future," said Professor Wilson. "We can't easily fix a problem until we know what's wrong and we can't know what's wrong until we're clear as to how it's supposed to work.

"'Export factors have changed very little throughout evolution, so those found in humans are very similar to those in simpler organisms such as yeast and insects. Our research was in human cells, but we believe that the process we've uncovered will be pretty much the same in any animal on the planet.'"

"'Co-transcriptional loading of RNA export factors shapes the human transcriptome", by Nicolas Viphakone, Ian Sudbery, Llywelyn Griffith, Catherine G. Heath, David Sims and Stuart A Wilson, is published in Molecular Cell. "

Comment: This illustrates the tight controls within the cell. The cells produce proteins at such high speed it has to be automatic. feedback loops will be present.

Biological complexity: white blood cells from stem cells

by David Turell @, Monday, May 20, 2019, 17:54 (1775 days ago) @ David Turell

A complex ballet of protein molecules:

https://phys.org/news/2019-05-zebrafish-explore-alternatives-bone-marrow.html

"To bypass the need for donations, University of California San Diego School of Medicine researchers are using zebrafish and human cells to determine how to grow blood stem cells in a laboratory dish.

"Whether it's humans or zebrafish, a major player driving embryonic and blood cell development is the Wnt family of molecules. These molecules tell cells what to do by docking on Frizzled receptors, which sit on cell surfaces like antennae.

"In their latest study, published May 20, 2019 by Nature Cell Biology, the team was surprised to discover that when one particular Wnt signaling molecule, Wnt9a, is received by blood stem cells, three different molecules are involved. Scientist had previously thought there were only two.

"That third—and, it turns out, crucial—factor is the epidermal growth factor receptor, or EGFR. This finding may help advance the development of blood stem cells in the laboratory.
"Previous attempts to develop blood stem cells in a laboratory dish have failed, and that may be in part because they didn't take the interaction between EGFR and Wnt into account," said first author Stephanie Grainger, Ph.D., assistant project scientist at UC San Diego School of Medicine.

"Researchers commonly use zebrafish—a pet shop staple—to study how blood stem cells develop in a normal organism. Zebrafish are an ideal model for this because they use the same mechanisms to make blood stem cells that humans do, but they are translucent as they develop. That means researchers can watch their blood stem cells arise in real time, and test how genetic modifications affect them.

"According to the study, blood stem cell development works like this: The Wnt9a molecule touches down on a Frizzled receptor on the outer surface of a blood stem cell (Fzd9b, to be exact). At the same time, Wnt9a also brings EGFR into the mix from the outside of the cell, bringing Fzd9b and EGFR closer together. Then, inside the cell, EGFR tags Fzd9b's inner tail with a chemical, a phosphate group. This last step triggers a cascade of cellular events necessary to turn a stem cell into a blood cell."

Comment: This complex development system requires three specific proteins to work in combination and finally add a phosphate group to Fzd9b's tail to set off production by a stem cell. This has to be designed from the beginning. Chance attempts won't work to put this series of reactions in place.

Biological complexity: single protein fights acidity

by David Turell @, Monday, May 20, 2019, 18:21 (1775 days ago) @ David Turell

Hypoxia of tissue from any cause has a cell channel help from a single gene making a single protein:

https://www.sciencedaily.com/releases/2019/05/190520081928.htm

"Johns Hopkins researchers have discovered a long-sought protein, the proton-activated chloride channel (PAC), that is activated in acidic environments and could protect against the tissue-damaging effects of stroke, heart attack, cancer and inflammation.

***

"Acidity builds in tissues as a result of oxygen deprivation caused by damage or disease. As the acidity of the tissues grows, it damages cells and can cause them to die. The acidic buildup, say researchers, is known to open the gate of specialized channels through the cell membrane, causing an abnormal accumulation of ions inside the cell, which eventually causes it to swell and die. However, the identity of this channel has remained a mystery until now.

"To solve this long-standing puzzle, the research team set up a method to rapidly test cells for these channel proteins. The researchers engineered human cell lines to produce a fluorescent molecule -- its glow would be turned off when channels through the cell membrane open in response to acid. Using these cells, the researchers systematically tested a library of 2,725 genes one by one. In this way, they found a single gene, called TMEM206, the inactivation of which reliably eliminated channel activity in response to acid. Through further study, the researchers found that the gene corresponded to a single protein, which they named PAC.

"This gene can be found from the human genome all the way to fish. "Its evolutionary conservation and wide expression suggest a broad role for this new channel family in physiology and disease -- now we are very excited to figure it all out," says Qiu.
Curiously, the PAC gene is one of the genes most frequently different between Tibetan highlanders and Han Chinese. "This leads us to believe," says Qiu, "PAC could have a conserved role in the adaptation to hypoxia," a condition that also results in increased acidity in the body."

Comment: Another complex mechanism that has to have been designed

Biological complexity: unclogging mitochondria

by David Turell @, Thursday, May 23, 2019, 23:35 (1772 days ago) @ David Turell

A new complex mechanism to move along protein molecules is discovered:

https://www.sciencedaily.com/releases/2019/05/190523143046.htm

"Mitochondria produce the bulk of cellular energy and are therefore referred to as powerhouses of the cell. In order to fulfill their functions, mitochondria depend on the import of about 1,000 different proteins. These proteins are synthesized as precursors in the cytosol. Specific protein machineries, termed protein translocases, transport these precursor proteins across the two surrounding membranes of mitochondria. The translocase of the outer membrane, TOM complex, forms the entry gate for almost all precursor proteins. A small portion of the precursors proteins can be stalled in the translocation channel of the TOM complex and blocks the import of further proteins into mitochondria. Impaired protein translocation into mitochondria is deleterious for the cell and leads to a number of cellular stress responses. How the cell prevents an accumulation of such clogged TOM complex is unclear.

"Researchers from the research training group 2202 "Transport Across and Into Membranes," and the cluster of excellence CIBSS -- Centre for Integrative Biological Signalling Studies at the University of Freiburg discovered a new mechanism that clears TOM complexes from stalled precursor proteins. Christoph Mårtensson from the Becker lab showed in collaboration with the group of Prof. Dr. Bettina Warscheid an interaction of the protein Ubx2 with the TOM complex. This finding was unexpected for the researchers since Ubx2 was previously found to function in the removal of misfolded proteins from the endoplasmic reticulum, another cell organelle. Becker´s team showed that Ubx2 is also present in mitochondria, where it binds to the TOM complex to recruit the cytosolic Cdc48. Cdc48 powers the extraction of stalled precursor protein from the TOM complex and transfers it to the cellular protein degradation machinery, the proteasome.

"The researchers termed this pathway the "mitochondrial protein translocation-associated degradation," mitoTAD. The mitoTAD mechanism allows efficient removal of clogged precursor proteins from the TOM complex and ensures unimpeded protein traffic into mitochondria."

Comment: The use of this group of helpful proteins requires specialized molecules, which can recognize misfolded (useless) protein products, obviously requires design at the start of the use of mitochondria, which are thought to come from ingested bacteria. If the logjams occurred and a mechanism to clear them was not present, advancing to fully developed eukaryote cells would not have occurred.

Biological complexity: cell pore controls

by David Turell @, Tuesday, June 25, 2019, 18:40 (1739 days ago) @ David Turell

These are very complex mechanisms allowing ions in and out of cells:

https://phys.org/news/2019-06-ph-calcium-ions-ion-channel.html

"Ion channels are pores in the membrane of cells or cell organelles. They allow positively or negatively charged particles, so-called ions, to be transported across the membrane. Biochemists at Johannes Gutenberg University Mainz (JGU) have now succeeded in imaging an important regulatory region of the human TRPML2 calcium ion channel at high resolution, an area of the channel shaped like a large ring on one side of the membrane. This ring acts like a doorman, deciding whether ions can move through the channel. "Our study has revealed the structure of the ring, which is also called the extracytosolic/lumenal domain (ELD), in human TRPML2 channels, and also that it is this domain that is responsible for the channel's interaction with calcium," said Professor Ute Hellmich of the JGU Institute of Pharmacy and Biochemistry—Therapeutical Life Sciences. Depending on the pH value, the calcium ions can open or block the channel, and therefore control their transport across cellular membranes.

"Hellmich's research group investigated which structural properties of the ion channel ring are responsible for allowing calcium ions to pass. "Calcium is an important cellular messenger that also plays a role in many diseases," explained Hellmich. The element performs numerous tasks in the body, including regulating enzymes and helping with membrane fusion.

"TRPML2, short for transient receptor potential mucolipin 2, is an ion channel of the mucolipin subfamily of TRP channels involved in sensory perception in humans. TRPML2 plays a role in the immune response to infections and increases the infectivity of Zika and dengue viruses.

***

"As Hellmich makes clear, ion channels are not simple holes. They can be actively opened and closed. This, in turn, activates and controls cellular pathways. "We have now discovered that binding of calcium to the TRPML2 extracytosolic/lumenal domain on top of the channel is dependent on pH," stated Kerstin Viet, first author of the paper in the scientific journal Structure. This research was part of her Master's thesis and resulted in her being awarded the Adolf Todt Foundation Prize.

"At a higher pH value of around seven, found at the outside of the cell, the calcium ions can bind to the ring and thus block it. Conversely, the calcium ions are no longer able to block the opening at a lower pH typical of certain intracellular compartments. "The ring acts like a gatekeeper for the rest of the ion channel," said Viet.

"This therefore regulates the activity of the channel: It is important that the ion channel is only activated within the cell, where the pH is generally low; in effect the channel is only opened when a particular cellular mechanism signals that it requires calcium. Unprompted activation on the cell surface could well result in damage to the cell. "The regulation mechanism is clever. It is also relevant, for example, to how the cell reacts to a viral infection," said Hellmich, adding that the entire process just when and how an ion channel is opened or closed is not yet fully understood. The other two ion channels of the human mucolipin subfamily, TRPML1 and TRPML3, also have a similar doorkeeper ring. The study's results therefore make it possible for the first time to compare all three subtypes. "

Comment: Cells cannot operate properly unless these pores are under precise controls. this complexity cannot be developed by chance mutations. Look at the diagram to understand the degree of complexity.

Biological complexity: unfolding used proteins

by David Turell @, Thursday, June 27, 2019, 20:24 (1737 days ago) @ David Turell

Cells must unfold proteins to remove them:

https://phys.org/news/2019-06-cells-unfold-proteins.html

"A happy cell is a balanced cell, but for every stupendously twisted protein it creates, it must tear the old ones asunder. That means untangling a convoluted pretzel-like mass for recycling. Cdc48 plays a critical role in unraveling the spent proteins.

"'Cdc48 is the swiss army knife of the cell and can interact with so many different substrates," said Peter Shen, Ph.D.,

***

"In the study, the research team purified Cdc48 directly from yeast cells (Saccharomyces cerevisiae) and took snapshots of the purified particles in different configurations after it was flash frozen using cryogenic electron microscopy (cryo-EM).

"'The cells are already doing the hard work for us by making these complexes," Shen said.
"Because this method is so fast, we have captured Cdc48 in the act of unfolding a protein substrate."

"Using this approach, the research team demonstrated how Cdc48 unfolds the protein by threading it through a central pore of the complex, using a hand-over-hand conveyor-like movement. The recycled tangle they were imaging was a mystery until collaborators at Brigham Young University applied mass spectrometry proteomics to the same harvested complex to unmask the anonymous proteinan inactive protein phosphatase 1 complex.

"Shen believes these results are applicable to human cells, because Cdc48 is highly conserved.

***

"The research team was unable to visualize the entire complex because Cdc48 interacts with multiple binding partners almost simultaneously. This efficient multitasking blurs the reconstruction; however, Shen wants to continue to explore how Cdc48 manages to bind with so many partners at roughly the same time."

Comment: I process of this complexity can not have arrived by chance.

Biological complexity: liver study of liquid crystal form

by David Turell @, Wednesday, July 03, 2019, 15:30 (1731 days ago) @ David Turell

An attempt to understand how hepatocytes work:

https://medicalxpress.com/news/2019-07-technique-liquid-crystal-liver-tissue.html

"The liver is the largest metabolic organ of the human body with a complex tissue architecture. It is vital for blood detoxification and metabolism. Blood flows through blood vessels to the liver cells, called hepatocytes, which take up and metabolize substances and secrete bile for discharge into the intestine. How do cells interact with each other and self-organize to form a functional tissue? For this, its three-dimensional structure must be known. The architecture of tissues and its relation to their function are still poorly understood today.

***

"A structural model of the liver lobule was made and hand-drawn by the anatomist Hans Elias in 1949. Since then, very little progress has been made. To solve this outstanding problem, the Dresden researchers computationally reconstructed the three-dimensional geometry of the tissue from microscopy images of mouse liver tissue and analyzed it applying concepts from Physics. Surprisingly, given the amorphous appearance of liver tissue, the researchers found that the hepatocytes follow a liquid-crystal order, similar to the one making electronic displays. Liquid crystals are less structured than crystals but are more organized than molecules in a liquid.

"Hernán Morales-Navarrete, postdoctoral researcher in the lab of Marino Zerial at the Max Planck Institute of Molecular Cell Biology and Genetics, explains: "Our results suggest that liver cells and sinusoids, which are the smallest blood vessels in the body, communicate with each other in both directions: The blood vessels instruct the hepatocytes and the hepatocytes send signals back to the blood vessels to establish and preserve the liquid-crystal order. This bi-directional communication is a central part of the self-organization of liver tissue." Such an architecture gives the tissue function and robustness against local damage.

Comment: This degree of complexity is not fully understood but the description is at least a beginning in understanding liver function. We know the functions, not the how. This must have been designed.

Biological complexity: blocked mRNA 'standby site'

by David Turell @, Monday, July 15, 2019, 21:15 (1719 days ago) @ David Turell

More extreme complexity in bacterial genome:

https://phys.org/news/2019-07-ribosome-standby-bacteria-proteins-blocked.html

"Bacterial ribosomes need a single-stranded ribosome binding site (RBS) to initiate protein synthesis, whereas stable RNA structure blocks initiation. Paradoxically, structured mRNAs can nevertheless be efficiently translated. Researchers at Uppsala University have now elucidated the anatomy of a "standby" site and its requirements, to overcome RNA structure problems for translation.

"Bacterial protein synthesis has been studied for decades. Ribosomes needs access to a single-stranded RBS to initiate translation. However, some mRNAs with stably structured RBS regions are efficiently translated. About 25 years ago, Dutch researchers proposed a new mechanism to account for this, "ribosome standby": a ribosome binds to an accessible, unstructured region elsewhere, waits for a while, and then moves to the RBS when its structure temporarily opens.

***

"researchers at Uppsala University have unveiled the anatomy of a standby site, and reported on the key role of ribosomal protein S1 in this process. S1 binds to a standby site consisting of two elements, a single-stranded region and—unexpectedly—a short RNA hairpin. Standby binding permits the ribosome to move through downstream RNA structure and to access the blocked RBS.

"'We felt that it was time to figure out what exactly a standby site looks like, and what is needed to make it work. Standby is an old idea that up to now lacked strong direct evidence," says Cédric Romilly, the study's first author.

"Following studies conducted by the Wagner group for years, they investigated a short mRNA that encodes a toxin, TisB. Translation of this protein is entirely dependent on a standby site located >100 nucleotides upstream of the stable and inaccessible RBS structure. Using sophisticated biochemical methods, such as fluorescence anisotropy and UV-crosslinking/ RNA footprinting, the researchers were able to catch the ribosome on the standby site. The experiments show that it is protein S1 that guides the ribosome to the standby site, thus likely promoting downstream RNA structure opening to access the TisB RBS."

Comment: The earliest life was bacteria, and they are obviously not simple. I doubt first life was either. No chance events can create this. Only a designer fits.

Biological complexity: nucleolus functions to protect

by David Turell @, Wednesday, July 17, 2019, 19:26 (1717 days ago) @ David Turell

The nucleolus protects cells fro misfolded protein molecules:

https://phys.org/news/2019-07-function-nucleolus.html

" A new study shows that the nucleolus is also a site of quality control for proteins.

"When cells are stressed, proteins tend to misfold and to aggregate. To prevent proteins from clumping, some are temporarily stored in the nucleolus. The special biophysical conditions found in this organelle help to prevent harmful protein aggregation,

***

"The nucleolus is a structure found in the cell nucleus, which was first described in the 1830s. In the 1960s it was recognized that ribosomes, the cell's protein factories, are assembled in this organelle. Researchers have known for some time that proteins known as chaperones move into the nucleolus under certain circumstances. It has been suggested that this relocation is related to protein production. However, the new work shows that the chaperones that migrate to the nucleolus are already bound to stress-sensitive proteins.

"As a pioneer of chaperone research, F.-Ulrich Hartl and his team previously discovered that chaperones are crucial for the correct folding of proteins, and play a central role in protein quality control. If proteins fail to fold correctly, their misfolded forms can accumulate and clump together.

***

"Together they were able to show that the misfolded luciferase protein behaved differently within the nucleolus than in the rest of the cell. "In the nucleolus, misfolded proteins were kept in a liquid-like state instead of aggregating," explains Frédéric Frottin, first author of the study. This is possible due to the specific biophysical conditions that prevail within the organelle.

"'Proteins that usually tend to aggregate are stored in a less dangerous form during stress, which protects cells from damage. Once the cell has had time to recover, the proteins can be refolded and released from the nucleolus," continues Frottin. At this point, the cells have the capacity to activate further mechanisms that enable the protein to be repaired or degraded. The researchers also demonstrated that this protective mechanism fails if the cell stress lasts too long. "This is a new mechanism that maintains the integrity of the cell," says Mark Hipp. Maintaining this integrity is ultimately essential to inhibit the development of disease and retard the aging process. "

Comment: Protein molecules can perform proper functions only when folded in just the right configurations. Living biochemistry performs functions at high speed and must be protected from misfolding. This mechanism had to present when first life began or it would have continued to live. Only design fits.

Biological complexity: potassium ion channels

by David Turell @, Saturday, August 10, 2019, 19:38 (1693 days ago) @ David Turell
edited by David Turell, Saturday, August 10, 2019, 19:57

Highly complex to control positively-charged potassium ions which are necessary for many cellular functions:

https://phys.org/news/2019-08-molecules-ions-filter-potassium-channels.html

"Our cells need potassium ions to transmit nerve impulses and to control the heart rate, among other functions. Virtually every human cell membrane is equipped with potassium channels. Because potassium channels are of fundamental importance for biological processes, and even the most minute changes can result in serious diseases, the tiny protein molecules are the focus of research efforts around the world. In 2003, a U.S. researcher was awarded the Nobel Prize in Chemistry for his elucidation of the structure of potassium channels.

"However, the question of how potassium actually passes through the channel in order to cross the cell membrane has remained unclear. For a long time, it was assumed that each potassium ion was followed by a water molecule and that the elements then lined up, like links in a chain, and passed through the narrowest part of the potassium channel, the so-called selectivity filter, one after the other. This was based on the fact that potassium ions are positively charged and would repel each other without the intermediate water molecules.

***

"Now, researchers from the FMP in Berlin have brought clarity to the debate: Dr. Carl Öster and Kitty Hendriks of Prof. Adam Lange's research group and other colleagues at the FMP used solid-state nuclear magnetic resonance (NMR) spectroscopy to show that potassium ions actually do migrate through the potassium channels without water molecules in between. Their findings show that the potassium ions are positioned directly behind each other and push each other through the potassium channel, from bottom to top.

"'The technology we used enables us to look at membrane proteins in real cell membranes under natural conditions, for example, at room temperature or physiological salt concentrations," explains Kitty Hendriks. "Thus, we have been able to show that under these conditions, there is definitely no water between the potassium ions in the selectivity filter."

***

"'Five years ago, we certainly would not have been able to demonstrate this in such a manner, but now we have reached a point where we are able to effectively answer this important question," said Prof. Adam Lange, head of the research group that focuses on the investigation of membrane proteins, such as ion channels. He adds: "Since the processes in potassium channels are fundamental to our health, our results have great significance that also extends beyond basic research.'"

Comment: Potassium ions play such a vital role in living processes, life could not have begun without these channels designed to be in place at the life appeared. The channel overcomes the problem of the ions repelling each other. Only design by a designer fits as the source of such complexity.

What is interesting and obvious from the comments made by dhw is that except for the very strong evidence of design, he would be an atheist. I think his early exposure to religion has caused some confusion in his thinking. The designer does not have to be religion's God as the ID folks constantly point out, but logic indicates there must be a designer. dhw can still be agnostic about who or what the designer represents while accepting a designer's existence and leave it at that. The next step is to recognize it requires a thinking, planning mind. No further step is necessary.

Biological complexity: power supply

by David Turell @, Friday, August 23, 2019, 15:04 (1680 days ago) @ David Turell

From ATP rotary mechanisms:

https://www.sciencedaily.com/releases/2019/08/190822141912.htm

"Cells rely on protein complexes known as ATP synthases or ATPases for their energy needs -- adenosine triphosphate (ATP) molecules power most of the processes sustaining life. Structural biologist Professor Leonid Sazanov and his research group from the Institute of Science and Technology Austria (IST Austria) in Klosterneuburg, Austria have now determined the first atomic structure of the representative of the V/A-ATPase family, filling in the gap in the evolutionary tree of these essential molecular machines.

***

"ATP synthases/ATPases are large membrane protein complexes which share overall gross building plans and rotary catalysis mechanisms. This protein family includes F-type enzyme found in mitochondria (power factories of the cell), chloroplasts (organelles that conduct photosynthesis in plants) and bacteria; V (vacuolar)-type found in intracellular compartments in eukaryotes (higher organisms with a nucleus) and A (archaeal)-type found in prokaryotes -- archaea (ancient microorganisms) and some bacteria.

"F- and A-type enzymes usually function to produce ATP, driven by proton flow across the membrane. V-type enzymes usually work in reverse, using ATP to pump protons. V- and A-ATPases are similar structurally but they differ from the F-type by having two or three peripheral stalks and additional connecting protein subunits between V1 and Vo.

***

"Instead of a single peripheral stalk of F-type enzymes, A-types such as ThV1Vo have two peripheral stalks, while eukaryotic V-types have three. But what is the advantage of the additional complexity in the already very large protein assembly, along with additional subunits linking V1 and Vo? The F1/V1 domain has a three-fold symmetry and so one ATP molecule is produced (or consumed) per each 120° rotation of the stator inside F1/V1. Professor Leonid Sazanov says: "In V/A-ATPases this step is a one-off 120° rotation, in contrast to F-ATP synthase where it is divided into several sub-steps. Thus, greater plasticity may be required in ThV1Vo in order to link these 120° steps in V1 to smaller per c subunit steps in the Vo c12-ring. This additional flexibility may be afforded in V-types by the additional peripheral stalks and connecting subunits. Our new structures show how this is achieved, providing a framework for the entire V-ATPase family.'"

Comment: Power sources of this degree of complexity require exact design, not chance development.

Biological complexity: sensing cold

by David Turell @, Saturday, August 31, 2019, 18:42 (1672 days ago) @ David Turell

All organisms do it roughly the same way with the same specific protein receptors:

https://www.sciencedaily.com/releases/2019/08/190829150803.htm

"When environmental temperatures drop to uncomfortable, and even dangerous levels, receptor proteins within the sensory nerves in the skin perceive the change, and they relay that information to the brain. This is true for organisms from humans all the way down to the tiny, millimeter-long worms that researchers study in Xu's lab at the Life Sciences Institute: the model system Caenorhabditis elegans.

***

"The researchers found that worms missing the glutamate receptor gene glr-3 no longer responded when temperatures dipped below 18 degrees Celsius (64 F). This gene is responsible for making the GLR-3 receptor protein. Without this protein, the worms became insensitive to cold temperatures, indicating that the protein is required for the worms to sense cold.

"What's more, the glr-3 gene is evolutionarily conserved across species, including humans. And it turns out the vertebrate versions of the gene can also function as a cold-sensing receptor.
When the researchers added the mammalian version of the gene to mutant worms lacking glr-3 -- and were thus insensitive to cold -- they found that it rescued the worms' cold sensitivity.

"They also added the worm, zebrafish, mouse and human versions of the genes to cold-insensitive mammalian cells. With all versions of the gene, the cells became sensitive to cold temperatures.

"The mouse version of the gene, GluK2 (for glutamate ionotropic receptor kainate type subunit 2), is well known for its role in transmitting chemical signals within the brain. The researchers discovered, however, that this gene is also active in a group of mouse sensory neurons that detect environmental stimuli, such as temperature, through sensory endings in the animals' skin.

"Reducing the expression of GluK2 in mouse sensory neurons suppressed their ability to sense cold, but not cool, temperatures. The findings provide additional evidence that the GluK2 protein serves as a cold receptor in mammals.

"'For all these years, attention has been focused on this gene's function in the brain. Now, we've found that it has a role in the peripheral sensory system, as well," Xu said. "It's really exciting. This was one of the few remaining sensory receptors that had not yet been identified in nature.'"

Comment: As usual the question is how did a chance evolutionary process find these exact proteins with their exact functions? Only design fits.

Biological complexity: cell pore complex controls

by David Turell @, Monday, May 04, 2020, 19:05 (1425 days ago) @ David Turell

More complexity described:

https://phys.org/news/2020-05-nuclear-pore-puzzle-super-resolution-microscopy.html

"The results reveal that most Nuclear Envelope Transmembrane (NET) proteins travel into the cell's nucleus through small tunnels, known as peripheral channels, whose existence has long been debated by scientists.

"Mistakes in the location or function of NET proteins are linked to many human diseases such as muscular dystrophies, cardiomyopathy, blood and bone disorders, and cancers.

"Most soluble proteins travel via Nuclear Pore Complexes (NPCs), vast tunnel-like structures spanning the nuclear envelope—the protective membrane that surrounds the nucleus, the command centre of the cell.

"'NPCs are one of the cells most important molecular machines, controlling the transport of proteins and RNA into and out of the nucleus, but their size and complexity has led to many different theories emerging on NET protein transport." says a lead author of the study, Professor Eric Schirmer at the University of Edinburgh.

***

"The study is the first to find conclusive functional proof of the existence and importance of smaller peripheral channels, at the edge of central NPC channels, for NET protein transport.

***

"Blocking the NPC tunnels did not disrupt transport, although the team found that 10% of NET proteins straddle both tunnels, using them simultaneously for faster and more efficient transport.

"'Nobel Laureate Gunter Blobel was a visionary in his suggesting that the NPCs—huge tunnel complexes containing hundreds of structural proteins—were highly plastic and dynamic." says Schirmer. "This is underscored by this study where NETs simultaneous usage of both central and peripheral channels could only happen if the NETs effectively slice through this dynamic protein complex.'"

Comment: If this degree of complexity doesn't convince a designer is needed and does exist, nothing will.

Biological complexity: cell division is complicated

by David Turell @, Sunday, September 15, 2019, 23:38 (1657 days ago) @ David Turell

Newly discovered cell division by microtubules purse-string mechanism:

https://www.sciencedaily.com/releases/2019/09/190913191442.htm

"Cell biologist Thomas Maresca and senior research fellow Vikash Verma at the University of Massachusetts Amherst say they have, for the first time, directly observed and recorded in animal cells a pathway called branching microtubule nucleation, a mechanism in cell division that had been imaged in cellular extracts and plant cells but not directly observed in animal cells.

***

"In particular, they want to understand how structures called microtubules help to define where the cell splits in half during the division process.

***

"In normal cell division, chromosomes line up near the center of the cell, where a structure called the spindle aligns copies of each chromosome by interacting with a bridge-like structure called the kinetochore. When all the chromosomes have been aligned, microtubules pull the chromosome copies apart like a zipper. The cell then physically divides at a location positioned between the segregated chromosomes to produce two daughter cells, each with a complete copy of the genome.

***

"...the division plane requires microtubules, Maresca says. "They grow out to touch the edges inside the cell membrane. Vikash found that the growing tips of the tubes, the 'plus-ends' that touch the membrane, say to the cell, 'This is where to divide.' Regulatory proteins get recruited to the site contacted by the plus-ends kicking into gear and a whole new pathway assembles a ring that will constrict like a purse string to split one large cell into two smaller ones."

"Timing plays a role, as well, the researchers found. "It seems that all the microtubule tips have the special ability to trigger the purse-string pathway," Maresca says, "but over time, something changes and only the tips in the middle of the cell retain that ability." Referring to work published in eLife in February, he adds, "We found what we think is a very important spatial cue for how the cell positions its division plane."

***

"Once they could visualize the entire process of branching nucleation in a cell, he adds, "We knew we could next 'tag' proteins that regulate the process with different colors to further quantify fundamental parameters of the phenomenon. All of a sudden we realized that this is the first time one could see this happening in living animals cells."

"Branching nucleation is fundamental and conserved, one of the essential parts of mitosis, but it's been difficult to directly visualize in other model systems, Maresca points out. "The course of this project was a reminder that some of the most exciting work we do as scientists is unplanned and, especially for microscopists, begins with seeing something in the cell unfold right before your eyes.'"

Comment: Highly complex protein molecular movements of this type require exact design so that each new daughter cell is the same as the original cell. This cannot be accomplished by chance, and requires guidance by a designing mind.

Biological complexity: bacteria fix iron from soil

by David Turell @, Tuesday, September 17, 2019, 17:23 (1655 days ago) @ David Turell
edited by David Turell, Tuesday, September 17, 2019, 17:43

Iron is vital to life in small amounts:

https://phys.org/news/2019-09-nitrogen-fixing-bacteria-iron.html

"Virtually all life forms require iron to survive, yet too much of the metal can be catastrophic. In healthy cells, many systems regulate this delicate balance.

"In many nitrogen-fixing bacteria, a protein called RirA plays a key role in regulating iron. It senses high levels of the metal and helps to shut down the production of proteins that bring in more iron.

"RirA contains a cluster of four iron and four sulfur atoms, which acts as a sensor for iron availability. But until now, exactly how this cluster structure detects iron levels in a cell was unclear

"The results revealed a 'loose' iron atom in the cluster. When iron levels drop, this atom is rapidly lost as it is scavenged for use in other essential cellular processes.

"Without it, the cluster in RirA collapses and the protein becomes inactive, which prompts the cell to produce proteins that enable the cell to take up iron from its surroundings.

"Once iron levels are sufficient again, RirA regains its cluster and becomes active again, stopping the production of proteins that bring in more iron.

"Iron-sulfur clusters are common in many proteins, and this work offers new insight into their various roles. It also highlights the potential to use time-resolved mass spectrometry to examine biological processes in depth.

"Prof Le Brun said 'This research provides unprecedented detail of how the iron-sensing cluster of RirA responds to low iron conditions, and establishes, for the first time, how an iron-sulfur cluster can be used to sense iron.

"'This is an important piece in the bigger puzzle of how life deals with iron, a nutrient it cannot do without but one it must also avoid having in excess.'"

Comment: This requires a special protein complex for life to use iron. Required as life began and must have been designed from the beginning. Controlling iron levels cannot be developed by hunt and peck chance. Once again this shows why bacteria are still around, having started life to now fixing the needed chemicals in the soil, and are absolutely necessary.

Biological complexity: feedback loops are vital

by David Turell @, Thursday, September 19, 2019, 20:07 (1653 days ago) @ David Turell

Without precise controls of chemical levels, life cannot survive. There are chemical cycles which produce necessary outputs and there are feedback controls which are also loops and control outputs when too low or too high. They are fully automatic and have to be:

https://www.quantamagazine.org/math-reveals-the-secrets-of-cells-feedback-circuitry-201...

"Whether in industrial control systems or in nature, negative feedback is an omnipresent strategy to help systems cope with disturbances. “People have noticed these feedback systems in physiology for as long as people have been studying physiology,” said Noah Olsman, a control theorist at Harvard University. Homeostasis, the self-regulation of biological systems, keeps many physiological parameters like body temperature, blood pressure and levels of blood glucose within exacting limits, whether we’ve run a marathon, gone scuba diving, or binge-watched Netflix all day. And for good reason: “If life couldn’t respond to changes and learn, it wouldn’t last very long,” Olsman said.

"Vital as that negative feedback is, however, biologists have been hard pressed to explain how cells and more complex organisms implement feedback systems with the necessary responsiveness and precision... Most recently, in an important advance this past summer, a team led by Khammash demonstrated a synthetic feedback system that could be installed in cells to help them adapt perfectly to disturbances, just like the robot. The work is backed by a mathematical proof that no simpler answer exists — a good indication that natural feedback systems probably work the same way.

***

"When blood calcium plunges, the parathyroid gland produces more parathyroid hormone, which stimulates calcium ions to leave the skeleton and corrects the error proportionally. In turn, elevated parathyroid hormone levels ramp up the rate of 1,25-DHCC production in the gut, which promotes absorption of calcium in the small intestine. Because the rate of 1,25-DHCC [a special form of vitamin D called 1,25-dihydroxycholecalciferol] production is tied to the concentration of parathyroid hormone, this feedback mechanism takes on a mathematically integral nature.

"Khammash wasn’t the only one realizing nature uses integral feedback to achieve robust perfect adaptation. Earlier, in 2000, Doyle showed mathematically that the effectiveness of bacteria’s directed movements to find food was due to integral feedback. Later, El-Samad, Khammash and Doyle collaborated and showed that heat shock responses in bacteria — their production of protective “chaperone” molecules when overheated — are robust for the same reason. (my bold)

***

'the two controller molecules must have a very specific relationship: They have to bind to each other and neutralize each other’s biological activity. One must be the antithesis of the other.

***

(attempts in the lab to reproduce natural control)

"In the fall of 2017, while his colleagues continued struggling in the lab, Gupta attended a conference in Ohio. There, he met other researchers also trying to build integrators in cells using the theory of the antithetical controller. All of them were struggling. Gupta thought there might be another design that would be easier to execute, making life easier for the experimentalists.

“It’s a legitimate question to ask whether, maybe, there is a simpler way,” Lillacci said. “And then it turns out that there isn’t.”

"Gupta found that the mathematical constraints for robust perfect adaptation were so huge, they restricted the circuit designs that would be stable in a noisy setting. All of them required an antithetical pair of controller molecules.

'Khammash and Gupta were elated at the mathematical proof that their approach, while arduous, was not just sound but inescapable. And for Aoki and Lillacci, who were already seeing signs that their cells could adapt to disturbances, the news kept them going.

“'To find out that there’s really only one underlying topology that should be able to achieve this is really, really quite amazing to me,” Aoki said."

Comment: Without these control loops, homeostasis in life is impossible, as is life itself. This research supports my contention that most bacterial and cellular responses are automatic or tightly controlled. So much for free-thinking and free-acting bacteria or cells.

Biological complexity: feedback loops are vital

by dhw, Friday, September 20, 2019, 08:59 (1652 days ago) @ David Turell

DAVID: Without precise controls of chemical levels, life cannot survive. There are chemical cycles which produce necessary outputs and there are feedback controls which are also loops and control outputs when too low or too high. They are fully automatic and have to be:

https://www.quantamagazine.org/math-reveals-the-secrets-of-cells-feedback-circuitry-201...

DAVID: Without these control loops, homeostasis in life is impossible, as is life itself. This research supports my contention that most bacterial and cellular responses are automatic or tightly controlled. So much for free-thinking and free-acting bacteria or cells.

Of course life would be impossible without homeostasis, and of course most bacterial and cellular responses are automatic and tightly controlled, just as most of our own responses are automatic and tightly controlled. If they weren’t, we too would drop dead any second. The key word in your comment is “most”. Cellular intelligence manifests itself in the responses that are not automatic! Those scientists who support the concept have observed bacteria solving new problems. Yes, the solutions always involve chemical processes – in us as in them – but the information demanding new actions has to be processed first, and then decisions have to be taken in order to change the existing structure/behaviour of the cell(s)/bacteria. You have always agreed that the decision-making process shows intelligence, but you attribute that to your God’s preprogramming, though allowing for a 50/50 chance that “my” scientists might be right. Please stop pretending that automatic chemical responses in bacteria prove they are not intelligent and have been preprogrammed by your God. But thank you for your all-important “most”. It’s the rest that demonstrate intelligence.

Biological complexity: feedback loops are vital

by David Turell @, Friday, September 20, 2019, 18:58 (1652 days ago) @ dhw

DAVID: Without precise controls of chemical levels, life cannot survive. There are chemical cycles which produce necessary outputs and there are feedback controls which are also loops and control outputs when too low or too high. They are fully automatic and have to be:

https://www.quantamagazine.org/math-reveals-the-secrets-of-cells-feedback-circuitry-201...

DAVID: Without these control loops, homeostasis in life is impossible, as is life itself. This research supports my contention that most bacterial and cellular responses are automatic or tightly controlled. So much for free-thinking and free-acting bacteria or cells.

dhw:Of course life would be impossible without homeostasis, and of course most bacterial and cellular responses are automatic and tightly controlled, just as most of our own responses are automatic and tightly controlled. If they weren’t, we too would drop dead any second. The key word in your comment is “most”. Cellular intelligence manifests itself in the responses that are not automatic! Those scientists who support the concept have observed bacteria solving new problems. Yes, the solutions always involve chemical processes – in us as in them – but the information demanding new actions has to be processed first, and then decisions have to be taken in order to change the existing structure/behaviour of the cell(s)/bacteria.

My 'most' is not your most. Please describe the new problems bacteria solve. I don't see any but I do see epigenetic alterations of their DNA for very minor adaptations. And where did the information bacteria use come from? They didn't think it up on their own.

dhw: You have always agreed that the decision-making process shows intelligence, but you attribute that to your God’s preprogramming, though allowing for a 50/50 chance that “my” scientists might be right. Please stop pretending that automatic chemical responses in bacteria prove they are not intelligent and have been preprogrammed by your God. But thank you for your all-important “most”. It’s the rest that demonstrate intelligence.

You persist is misinterpreting my 50/50 as it simply describes the possibilities for the existence of information. Either it was implanted in the beginning or bacteria developed it on their own. I totally reject the latter possibility as you well know. Bacteria cannot and do not think, much as you want them to, as a way of avoiding God..

Biological complexity: feedback loops are vital

by dhw, Saturday, September 21, 2019, 10:10 (1651 days ago) @ David Turell

DAVID: Without precise controls of chemical levels, life cannot survive. There are chemical cycles which produce necessary outputs and there are feedback controls which are also loops and control outputs when too low or too high. They are fully automatic and have to be:
https://www.quantamagazine.org/math-reveals-the-secrets-of-cells-feedback-circuitry-201...

DAVID: Without these control loops, homeostasis in life is impossible, as is life itself. This research supports my contention that most bacterial and cellular responses are automatic or tightly controlled. So much for free-thinking and free-acting bacteria or cells.

dhw: Of course life would be impossible without homeostasis, and of course most bacterial and cellular responses are automatic and tightly controlled, just as most of our own responses are automatic and tightly controlled. If they weren’t, we too would drop dead any second. The key word in your comment is “most”. Cellular intelligence manifests itself in the responses that are not automatic! Those scientists who support the concept have observed bacteria solving new problems. Yes, the solutions always involve chemical processes – in us as in them – but the information demanding new actions has to be processed first, and then decisions have to be taken in order to change the existing structure/behaviour of the cell(s)/bacteria.

DAVID: My 'most' is not your most. Please describe the new problems bacteria solve. I don't see any but I do see epigenetic alterations of their DNA for very minor adaptations. And where did the information bacteria use come from? They didn't think it up on their own.

The proposal is that bacteria process information from their environment, presumably with what would be their equivalent of a brain. I don’t have time to research all the experiments and observations made by McClintock, Margulis, James Shapiro, Albrecht Bühler or all the other scientists who support the theory that bacteria are intelligent, but earlier you admitted that they are in a majority.

dhw: You have always agreed that the decision-making process shows intelligence, but you attribute that to your God’s preprogramming, though allowing for a 50/50 chance that “my” scientists might be right. Please stop pretending that automatic chemical responses in bacteria prove they are not intelligent and have been preprogrammed by your God. But thank you for your all-important “most”. It’s the rest that demonstrate intelligence.

DAVID: You persist is misinterpreting my 50/50 as it simply describes the possibilities for the existence of information. Either it was implanted in the beginning or bacteria developed it on their own. I totally reject the latter possibility as you well know. Bacteria cannot and do not think, much as you want them to, as a way of avoiding God.

Yes, you totally reject the autonomously intelligent 50, although many scientists accept it, and for the hundredth time, this is NOT a way of avoiding God, because in hundreds of posts I keep reiterating that your God may be the inventor of cellular intelligence.But it is certainly a way of avoiding a particular theory about God's motives and methods which we humans, yourself included, find illogical.

Biological complexity: feedback loops are vital

by David Turell @, Saturday, September 21, 2019, 19:12 (1651 days ago) @ dhw

DAVID: Without precise controls of chemical levels, life cannot survive. There are chemical cycles which produce necessary outputs and there are feedback controls which are also loops and control outputs when too low or too high. They are fully automatic and have to be:
https://www.quantamagazine.org/math-reveals-the-secrets-of-cells-feedback-circuitry-201...

DAVID: Without these control loops, homeostasis in life is impossible, as is life itself. This research supports my contention that most bacterial and cellular responses are automatic or tightly controlled. So much for free-thinking and free-acting bacteria or cells.

dhw: Of course life would be impossible without homeostasis, and of course most bacterial and cellular responses are automatic and tightly controlled, just as most of our own responses are automatic and tightly controlled. If they weren’t, we too would drop dead any second. The key word in your comment is “most”. Cellular intelligence manifests itself in the responses that are not automatic! Those scientists who support the concept have observed bacteria solving new problems. Yes, the solutions always involve chemical processes – in us as in them – but the information demanding new actions has to be processed first, and then decisions have to be taken in order to change the existing structure/behaviour of the cell(s)/bacteria.

DAVID: My 'most' is not your most. Please describe the new problems bacteria solve. I don't see any but I do see epigenetic alterations of their DNA for very minor adaptations. And where did the information bacteria use come from? They didn't think it up on their own.

dhw: The proposal is that bacteria process information from their environment, presumably with what would be their equivalent of a brain. I don’t have time to research all the experiments and observations made by McClintock, Margulis, James Shapiro, Albrecht Bühler or all the other scientists who support the theory that bacteria are intelligent, but earlier you admitted that they are in a majority.

Newer concepts come from a minority (Thomas Kuhn). Yes bacteria process information from their environment but decision making for responses requires the use of internal information at their disposal . Where did that information come from? Your favorite scientists cannot tell you


dhw: You have always agreed that the decision-making process shows intelligence, but you attribute that to your God’s preprogramming, though allowing for a 50/50 chance that “my” scientists might be right. Please stop pretending that automatic chemical responses in bacteria prove they are not intelligent and have been preprogrammed by your God. But thank you for your all-important “most”. It’s the rest that demonstrate intelligence.

DAVID: You persist is misinterpreting my 50/50 as it simply describes the possibilities for the existence of information. Either it was implanted in the beginning or bacteria developed it on their own. I totally reject the latter possibility as you well know. Bacteria cannot and do not think, much as you want them to, as a way of avoiding God.

dhw: Yes, you totally reject the autonomously intelligent 50, although many scientists accept it, and for the hundredth time, this is NOT a way of avoiding God, because in hundreds of posts I keep reiterating that your God may be the inventor of cellular intelligence.But it is certainly a way of avoiding a particular theory about God's motives and methods which we humans, yourself included, find illogical.

I find nothing illogical in my theories. Pretending that I do is silly. It dos not advance our discussion.

Biological complexity: feedback loops are vital

by dhw, Sunday, September 22, 2019, 10:51 (1650 days ago) @ David Turell

dhw: The proposal is that bacteria process information from their environment, presumably with what would be their equivalent of a brain. I don’t have time to research all the experiments and observations made by McClintock, Margulis, James Shapiro, Albrecht Bühler or all the other scientists who support the theory that bacteria are intelligent, but earlier you admitted that they are in a majority.

DAVID: Newer concepts come from a minority (Thomas Kuhn). Yes bacteria process information from their environment but decision making for responses requires the use of internal information at their disposal. Where did that information come from? Your favorite scientists cannot tell you.

Or to put it a different way, decision-making requires the use of intelligence. Where did that intelligence come from? Maybe from your God. Nobody knows. Materialists believe intelligence comes from the brain, which is a mass of individual cells. In that case bacterial intelligence would come from the bacterial equivalent of a brain within a cell.

DAVID: Bacteria cannot and do not think, much as you want them to, as a way of avoiding God.

dhw: Yes, you totally reject the autonomously intelligent 50, although many scientists accept it, and for the hundredth time, this is NOT a way of avoiding God, because in hundreds of posts I keep reiterating that your God may be the inventor of cellular intelligence.But it is certainly a way of avoiding a particular theory about God's motives and methods which we humans, yourself included, find illogical.

DAVID: I find nothing illogical in my theories. Pretending that I do is silly. It dos not advance our discussion.

Your theory is that your God’s only purpose was to design H. sapiens, but he decided to wait 3.X billion years before starting to evolve (= specially design) all the different hominids and homos that led to his goal, and therefore had to evolve (= specially design) billions of life forms to keep life going. And you say to me: “Haven’t you realized by now, I have no idea why God chose to evolve humans over time.” I suggest that if you have no idea why God would choose this way of achieving his goal, you do not find it logical. Indeed, you even go so far as to say that God’s logic must be different from human logic!

Biological complexity: feedback loops are vital

by David Turell @, Sunday, September 22, 2019, 16:12 (1650 days ago) @ dhw

dhw: The proposal is that bacteria process information from their environment, presumably with what would be their equivalent of a brain. I don’t have time to research all the experiments and observations made by McClintock, Margulis, James Shapiro, Albrecht Bühler or all the other scientists who support the theory that bacteria are intelligent, but earlier you admitted that they are in a majority.

DAVID: Newer concepts come from a minority (Thomas Kuhn). Yes bacteria process information from their environment but decision making for responses requires the use of internal information at their disposal. Where did that information come from? Your favorite scientists cannot tell you.

dhw: Or to put it a different way, decision-making requires the use of intelligence. Where did that intelligence come from? Maybe from your God. Nobody knows. Materialists believe intelligence comes from the brain, which is a mass of individual cells.

Back to the discussion ab out the bab y brain being a blank slate, except for inherited tendencies.

dhw: In that case bacterial intelligence would come from the bacterial equivalent of a brain within a cell.

Such brainy organelle has never been described.


DAVID: Bacteria cannot and do not think, much as you want them to, as a way of avoiding God.

dhw: Yes, you totally reject the autonomously intelligent 50, although many scientists accept it, and for the hundredth time, this is NOT a way of avoiding God, because in hundreds of posts I keep reiterating that your God may be the inventor of cellular intelligence.But it is certainly a way of avoiding a particular theory about God's motives and methods which we humans, yourself included, find illogical.

DAVID: I find nothing illogical in my theories. Pretending that I do is silly. It does not advance our discussion.

dhw: Your theory is that your God’s only purpose was to design H. sapiens, but he decided to wait 3.X billion years before starting to evolve (= specially design) all the different hominids and homos that led to his goal, and therefore had to evolve (= specially design) billions of life forms to keep life going. And you say to me: “Haven’t you realized by now, I have no idea why God chose to evolve humans over time.” I suggest that if you have no idea why God would choose this way of achieving his goal, you do not find it logical. Indeed, you even go so far as to say that God’s logic must be different from human logic!

Same tired mantra: I don't try to guess at God's reasoning. And I do fully feel His choice was logical and reasonable for Him. As you humanize god, you don't.

Biological complexity: how cholesterol enters cells

by David Turell @, Monday, September 23, 2019, 01:42 (1649 days ago) @ David Turell

Cholesterol is carried in the blood and must enter cells to be used. A very complex protein mechanism is shown:

https://www.sciencedaily.com/releases/2019/09/190920111345.htm

"Most people have heard of "cholesterol levels" and the dangers of high blood cholesterol, which is one of the main causes of cardiovascular disease. But besides the harmful side effects of high cholesterol, cholesterol is an essential component of all cells and fundamental to a host of important functions of the body. Hormones like estrogen and testosterone are made from cholesterol, for example.

"It has been known for a long time that cholesterol is transported around the body in the blood as small particles consisting of fat and protein. In the body's cells, these particles are broken down and cholesterol is released and integrated as part of the cell. Although this process is essential, not just for humans, but for all animals and plants, surprisingly little is known about how cholesterol is actually incorporated into the cells after the breakdown of these particles.

From the study itself:

https://www.cell.com/cell/fulltext/S0092-8674(19)30957-2?_returnURL=https%3A%2F%2Flinki...

Summary: "Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, using a combination of crystallography, cryo-electron microscopy, and biochemical and in vivo studies on the Saccharomyces cerevisiae NPC system (NCR1 and NPC2), we present a framework for sterol membrane integration. Sterols are transferred between hydrophobic pockets of vacuolar NPC2 and membrane-protein NCR1. NCR1 has its N-terminal domain (NTD) positioned to deliver a sterol to a tunnel connecting NTD to the luminal membrane leaflet 50 Å away. A sterol is caught inside this tunnel during transport, and a proton-relay network of charged residues in the transmembrane region is linked to this tunnel supporting a proton-driven transport mechanism. We propose a model for sterol integration that clarifies the role of NPC proteins in this essential eukaryotic pathway and that rationalizes mutations in patients with Niemann-Pick disease type C."

Comment: The description is difficult to follow. Look at the diagram on the website to see how complex is this protein arrangement. Not by chance. Requires design in the very beginning of this geologic period for organisms like the Cambrian animals to have survived.

Biological complexity: feedback loops are vital

by dhw, Monday, September 23, 2019, 11:34 (1649 days ago) @ David Turell

dhw: The proposal is that bacteria process information from their environment, presumably with what would be their equivalent of a brain. I don’t have time to research all the experiments and observations made by McClintock, Margulis, James Shapiro, Albrecht Bühler or all the other scientists who support the theory that bacteria are intelligent, but earlier you admitted that they are in a majority.

DAVID: Newer concepts come from a minority (Thomas Kuhn). Yes bacteria process information from their environment but decision making for responses requires the use of internal information at their disposal. Where did that information come from? Your favorite scientists cannot tell you.

dhw: Or to put it a different way, decision-making requires the use of intelligence. Where did that intelligence come from? Maybe from your God. Nobody knows. Materialists believe intelligence comes from the brain, which is a mass of individual cells.

DAVID: Back to the discussion about the baby brain being a blank slate, except for inherited tendencies.

We are talking about bacterial intelligence.

dhw: In that case bacterial intelligence would come from the bacterial equivalent of a brain within a cell.

DAVID: Such brainy organelle has never been described.

Albrecht-Buehler thinks the centrosome and centrioles constitute the “brain” and “eyes” of the cell. Who knows? Nobody has yet succeeded in describing how ANY form of intelligence is generated. We only have theories.

DAVID: Comment (under “Genome complexity”): The importance of activating the correct genes in each cell is backed up by a complex of six special proteins each of which can do the job. Such a system has to be designed, and cannot develop by chance. How does a mindless mechanism recognize the need for such an important backup system?

There is a similar comment under “How cholesterol enters cells”. It is unfortunate that there are no atheists currently contributing to this forum. I do miss George Jelliss! For me, the complexity of the cell alone is sufficient to cast doubt on the chance theory that is the atheist alternative to design. I accept the atheist argument that one mystery (God) doesn’t solve another mystery (life’s complexity), which is why I stay on my agnostic fence, but I would really like to know how an atheist justifies his faith in the ability of chance to create the mechanisms of the cell.

The rest of your post is quoted and amply covered under "Natural Wonders and Evolution".

Biological complexity: feedback loops are vital

by David Turell @, Monday, September 23, 2019, 18:22 (1649 days ago) @ dhw

dhw: Or to put it a different way, decision-making requires the use of intelligence. Where did that intelligence come from? Maybe from your God. Nobody knows. Materialists believe intelligence comes from the brain, which is a mass of individual cells.

DAVID: Back to the discussion about the baby brain being a blank slate, except for inherited tendencies.

dhw: We are talking about bacterial intelligence.

No, intelligent responses requires intelligent information or a brain that creates its own intelligence as babies eventually do.


dhw: In that case bacterial intelligence would come from the bacterial equivalent of a brain within a cell.

DAVID: Such brainy organelle has never been described.

dhw: Albrecht-Buehler thinks the centrosome and centrioles constitute the “brain” and “eyes” of the cell. Who knows? Nobody has yet succeeded in describing how ANY form of intelligence is generated. We only have theories.

A-B is a solo practitioner of his theory. Intelligence is part of consciousness, by learning and thinking. it is consciousness we don't understand. Intelligence involves information, a concept in cells, which you have problems in understanding. I think God supplied it when He started life.


DAVID: Comment (under “Genome complexity”): The importance of activating the correct genes in each cell is backed up by a complex of six special proteins each of which can do the job. Such a system has to be designed, and cannot develop by chance. How does a mindless mechanism recognize the need for such an important backup system?

dhw: There is a similar comment under “How cholesterol enters cells”. It is unfortunate that there are no atheists currently contributing to this forum. I do miss George Jelliss! For me, the complexity of the cell alone is sufficient to cast doubt on the chance theory that is the atheist alternative to design. I accept the atheist argument that one mystery (God) doesn’t solve another mystery (life’s complexity), which is why I stay on my agnostic fence, but I would really like to know how an atheist justifies his faith in the ability of chance to create the mechanisms of the cell.

What you do not accept is the necessity of a signing mind having to exist.

Biological complexity: feedback loops are vital

by dhw, Tuesday, September 24, 2019, 09:03 (1648 days ago) @ David Turell

dhw: Or to put it a different way, decision-making requires the use of intelligence. Where did that intelligence come from? Maybe from your God. Nobody knows. Materialists believe intelligence comes from the brain, which is a mass of individual cells.

DAVID: Back to the discussion about the baby brain being a blank slate, except for inherited tendencies.

dhw: We are talking about bacterial intelligence.

DAVID: No, intelligent responses requires intelligent information or a brain that creates its own intelligence as babies eventually do.

Please explain how information can be intelligent. Does information think, communicate, make decisions? Intelligent responses demand the ability to process information from outside (e.g. changing conditions) and from inside (e.g. the organism’s possible limitations: the pre-whale would know that it cannot escape from barren land by flying, but taking to the water is a viable proposition). Bacteria appear to be able to use both forms of information, and to take their decisions accordingly. Bacteria do not have a brain as such, but perhaps they have the equivalent of a brain. After all, we don’t even know how brains generate intelligence.

DAVID: Such brainy organelle has never been described.

dhw: Albrecht-Buehler thinks the centrosome and centrioles constitute the “brain” and “eyes” of the cell. Who knows? Nobody has yet succeeded in describing how ANY form of intelligence is generated. We only have theories.

DAVID: A-B is a solo practitioner of his theory. Intelligence is part of consciousness, by learning and thinking. it is consciousness we don't understand. Intelligence involves information, a concept in cells, which you have problems in understanding. I think God supplied it when He started life.

That is precisely the theistic version of my theory: that God supplied the cells with consciousness (not to be confused with human self-awareness), of which intelligence is part, when he started life. Thank you.

DAVID: Comment (under “Genome complexity”): […] Such a system has to be designed, and cannot develop by chance. How does a mindless mechanism recognize the need for such an important backup system?

dhw: […] It is unfortunate that there are no atheists currently contributing to this forum. I do miss George Jelliss! For me, the complexity of the cell alone is sufficient to cast doubt on the chance theory that is the atheist alternative to design. I accept the atheist argument that one mystery (God) doesn’t solve another mystery (life’s complexity), which is why I stay on my agnostic fence, but I would really like to know how an atheist justifies his faith in the ability of chance to create the mechanisms of the cell.

DAVID: What you do not accept is the necessity of a signing mind having to exist.

What you do not accept is that a designing mind (which even you say is “hidden”) is just as great a mystery as the origin of life’s complexities. Hence my agnosticism.

Biological complexity: feedback loops are vital

by David Turell @, Tuesday, September 24, 2019, 17:54 (1648 days ago) @ dhw

DAVID: No, intelligent responses requires intelligent information or a brain that creates its own intelligence as babies eventually do.

dhw: Please explain how information can be intelligent. Does information think, communicate, make decisions? Intelligent responses demand the ability to process information from outside (e.g. changing conditions) and from inside (e.g. the organism’s possible limitations: the pre-whale would know that it cannot escape from barren land by flying, but taking to the water is a viable proposition). Bacteria appear to be able to use both forms of information, and to take their decisions accordingly. Bacteria do not have a brain as such, but perhaps they have the equivalent of a brain. After all, we don’t even know how brains generate intelligence.

Properly functioning information must be designed by an intelligent mind, which provides meaningful processes in the cell and appropriate responses to challenges. I agree information itself is not intelligent, but its source must be. I was writing a sort of shorthand in my response.


DAVID: Such brainy organelle has never been described.

dhw: Albrecht-Buehler thinks the centrosome and centrioles constitute the “brain” and “eyes” of the cell. Who knows? Nobody has yet succeeded in describing how ANY form of intelligence is generated. We only have theories.

DAVID: A-B is a solo practitioner of his theory. Intelligence is part of consciousness, by learning and thinking. it is consciousness we don't understand. Intelligence involves information, a concept in cells, which you have problems in understanding. I think God supplied it when He started life.

dhw: That is precisely the theistic version of my theory: that God supplied the cells with consciousness (not to be confused with human self-awareness), of which intelligence is part, when he started life. Thank you.

I don't think He made bacteria or cells conscious in the usual way we mean. He gave them intelligently drawn information to use in appropriate ways.


DAVID: Comment (under “Genome complexity”): […] Such a system has to be designed, and cannot develop by chance. How does a mindless mechanism recognize the need for such an important backup system?

dhw: […] It is unfortunate that there are no atheists currently contributing to this forum. I do miss George Jelliss! For me, the complexity of the cell alone is sufficient to cast doubt on the chance theory that is the atheist alternative to design. I accept the atheist argument that one mystery (God) doesn’t solve another mystery (life’s complexity), which is why I stay on my agnostic fence, but I would really like to know how an atheist justifies his faith in the ability of chance to create the mechanisms of the cell.

DAVID: What you do not accept is the necessity of a signing mind having to exist.

dhw: What you do not accept is that a designing mind (which even you say is “hidden”) is just as great a mystery as the origin of life’s complexities. Hence my agnosticism.

Of course the designing mind is a mystery, but an obvious requirement to explain the designs in life. Life's designs do not occur by chance.

Biological complexity: feedback loops are vital

by dhw, Wednesday, September 25, 2019, 11:54 (1647 days ago) @ David Turell

DAVID: intelligent responses requires intelligent information or a brain that creates its own intelligence as babies eventually do.

dhw: Please explain how information can be intelligent.

DAVID: Properly functioning information must be designed by an intelligent mind, which provides meaningful processes in the cell and appropriate responses to challenges. I agree information itself is not intelligent, but its source must be. I was writing a sort of shorthand in my response.

Not only is information not intelligent, but information doesn’t function. It requires intelligence to make it function. Your shorthand simply obscures the argument.

DAVID: Intelligence is part of consciousness, by learning and thinking. it is consciousness we don't understand. Intelligence involves information, a concept in cells, which you have problems in understanding. I think God supplied it when He started life.

dhw: That is precisely the theistic version of my theory: that God supplied the cells with consciousness (not to be confused with human self-awareness), of which intelligence is part, when he started life. Thank you.

DAVID: I don't think He made bacteria or cells conscious in the usual way we mean. He gave them intelligently drawn information to use in appropriate ways.

What is the “usual way we mean”? Intelligence involves conscious use of information. Consciousness involves awareness, the ability to process information, to communicate, to make decisions etc., and is not confined to human self-awareness. And yes indeed, if God exists, I agree that he would have supplied it when He started life. Thank you again.

Under "Big brain evolution": "If the mouse needed to prioritize auditory information, the prefrontal cortex told the visual TRN to increase its activity to suppress the visual thalamus — stripping away irrelevant visual data."

What we have here is a process in which all parts of the body (i.e. cell communities) tell one another what to do. The pre-frontal cortex appears to be the controlling cell community. In micro-organisms, there would have to be an equivalent. Communication and cooperation between cells is integral to all aspects of our lives, as illustrated in the next example:

Under "Immunity complexity": "The cells of our immune system constantly communicate with one another by exchanging complex protein molecules. A team has now revealed how dedicated cellular control proteins, referred to as chaperones, detect immature immune signaling proteins and prevent them from leaving the cell."

Communication and cooperation are the key to survival on all levels of existence.

DAVID: the immune system is vital to protect organisms from attack. Proper targets must be identified accurately, and release of antibodies controlled and prompt. This protection must have been designed in the beginning of life as all organisms need ways to block infections

I don’t think every “attacker” or “infection” was present at the beginning of life. Perhaps it might be more accurate to propose that the first cells were provided with the intelligence to adapt themselves to new conditions as and when they arose. Immune systems would therefore have developed enormously over time as they worked out ways to combat new threats but also preserved ways of combating old threats, just as single-celled bacteria do.

Biological complexity: feedback loops are vital

by David Turell @, Wednesday, September 25, 2019, 19:54 (1647 days ago) @ dhw

DAVID: Properly functioning information must be designed by an intelligent mind, which provides meaningful processes in the cell and appropriate responses to challenges. I agree information itself is not intelligent, but its source must be. I was writing a sort of shorthand in my response.

dhw: Not only is information not intelligent, but information doesn’t function

Exactly. The organism's responses are guided by the information in its genome which then induces obviously intelligent responses to stimuli by activating a proper mechanism to answer.


DAVID: I don't think He made bacteria or cells conscious in the usual way we mean. He gave them intelligently drawn information to use in appropriate ways.

What is the “usual way we mean”? Intelligence involves conscious use of information. Consciousness involves awareness, the ability to process information, to communicate, to make decisions etc., and is not confined to human self-awareness. And yes indeed, if God exists, I agree that he would have supplied it when He started life. Thank you again.

It does not have to be conscious responses, but automatic, as you fully understand, but don't want to accept.


dhw: Under "Big brain evolution": "If the mouse needed to prioritize auditory information, the prefrontal cortex told the visual TRN to increase its activity to suppress the visual thalamus — stripping away irrelevant visual data."

What we have here is a process in which all parts of the body (i.e. cell communities) tell one another what to do. The pre-frontal cortex appears to be the controlling cell community. In micro-organisms, there would have to be an equivalent. Communication and cooperation between cells is integral to all aspects of our lives, as illustrated in the next example:

Under "Immunity complexity": "The cells of our immune system constantly communicate with one another by exchanging complex protein molecules. A team has now revealed how dedicated cellular control proteins, referred to as chaperones, detect immature immune signaling proteins and prevent them from leaving the cell." (my bold)

Communication and cooperation are the key to survival on all levels of existence.

Of course, the exchange in my bold above can all be fully automatic.


DAVID: the immune system is vital to protect organisms from attack. Proper targets must be identified accurately, and release of antibodies controlled and prompt. This protection must have been designed in the beginning of life as all organisms need ways to block infections

dhw: I don’t think every “attacker” or “infection” was present at the beginning of life. Perhaps it might be more accurate to propose that the first cells were provided with the intelligence to adapt themselves to new conditions as and when they arose. Immune systems would therefore have developed enormously over time as they worked out ways to combat new threats but also preserved ways of combating old threats, just as single-celled bacteria do.

But the immune cells have to be given a way to code future responses. They can't invent those mechanisms by themselves on the fly while being attacked as attackers evolve. They must have had the basic mechanism from the beginning of life given to them by God.

Biological complexity: feedback loops are vital

by dhw, Thursday, September 26, 2019, 08:45 (1646 days ago) @ David Turell

DAVID: Properly functioning information must be designed by an intelligent mind, which provides meaningful processes in the cell and appropriate responses to challenges. I agree information itself is not intelligent, but its source must be. I was writing a sort of shorthand in my response.

dhw: Not only is information not intelligent, but information doesn’t function

DAVID: Exactly. The organism's responses are guided by the information in its genome which then induces obviously intelligent responses to stimuli by activating a proper mechanism to answer.

Thank you for once more agreeing with me, though in an extraordinarily roundabout fashion. Information is not intelligent and information is not functioning. The “proper mechanism” which provides intelligent responses to stimuli is what we call intelligence.

DAVID: I don't think He made bacteria or cells conscious in the usual way we mean. He gave them intelligently drawn information to use in appropriate ways.

dhw: What is the “usual way we mean”? Intelligence involves conscious use of information. consciousness involves awareness, the ability to process information, to communicate, to make decisions etc., and is not confined to human self-awareness. And yes indeed, if God exists, I agree that he would have supplied it when He started life. Thank you again.

DAVID: It does not have to be conscious responses, but automatic, as you fully understand, but don't want to accept.

No, it does not “have to be”, but it may be. If it is automatic, that means your God must have preprogrammed the first cells with every single undabbled intelligent response to every single situation that would arise then, now and for evermore. However, the responses do not “have to be” automatic but may be conscious, “as you fully understand but don’t want to accept”.

Under "Immunity complexity": "The cells of our immune system constantly communicate with one another by exchanging complex protein molecules. A team has now revealed how dedicated cellular control proteins, referred to as chaperones, detect immature immune signaling proteins and prevent them from leaving the cell."

dhw: Communication and cooperation are the key to survival on all levels of existence.

DAVID: Of course, the exchange in my bold above can all be fully automatic.

Or, of course, can be fully conscious.

DAVID (re “stromatolites”: If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

Very interesting. I like your use of the word “organized”. Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: ..the immune system is vital to protect organisms from attack. Proper targets must be identified accurately, and release of antibodies controlled and prompt. This protection must have been designed in the beginning of life as all organisms need ways to block infections

dhw: I don’t think every “attacker” or “infection” was present at the beginning of life. Perhaps it might be more accurate to propose that the first cells were provided with the intelligence to adapt themselves to new conditions as and when they arose. Immune systems would therefore have developed enormously over time as they worked out ways to combat new threats but also preserved ways of combating old threats, just as single-celled bacteria do.

DAVID: But the immune cells have to be given a way to code future responses. They can't invent those mechanisms by themselves on the fly while being attacked as attackers evolve. They must have had the basic mechanism from the beginning of life given to them by God.

Precisely. Thank you for once more accepting the theistic version of my hypothesis. The way to respond as attackers evolve is provided by a basic mechanism which must have been there from the beginning – and possibly given to them by your God. I have called it cellular intelligence. What do you call it?

Biological complexity: feedback loops are vital

by David Turell @, Thursday, September 26, 2019, 19:56 (1646 days ago) @ dhw

dhw: Not only is information not intelligent, but information doesn’t function

DAVID: Exactly. The organism's responses are guided by the information in its genome which then induces obviously intelligent responses to stimuli by activating a proper mechanism to answer.

dhw: Thank you for once more agreeing with me, though in an extraordinarily roundabout fashion. Information is not intelligent and information is not functioning. The “proper mechanism” which provides intelligent responses to stimuli is what we call intelligence.

I'll remind you, the intelligent responses are in my view all automatic, because of the quality of the information


DAVID: It does not have to be conscious responses, but automatic, as you fully understand, but don't want to accept.

dhw: No, it does not “have to be”, but it may be. If it is automatic, that means your God must have preprogrammed the first cells with every single undabbled intelligent response to every single situation that would arise then, now and for evermore. However, the responses do not “have to be” automatic but may be conscious, “as you fully understand but don’t want to accept”.

no , I don't.


Under "Immunity complexity": "The cells of our immune system constantly communicate with one another by exchanging complex protein molecules. A team has now revealed how dedicated cellular control proteins, referred to as chaperones, detect immature immune signaling proteins and prevent them from leaving the cell."

dhw: Communication and cooperation are the key to survival on all levels of existence.

DAVID: Of course, the exchange in my bold above can all be fully automatic.

dhw: Or, of course, can be fully conscious.

DAVID (re “stromatolites”: If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

dhw: Very interesting. I like your use of the word “organized”. Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

Each cell is alive and fully organized, no more.


dhw: I don’t think every “attacker” or “infection” was present at the beginning of life. Perhaps it might be more accurate to propose that the first cells were provided with the intelligence to adapt themselves to new conditions as and when they arose. Immune systems would therefore have developed enormously over time as they worked out ways to combat new threats but also preserved ways of combating old threats, just as single-celled bacteria do.

DAVID: But the immune cells have to be given a way to code future responses. They can't invent those mechanisms by themselves on the fly while being attacked as attackers evolve. They must have had the basic mechanism from the beginning of life given to them by God.

dhw: Precisely. Thank you for once more accepting the theistic version of my hypothesis. The way to respond as attackers evolve is provided by a basic mechanism which must have been there from the beginning – and possibly given to them by your God. I have called it cellular intelligence. What do you call it?

An appropriate mechanism provided by God.

Biological complexity: feedback loops are vital

by dhw, Friday, September 27, 2019, 18:25 (1645 days ago) @ David Turell

dhw: Not only is information not intelligent, but information doesn’t function

DAVID: Exactly. The organism's responses are guided by the information in its genome which then induces obviously intelligent responses to stimuli by activating a proper mechanism to answer.

dhw: Thank you for once more agreeing with me, though in an extraordinarily roundabout fashion. Information is not intelligent and information is not functioning. The “proper mechanism” which provides intelligent responses to stimuli is what we call intelligence.

DAVID: I'll remind you, the intelligent responses are in my view all automatic, because of the quality of the information.

What information are you talking about? The information which you now agree is not intelligent, or the information which you now agree doesn’t function? Stop tying yourself in knots with “information” and stick to the fact that you believe every single intelligent response was either divinely preprogrammed 3.8 billion years ago to be passed on by the very first cells, or was directly dabbled by your God.

DAVID (re “stromatolites”): If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

dhw: Very interesting. I like your use of the word “organized”. Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: Each cell is alive and fully organized, no more.

If organized cells bunched together, why do you ignore cooperation?

dhw: I don’t think every “attacker” or “infection” was present at the beginning of life. Perhaps it might be more accurate to propose that the first cells were provided with the intelligence to adapt themselves to new conditions as and when they arose. Immune systems would therefore have developed enormously over time as they worked out ways to combat new threats but also preserved ways of combating old threats, just as single-celled bacteria do.

DAVID: But the immune cells have to be given a way to code future responses. They can't invent those mechanisms by themselves on the fly while being attacked as attackers evolve. They must have had the basic mechanism from the beginning of life given to them by God.

dhw: Precisely. Thank you for once more accepting the theistic version of my hypothesis. The way to respond as attackers evolve is provided by a basic mechanism which must have been there from the beginning – and possibly given to them by your God. I have called it cellular intelligence. What do you call it?

DAVID: An appropriate mechanism provided by God.

I’ve already allowed for “provided by God”. So you call the basic mechanism an appropriate mechanism. Obviously it’s appropriate since it works!

Biological complexity: feedback loops are vital

by David Turell @, Friday, September 27, 2019, 22:38 (1645 days ago) @ dhw

DAVID: I'll remind you, the intelligent responses are in my view all automatic, because of the quality of the information.

d hwK: What information are you talking about? The information which you now agree is not intelligent, or the information which you now agree doesn’t function? Stop tying yourself in knots with “information” and stick to the fact that you believe every single intelligent response was either divinely preprogrammed 3.8 billion years ago to be passed on by the very first cells, or was directly dabbled by your God.

you still don't understand the meaning of 'intelligent information'. It is a carefully set of instructions for the organisms to follow. Information is not active, as you note, but the organisms c an use it to activate processes.


DAVID (re “stromatolites”): If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

dhw: Very interesting. I like your use of the word “organized”. Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: Each cell is alive and fully organized, no more.

dhw: If organized cells bunched together, why do you ignore cooperation?

I agree. As in bacterial mats cells will function somewhat differently, but each cell has its own c omplete internal organization


dhw: I don’t think every “attacker” or “infection” was present at the beginning of life. Perhaps it might be more accurate to propose that the first cells were provided with the intelligence to adapt themselves to new conditions as and when they arose. Immune systems would therefore have developed enormously over time as they worked out ways to combat new threats but also preserved ways of combating old threats, just as single-celled bacteria do.

DAVID: But the immune cells have to be given a way to code future responses. They can't invent those mechanisms by themselves on the fly while being attacked as attackers evolve. They must have had the basic mechanism from the beginning of life given to them by God.

dhw: Precisely. Thank you for once more accepting the theistic version of my hypothesis. The way to respond as attackers evolve is provided by a basic mechanism which must have been there from the beginning – and possibly given to them by your God. I have called it cellular intelligence. What do you call it?

DAVID: An appropriate mechanism provided by God.

d hw: I’ve already allowed for “provided by God”. So you call the basic mechanism an appropriate mechanism. Obviously it’s appropriate since it works!

Yes, it works. agreed.

Biological complexity: feedback loops are vital

by dhw, Saturday, September 28, 2019, 10:52 (1644 days ago) @ David Turell

DAVID: I'll remind you, the intelligent responses are in my view all automatic, because of the quality of the information.

dhw: What information are you talking about? The information which you now agree is not intelligent, or the information which you now agree doesn’t function? Stop tying yourself in knots with “information” and stick to the fact that you believe every single intelligent response was either divinely preprogrammed 3.8 billion years ago to be passed on by the very first cells, or was directly dabbled by your God.

DAVID: you still don't understand the meaning of 'intelligent information'. It is a carefully set of instructions for the organisms to follow. Information is not active, as you note, but the organisms can use it to activate processes.

DAVID (September 25): I agree information is not intelligent, but its source must be. I was writing a sort of shorthand in my response.

And now back you go to your shorthand. We have intelligent information which is not intelligent, and we have functioning information which is not functioning, and now we have intelligent information which is instructions. Why don’t you just use the word instructions instead of faffing about with “information”? And yes, that is another way of saying you believe your God provided the very first cells with instructions or programmes for every bacterial response, organismal innovation, lifestyle and natural wonder in the history of life past, present and future. Meanwhile, I suggest you stick to your excellent last sentence: information is not active (and not intelligent, and not functioning), and it requires the intelligence of organisms to use it. Perfectly simple.

DAVID (re “stromatolites”): If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

dhw: Very interesting. I like your use of the word “organized”. Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: Each cell is alive and fully organized, no more.

dhw: If organized cells bunched together, why do you ignore cooperation?

DAVID: I agree. As in bacterial mats cells will function somewhat differently, but each cell has its own complete internal organization,

Precisely: a neat description of how different, autonomous, intelligent cells cooperate to form “mats” and organs and organisms. That is the gist of my hypothesis.

Biological complexity: feedback loops are vital

by David Turell @, Saturday, September 28, 2019, 16:00 (1644 days ago) @ dhw

DAVID: I'll remind you, the intelligent responses are in my view all automatic, because of the quality of the information.

dhw: What information are you talking about? The information which you now agree is not intelligent, or the information which you now agree doesn’t function? Stop tying yourself in knots with “information” and stick to the fact that you believe every single intelligent response was either divinely preprogrammed 3.8 billion years ago to be passed on by the very first cells, or was directly dabbled by your God.

DAVID: you still don't understand the meaning of 'intelligent information'. It is a carefully set of instructions for the organisms to follow. Information is not active, as you note, but the organisms can use it to activate processes.

DAVID (September 25): I agree information is not intelligent, but its source must be. I was writing a sort of shorthand in my response.

dhw: And now back you go to your shorthand. We have intelligent information which is not intelligent, and we have functioning information which is not functioning, and now we have intelligent information which is instructions. Why don’t you just use the word instructions instead of faffing about with “information”? And yes, that is another way of saying you believe your God provided the very first cells with instructions or programmes for every bacterial response, organismal innovation, lifestyle and natural wonder in the history of life past, present and future. Meanwhile, I suggest you stick to your excellent last sentence: information is not active (and not intelligent, and not functioning), and it requires the intelligence of organisms to use it. Perfectly simple. (my bold)

The bold is not my concept. The organisms automatically use the information to guide their actions


DAVID (re “stromatolites”): If it is agreed this is acceptable evidence, then life was certainly on Earth very early, considering that the Earth formed about 4.5 byo and is considered to have been too hot of life at 4 byo. These appear to be organized organisms, advanced beyond what simple early life may have looked like.

dhw: Very interesting. I like your use of the word “organized”. Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: Each cell is alive and fully organized, no more.

dhw: If organized cells bunched together, why do you ignore cooperation?

DAVID: I agree. As in bacterial mats cells will function somewhat differently, but each cell has its own complete internal organization,

dhw: Precisely: a neat description of how different, autonomous, intelligent cells cooperate to form “mats” and organs and organisms. That is the gist of my hypothesis.

Neat try: The leap from mats to organs requires intelligent design.

Biological complexity: feedback loops are vital

by dhw, Sunday, September 29, 2019, 08:35 (1643 days ago) @ David Turell

dhw:[…] . We have intelligent information which is not intelligent, and we have functioning information which is not functioning, and now we have intelligent information which is instructions. Why don’t you just use the word instructions instead of faffing about with “information”? And yes, that is another way of saying you believe your God provided the very first cells with instructions or programmes for every bacterial response, organismal innovation, lifestyle and natural wonder in the history of life past, present and future. Meanwhile, I suggest you stick to your excellent last sentence: information is not active (and not intelligent, and not functioning), and it requires the intelligence of organisms to use it. Perfectly simple. (my bold)

DAVID: The bold is not my concept. The organisms automatically use the information to guide their actions.

Which information are you talking about now? You wrote: "you still don't understand the meaning of 'intelligent information'. It is a carefully set of instructions for the organisms to follow. Information is not active, as you note, but the organisms can use it to activate processes." So now we have a set of instructions, and the organisms “automatically” use the instructions, which means they have received a set of instructions telling them how to use the set of instructions in order to activate processes. And this simply doubles the problem because you say that instructions are information, but information is not active. How, then, can organisms actively use information about how to use information? Counter proposal: Organisms actively use information about outside conditions and about their own composition in order to activate processes. Many scientists believe that their ability to use this information springs from autonomous intelligence, but I know of one who believes that they are all machines that were preprogrammed 3.8 billion years ago.

dhw: (re “stromatolites”): Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: Each cell is alive and fully organized, no more.

dhw: If organized cells bunched together, why do you ignore cooperation?

DAVID: I agree. As in bacterial mats cells will function somewhat differently, but each cell has its own complete internal organization,

dhw: Precisely: a neat description of how different, autonomous, intelligent cells cooperate to form “mats” and organs and organisms. That is the gist of my hypothesis.

DAVID: Neat try: The leap from mats to organs requires intelligent design.

Yes of course, and my point is that mats are the product of intelligent design by individual cells combining, and organs are the product of intelligent design by increasingly complex combinations or communities of cells.


Under "Natural Wonders":
QUOTE: "Like a brain, an ant colony operates without central control. Each is a set of interacting individuals, either neurons or ants, using simple chemical interactions that in the aggregate generate their behaviour."

This is the analogy I have often used myself, and it illustrates perfectly how intelligent cells/ants cooperate to produce a functioning brain/colony.

QUOTES: "From day to day, the colony’s behaviour changes, and what happens on one day affects the next."

"Ants use the rate at which they meet and smell other ants, or the chemicals deposited by other ants, to decide what to do next...".

DAVID: As with bridges, automatic individual reactions make the whole colony operate as a unit.

They take new decisions every day according to individual reactions, but clearly they retain memory of earlier successful discoveries (e.g. how to form a bridge). Where have you found the word “automatic”? Do you really believe your God dabbles each new decision, or preprogrammed it 3.8 billion years ago?

Biological complexity: feedback loops are vital

by David Turell @, Sunday, September 29, 2019, 19:28 (1643 days ago) @ dhw

DAVID: The bold is not my concept. The organisms automatically use the information to guide their actions.

dhw: Which information are you talking about now? You wrote: "you still don't understand the meaning of 'intelligent information'. It is a carefully set of instructions for the organisms to follow. Information is not active, as you note, but the organisms can use it to activate processes." So now we have a set of instructions, and the organisms “automatically” use the instructions, which means they have received a set of instructions telling them how to use the set of instructions in order to activate processes. And this simply doubles the problem because you say that instructions are information, but information is not active. How, then, can organisms actively use information about how to use information? Counter proposal: Organisms actively use information about outside conditions and about their own composition in order to activate processes. Many scientists believe that their ability to use this information springs from autonomous intelligence, but I know of one who believes that they are all machines that were preprogrammed 3.8 billion years ago.

I agree my theories are mine. In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created. The organisms are programmed to automatically respond to instructions in the information. It is a complexity created by God.


dhw: (re “stromatolites”): Here we seem to have the beginnings of the cooperation between cells which forms the whole basis of evolution.

DAVID: Each cell is alive and fully organized, no more.

dhw: If organized cells bunched together, why do you ignore cooperation?

DAVID: I agree. As in bacterial mats cells will function somewhat differently, but each cell has its own complete internal organization,

dhw: Precisely: a neat description of how different, autonomous, intelligent cells cooperate to form “mats” and organs and organisms. That is the gist of my hypothesis.

DAVID: Neat try: The leap from mats to organs requires intelligent design.

dhw: Yes of course, and my point is that mats are the product of intelligent design by individual cells combining, and organs are the product of intelligent design by increasingly complex combinations or communities of cells.

I know your theory. For me it stretches credulity


Under "Natural Wonders":
QUOTE: "Like a brain, an ant colony operates without central control. Each is a set of interacting individuals, either neurons or ants, using simple chemical interactions that in the aggregate generate their behaviour."

dhw: This is the analogy I have often used myself, and it illustrates perfectly how intelligent cells/ants cooperate to produce a functioning brain/colony.

QUOTES: "From day to day, the colony’s behaviour changes, and what happens on one day affects the next."

"Ants use the rate at which they meet and smell other ants, or the chemicals deposited by other ants, to decide what to do next...".

DAVID: As with bridges, automatic individual reactions make the whole colony operate as a unit.

dhw: They take new decisions every day according to individual reactions, but clearly they retain memory of earlier successful discoveries (e.g. how to form a bridge). Where have you found the word “automatic”? Do you really believe your God dabbles each new decision, or preprogrammed it 3.8 billion years ago?

You miss the point above. The individual ants are programmed for exactly the same responses in each situation. Results differ for the whole colony because of those individual responses under different circumstances.

Biological complexity: feedback loops are vital

by dhw, Monday, September 30, 2019, 13:24 (1642 days ago) @ David Turell

dhw: [...] information is not active (and not intelligent and not functioning), and it requires the intelligence of organisms to use it. Perfectly simple.

DAVID: In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created.

Precisely. I am an intelligent organism (I hope you’ll agree), and I actively use my intelligence to create something out of whatever non-intelligent, non-functioning instructions/information are at my disposal. Thank you for an excellent analogy.

DAVID: The organisms are programmed to automatically respond to instructions in the information. It is a complexity created by God.

If they are programmed to respond automatically to the instructions, it means they have instructions on how to use the instructions, so what do they use to follow the instructions on how to use the instructions in order to create or respond to something? Whether the complexity was created by God or not makes no difference to the process whereby organisms actively use non-active information.

Under "Natural Wonders":

QUOTE: "Like a brain, an ant colony operates without central control. Each is a set of interacting individuals, either neurons or ants, using simple chemical interactions that in the aggregate generate their behaviour."

dhw: This is the analogy I have often used myself, and it illustrates perfectly how intelligent cells/ants cooperate to produce a functioning brain/colony.

QUOTES: "From day to day, the colony’s behaviour changes, and what happens on one day affects the next."
"Ants use the rate at which they meet and smell other ants, or the chemicals deposited by other ants, to decide what to do next..
.".

DAVID: As with bridges, automatic individual reactions make the whole colony operate as a unit.

dhw: They take new decisions every day according to individual reactions, but clearly they retain memory of earlier successful discoveries (e.g. how to form a bridge). Where have you found the word “automatic”? Do you really believe your God dabbles each new decision, or preprogrammed it 3.8 billion years ago?

DAVID: You miss the point above. The individual ants are programmed for exactly the same responses in each situation. Results differ for the whole colony because of those individual responses under different circumstances.

It is you with your “automatic” and “programmed” who have missed the point above! In situations for which solutions have already been found, individuals will combine to repeat the same actions. The information has been passed on. It is when new conditions arise that individuals pool their intelligence to find new solutions (“from day to day the colony’s behaviour changes” and they “decide what to do next”…) Your theory means that your God programmed the first cells to pass on instructions for every single day-to-day decision taken by the ants (not to mention bacteria, and not to mention instructions for every single undabbled major adaptation/innovation, lifestyle and natural wonder in the history of life). Thousands and thousands of millions of programmes, all specially devised to cover the time before your God's "humans now" programmes either switched themselves on or he popped in 21 million years ago to start dabbling with a vertebra.

Biological complexity: feedback loops are vital

by David Turell @, Monday, September 30, 2019, 19:00 (1642 days ago) @ dhw

dhw: [...] information is not active (and not intelligent and not functioning), and it requires the intelligence of organisms to use it. Perfectly simple.

DAVID: In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created.

dhw: Precisely. I am an intelligent organism (I hope you’ll agree), and I actively use my intelligence to create something out of whatever non-intelligent, non-functioning instructions/information are at my disposal. Thank you for an excellent analogy.

DAVID: The organisms are programmed to automatically respond to instructions in the information. It is a complexity created by God.

dhw: If they are programmed to respond automatically to the instructions, it means they have instructions on how to use the instructions, so what do they use to follow the instructions on how to use the instructions in order to create or respond to something? Whether the complexity was created by God or not makes no difference to the process whereby organisms actively use non-active information.

The organisms work just as you do in the analogy. You are free to act. They are automatic with programmed reponses to the instructional information.


Under "Natural Wonders":

QUOTE: "Like a brain, an ant colony operates without central control. Each is a set of interacting individuals, either neurons or ants, using simple chemical interactions that in the aggregate generate their behaviour."

dhw: This is the analogy I have often used myself, and it illustrates perfectly how intelligent cells/ants cooperate to produce a functioning brain/colony.

QUOTES: "From day to day, the colony’s behaviour changes, and what happens on one day affects the next."
"Ants use the rate at which they meet and smell other ants, or the chemicals deposited by other ants, to decide what to do next..
.".

DAVID: As with bridges, automatic individual reactions make the whole colony operate as a unit.

dhw: They take new decisions every day according to individual reactions, but clearly they retain memory of earlier successful discoveries (e.g. how to form a bridge). Where have you found the word “automatic”? Do you really believe your God dabbles each new decision, or preprogrammed it 3.8 billion years ago?

DAVID: You miss the point above. The individual ants are programmed for exactly the same responses in each situation. Results differ for the whole colony because of those individual responses under different circumstances.

dhw: It is you with your “automatic” and “programmed” who have missed the point above! In situations for which solutions have already been found, individuals will combine to repeat the same actions. The information has been passed on. It is when new conditions arise that individuals pool their intelligence to find new solutions (“from day to day the colony’s behaviour changes” and they “decide what to do next”…) Your theory means that your God programmed the first cells to pass on instructions for every single day-to-day decision taken by the ants (not to mention bacteria, and not to mention instructions for every single undabbled major adaptation/innovation, lifestyle and natural wonder in the history of life). Thousands and thousands of millions of programmes, all specially devised to cover the time before your God's "humans now" programmes either switched themselves on or he popped in 21 million years ago to start dabbling with a vertebra.

You should go back to ant bridge studies: individual ants do what they are programmed to individually do in that circumstance as all other situations. The overall colony acts through these individual actions, as the Article shows..

Biological complexity: protein sensors

by David Turell @, Monday, September 30, 2019, 19:54 (1642 days ago) @ David Turell

There are about 800 of them at work:

https://phys.org/news/2019-09-reveal-molecular-basis-vision.html

"Researchers have solved the three-dimensional structure of a protein complex involved in vertebrate vision at atomic resolution, a finding that has broad implications for our understanding of biological signaling processes and the design of over a third of the drugs on the market today.

"The findings illuminate how signals from photons (particles of light) get amplified in the eye. More importantly, the study provides insights into how the largest family of cell membrane proteins—G-protein-coupled receptors (GPCRs) - work in humans.

"'They're involved in almost all the biological processes in a human body—how we perceive light, taste, smell, or how the heart rate is regulated or muscles contract—and they are targets for over 30% of the drugs that are used today," said Yang Gao, co-first author of the paper and a postdoctoral researcher...

***

"There are over 800 GPCRs in humans that signal through about 20 different G proteins. GPCRs are responsible for sensing a wide range of outside signals—such as hormones, light, and sense of smell and taste—and inducing corresponding responses inside the cell. In vertebrate vision, the GPCR rhodopsin is capable of detecting the signal from just one photon and through the activation of the G protein transducin and downstream effectors, amplify it 100,000 times. (my bold)

"The researchers used cryo-electron microscopy to obtain atomic-resolution structures of the rhodopsin-transducin complex. The structures not only provide the molecular basis of vertebrate vision, but also reveal a previously unknown mechanism of how GPCRs in general activate G proteins.

"'What we've learnt from these structures at an atomic level may be broadly applicable to other GPCR signaling systems," said co-first author Sekar Ramachandran, a senior research associate in Cerione's lab."

Comment: this is an intensely designed system of responding to stimuli. Chance mutation could not invent these precise sensory receptors. They had to be present when organisms appeared to protect the organisms.

Biological complexity: feedback loops are vital

by dhw, Tuesday, October 01, 2019, 09:42 (1641 days ago) @ David Turell

dhw: [...] information is not active (and not intelligent and not functioning), and it requires the intelligence of organisms to use it. Perfectly simple.

DAVID: In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created.

dhw: Precisely. I am an intelligent organism (I hope you’ll agree), and I actively use my intelligence to create something out of whatever non-intelligent, non-functioning instructions/information are at my disposal. Thank you for an excellent analogy.[…]

DAVID: The organisms work just as you do in the analogy. You are free to act. They are automatic with programmed responses to the instructional information.

If organisms work just as I do, and I am free to act, how do you manage to conclude that organisms are not free to act but are automatic and your God preprogrammed them 3.8 billion years ago?!

DAVID: (re ant colonies) As with bridges, automatic individual reactions make the whole colony operate as a unit.

dhw: They take new decisions every day according to individual reactions, but clearly they retain memory of earlier successful discoveries (e.g. how to form a bridge). Where have you found the word “automatic”? Do you really believe your God dabbles each new decision, or preprogrammed it 3.8 billion years ago? […]

DAVID: You should go back to ant bridge studies: individual ants do what they are programmed to individually do in that circumstance as all other situations. The overall colony acts through these individual actions, as the Article shows.

Once again: the bridge would have been the result of individuals pooling their intelligence to find a solution to a problem. Once the solution had proved successful, it would have been passed on, and so of course subsequent generations would follow the same procedure. It is when new conditions arise that individuals pool their intelligence to find new solutions. This is what “the article shows”: “from day to day the colony’s behaviour changes” and they “decide what to do next”… Not “3.8 billion years ago God supplied the first cells with a programme to pass on for whatever ants do next, on a day to day basis.”

Biological complexity: feedback loops are vital

by David Turell @, Wednesday, October 02, 2019, 00:35 (1640 days ago) @ dhw

DAVID: In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created.

dhw: Precisely. I am an intelligent organism (I hope you’ll agree), and I actively use my intelligence to create something out of whatever non-intelligent, non-functioning instructions/information are at my disposal. Thank you for an excellent analogy.[…]

DAVID: The organisms work just as you do in the analogy. You are free to act. They are automatic with programmed responses to the instructional information.

dhw: If organisms work just as I do, and I am free to act, how do you manage to conclude that organisms are not free to act but are automatic and your God preprogrammed them 3.8 billion years ago?!

The 'organisms work as you do' following instructions, as in the analogy. You think as you follow instructions. They are programmed to act automatically and follow them.


DAVID: (re ant colonies) As with bridges, automatic individual reactions make the whole colony operate as a unit.

dhw: They take new decisions every day according to individual reactions, but clearly they retain memory of earlier successful discoveries (e.g. how to form a bridge). Where have you found the word “automatic”? Do you really believe your God dabbles each new decision, or preprogrammed it 3.8 billion years ago? […]

DAVID: You should go back to ant bridge studies: individual ants do what they are programmed to individually do in that circumstance as all other situations. The overall colony acts through these individual actions, as the Article shows.

dhw: Once again: the bridge would have been the result of individuals pooling their intelligence to find a solution to a problem. Once the solution had proved successful, it would have been passed on, and so of course subsequent generations would follow the same procedure.

The bridge study specifically said each ant did its own programmed response.

dhw: It is when new conditions arise that individuals pool their intelligence to find new solutions. This is what “the article shows”: “from day to day the colony’s behaviour changes” and they “decide what to do next”… Not “3.8 billion years ago God supplied the first cells with a programme to pass on for whatever ants do next, on a day to day basis.”

it is true that older ants teach younger ones and that a leader ant will make a trip-change- in-direction decision, but all the following ants will automatically follow the leader. The colonies' memory is mainly due to the individuals' constant similar responses.

Biological complexity: feedback loops are vital

by dhw, Wednesday, October 02, 2019, 10:26 (1640 days ago) @ David Turell

DAVID: In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created.

dhw: Precisely. I am an intelligent organism (I hope you’ll agree), and I actively use my intelligence to create something out of whatever non-intelligent, non-functioning instructions/information are at my disposal. Thank you for an excellent analogy.[…]

DAVID: The organisms work just as you do in the analogy. You are free to act. They are automatic with programmed responses to the instructional information.

dhw: If organisms work just as I do, and I am free to act, how do you manage to conclude that organisms are not free to act but are automatic and your God preprogrammed them 3.8 billion years ago?!

DAVID: The 'organisms work as you do' following instructions, as in the analogy. You think as you follow instructions. They are programmed to act automatically and follow them.

So your analogy ceases to apply as soon as we reach the all-important point of how organisms use information! Let’s move on.

DAVID: You should go back to ant bridge studies: individual ants do what they are programmed to individually do in that circumstance as all other situations. The overall colony acts through these individual actions, as the Article shows.

dhw: Once again: the bridge would have been the result of individuals pooling their intelligence to find a solution to a problem. Once the solution had proved successful, it would have been passed on, and so of course subsequent generations would follow the same procedure.

DAVID: The bridge study specifically said each ant did its own programmed response.

Once a strategy has proved successful, each ant will know (or will have been taught) what it has to do. That doesn’t mean your God provided the first cells with an ant bridge-building programme to be passed on through billions of years.

dhw: It is when new conditions arise that individuals pool their intelligence to find new solutions. This is what “the article shows”: “from day to day the colony’s behaviour changes” and they “decide what to do next”… Not “3.8 billion years ago God supplied the first cells with a programme to pass on for whatever ants do next, on a day to day basis.”

DAVID: it is true that older ants teach younger ones and that a leader ant will make a trip-change- in-direction decision, but all the following ants will automatically follow the leader. The colonies' memory is mainly due to the individuals' constant similar responses.

In all societies there are leaders and followers. That doesn’t mean the leaders and the followers are all automatons! You refuse to acknowledge that every form of behaviour has to have an origin. Once it is established, of course individuals will perpetuate the responses. But the article makes it crystal clear that new decisions are taken every day. If you really think every new decision was preprogrammed 3.8 billion years ago, so be it.

Biological complexity: feedback loops are vital

by David Turell @, Wednesday, October 02, 2019, 19:25 (1640 days ago) @ dhw

DAVID: In regard as to how organisms operate, let me ask a question. Have you ever followed instructions from a pamphlet or book to create something or respond to something? That is how I view organisms and information. You used the information actively and created.

dhw: Precisely. I am an intelligent organism (I hope you’ll agree), and I actively use my intelligence to create something out of whatever non-intelligent, non-functioning instructions/information are at my disposal. Thank you for an excellent analogy.[…]

DAVID: The organisms work just as you do in the analogy. You are free to act. They are automatic with programmed responses to the instructional information.

dhw: If organisms work just as I do, and I am free to act, how do you manage to conclude that organisms are not free to act but are automatic and your God preprogrammed them 3.8 billion years ago?!

DAVID: The 'organisms work as you do' following instructions, as in the analogy. You think as you follow instructions. They are programmed to act automatically and follow them.

dhw: So your analogy ceases to apply as soon as we reach the all-important point of how organisms use information! Let’s move on.

DAVID: You should go back to ant bridge studies: individual ants do what they are programmed to individually do in that circumstance as all other situations. The overall colony acts through these individual actions, as the Article shows.

dhw: Once again: the bridge would have been the result of individuals pooling their intelligence to find a solution to a problem. Once the solution had proved successful, it would have been passed on, and so of course subsequent generations would follow the same procedure.

DAVID: The bridge study specifically said each ant did its own programmed response.

dhw: Once a strategy has proved successful, each ant will know (or will have been taught) what it has to do. That doesn’t mean your God provided the first cells with an ant bridge-building programme to be passed on through billions of years.

dhw: It is when new conditions arise that individuals pool their intelligence to find new solutions. This is what “the article shows”: “from day to day the colony’s behaviour changes” and they “decide what to do next”… Not “3.8 billion years ago God supplied the first cells with a programme to pass on for whatever ants do next, on a day to day basis.”

DAVID: it is true that older ants teach younger ones and that a leader ant will make a trip-change- in-direction decision, but all the following ants will automatically follow the leader. The colonies' memory is mainly due to the individuals' constant similar responses.

dhw: In all societies there are leaders and followers. That doesn’t mean the leaders and the followers are all automatons! You refuse to acknowledge that every form of behaviour has to have an origin. Once it is established, of course individuals will perpetuate the responses. But the article makes it crystal clear that new decisions are taken every day. If you really think every new decision was preprogrammed 3.8 billion years ago, so be it.

Yes, so be it.

Biological complexity: feedback loops are vital

by dhw, Thursday, October 03, 2019, 13:06 (1639 days ago) @ David Turell

DAVID: ...it is true that older ants teach younger ones and that a leader ant will make a trip-change- in-direction decision, but all the following ants will automatically follow the leader. The colonies' memory is mainly due to the individuals' constant similar responses.

dhw: In all societies there are leaders and followers. That doesn’t mean the leaders and the followers are all automatons! You refuse to acknowledge that every form of behaviour has to have an origin. Once it is established, of course individuals will perpetuate the responses. But the article makes it crystal clear that new decisions are taken every day. If you really think every new decision was preprogrammed 3.8 billion years ago, so be it.

DAVID: Yes, so be it.

Again, as with your theory of evolution, it’s important to understand exactly what your proposals mean. Let us remember that ants have brains. It appears, however, that you believe every decision made not only by brainless bacteria but also by some organisms (I presume you exclude humans and other large organisms) with brains was preprogrammed 3.8 billion years ago, to be passed on by the very first cells. These decisions apply to all the natural wonders you have listed, such as the monarch butterfly’s lifestyle and the weaverbird’s nest, and all stages of the pre-whale’s adaptations to marine life – all laid out in those very first cells, even though your God’s one and only intention was to specially design H. sapiens. You agree that this seems illogical (you have “no idea” why he chose this method), but it is logical so long as we do not apply human logic it. Since you are not prepared to use human reasoning, the discussion could well end there, but it is bound to be reopened whenever you try to justify your preprogramming theory.

Biological complexity: feedback loops are vital

by David Turell @, Thursday, October 03, 2019, 20:43 (1639 days ago) @ dhw

DAVID: ...it is true that older ants teach younger ones and that a leader ant will make a trip-change- in-direction decision, but all the following ants will automatically follow the leader. The colonies' memory is mainly due to the individuals' constant similar responses.

dhw: In all societies there are leaders and followers. That doesn’t mean the leaders and the followers are all automatons! You refuse to acknowledge that every form of behaviour has to have an origin. Once it is established, of course individuals will perpetuate the responses. But the article makes it crystal clear that new decisions are taken every day. If you really think every new decision was preprogrammed 3.8 billion years ago, so be it.

DAVID: Yes, so be it.

dhw: Again, as with your theory of evolution, it’s important to understand exactly what your proposals mean. Let us remember that ants have brains. It appears, however, that you believe every decision made not only by brainless bacteria but also by some organisms (I presume you exclude humans and other large organisms) with brains was preprogrammed 3.8 billion years ago, to be passed on by the very first cells. These decisions apply to all the natural wonders you have listed, such as the monarch butterfly’s lifestyle and the weaverbird’s nest, and all stages of the pre-whale’s adaptations to marine life – all laid out in those very first cells, even though your God’s one and only intention was to specially design H. sapiens. You agree that this seems illogical (you have “no idea” why he chose this method),

Your constant distortion: My 'no idea' simply means I don't guess at His reasons for his choices, not that I think it is illogical. I'm sure God is perfectly logical.

dhw: but it is logical so long as we do not apply human logic it. Since you are not prepared to use human reasoning, the discussion could well end there, but it is bound to be reopened whenever you try to justify your preprogramming theory.

I don't try to apply human logic to it, that is the point, which for some unknown reason you refuse to recognize.

Biological complexity: managing cellular oxygen levels

by David Turell @, Tuesday, October 08, 2019, 02:01 (1634 days ago) @ David Turell

A cascade of molecular controls to vary oxygen levels under all circumstances:

https://www.quantamagazine.org/nobel-prize-awarded-for-cells-adaptations-to-oxygen-2019...

"Through their separate contributions, the three scientists uncovered how cells sense and respond to the availability of oxygen, that key ingredient complex organisms need to move, build tissues and perform the diverse jobs that keep them alive.

"Levels of oxygen can fluctuate greatly: It naturally thins out at higher altitudes, but during exercise it also floods into active muscles while dropping elsewhere in the body. In tissues, oxygen concentrations can also decrease rapidly in and around wounds. When oxygen surges or plummets, cells have to adapt their metabolism accordingly — and quickly.

"They do so with what the Nobel committee called an “elegant switch.” For decades, scientists were aware that in low-oxygen conditions, the kidneys secrete a hormone called EPO (erythropoietin), which boosts the production of red blood cells in an effort to bring oxygen levels back to normal. But it wasn’t until the 1990s that researchers started to tease apart just how the body knows to do that.

"That’s where Semenza, Ratcliffe and Kaelin came in. Semenza pinpointed a section of DNA located near the EPO gene that seemed to be involved in the hormone’s expression, and he isolated the protein complex it encoded. When oxygen levels drop, he found, the protein — HIF (hypoxia-inducible factor) — is produced and accumulates in the cell. This in turn induces a slew of other oxygen-sensitive genes, including the one for EPO, to jump into action.

"On the other hand, when there’s enough oxygen around, HIF gets degraded, and the cascade is stopped in its tracks. Ratcliffe and Kaelin independently delineated the series of reactions that enable the degradation, as well as the way the cell prevents these reactions when oxygen gets too low.

***

“'Discovering the hypoxia-inducible-factor pathway answered the fundamental question of how cells adapt to less oxygen or to low oxygen, and ultimately how it allows cells, tissues and our human body to adapt. It’s a vital piece of fundamental research that’s got huge implications.'”

Comment: Any time there is a cascade of critical control reactions it must be developed all at once, never by hunt and peck. Only design at the beginning will work.

Biological complexity: managing cellular oxygen levels

by dhw, Tuesday, October 08, 2019, 13:33 (1634 days ago) @ David Turell

QUOTES: "Through their separate contributions, the three scientists uncovered how cells sense and respond to the availability of oxygen, that key ingredient complex organisms need to move, build tissues and perform the diverse jobs that keep them alive.
"When oxygen surges or plummets, cells have to adapt their metabolism accordingly — and quickly.
"

"Discovering the hypoxia-inducible-factor pathway answered the fundamental question of how cells adapt to less oxygen or to low oxygen, and ultimately how it allows cells, tissues and our human body to adapt. It’s a vital piece of fundamental research that’s got huge implications.'”

DAVID: Any time there is a cascade of critical control reactions it must be developed all at once, never by hunt and peck. Only design at the beginning will work.

With all forms of adaptation, the cells must find a way to adjust themselves, and if we take the example of bacteria, we know that millions of them may die before the correct balance is found. No doubt if organisms were once subjected to sudden changes in the oxygen level, there would have been millions of deaths until the cell communities found a way to correct the balance. Once the solution has been found, it will be passed on, and just as bacteria will then have a defence against the latest threat, so too will multicellular organisms inherit the new patterns that enable them to survive. What the scientists are now observing may have been at the cost of countless deaths until the hectic “hunting and pecking” produced the desired result.

Under "Magic embryology":

QUOTE: "'We are just beginning to understand how the 'software' of embryonic development (the electrical patterns) are created and interpreted by the 'hardware' (the cells' genes and proteins) to enable the cells to cooperate and organize into a highly-patterned body," said Michael Levin, Vannevar Bush Professor of Biology in the School of Arts & Sciences and director of the Allen Discovery Center at Tufts."

DAVID: Embryos just don't grow. They are design coded to follow designed plans electrically laid out.

The emphasis always seems to be on cooperation, with the cells creating and organizing patterns which must at one time have been new to life’s history. Once a pattern is successful, it survives. Every single one divinely preprogrammed 3.8 billion years ago, or separately designed by the cells themselves, using their perhaps God-given intelligence in response to new challenges and new opportunities?

Biological complexity: managing cellular oxygen levels

by David Turell @, Tuesday, October 08, 2019, 18:09 (1634 days ago) @ dhw

QUOTES: "Through their separate contributions, the three scientists uncovered how cells sense and respond to the availability of oxygen, that key ingredient complex organisms need to move, build tissues and perform the diverse jobs that keep them alive.
"When oxygen surges or plummets, cells have to adapt their metabolism accordingly — and quickly.
"

"Discovering the hypoxia-inducible-factor pathway answered the fundamental question of how cells adapt to less oxygen or to low oxygen, and ultimately how it allows cells, tissues and our human body to adapt. It’s a vital piece of fundamental research that’s got huge implications.'”

DAVID: Any time there is a cascade of critical control reactions it must be developed all at once, never by hunt and peck. Only design at the beginning will work.

dhw: With all forms of adaptation, the cells must find a way to adjust themselves, and if we take the example of bacteria, we know that millions of them may die before the correct balance is found. No doubt if organisms were once subjected to sudden changes in the oxygen level, there would have been millions of deaths until the cell communities found a way to correct the balance.

You are totally missing the point. Look back into the article. This is not environmental oxygen levels and use. Remember yourself in Cricket. At bat your body is tense but still. Everything is well-oxygenated. You hit and start running. Now certain areas (arm and leg muscles) need more oxygen. Other now will lack oxygen unless critical shifts in cells isn't accomplished.

dhw: Once the solution has been found, it will be passed on, and just as bacteria will then have a defence against the latest threat, so too will multicellular organisms inherit the new patterns that enable them to survive. What the scientists are now observing may have been at the cost of countless deaths until the hectic “hunting and pecking” produced the desired result.

Not a problem for single cellular organisms, but a coordinated system for multicellular organisms with many moving parts required for their development, and therefore must be totally in place as they developed. Only design fits.


Under "Magic embryology":

QUOTE: "'We are just beginning to understand how the 'software' of embryonic development (the electrical patterns) are created and interpreted by the 'hardware' (the cells' genes and proteins) to enable the cells to cooperate and organize into a highly-patterned body," said Michael Levin, Vannevar Bush Professor of Biology in the School of Arts & Sciences and director of the Allen Discovery Center at Tufts."

DAVID: Embryos just don't grow. They are design coded to follow designed plans electrically laid out.

dhw: The emphasis always seems to be on cooperation, with the cells creating and organizing patterns which must at one time have been new to life’s history. Once a pattern is successful, it survives. Every single one divinely preprogrammed 3.8 billion years ago, or separately designed by the cells themselves, using their perhaps God-given intelligence in response to new challenges and new opportunities?

This is a pattern with a future goal of construction. What is laid out in the total embryo is a guide to that future result. Each cell must follow instructions and do its singular part to follow the plan which is set up in advance to achieve the goal. Under your view I don't know how a new horse will appear after the egg is fertilized. The cells are programmed to follow the electrical patterns. They do not set up the pattern.

Biological complexity: managing cellular oxygen levels

by dhw, Wednesday, October 09, 2019, 12:08 (1633 days ago) @ David Turell

DAVID: Any time there is a cascade of critical control reactions it must be developed all at once, never by hunt and peck. Only design at the beginning will work.

dhw: With all forms of adaptation, the cells must find a way to adjust themselves, and if we take the example of bacteria, we know that millions of them may die before the correct balance is found. No doubt if organisms were once subjected to sudden changes in the oxygen level, there would have been millions of deaths until the cell communities found a way to correct the balance.

DAVID: You are totally missing the point. Look back into the article. This is not environmental oxygen levels and use. Remember yourself in Cricket. At bat your body is tense but still. Everything is well-oxygenated. You hit and start running. Now certain areas (arm and leg muscles) need more oxygen. Other now will lack oxygen unless critical shifts in cells isn't accomplished.

And I am pointing out that every form of adaptation must have had a beginning. Our own body is the consequence of millions of years in which cells and cell communities have had to adapt to millions of new situations. Now that each one is established, of course the reactions happen at once, and I agree that they are the product of intelligent design (and propose that the perhaps God-given intelligence of cells is the designing force). I do not agree that every adaptation must have been designed all at once, and never by hunt or peck. You have missed the point that even now we see organisms dying until the cells eventually find a way of adjusting their balance to the demands of the conditions.

DAVID: Not a problem for single cellular organisms, but a coordinated system for multicellular organisms with many moving parts required for their development, and therefore must be totally in place as they developed. Only design fits.

Of course the system must be coordinated in multicellular organisms - hence cooperation between the different cell communities.

Under "Magic embryology":
dhw: The emphasis always seems to be on cooperation, with the cells creating and organizing patterns which must at one time have been new to life’s history. Once a pattern is successful, it survives. Every single one divinely preprogrammed 3.8 billion years ago, or separately designed by the cells themselves, using their perhaps God-given intelligence in response to new challenges and new opportunities?

DAVID: This is a pattern with a future goal of construction. What is laid out in the total embryo is a guide to that future result. Each cell must follow instructions and do its singular part to follow the plan which is set up in advance to achieve the goal. Under your view I don't know how a new horse will appear after the egg is fertilized. The cells are programmed to follow the electrical patterns. They do not set up the pattern.

Again: once a pattern has been established, it will be repeated, but nobody knows how speciation – i.e. new patterns – first arise. You say every undabbled change in the history of life was divinely preprogrammed 3.8 billion years ago. I propose that every change was the result of cell communities responding to the demands or opportunities presented by new conditions. The embryo presumably inherits the patterns established by those changes, but nobody knows how it all works.

Under “Natural wonders”:
DAVID: this sort of avoidance activity suggest that the insect somehow knows the future consequences of its egg deposition. How do insects anticipate the future? I doubt they do and are programmed in this way to protect the larvae.

As usual, you forget the fact that all these strategies and wonders must have had a beginning! No matter how the strategy first arose, it worked, and from then on, the species followed the successful pattern. No anticipation of the future required, other than the knowledge that larvae must be protected from predators, and this has proved to be a good way to do it. But if you think your God specially designed this particular programme 3.8 billion years ago as part of his having to cover the time he’d decided to wait before he fulfilled his one and only purpose of specially designing H. sapiens, so be it.

Biological complexity: managing cellular oxygen levels

by David Turell @, Wednesday, October 09, 2019, 16:00 (1633 days ago) @ dhw

DAVID: Any time there is a cascade of critical control reactions it must be developed all at once, never by hunt and peck. Only design at the beginning will work.

dhw: With all forms of adaptation, the cells must find a way to adjust themselves, and if we take the example of bacteria, we know that millions of them may die before the correct balance is found. No doubt if organisms were once subjected to sudden changes in the oxygen level, there would have been millions of deaths until the cell communities found a way to correct the balance.

DAVID: You are totally missing the point. Look back into the article. This is not environmental oxygen levels and use. Remember yourself in Cricket. At bat your body is tense but still. Everything is well-oxygenated. You hit and start running. Now certain areas (arm and leg muscles) need more oxygen. Other now will lack oxygen unless critical shifts in cells isn't accomplished.

dhw: And I am pointing out that every form of adaptation must have had a beginning. Our own body is the consequence of millions of years in which cells and cell communities have had to adapt to millions of new situations. Now that each one is established, of course the reactions happen at once, and I agree that they are the product of intelligent design (and propose that the perhaps God-given intelligence of cells is the designing force). I do not agree that every adaptation must have been designed all at once, and never by hunt or peck. You have missed the point that even now we see organisms dying until the cells eventually find a way of adjusting their balance to the demands of the conditions.

And you do not understand biochemical cascades, which are a series of specific reactions that must interlock from the beginning. I'll remind you of blood clotting, 20 or so factors and tight control so teh whole body doesn't clot.

DAVID: Not a problem for single cellular organisms, but a coordinated system for multicellular organisms with many moving parts required for their development, and therefore must be totally in place as they developed. Only design fits.

dhw: Of course the system must be coordinated in multicellular organisms - hence cooperation between the different cell communities.

This doesn't describe cascades of chemicals.


Under "Magic embryology":
dhw: The emphasis always seems to be on cooperation, with the cells creating and organizing patterns which must at one time have been new to life’s history. Once a pattern is successful, it survives. Every single one divinely preprogrammed 3.8 billion years ago, or separately designed by the cells themselves, using their perhaps God-given intelligence in response to new challenges and new opportunities?

DAVID: This is a pattern with a future goal of construction. What is laid out in the total embryo is a guide to that future result. Each cell must follow instructions and do its singular part to follow the plan which is set up in advance to achieve the goal. Under your view I don't know how a new horse will appear after the egg is fertilized. The cells are programmed to follow the electrical patterns. They do not set up the pattern.

dhw: Again: once a pattern has been established, it will be repeated, but nobody knows how speciation – i.e. new patterns – first arise. You say every undabbled change in the history of life was divinely preprogrammed 3.8 billion years ago. I propose that every change was the result of cell communities responding to the demands or opportunities presented by new conditions. The embryo presumably inherits the patterns established by those changes, but nobody knows how it all works.

You think cells create the control cascades of a series of special proteins following special electrical patterns. I don't


Under “Natural wonders”:
DAVID: this sort of avoidance activity suggest that the insect somehow knows the future consequences of its egg deposition. How do insects anticipate the future? I doubt they do and are programmed in this way to protect the larvae.

dhw: As usual, you forget the fact that all these strategies and wonders must have had a beginning! No matter how the strategy first arose, it worked, and from then on, the species followed the successful pattern. No anticipation of the future required, other than the knowledge that larvae must be protected from predators, and this has proved to be a good way to do it. But if you think your God specially designed this particular programme 3.8 billion years ago as part of his having to cover the time he’d decided to wait before he fulfilled his one and only purpose of specially designing H. sapiens, so be it.

So now you have insects anticipating the future!!! That requires concepts in consciousness. So be it.

Biological complexity: managing cellular oxygen levels

by dhw, Thursday, October 10, 2019, 10:28 (1632 days ago) @ David Turell

dhw: And I am pointing out that every form of adaptation must have had a beginning. Our own body is the consequence of millions of years in which cells and cell communities have had to adapt to millions of new situations. Now that each one is established, of course the reactions happen at once, and I agree that they are the product of intelligent design (and propose that the perhaps God-given intelligence of cells is the designing force). I do not agree that every adaptation must have been designed all at once, and never by hunt or peck. You have missed the point that even now we see organisms dying until the cells eventually find a way of adjusting their balance to the demands of the conditions.

DAVID: And you do not understand biochemical cascades, which are a series of specific reactions that must interlock from the beginning. I'll remind you of blood clotting, 20 or so factors and tight control so teh whole body doesn't clot.

You can go through every single process of adaptation you like, including managing oxygen levels, cascades of chemicals, blood clotting, magic embryology, brain neuron clusters, immune and blood systems etc., but you still can’t escape the fact that all of them must have had a beginning, and the process we now observe may be the successful resolution of problems that killed off generations of organisms. NOBODY KNOWS how these processes evolved, but the proposal that a divine being preprogrammed every single one of them 3.8 billion years ago in the first cells, or suddenly popped in to dabble them, does not seem to me any less fanciful than the idea that the cells themselves had the perhaps God-given power to work out their own solutions as and when needed.

Under “Natural wonders”:
DAVID: this sort of avoidance activity suggest that the insect somehow knows the future consequences of its egg deposition. How do insects anticipate the future? I doubt they do and are programmed in this way to protect the larvae.

dhw: As usual, you forget the fact that all these strategies and wonders must have had a beginning! No matter how the strategy first arose, it worked, and from then on, the species followed the successful pattern. No anticipation of the future required, other than the knowledge that larvae must be protected from predators, and this has proved to be a good way to do it. But if you think your God specially designed this particular programme 3.8 billion years ago as part of his having to cover the time he’d decided to wait before he fulfilled his one and only purpose of specially designing H. sapiens, so be it.(David’s bold)

DAVID: So now you have insects anticipating the future!!! That requires concepts in consciousness. So be it.

Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions? Of course this knowledge and these actions require “concepts in consciousness”. That is why even you admit that our fellow animals are conscious. That does not mean they consciously analyse their own behaviour, write books about their findings, compose symphonies or philosophize about how they got here in the first place. Their form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

Biological complexity: managing cellular oxygen levels

by David Turell @, Thursday, October 10, 2019, 21:30 (1632 days ago) @ dhw

dhw: And I am pointing out that every form of adaptation must have had a beginning. Our own body is the consequence of millions of years in which cells and cell communities have had to adapt to millions of new situations. Now that each one is established, of course the reactions happen at once, and I agree that they are the product of intelligent design (and propose that the perhaps God-given intelligence of cells is the designing force). I do not agree that every adaptation must have been designed all at once, and never by hunt or peck. You have missed the point that even now we see organisms dying until the cells eventually find a way of adjusting their balance to the demands of the conditions.

DAVID: And you do not understand biochemical cascades, which are a series of specific reactions that must interlock from the beginning. I'll remind you of blood clotting, 20 or so factors and tight control so the whole body doesn't clot.

dhw: You can go through every single process of adaptation you like, including managing oxygen levels, cascades of chemicals, blood clotting, magic embryology, brain neuron clusters, immune and blood systems etc., but you still can’t escape the fact that all of them must have had a beginning, and the process we now observe may be the successful resolution of problems that killed off generations of organisms. NOBODY KNOWS how these processes evolved, but the proposal that a divine being preprogrammed every single one of them 3.8 billion years ago in the first cells, or suddenly popped in to dabble them, does not seem to me any less fanciful than the idea that the cells themselves had the perhaps God-given power to work out their own solutions as and when needed.

That removes God from total control, no matter how many modifications you add, and I don't think God acts second-hand. Cells cannot on their own work out complex protein cascades.


Under “Natural wonders”:
DAVID: this sort of avoidance activity suggest that the insect somehow knows the future consequences of its egg deposition. How do insects anticipate the future? I doubt they do and are programmed in this way to protect the larvae.

dhw: As usual, you forget the fact that all these strategies and wonders must have had a beginning! No matter how the strategy first arose, it worked, and from then on, the species followed the successful pattern. No anticipation of the future required, other than the knowledge that larvae must be protected from predators, and this has proved to be a good way to do it. But if you think your God specially designed this particular programme 3.8 billion years ago as part of his having to cover the time he’d decided to wait before he fulfilled his one and only purpose of specially designing H. sapiens, so be it.(David’s bold)

DAVID: So now you have insects anticipating the future!!! That requires concepts in consciousness. So be it.

dhw; Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions? Of course this knowledge and these actions require “concepts in consciousness”. That is why even you admit that our fellow animals are conscious. That does not mean they consciously analyse their own behaviour, write books about their findings, compose symphonies or philosophize about how they got here in the first place. Their form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

You have again glibly assumed insects can imagine the future in order to protect their larvae. Really? Do you think monarchs go through four generations each year and 'know' about each one? Totally illogical. I view the bolded as a fairy tale of thought and reminiscent of the just-so stories from Darwinism. Insects are totally programmed in their genome. Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory? Preposterous and totally illogical.

Biological complexity: managing cellular oxygen levels

by dhw, Friday, October 11, 2019, 13:25 (1631 days ago) @ David Turell

dhw: NOBODY KNOWS how these processes evolved, but the proposal that a divine being preprogrammed every single one of them 3.8 billion years ago in the first cells, or suddenly popped in to dabble them, does not seem to me any less fanciful than the idea that the cells themselves had the perhaps God-given power to work out their own solutions as and when needed.

DAVID: That removes God from total control, no matter how many modifications you add, and I don't think God acts second-hand. Cells cannot on their own work out complex protein cascades.

Of course it removes him from total control. Why do you always insist that he wanted to create a world of automatons? In your more open-minded moments you have conceded that he may be watching the world with interest. Which do you find more interesting – a show in which everything is totally predictable, or a show full of wonderful surprises? “You’re humanizing him!” will be the cry. And the next moment you’ll agree that he “very well could think like us”. So why not accept the possibility that in certain respects he “very well could think like us”, instead of pretending that you know he doesn’t?

DAVID: So now you have insects anticipating the future!!! That requires concepts in consciousness. So be it.

dhw: Their form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

DAVID: You have again glibly assumed insects can imagine the future in order to protect their larvae. Really? Do you think monarchs go through four generations each year and 'know' about each one? Totally illogical. I view the bolded as a fairy tale of thought and reminiscent of the just-so stories from Darwinism. Insects are totally programmed in their genome. Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory? Preposterous and totally illogical.

“Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise. I have no idea how every single natural wonder originated, but I stand by the bold as a more than convincing alternative to your theory (which many would call a just-so story) that there is an unknown sourceless supermind which provided the first living cells with programmes to pass on through thousands of millions of years and organisms for every single innovation, lifestyle and natural wonder throughout the history of life. There can, however, be little doubt that even within your own theory, once a life form, style or wonder has come into being, every one of these will be perpetuated by some form of cellular memory, since changes are passed on. Unless you think your God is sitting there pulling the strings of every single organism on the planet. Another just-so story?

Biological complexity: managing cellular oxygen levels

by David Turell @, Friday, October 11, 2019, 19:38 (1631 days ago) @ dhw

dhw: NOBODY KNOWS how these processes evolved, but the proposal that a divine being preprogrammed every single one of them 3.8 billion years ago in the first cells, or suddenly popped in to dabble them, does not seem to me any less fanciful than the idea that the cells themselves had the perhaps God-given power to work out their own solutions as and when needed.

DAVID: That removes God from total control, no matter how many modifications you add, and I don't think God acts second-hand. Cells cannot on their own work out complex protein cascades.

dhw; Of course it removes him from total control. Why do you always insist that he wanted to create a world of automatons? In your more open-minded moments you have conceded that he may be watching the world with interest. Which do you find more interesting – a show in which everything is totally predictable, or a show full of wonderful surprises? “You’re humanizing him!” will be the cry. And the next moment you’ll agree that he “very well could think like us”. So why not accept the possibility that in certain respects he “very well could think like us”, instead of pretending that you know he doesn’t?

Your imagined God sits in the stands and watches the show. Pure humanization.


DAVID: So now you have insects anticipating the future!!! That requires concepts in consciousness. So be it.

dhw: Their form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

DAVID: You have again glibly assumed insects can imagine the future in order to protect their larvae. Really? Do you think monarchs go through four generations each year and 'know' about each one? Totally illogical. I view the bolded as a fairy tale of thought and reminiscent of the just-so stories from Darwinism. Insects are totally programmed in their genome. Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory? Preposterous and totally illogical.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

Your insects still foretell the dangers in the future. I don't understand why you cannot see the problem in your totally illogical thoughts? Your insects are prescient. Really? Do you think the eaten larvae tell their parents what happened?

dhw: I have no idea how every single natural wonder originated, but I stand by the bold as a more than convincing alternative to your theory (which many would call a just-so story) that there is an unknown sourceless supermind which provided the first living cells with programmes to pass on through thousands of millions of years and organisms for every single innovation, lifestyle and natural wonder throughout the history of life. There can, however, be little doubt that even within your own theory, once a life form, style or wonder has come into being, every one of these will be perpetuated by some form of cellular memory, since changes are passed on. Unless you think your God is sitting there pulling the strings of every single organism on the planet. Another just-so story?

And what is the source of the designs you see but cannot explain, which therefore keeps you agnostic? There must be a designing mind. Mind is required.

Biological complexity: managing cellular oxygen levels

by dhw, Saturday, October 12, 2019, 12:38 (1630 days ago) @ David Turell

dhw: Why do you always insist that [God] wanted to create a world of automatons? In your more open-minded moments you have conceded that he may be watching the world with interest. Which do you find more interesting – a show in which everything is totally predictable, or a show full of wonderful surprises? “You’re humanizing him!” will be the cry. And the next moment you’ll agree that he “very well could think like us”. So why not accept the possibility that in certain respects he “very well could think like us”, instead of pretending that you know he doesn’t?

DAVID: Your imagined God sits in the stands and watches the show. Pure humanization.

I think you had him sitting behind a quantum wall watching with interest. Your response is anticipated by the first bold, and your inconsistency is highlighted by the second bold.
NB this “deistic” hypothesis is only one of the alternatives I offer.

dhw: Their form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

DAVID: You have again glibly assumed insects can imagine the future in order to protect their larvae. Really? Do you think monarchs go through four generations each year and 'know' about each one? Totally illogical. I view the bolded as a fairy tale of thought and reminiscent of the just-so stories from Darwinism. Insects are totally programmed in their genome. Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory? Preposterous and totally illogical.

DAVID (under “IMMUNITY SYSTEM COMPLEXITY”): Once an infection is defeated there must be a memory for the next time that same infection is attempted.

But it doesn’t occur to you that precisely the same argument applies to every innovation, strategy, lifestyle,and natural wonder. As soon as something is successful, “there must be a memory for the next time”.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

DAVID: Your insects still foretell the dangers in the future. I don't understand why you cannot see the problem in your totally illogical thoughts? Your insects are prescient. Really? Do you think the eaten larvae tell their parents what happened?

If a solution to an EXISTING (not a future) problem had not been found, the species would have died out, as happens all the time in life’s history. I do not claim to know any more than you do how every strategy was first discovered, but do please answer the question bolded above and the bolded comment that follows.

dhw: I have no idea how every single natural wonder originated, but I stand by the bold as a more than convincing alternative to your theory (which many would call a just-so story) that there is an unknown sourceless supermind which provided the first living cells with programmes to pass on through thousands of millions of years and organisms for every single innovation, lifestyle and natural wonder throughout the history of life. There can, however, be little doubt that even within your own theory, once a life form, style or wonder has come into being, every one of these will be perpetuated by some form of cellular memory, since changes are passed on. Unless you think your God is sitting there pulling the strings of every single organism on the planet. Another just-so story?

DAVID: And what is the source of the designs you see but cannot explain, which therefore keeps you agnostic? There must be a designing mind. Mind is required.

I keep agreeing that the source of cellular intelligence may be your God. Your question is a complete digression from the unlikelihood of your own theory, and you have failed to comment on the need for cellular memory in both theories.

Biological complexity: managing cellular oxygen levels

by David Turell @, Sunday, October 13, 2019, 05:23 (1629 days ago) @ dhw

dhw: Why do you always insist that [God] wanted to create a world of automatons? In your more open-minded moments you have conceded that he may be watching the world with interest. Which do you find more interesting – a show in which everything is totally predictable, or a show full of wonderful surprises? “You’re humanizing him!” will be the cry. And the next moment you’ll agree that he “very well could think like us”. So why not accept the possibility that in certain respects he “very well could think like us”, instead of pretending that you know he doesn’t?

My guesses about God's personality and thoughts is a result of trying to politely answering your queries. Only guesses .


DAVID: Your imagined God sits in the stands and watches the show. Pure humanization.

dhw: I think you had him sitting behind a quantum wall watching with interest. Your response is anticipated by the first bold, and your inconsistency is highlighted by the second bold.
NB this “deistic” hypothesis is only one of the alternatives I offer.

And I think He is totally in charge. Your offers humanize, as you give him human thinking, like why did He wait so long to create humans? I don't know why, but that is the history.


dhw: Their form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

DAVID: You have again glibly assumed insects can imagine the future in order to protect their larvae. Really? Do you think monarchs go through four generations each year and 'know' about each one? Totally illogical. I view the bolded as a fairy tale of thought and reminiscent of the just-so stories from Darwinism. Insects are totally programmed in their genome. Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory? Preposterous and totally illogical.

DAVID (under “IMMUNITY SYSTEM COMPLEXITY”): Once an infection is defeated there must be a memory for the next time that same infection is attempted.

dhw: But it doesn’t occur to you that precisely the same argument applies to every innovation, strategy, lifestyle,and natural wonder. As soon as something is successful, “there must be a memory for the next time”.

Apples and oranges. The T cells are programmed to develop a memory. the insects in your view an foretell the future. totally illogical.


dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

DAVID: Your insects still foretell the dangers in the future. I don't understand why you cannot see the problem in your totally illogical thoughts? Your insects are prescient. Really? Do you think the eaten larvae tell their parents what happened?

dhw: If a solution to an EXISTING (not a future) problem had not been found, the species would have died out, as happens all the time in life’s history. I do not claim to know any more than you do how every strategy was first discovered, but do please answer the question bolded above and the bolded comment that follows.

My point is God steps in and helps.


dhw: I have no idea how every single natural wonder originated, but I stand by the bold as a more than convincing alternative to your theory (which many would call a just-so story) that there is an unknown sourceless supermind which provided the first living cells with programmes to pass on through thousands of millions of years and organisms for every single innovation, lifestyle and natural wonder throughout the history of life. There can, however, be little doubt that even within your own theory, once a life form, style or wonder has come into being, every one of these will be perpetuated by some form of cellular memory, since changes are passed on. Unless you think your God is sitting there pulling the strings of every single organism on the planet. Another just-so story?

DAVID: And what is the source of the designs you see but cannot explain, which therefore keeps you agnostic? There must be a designing mind. Mind is required.

dhw: I keep agreeing that the source of cellular intelligence may be your God. Your question is a complete digression from the unlikelihood of your own theory, and you have failed to comment on the need for cellular memory in both theories.

See above. T cells are obviously programmed to have a memory of previous infections. Insects can not see the future and if they plan to protect larvae, they are programmed to do so.

Biological complexity: managing cellular oxygen levels

by dhw, Sunday, October 13, 2019, 11:02 (1629 days ago) @ David Turell

dhw: Why do you always insist that [God] wanted to create a world of automatons? In your more open-minded moments you have conceded that he may be watching the world with interest. Which do you find more interesting – a show in which everything is totally predictable, or a show full of wonderful surprises? “You’re humanizing him!” will be the cry. And the next moment you’ll agree that he “very well could think like us”. So why not accept the possibility that in certain respects he “very well could think like us”, instead of pretending that you know he doesn’t?

DAVID: My guesses about God's personality and thoughts is a result of trying to politely answering your queries. Only guesses.

And your incongruous account of his purpose and method is also a mass of guesses, the logic of which depends on abandoning all human reason, although he “very well could think like us.” Your subsequent comments repeat this one or others made under “David’s theory of evolution”.

dhw: [Insects’] form of consciousness is vastly less advanced than our own. But it is sufficient for them to maximise their own chances of survival, and that means taking steps to protect themselves against future dangers already known from past experience.

DAVID: You have again glibly assumed insects can imagine the future in order to protect their larvae. […] Insects are totally programmed in their genome. Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory? Preposterous and totally illogical.

DAVID (under “IMMUNITY SYSTEM COMPLEXITY”): Once an infection is defeated there must be a memory for the next time that same infection is attempted.

dhw: But it doesn’t occur to you that precisely the same argument applies to every innovation, strategy, lifestyle,and natural wonder. As soon as something is successful, “there must be a memory for the next time”.

DAVID: Apples and oranges. The T cells are programmed to develop a memory. the insects in your view an foretell the future. totally illogical.

Cells have memory. I don’t know why you insert the word programmed. So do insects. I keep emphasizing that they do NOT foretell the future. They respond, just like bacteria and just like our fellow animals, to PRESENT conditions, and whatever they have learned is passed on through memory to enable them to take precautions against or to counter the same dangers or to solve the same problems.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

[…] If a solution to an EXISTING (not a future) problem had not been found, the species would have died out, as happens all the time in life’s history. I do not claim to know any more than you do how every strategy was first discovered, but do please answer the question bolded above and the bolded comment that follows.

DAVID: My point is God steps in and helps.

So now it’s not even a 3.8-billion-year-old programme for every single innovation, strategy, lifestyle and natural wonder. God personally steps in whenever he anticipates a new, i.e. not yet existing problem, except that one minute later you go back to pre-programming!

DAVID: T cells are obviously programmed to have a memory of previous infections. Insects can not see the future and if they plan to protect larvae, they are programmed to do so.

So 3.8 thousand million years ago, your God preprogrammed every solution to every problem that would ever be faced by every cell and every insect (except when he “steps in and helps”) – and all because he had to cover the time he’d decided to wait before he preprogrammed or dabbled the beginnings of human evolution, which was the only thing he actually wanted to do in the first place!

Biological complexity: managing cellular oxygen levels

by David Turell @, Sunday, October 13, 2019, 16:07 (1629 days ago) @ dhw

dhw: So why not accept the possibility that in certain respects he “very well could think like us”, instead of pretending that you know he doesn’t?[/i]

DAVID: My guesses about God's personality and thoughts is a result of trying to politely answering your queries. Only guesses.

dhw: And your incongruous account of his purpose and method is also a mass of guesses, the logic of which depends on abandoning all human reason, although he “very well could think like us.” Your subsequent comments repeat this one or others made under “David’s theory of evolution”.

My guesses are based on my belief in intelligent design, and design keeps you agnostic.


DAVID (under “IMMUNITY SYSTEM COMPLEXITY”): Once an infection is defeated there must be a memory for the next time that same infection is attempted.

dhw: But it doesn’t occur to you that precisely the same argument applies to every innovation, strategy, lifestyle,and natural wonder. As soon as something is successful, “there must be a memory for the next time”.

DAVID: Apples and oranges. The T cells are programmed to develop a memory. the insects in your view an foretell the future. totally illogical.

dhw; Cells have memory. I don’t know why you insert the word programmed. So do insects. I keep emphasizing that they do NOT foretell the future. They respond, just like bacteria and just like our fellow animals, to PRESENT conditions, and whatever they have learned is passed on through memory to enable them to take precautions against or to counter the same dangers or to solve the same problems.

Unless the insect parents watch the larvae until adulthood, they cannot know what might happen to them.


dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

[…] If a solution to an EXISTING (not a future) problem had not been found, the species would have died out, as happens all the time in life’s history. I do not claim to know any more than you do how every strategy was first discovered, but do please answer the question bolded above and the bolded comment that follows.

DAVID: My point is God steps in and helps.

dhw: So now it’s not even a 3.8-billion-year-old programme for every single innovation, strategy, lifestyle and natural wonder. God personally steps in whenever he anticipates a new, i.e. not yet existing problem, except that one minute later you go back to pre-programming!

You have accepted as a theist the possibility of God dabbling.


DAVID: T cells are obviously programmed to have a memory of previous infections. Insects can not see the future and if they plan to protect larvae, they are programmed to do so.

dhw: So 3.8 thousand million years ago, your God preprogrammed every solution to every problem that would ever be faced by every cell and every insect (except when he “steps in and helps”) – and all because he had to cover the time he’d decided to wait before he preprogrammed or dabbled the beginnings of human evolution, which was the only thing he actually wanted to do in the first place!

Same problem: I don't know why God chose to evolve humans, but He did as history shows.

Biological complexity: managing cellular oxygen levels

by dhw, Monday, October 14, 2019, 13:04 (1628 days ago) @ David Turell

DAVID (under “IMMUNITY SYSTEM COMPLEXITY”): Once an infection is defeated there must be a memory for the next time that same infection is attempted.

dhw: But it doesn’t occur to you that precisely the same argument applies to every innovation, strategy, lifestyle,and natural wonder. As soon as something is successful, “there must be a memory for the next time”.

DAVID: Apples and oranges. The T cells are programmed to develop a memory. the insects in your view an foretell the future. totally illogical.

dhw: Cells have memory. I don’t know why you insert the word programmed. So do insects. I keep emphasizing that they do NOT foretell the future. They respond, just like bacteria and just like our fellow animals, to PRESENT conditions, and whatever they have learned is passed on through memory to enable them to take precautions against or to counter the same dangers or to solve the same problems.

DAVID: Unless the insect parents watch the larvae until adulthood, they cannot know what might happen to them.

I do not pretend to know how every single survival strategy originated! But even if I accepted your belief that your God (whose sole purpose was apparently to design H. sapiens) watched over the larvae and dabbled this strategy into them, it would still have had to be handed down through memory to all subsequent generations, unless you think he sits there year after year doing the same old dabble! And the same applies if (just as incredibly) 3.8 billion years ago he provided the first living cells with a programme for this particular strategy to switch itself on when the first larvae of this particular species found themselves in trouble. There would still have had to be cellular memory to pass it on.
[…]
DAVID: You have accepted as a theist the possibility of God dabbling.

Yes, for instance by chucking Chixculub at the dinosaurs. I do not see him either dabbling or preprogramming every single strategy, innovation, lifestyle and natural wonder in the history of life.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

You have still not commented on this important issue.

dhw: So 3.8 thousand million years ago, your God preprogrammed every solution to every problem that would ever be faced by every cell and every insect (except when he “steps in and helps”) – and all because he had to cover the time he’d decided to wait before he preprogrammed or dabbled the beginnings of human evolution, which was the only thing he actually wanted to do in the first place!

DAVID: Same problem: I don't know why God chose to evolve humans, but He did as history shows.

Dealt with under “David’s theory of evolution”. Please stop leaving out the incongruities which – as you readily admit – demand the abandonment of all human reason. It’s boring for both of us if you keep making me repeat them!

Biological complexity: managing cellular oxygen levels

by David Turell @, Monday, October 14, 2019, 18:58 (1628 days ago) @ dhw

dhw: Cells have memory. I don’t know why you insert the word programmed. So do insects. I keep emphasizing that they do NOT foretell the future. They respond, just like bacteria and just like our fellow animals, to PRESENT conditions, and whatever they have learned is passed on through memory to enable them to take precautions against or to counter the same dangers or to solve the same problems.

DAVID: Unless the insect parents watch the larvae until adulthood, they cannot know what might happen to them.

dhw: I do not pretend to know how every single survival strategy originated! But even if I accepted your belief that your God (whose sole purpose was apparently to design H. sapiens) watched over the larvae and dabbled this strategy into them, it would still have had to be handed down through memory to all subsequent generations, unless you think he sits there year after year doing the same old dabble! And the same applies if (just as incredibly) 3.8 billion years ago he provided the first living cells with a programme for this particular strategy to switch itself on when the first larvae of this particular species found themselves in trouble. There would still have had to be cellular memory to pass it on.

Of course there is a cellular memory represented by instincts all animals follow, once established.

[…]
DAVID: You have accepted as a theist the possibility of God dabbling.

dhw: Yes, for instance by chucking Chixculub at the dinosaurs. I do not see him either dabbling or preprogramming every single strategy, innovation, lifestyle and natural wonder in the history of life.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

dhw: You have still not commented on this important issue.

Yes, I have. You want insect parents who do not tend their larvae to foretell the future needs for protection. They cannot conceptualize the future dangers.


dhw: So 3.8 thousand million years ago, your God preprogrammed every solution to every problem that would ever be faced by every cell and every insect (except when he “steps in and helps”) – and all because he had to cover the time he’d decided to wait before he preprogrammed or dabbled the beginnings of human evolution, which was the only thing he actually wanted to do in the first place!

DAVID: Same problem: I don't know why God chose to evolve humans, but He did as history shows.

dhw: Dealt with under “David’s theory of evolution”. Please stop leaving out the incongruities which – as you readily admit – demand the abandonment of all human reason. It’s boring for both of us if you keep making me repeat them!

I don't accept your reasoning so lets leave this

Biological complexity: managing cellular oxygen levels

by dhw, Tuesday, October 15, 2019, 10:12 (1627 days ago) @ David Turell

dhw: Cells have memory. I don’t know why you insert the word programmed. So do insects. I keep emphasizing that they do NOT foretell the future. They respond, just like bacteria and just like our fellow animals, to PRESENT conditions, and whatever they have learned is passed on through memory to enable them to take precautions against or to counter the same dangers or to solve the same problems.
[…]
DAVID: Of course there is a cellular memory represented by instincts all animals follow, once established.

Thank you. You had written “Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory. Preposterous and totally illogical.” I pointed out that this was precisely the process that must accompany all innovations, strategies, lifestyles and natural wonders. They must all be passed on through cellular memory. I’m glad you now agree.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

dhw: You have still not commented on this important issue.

DAVID: Yes, I have. You want insect parents who do not tend their larvae to foretell the future needs for protection. They cannot conceptualize the future dangers.

That is not an answer! I do not pretend that I can explain every single survival strategy devised by every single insect in the history of life, and I can understand your clinging desperately to a single example which presents special difficulties. But I reject totally the idea that insects foretell dangers which have never been experienced before. My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary.

Biological complexity: managing cellular oxygen levels

by David Turell @, Tuesday, October 15, 2019, 15:25 (1627 days ago) @ dhw

dhw: Cells have memory. I don’t know why you insert the word programmed. So do insects. I keep emphasizing that they do NOT foretell the future. They respond, just like bacteria and just like our fellow animals, to PRESENT conditions, and whatever they have learned is passed on through memory to enable them to take precautions against or to counter the same dangers or to solve the same problems.
[…]
DAVID: Of course there is a cellular memory represented by instincts all animals follow, once established.

Thank you. You had written “Metamorphosis calls for all cells to dissolve and become different cells in a different body, and you think that change is supposed to carry neuronal memory. Preposterous and totally illogical.” I pointed out that this was precisely the process that must accompany all innovations, strategies, lifestyles and natural wonders. They must all be passed on through cellular memory. I’m glad you now agree.

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.

dhw: You have still not commented on this important issue.

DAVID: Yes, I have. You want insect parents who do not tend their larvae to foretell the future needs for protection. They cannot conceptualize the future dangers.

dhw: That is not an answer! I do not pretend that I can explain every single survival strategy devised by every single insect in the history of life, and I can understand your clinging desperately to a single example which presents special difficulties. But I reject totally the idea that insects foretell dangers which have never been experienced before. My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary.

The bold is the problem. If insect parents try to hide unattended larvae from unforeseen dangers, how did they know there were future dangers? Some insects do shepherd their larvae. Why the difference? We can say instinct for the former, and the latter group of shepherders learned by experience. Fine, but how did the instinct develop in the former not with the abandoned larvae? No awareness is possible.

Biological complexity: managing cellular oxygen levels

by dhw, Wednesday, October 16, 2019, 10:10 (1626 days ago) @ David Turell

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.
dhw: You have still not commented on this important issue.

DAVID: Yes, I have. You want insect parents who do not tend their larvae to foretell the future needs for protection. They cannot conceptualize the future dangers.

dhw: That is not an answer! I do not pretend that I can explain every single survival strategy devised by every single insect in the history of life, and I can understand your clinging desperately to a single example which presents special difficulties. But I reject totally the idea that insects foretell dangers which have never been experienced before. (David’s bold) My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. (dhw’s bold) No crystal ball necessary.

DAVID: The bold is the problem. If insect parents try to hide unattended larvae from unforeseen dangers, how did they know there were future dangers? Some insects do shepherd their larvae. Why the difference? We can say instinct for the former, and the latter group of shepherders learned by experience. Fine, but how did the instinct develop in the former not with the abandoned larvae? No awareness is possible.

You are still clinging to this one example and refusing to comment on the general point I have made above. Maybe in this case the whole process began when Mr and Mrs did see what happened to their larvae and worked out a solution which then got handed down, and after that, succeeding generations of mummies and daddies knew they didn’t have to bother shepherding their larvae. We don’t know the origin of every single strategy, lifestyle and natural wonder in the history of life, but we do know that organisms including insects learn from experience etc. as now also bolded above and as totally ignored by you. So do you or do you not agree with my bold?

DAVID (under “water control in trees”): these are complex designs to help the trees handle changing wet and drier climates where they exist. The complexity can be appreciated by looking at the article's illustrations. Only design explains this system.

Further evidence that even plants learn from experience and refine their survival techniques in accordance with the demands of the environment. Or do you think your God preprogrammed every plant strategy 3.8 billion years ago, or steps in to dabble every time a tree gets into trouble?

Biological complexity: managing cellular oxygen levels

by David Turell @, Wednesday, October 16, 2019, 18:42 (1626 days ago) @ dhw

dhw: “Imagining the future” is your phrase, not mine. I wrote: “Do you honestly believe that organisms are not aware of dangers and do not learn from experience and do not take precautions”? These are manifestations of consciousness, and we know they are capable of solving new problems as and when they arise.
dhw: You have still not commented on this important issue.

DAVID: Yes, I have. You want insect parents who do not tend their larvae to foretell the future needs for protection. They cannot conceptualize the future dangers.

dhw: That is not an answer! I do not pretend that I can explain every single survival strategy devised by every single insect in the history of life, and I can understand your clinging desperately to a single example which presents special difficulties. But I reject totally the idea that insects foretell dangers which have never been experienced before. (David’s bold) My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. (dhw’s bold) No crystal ball necessary.

DAVID: The bold is the problem. If insect parents try to hide unattended larvae from unforeseen dangers, how did they know there were future dangers? Some insects do shepherd their larvae. Why the difference? We can say instinct for the former, and the latter group of shepherders learned by experience. Fine, but how did the instinct develop in the former not with the abandoned larvae? No awareness is possible.

dhw: You are still clinging to this one example and refusing to comment on the general point I have made above. Maybe in this case the whole process began when Mr and Mrs did see what happened to their larvae and worked out a solution which then got handed down, and after that, succeeding generations of mummies and daddies knew they didn’t have to bother shepherding their larvae. We don’t know the origin of every single strategy, lifestyle and natural wonder in the history of life, but we do know that organisms including insects learn from experience etc. as now also bolded above and as totally ignored by you. So do you or do you not agree with my bold?

Your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.


DAVID (under “water control in trees”): these are complex designs to help the trees handle changing wet and drier climates where they exist. The complexity can be appreciated by looking at the article's illustrations. Only design explains this system.

dhw; Further evidence that even plants learn from experience and refine their survival techniques in accordance with the demands of the environment. Or do you think your God preprogrammed every plant strategy 3.8 billion years ago, or steps in to dabble every time a tree gets into trouble?

Again you want consciousness in plants, and I don't accept it. Besides you are ignoring how complex the plant design has to be. It didn't develop by chance.

Biological complexity: inheriting actions and instinct

by David Turell @, Wednesday, October 16, 2019, 19:36 (1626 days ago) @ David Turell

Epigenetic research does not really tell us how this happens, especially related to the preceding discussion of insect/larval behavior and trees changing water controls:

https://www.quantamagazine.org/inherited-learning-it-happens-but-how-is-uncertain-20191...

"Most recently, some researchers have found evidence that even some learned behaviors and physiological responses can be epigenetically inherited. None of the new studies fully address exactly how information learned or acquired in the somatic tissues is communicated and incorporated into the germline. But mechanisms centering around small RNA molecules and forms of hormonal communication are actively being investigated.

***

"The evolutionary “why” for epigenetic inheritance is also an area of active investigation because it’s paradoxical. If learned adaptive behaviors can be passed on to the next generation, that would seem to eliminate the necessity for certain standard evolved changes to the genome. On the other hand, if epigenetically transmitted traits are adaptive, why not hardwire them into the genome so that they can be inherited more stably?

***

“'The possibility that the nervous system could generate heritable responses was especially intriguing, because the nervous system is a very unique system in its ability to organize information about the environment,” said Oded Rechavi, a neurobiologist at Tel Aviv University who studies inheritance and evolution. “It has [a] unique capability of planning.” (my bold)

"Rechavi is one of the scientists behind a series of studies published in the past few months that point to small noncoding RNAs — RNA molecules that serve functions other than the production of peptides — as key mediators of some epigenetic effects in a simple model animal, the roundworm Caenorhabditis elegans. Different mechanisms, probably including ones as yet unknown, may govern other instances of inherited learning in the worms and in more complex organisms. Indeed, some scientists don’t agree that small noncoding RNAs have a singularly important role in the phenomenon at all. And in general, researchers are cautious in approaching the argument that epigenetics enables the transmission of specific, adaptive traits to new generations.

***

"Rechavi investigated the inheritance of a learned behavior: chemotaxis, the ability to orient and move toward food sources. He wanted to know whether small RNAs made specifically in nerve cells could somehow communicate with the germline and generate heritable behavioral responses.

***

"Further work determined that the worms’ chemotaxis depended mainly on so-called small interfering RNAs (siRNAs) that muted the effects of a particular gene, saeg-2, in the neurons.

"The surprise came when they looked at the worms’ gonads: More than 1,000 siRNAs had changed in abundance relative to those in worms that lacked rde-4 entirely. And although none of the progeny’s cells carried a working rde-4 gene, the worms could still perform chemotaxis. Somehow, their germ cells still had siRNAs targeting saeg-2. Rechavi and his colleagues concluded that these worms had inherited the siRNAs from their parents — evidence that the production of specific small RNAs in the parental neurons could generate a heritable response that showed up in the worms’ progeny.

***

“'What I would suggest is that our brains are our pharmacies,” Bosco said. “Our brains are making chemicals all the time,” such as neuropeptides and other neuromodulatory molecules with diverse functions. Some of those functions impinge directly on processes in other organs, including the reproductive system. “If we can ingest a chemical from our environment that changes the epigenomes of the egg or sperm, why couldn’t our brain make a similar molecule that does the same thing?” he said.

***

"One of the outstanding questions in the field is why epigenetic inheritance only lasts for a handful of generations and then stops, said Eric Greer, an epigeneticist at Harvard Medical School and Boston Children’s Hospital who studies the epigenetic inheritance of longevity and fertility in C. elegans. It appears to be a regulated process, in part because the effect persists at the same magnitude from one generation to the next, and then abruptly disappears. Moreover, in a paper published in Cell in 2016, Rechavi and colleagues described dedicated cell machinery and specific genes that control the duration of the epigenetically inherited response. “So it’s an evolved mechanism that likely serves many important functions,” Rechavi said.

***

"Greer concurs that there could generally be a cost to deploying an adaptive response permanently. For example, deploying antiviral defenses when pathogens aren’t around is a waste of resources that could be used instead for growth and reproduction."

Comment: We just do not know how instinctual behavior is generated, but it exists. That animals are adaptable is obvious as is the role of the brain. (note my bold).

Biological complexity: managing cellular oxygen levels

by dhw, Thursday, October 17, 2019, 12:59 (1625 days ago) @ David Turell

dhw: My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. (dhw’s bold) No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level

DAVID (under “water control in trees”): these are complex designs to help the trees handle changing wet and drier climates where they exist. The complexity can be appreciated by looking at the article's illustrations. Only design explains this system.

dhw: Further evidence that even plants learn from experience and refine their survival techniques in accordance with the demands of the environment. Or do you think your God preprogrammed every plant strategy 3.8 billion years ago, or steps in to dabble every time a tree gets into trouble?

DAVID: Again you want consciousness in plants, and I don't accept it. Besides you are ignoring how complex the plant design has to be. It didn't develop by chance.

I don’t “want” it. I see their behaviour as evidence that their actions are dictated by awareness of what they need to do in order to survive and of the means whereby they can do it. I discount chance, and allow for the possibility that the cognitive powers of ALL cell communities may be the result of your God’s invention of cellular intelligence. I find this more likely than the vision of your hidden God individually preprogramming every undabbled strategy of plants, bacteria, insects, fish, birds, and animals throughout the whole history of life, especially in view of your insistence that the only thing he really wanted to design was H. sapiens.

Under "Biological complexity"
DAVID: We just do not know how instinctual behavior is generated, but it exists. That animals are adaptable is obvious as is the role of the brain.

Agreed.

Under "Big brain evolution"

"Human brains are certainly bigger than those of our nearest primate relatives, but there are surprisingly few differences in structure. So it is unclear what gives rise to the huge differences in our mental abilities."

DAVID: Why are similar genes handled differently and how did that happen? Perhaps God designing. The other difference is the slower speed of growth of human brains compare to chimps. Why did that happen? God in action.

Yet again, nobody knows the answers, and so we can only speculate: your God preprogrammed every undabbled variation and innovation 3.8 billion years ago (your proposal), or cells/cell communities work out every variation and innovation autonomously (this ability possibly being your God’s invention).

Biological complexity: managing cellular oxygen levels

by David Turell @, Thursday, October 17, 2019, 22:57 (1625 days ago) @ dhw

dhw: My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. (dhw’s bold) No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

Not knowing the source of consciousness does't answer the issue of possible precognition of future events.


DAVID (under “water control in trees”): these are complex designs to help the trees handle changing wet and drier climates where they exist. The complexity can be appreciated by looking at the article's illustrations. Only design explains this system.

dhw: Further evidence that even plants learn from experience and refine their survival techniques in accordance with the demands of the environment. Or do you think your God preprogrammed every plant strategy 3.8 billion years ago, or steps in to dabble every time a tree gets into trouble?

DAVID: Again you want consciousness in plants, and I don't accept it. Besides you are ignoring how complex the plant design has to be. It didn't develop by chance.

dhw: I don’t “want” it. I see their behaviour as evidence that their actions are dictated by awareness of what they need to do in order to survive and of the means whereby they can do it. I discount chance, and allow for the possibility that the cognitive powers of ALL cell communities may be the result of your God’s invention of cellular intelligence. I find this more likely than the vision of your hidden God individually preprogramming every undabbled strategy of plants, bacteria, insects, fish, birds, and animals throughout the whole history of life, especially in view of your insistence that the only thing he really wanted to design was H. sapiens.

God may well have given cells the ability to recognize dangers and also good items. Design by Him fits.


Under "Biological complexity"
DAVID: We just do not know how instinctual behavior is generated, but it exists. That animals are adaptable is obvious as is the role of the brain.

Agreed.

Under "Big brain evolution"

"Human brains are certainly bigger than those of our nearest primate relatives, but there are surprisingly few differences in structure. So it is unclear what gives rise to the huge differences in our mental abilities."

DAVID: Why are similar genes handled differently and how did that happen? Perhaps God designing. The other difference is the slower speed of growth of human brains compare to chimps. Why did that happen? God in action.

dhw; Yet again, nobody knows the answers, and so we can only speculate: your God preprogrammed every undabbled variation and innovation 3.8 billion years ago (your proposal), or cells/cell communities work out every variation and innovation autonomously (this ability possibly being your God’s invention).

Yes, it must be speculation, but the overwhelming evidence for design overcomes that to a marked degree. It keeps you agnostic.

Biological complexity: managing cellular oxygen levels

by dhw, Friday, October 18, 2019, 10:51 (1624 days ago) @ David Turell

dhw: My argument is that once a danger has been experienced, either the cell communities devise a means of combating it, or the species dies out. This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. (dhw’s bold) No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

DAVID: Not knowing the source of consciousness does't answer the issue of possible precognition of future events.

There is no precognition of future events, as I keep trying to explain.

DAVID (under “water control in trees”): Again you want consciousness in plants, and I don't accept it. Besides you are ignoring how complex the plant design has to be. It didn't develop by chance.

dhw: I don’t “want” it. I see their behaviour as evidence that their actions are dictated by awareness of what they need to do in order to survive and of the means whereby they can do it. I discount chance, and allow for the possibility that the cognitive powers of ALL cell communities may be the result of your God’s invention of cellular intelligence. I find this more likely than the vision of your hidden God individually preprogramming every undabbled strategy of plants, bacteria, insects, fish, birds, and animals throughout the whole history of life, especially in view of your insistence that the only thing he really wanted to design was H. sapiens.

DAVID: God may well have given cells the ability to recognize dangers and also good items. Design by Him fits.

“Design by Him fits” cellular intelligence, i.e. the autonomous means of combating dangers and exploiting good items.


DAVID ( Under "Big brain evolution"): Why are similar genes handled differently and how did that happen? Perhaps God designing. The other difference is the slower speed of growth of human brains compare to chimps. Why did that happen? God in action.

dhw; Yet again, nobody knows the answers, and so we can only speculate: your God preprogrammed every undabbled variation and innovation 3.8 billion years ago (your proposal), or cells/cell communities work out every variation and innovation autonomously (this ability possibly being your God’s invention).

DAVID: Yes, it must be speculation, but the overwhelming evidence for design overcomes that to a marked degree. It keeps you agnostic.

It does indeed. But it doesn’t in any way lessen the incongruity of your preprogramming/dabbling theory allied to your anthropocentric interpretation of the bush of life!

Biological complexity: managing cellular oxygen levels

by David Turell @, Friday, October 18, 2019, 17:55 (1624 days ago) @ dhw

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

DAVID: Not knowing the source of consciousness does't answer the issue of possible precognition of future events.

dhw: There is no precognition of future events, as I keep trying to explain.

How do the insects know the future of their larvae, if they do not watch in the future?


DAVID (under “water control in trees”): Again you want consciousness in plants, and I don't accept it. Besides you are ignoring how complex the plant design has to be. It didn't develop by chance.

dhw: I don’t “want” it. I see their behaviour as evidence that their actions are dictated by awareness of what they need to do in order to survive and of the means whereby they can do it. I discount chance, and allow for the possibility that the cognitive powers of ALL cell communities may be the result of your God’s invention of cellular intelligence. I find this more likely than the vision of your hidden God individually preprogramming every undabbled strategy of plants, bacteria, insects, fish, birds, and animals throughout the whole history of life, especially in view of your insistence that the only thing he really wanted to design was H. sapiens.

DAVID: God may well have given cells the ability to recognize dangers and also good items. Design by Him fits.

dhw: “Design by Him fits” cellular intelligence, i.e. the autonomous means of combating dangers and exploiting good items.

I've admitted its possible.>


DAVID ( Under "Big brain evolution"): Why are similar genes handled differently and how did that happen? Perhaps God designing. The other difference is the slower speed of growth of human brains compare to chimps. Why did that happen? God in action.

dhw; Yet again, nobody knows the answers, and so we can only speculate: your God preprogrammed every undabbled variation and innovation 3.8 billion years ago (your proposal), or cells/cell communities work out every variation and innovation autonomously (this ability possibly being your God’s invention).

DAVID: Yes, it must be speculation, but the overwhelming evidence for design overcomes that to a marked degree. It keeps you agnostic.

dhw; It does indeed. But it doesn’t in any way lessen the incongruity of your preprogramming/dabbling theory allied to your anthropocentric interpretation of the bush of life!

We are here, and history tells us the actual story, if not God's reasoning, which you constantly delve into, and He's not talking ..

Biological complexity: managing cellular oxygen levels

by dhw, Saturday, October 19, 2019, 10:34 (1623 days ago) @ David Turell

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

DAVID: Not knowing the source of consciousness does't answer the issue of possible precognition of future events.

dhw: There is no precognition of future events, as I keep trying to explain.

DAVID: How do the insects know the future of their larvae, if they do not watch in the future?

I keep repeating that I cannot give you an explanation for how each and every natural wonder originated, but it is perfectly possible that the method was invented when Mr and Mrs Insect noticed that their larvae were being killed off, and so they devised a method to ensure their survival, and when the method succeeded, it was passed on to subsequent generations, and then they didn’t have to watch any more. In your desperation to have your God anticipating the future on behalf of all the organisms he designed before designing the only organism he wanted to design, you persist in focusing on one out of millions of strategies, and trying to wriggle out of the sheer common sense of the bold at the start of this post.

Biological complexity: managing cellular oxygen levels

by David Turell @, Saturday, October 19, 2019, 19:34 (1623 days ago) @ dhw

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

DAVID: Not knowing the source of consciousness does't answer the issue of possible precognition of future events.

dhw: There is no precognition of future events, as I keep trying to explain.

DAVID: How do the insects know the future of their larvae, if they do not watch in the future?

dhw: I keep repeating that I cannot give you an explanation for how each and every natural wonder originated, but it is perfectly possible that the method was invented when Mr and Mrs Insect noticed that their larvae were being killed off, and so they devised a method to ensure their survival, and when the method succeeded, it was passed on to subsequent generations, and then they didn’t have to watch any more. In your desperation to have your God anticipating the future on behalf of all the organisms he designed before designing the only organism he wanted to design, you persist in focusing on one out of millions of strategies, and trying to wriggle out of the sheer common sense of the bold at the start of this post.

I agreed above, your theory is a possibility, if they watched and the quit watching when the problem was solved. But we cannot know if they watched in the beginning, because we do not know if they can conceptualize a solution like we would with our abilities. I think you hope for special insects with some degree of our consciousness. I still doubt it.

Biological complexity: managing cellular oxygen levels

by dhw, Sunday, October 20, 2019, 10:20 (1622 days ago) @ David Turell

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

DAVID: Not knowing the source of consciousness does't answer the issue of possible precognition of future events.

dhw: There is no precognition of future events, as I keep trying to explain.

DAVID: How do the insects know the future of their larvae, if they do not watch in the future?

dhw: I keep repeating that I cannot give you an explanation for how each and every natural wonder originated, but it is perfectly possible that the method was invented when Mr and Mrs Insect noticed that their larvae were being killed off, and so they devised a method to ensure their survival, and when the method succeeded, it was passed on to subsequent generations, and then they didn’t have to watch any more. In your desperation to have your God anticipating the future on behalf of all the organisms he designed before designing the only organism he wanted to design, you persist in focusing on one out of millions of strategies, and trying to wriggle out of the sheer common sense of the bold at the start of this post.

DAVID: I agreed above, your theory is a possibility, if they watched and the quit watching when the problem was solved. But we cannot know if they watched in the beginning, because we do not know if they can conceptualize a solution like we would with our abilities. I think you hope for special insects with some degree of our consciousness. I still doubt it.

I don’t hope for anything. You asked me for a possible explanation, and I gave you one. I don’t know why you refer to “special insects with some degree of our consciousness”. Insects were here long before us, and I do not regard consciousness as the exclusive property of H. sapiens. What I have described in bold is consciousness, but it is not “conceptualization” in the sense of abstract planning for the future. They don’t need a crystal ball to know that they are confronted by a present danger and must find a means of combating it if they are to survive.

Biological complexity: managing cellular oxygen levels

by David Turell @, Sunday, October 20, 2019, 23:18 (1622 days ago) @ dhw

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary.

DAVID: your bold is a possible just-so story. It requires conceptualization, so I don't know if it fully explains the insects' instinctual behavior.

dhw: So at least you now think that the above is possible. That’s progress. Thank you. I accept the cavil that we don’t know if it “fully explains” their behaviour, since nobody has yet found a “full” explanation of how consciousness and speciation work at any level.

DAVID: Not knowing the source of consciousness does't answer the issue of possible precognition of future events.

dhw: There is no precognition of future events, as I keep trying to explain.

DAVID: How do the insects know the future of their larvae, if they do not watch in the future?

dhw: I keep repeating that I cannot give you an explanation for how each and every natural wonder originated, but it is perfectly possible that the method was invented when Mr and Mrs Insect noticed that their larvae were being killed off, and so they devised a method to ensure their survival, and when the method succeeded, it was passed on to subsequent generations, and then they didn’t have to watch any more. In your desperation to have your God anticipating the future on behalf of all the organisms he designed before designing the only organism he wanted to design, you persist in focusing on one out of millions of strategies, and trying to wriggle out of the sheer common sense of the bold at the start of this post.

DAVID: I agreed above, your theory is a possibility, if they watched and the quit watching when the problem was solved. But we cannot know if they watched in the beginning, because we do not know if they can conceptualize a solution like we would with our abilities. I think you hope for special insects with some degree of our consciousness. I still doubt it.

dhw: I don’t hope for anything. You asked me for a possible explanation, and I gave you one. I don’t know why you refer to “special insects with some degree of our consciousness”. Insects were here long before us, and I do not regard consciousness as the exclusive property of H. sapiens. What I have described in bold is consciousness, but it is not “conceptualization” in the sense of abstract planning for the future. They don’t need a crystal ball to know that they are confronted by a present danger and must find a means of combating it if they are to survive.

The only consciousness I'll agree to for insects is that they are obviously aware of their environment and can react to it. Most of what they do is pure instinct as in monarchs metamorphosing and migrating and nothing more.

Biological complexity: managing cellular oxygen levels

by dhw, Monday, October 21, 2019, 14:20 (1621 days ago) @ David Turell

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary. […]

DAVID […] I agreed above, your theory is a possibility, if they watched and the quit watching when the problem was solved. But we cannot know if they watched in the beginning, because we do not know if they can conceptualize a solution like we would with our abilities. I think you hope for special insects with some degree of our consciousness. I still doubt it.

dhw: I don’t hope for anything. You asked me for a possible explanation, and I gave you one. I don’t know why you refer to “special insects with some degree of our consciousness”. Insects were here long before us, and I do not regard consciousness as the exclusive property of H. sapiens. What I have described in bold is consciousness, but it is not “conceptualization” in the sense of abstract planning for the future. They don’t need a crystal ball to know that they are confronted by a present danger and must find a means of combating it if they are to survive.

DAVID: The only consciousness I'll agree to for insects is that they are obviously aware of their environment and can react to it. Most of what they do is pure instinct as in monarchs metamorphosing and migrating and nothing more.

I’m happy with “most of what they do”. The same applies to all organisms, including ourselves – or do you consciously control every single process that takes place in your body? You simply refuse to accept that all the processes and decisions and variations and behaviours and strategies must have had an origin. If problems created by the environment have been solved in the past, the solutions will be passed on (in ALL forms of life, including our own). That is your “most of”. If they are new, then new solutions must be found - and that is where consciousness comes into play. All summed up in the bold at the start of this post, which you grudgingly accept and then try to brush aside..

Biological complexity: managing cellular oxygen levels

by David Turell @, Monday, October 21, 2019, 17:46 (1621 days ago) @ dhw

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary. […]

DAVID […] I agreed above, your theory is a possibility, if they watched and the quit watching when the problem was solved. But we cannot know if they watched in the beginning, because we do not know if they can conceptualize a solution like we would with our abilities. I think you hope for special insects with some degree of our consciousness. I still doubt it.

dhw: I don’t hope for anything. You asked me for a possible explanation, and I gave you one. I don’t know why you refer to “special insects with some degree of our consciousness”. Insects were here long before us, and I do not regard consciousness as the exclusive property of H. sapiens. What I have described in bold is consciousness, but it is not “conceptualization” in the sense of abstract planning for the future. They don’t need a crystal ball to know that they are confronted by a present danger and must find a means of combating it if they are to survive.

DAVID: The only consciousness I'll agree to for insects is that they are obviously aware of their environment and can react to it. Most of what they do is pure instinct as in monarchs metamorphosing and migrating and nothing more.

dhw: I’m happy with “most of what they do”. The same applies to all organisms, including ourselves – or do you consciously control every single process that takes place in your body? You simply refuse to accept that all the processes and decisions and variations and behaviours and strategies must have had an origin. If problems created by the environment have been solved in the past, the solutions will be passed on (in ALL forms of life, including our own). That is your “most of”. If they are new, then new solutions must be found - and that is where consciousness comes into play. All summed up in the bold at the start of this post, which you grudgingly accept and then try to brush aside..

I'm glad you accept automatic instinct. whose origin is not understood.

Biological complexity: managing cellular oxygen levels

by dhw, Tuesday, October 22, 2019, 11:03 (1620 days ago) @ David Turell

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary. […]

DAVID: The only consciousness I'll agree to for insects is that they are obviously aware of their environment and can react to it. Most of what they do is pure instinct as in monarchs metamorphosing and migrating and nothing more.

dhw: I’m happy with “most of what they do”. The same applies to all organisms, including ourselves – or do you consciously control every single process that takes place in your body? You simply refuse to accept that all the processes and decisions and variations and behaviours and strategies must have had an origin. If problems created by the environment have been solved in the past, the solutions will be passed on (in ALL forms of life, including our own). That is your “most of”. If they are new, then new solutions must be found - and that is where consciousness comes into play. All summed up in the bold at the start of this post, which you grudgingly accept and then try to brush aside..

DAVID: I'm glad you accept automatic instinct. whose origin is not understood.

Of course I accept automatic instinct. All organisms, including ourselves, function through automatic processes. That is your “most of what they do”. Now would you please accept that the rest of what they do, such as responding intelligently to new conditions, learning from experience, finding ways of combating existing dangers and passing solutions on to subsequent generations, are all evidence of consciousness.

Biological complexity: managing cellular oxygen levels

by David Turell @, Tuesday, October 22, 2019, 15:15 (1620 days ago) @ dhw

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary. […]

DAVID: The only consciousness I'll agree to for insects is that they are obviously aware of their environment and can react to it. Most of what they do is pure instinct as in monarchs metamorphosing and migrating and nothing more.

dhw: I’m happy with “most of what they do”. The same applies to all organisms, including ourselves – or do you consciously control every single process that takes place in your body? You simply refuse to accept that all the processes and decisions and variations and behaviours and strategies must have had an origin. If problems created by the environment have been solved in the past, the solutions will be passed on (in ALL forms of life, including our own). That is your “most of”. If they are new, then new solutions must be found - and that is where consciousness comes into play. All summed up in the bold at the start of this post, which you grudgingly accept and then try to brush aside..

DAVID: I'm glad you accept automatic instinct, whose origin is not understood.

dhw: Of course I accept automatic instinct. All organisms, including ourselves, function through automatic processes. That is your “most of what they do”. Now would you please accept that the rest of what they do, such as responding intelligently to new conditions, learning from experience, finding ways of combating existing dangers and passing solutions on to subsequent generations, are all evidence of consciousness.

The usual answer, intelligent information provided by God. Weaverbird nest knots would challenge a boy scout.

Biological complexity: managing cellular oxygen levels

by dhw, Wednesday, October 23, 2019, 11:53 (1619 days ago) @ David Turell

dhw: This means that organisms are aware of existing dangers, learn from experience, find ways of combating the dangers they know exist, and these ways are passed on by cellular memory to subsequent generations. No crystal ball necessary. […]

DAVID: The only consciousness I'll agree to for insects is that they are obviously aware of their environment and can react to it. Most of what they do is pure instinct as in monarchs metamorphosing and migrating and nothing more.

dhw: I’m happy with “most of what they do”. The same applies to all organisms, including ourselves – or do you consciously control every single process that takes place in your body? You simply refuse to accept that all the processes and decisions and variations and behaviours and strategies must have had an origin. If problems created by the environment have been solved in the past, the solutions will be passed on (in ALL forms of life, including our own). That is your “most of”. If they are new, then new solutions must be found - and that is where consciousness comes into play. All summed up in the bold at the start of this post, which you grudgingly accept and then try to brush aside..

DAVID: I'm glad you accept automatic instinct, whose origin is not understood.

dhw: Of course I accept automatic instinct. All organisms, including ourselves, function through automatic processes. That is your “most of what they do”. Now would you please accept that the rest of what they do, such as responding intelligently to new conditions, learning from experience, finding ways of combating existing dangers and passing solutions on to subsequent generations, are all evidence of consciousness.

DAVID: The usual answer, intelligent information provided by God. Weaverbird nest knots would challenge a boy scout.

Information is not intelligent. Intelligence is required to use information. Do you mean instructions? A 3.8-billion-year-old programme that the robot automatically switches on when new problems arise? Or do you mean that God popped down to earth to teach the weaverbird to tie its knots because weaverbird knots were “an absolute requirement for the evolutionary appearance of humans”? If organisms consciously observe and react to their environment, I suggest it makes more sense to have them consciously seek for solutions to new problems rather than switch off their consciousness and unconsciously switch on God’s programme, or hang around for him to hold a knot-tying lesson.

DAVID: (under “Ant intelligence”): Human traffic jams are the result of individual driver's decisions. The ants make group decisions as each individual makes the same move in coordination. I suspect a learned instinctual behavior based on standardized individual responses to stimuli, as shown in the bridge building study.

I’m glad you use the word “learned”, as opposed to preprogrammed or dabbled. How do you think the strategy first arose, and how do you think subsequent generations learned it? Don’t you think this is a prime example of the bolded statement with which I have begun this post?

Biological complexity: managing cellular oxygen levels

by David Turell @, Wednesday, October 23, 2019, 20:11 (1619 days ago) @ dhw

DAVID: I'm glad you accept automatic instinct, whose origin is not understood.

dhw: Of course I accept automatic instinct. All organisms, including ourselves, function through automatic processes. That is your “most of what they do”. Now would you please accept that the rest of what they do, such as responding intelligently to new conditions, learning from experience, finding ways of combating existing dangers and passing solutions on to subsequent generations, are all evidence of consciousness.

DAVID: The usual answer, intelligent information provided by God. Weaverbird nest knots would challenge a boy scout.

dhw: Information is not intelligent. Intelligence is required to use information. Do you mean instructions? A 3.8-billion-year-old programme that the robot automatically switches on when new problems arise? Or do you mean that God popped down to earth to teach the weaverbird to tie its knots because weaverbird knots were “an absolute requirement for the evolutionary appearance of humans”? If organisms consciously observe and react to their environment, I suggest it makes more sense to have them consciously seek for solutions to new problems rather than switch off their consciousness and unconsciously switch on God’s programme, or hang around for him to hold a knot-tying lesson.

Yes "Intelligent information" is instructional information which can be used directly and automatically to solve problems, by organisms that cannot conceptualize. I fully believe God helped the weaverbirds. See my entry on self-awareness and who can conceptualize solutions.


DAVID: (under “Ant intelligence”): Human traffic jams are the result of individual driver's decisions. The ants make group decisions as each individual makes the same move in coordination. I suspect a learned instinctual behavior based on standardized individual responses to stimuli, as shown in the bridge building study.

dhw: I’m glad you use the word “learned”, as opposed to preprogrammed or dabbled. How do you think the strategy first arose, and how do you think subsequent generations learned it? Don’t you think this is a prime example of the bolded statement with which I have begun this post?

But it is based on expecting rote behavior by programmed ants, as previously shown.

Biological complexity: managing cellular oxygen levels

by dhw, Thursday, October 24, 2019, 10:39 (1618 days ago) @ David Turell

DAVID: I'm glad you accept automatic instinct, whose origin is not understood.

dhw: Of course I accept automatic instinct. All organisms, including ourselves, function through automatic processes. That is your “most of what they do”. Now would you please accept that the rest of what they do, such as responding intelligently to new conditions, learning from experience, finding ways of combating existing dangers and passing solutions on to subsequent generations, are all evidence of consciousness.

DAVID: The usual answer, intelligent information provided by God. Weaverbird nest knots would challenge a boy scout.

dhw: Information is not intelligent. Intelligence is required to use information. Do you mean instructions? A 3.8-billion-year-old programme that the robot automatically switches on when new problems arise? Or do you mean that God popped down to earth to teach the weaverbird to tie its knots because weaverbird knots were “an absolute requirement for the evolutionary appearance of humans”? If organisms consciously observe and react to their environment, I suggest it makes more sense to have them consciously seek for solutions to new problems rather than switch off their consciousness and unconsciously switch on God’s programme, or hang around for him to hold a knot-tying lesson.

DAVID: Yes "Intelligent information" is instructional information which can be used directly and automatically to solve problems, by organisms that cannot conceptualize. I fully believe God helped the weaverbirds. See my entry on self-awareness and who can conceptualize solutions.

See my response to that entry on the Dennett thread. I realize that you fully believe your God preprogrammed the weaverbird’s nest 3.8 billion years ago, or popped in to give the bird a course in knot-tying, and that this was an indispensable factor in his preparations for the design of H. sapiens, which was his one and only purpose. I remain sceptical.

DAVID: (under “Ant intelligence”): Human traffic jams are the result of individual driver's decisions. The ants make group decisions as each individual makes the same move in coordination. I suspect a learned instinctual behavior based on standardized individual responses to stimuli, as shown in the bridge building study.

dhw: I’m glad you use the word “learned”, as opposed to preprogrammed or dabbled. How do you think the strategy first arose, and how do you think subsequent generations learned it? Don’t you think this is a prime example of the bolded statement with which I have begun this post?

DAVID: But it is based on expecting rote behavior by programmed ants, as previously shown.

You have never shown that the first ants to solve problems of traffic jams and gaps to be bridged were preprogrammed to do so 3.8 billion years ago in the first cells. Once a problem has been solved, the solution will be passed on, but it takes intelligence to solve the problem in the first place.

Biological complexity: managing cellular oxygen levels

by David Turell @, Thursday, October 24, 2019, 18:59 (1618 days ago) @ dhw

DAVID: I'm glad you accept automatic instinct, whose origin is not understood.

dhw: Of course I accept automatic instinct. All organisms, including ourselves, function through automatic processes. That is your “most of what they do”. Now would you please accept that the rest of what they do, such as responding intelligently to new conditions, learning from experience, finding ways of combating existing dangers and passing solutions on to subsequent generations, are all evidence of consciousness.

DAVID: The usual answer, intelligent information provided by God. Weaverbird nest knots would challenge a boy scout.

dhw: Information is not intelligent. Intelligence is required to use information. Do you mean instructions? A 3.8-billion-year-old programme that the robot automatically switches on when new problems arise? Or do you mean that God popped down to earth to teach the weaverbird to tie its knots because weaverbird knots were “an absolute requirement for the evolutionary appearance of humans”? If organisms consciously observe and react to their environment, I suggest it makes more sense to have them consciously seek for solutions to new problems rather than switch off their consciousness and unconsciously switch on God’s programme, or hang around for him to hold a knot-tying lesson.

DAVID: Yes "Intelligent information" is instructional information which can be used directly and automatically to solve problems, by organisms that cannot conceptualize. I fully believe God helped the weaverbirds. See my entry on self-awareness and who can conceptualize solutions.

dhw: See my response to that entry on the Dennett thread. I realize that you fully believe your God preprogrammed the weaverbird’s nest 3.8 billion years ago, or popped in to give the bird a course in knot-tying, and that this was an indispensable factor in his preparations for the design of H. sapiens, which was his one and only purpose. I remain sceptical.

Of course you do.


DAVID: (under “Ant intelligence”): Human traffic jams are the result of individual driver's decisions. The ants make group decisions as each individual makes the same move in coordination. I suspect a learned instinctual behavior based on standardized individual responses to stimuli, as shown in the bridge building study.

dhw: I’m glad you use the word “learned”, as opposed to preprogrammed or dabbled. How do you think the strategy first arose, and how do you think subsequent generations learned it? Don’t you think this is a prime example of the bolded statement with which I have begun this post?

DAVID: But it is based on expecting rote behavior by programmed ants, as previously shown.

dhw: You have never shown that the first ants to solve problems of traffic jams and gaps to be bridged were preprogrammed to do so 3.8 billion years ago in the first cells. Once a problem has been solved, the solution will be passed on, but it takes intelligence to solve the problem in the first place.

The finding in bridges was that each ant was programmed to do his own individual standardized response. Intelligence involves conceptualizing a solution. In this case according to the article:

"What they saw surprised them: when density increases, ant flows (1) swell and then become constant, whereas human traffic, above a certain density threshold, slows to zero flow and causes a jam (2). Ants, on the other hand, accelerate until a maximum flow or capacity on the path is reached. When traffic becomes too dense and causes too many collisions between ants, they change tactics, preferring to avoid time-consuming collisions instead of continuing to accelerate. Similarly, researchers noted that at excessively high density levels, ants refrain from joining the flow of traffic and wait for it to thin out instead."

Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

Biological complexity: managing cellular oxygen levels

by dhw, Friday, October 25, 2019, 11:05 (1617 days ago) @ David Turell

dhw: I realize that you fully believe your God preprogrammed the weaverbird’s nest 3.8 billion years ago, or popped in to give the bird a course in knot-tying, and that this was an indispensable factor in his preparations for the design of H. sapiens, which was his one and only purpose. I remain sceptical.

DAVID: Of course you do.

I’m glad you acknowledge that my scepticism is only natural!

DAVID: (under “Ant intelligence”): Human traffic jams are the result of individual driver's decisions. The ants make group decisions as each individual makes the same move in coordination. I suspect a learned instinctual behavior based on standardized individual responses to stimuli, as shown in the bridge building study.

dhw: I’m glad you use the word “learned”, as opposed to preprogrammed or dabbled. How do you think the strategy first arose, and how do you think subsequent generations learned it? Don’t you think this is a prime example of the bolded statement with which I have begun this post?

DAVID: But it is based on expecting rote behavior by programmed ants, as previously shown.

dhw: You have never shown that the first ants to solve problems of traffic jams and gaps to be bridged were preprogrammed to do so 3.8 billion years ago in the first cells. Once a problem has been solved, the solution will be passed on, but it takes intelligence to solve the problem in the first place.

DAVID: The finding in bridges was that each ant was programmed to do his own individual standardized response. Intelligence involves conceptualizing a solution. In this case according to the article:
"What they saw surprised them: when density increases, ant flows (1) swell and then become constant, whereas human traffic, above a certain density threshold, slows to zero flow and causes a jam (2). Ants, on the other hand, accelerate until a maximum flow or capacity on the path is reached. When traffic becomes too dense and causes too many collisions between ants, they change tactics, preferring to avoid time-consuming collisions instead of continuing to accelerate. Similarly, researchers noted that at excessively high density levels, ants refrain from joining the flow of traffic and wait for it to thin out instead."

Where do you see preprogramming? Every sentence tells us what they do and how they adapt to changing circumstances: they accelerate, they change tactics, they refrain and wait...Do you honestly think all this was preprogrammed 3.8 billion years ago? Clearly they think on their feet!

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

Biological complexity: managing cellular oxygen levels

by David Turell @, Friday, October 25, 2019, 23:05 (1617 days ago) @ dhw

dhw: I realize that you fully believe your God preprogrammed the weaverbird’s nest 3.8 billion years ago, or popped in to give the bird a course in knot-tying, and that this was an indispensable factor in his preparations for the design of H. sapiens, which was his one and only purpose. I remain sceptical.

DAVID: Of course you do.

I’m glad you acknowledge that my scepticism is only natural!

DAVID: (under “Ant intelligence”): Human traffic jams are the result of individual driver's decisions. The ants make group decisions as each individual makes the same move in coordination. I suspect a learned instinctual behavior based on standardized individual responses to stimuli, as shown in the bridge building study.

dhw: I’m glad you use the word “learned”, as opposed to preprogrammed or dabbled. How do you think the strategy first arose, and how do you think subsequent generations learned it? Don’t you think this is a prime example of the bolded statement with which I have begun this post?

DAVID: But it is based on expecting rote behavior by programmed ants, as previously shown.

dhw: You have never shown that the first ants to solve problems of traffic jams and gaps to be bridged were preprogrammed to do so 3.8 billion years ago in the first cells. Once a problem has been solved, the solution will be passed on, but it takes intelligence to solve the problem in the first place.

DAVID: The finding in bridges was that each ant was programmed to do his own individual standardized response. Intelligence involves conceptualizing a solution. In this case according to the article:
"What they saw surprised them: when density increases, ant flows (1) swell and then become constant, whereas human traffic, above a certain density threshold, slows to zero flow and causes a jam (2). Ants, on the other hand, accelerate until a maximum flow or capacity on the path is reached. When traffic becomes too dense and causes too many collisions between ants, they change tactics, preferring to avoid time-consuming collisions instead of continuing to accelerate. Similarly, researchers noted that at excessively high density levels, ants refrain from joining the flow of traffic and wait for it to thin out instead."

dhw: Where do you see preprogramming? Every sentence tells us what they do and how they adapt to changing circumstances: they accelerate, they change tactics, they refrain and wait...Do you honestly think all this was preprogrammed 3.8 billion years ago? Clearly they think on their feet!

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

dhw: Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

That the ants start and stop or move along in unison is their individual programming. If you have ever marched. as I did in the Army, you'd understand. Soldiers don't bump in formations.

Biological complexity: managing cellular oxygen levels

by dhw, Saturday, October 26, 2019, 12:53 (1616 days ago) @ David Turell

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

dhw: Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

DAVID: That the ants start and stop or move along in unison is their individual programming. If you have ever marched. as I did in the Army, you'd understand. Soldiers don't bump in formations.

So did your God preprogramme your march 3.8 billion years ago? Or did he pop in to give you marching lessons?

Biological complexity: managing cellular oxygen levels

by David Turell @, Saturday, October 26, 2019, 15:30 (1616 days ago) @ dhw

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

dhw: Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

DAVID: That the ants start and stop or move along in unison is their individual programming. If you have ever marched. as I did in the Army, you'd understand. Soldiers don't bump in formations.

dhw: So did your God preprogramme your march 3.8 billion years ago? Or did he pop in to give you marching lessons?

If I was trained to act like ants, the ant instinct could give the same result. You wouldn't want to bump into other people.

Biological complexity: managing cellular oxygen levels

by David Turell @, Saturday, October 26, 2019, 15:31 (1616 days ago) @ David Turell

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

dhw: Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

DAVID: That the ants start and stop or move along in unison is their individual programming. If you have ever marched. as I did in the Army, you'd understand. Soldiers don't bump in formations.

dhw: So did your God preprogramme your march 3.8 billion years ago? Or did he pop in to give you marching lessons?


If I was trained to act like ants, the ant instinct could give the same result. You wouldn't want to bump into other people. Ants don't either, as the article notes.

Biological complexity: managing cellular oxygen levels

by dhw, Sunday, October 27, 2019, 09:02 (1615 days ago) @ David Turell

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

dhw: Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

DAVID: That the ants start and stop or move along in unison is their individual programming. If you have ever marched. as I did in the Army, you'd understand. Soldiers don't bump in formations.

dhw: So did your God preprogramme your march 3.8 billion years ago? Or did he pop in to give you marching lessons?

DAVID: If I was trained to act like ants, the ant instinct could give the same result. You wouldn't want to bump into other people.

I can’t follow this. If you were trained to act like ants, your behaviour would be the same as that of ants. But you think you have an autonomous intelligence and they don’t. We’re back to the same point made on the “Dennett” thread. If we can’t tell from the outside whether their behaviour is preprogrammed or autonomous, the same applies to our own. So please answer my question: since you firmly believe that your God preprogrammed the ant march 3.8 billion years ago, or popped in to give them marching lessons, do you believe he did the same for you? If not, how can you tell the difference?

Biological complexity: managing cellular oxygen levels

by David Turell @, Sunday, October 27, 2019, 17:20 (1615 days ago) @ dhw

DAVID: Individual ants work in unison as programmed, while humans act individually. No conceptualization required.

dhw: Why “as programmed”? Yes, they work in unison – so do humans when the action requires teamwork. And you still refuse to acknowledge that all strategies such as bridge-building must have had an origin which requires an inventive intelligence, and once a solution had been found to a particular problem, it would have been passed down to subsequent generations.

DAVID: That the ants start and stop or move along in unison is their individual programming. If you have ever marched. as I did in the Army, you'd understand. Soldiers don't bump in formations.

dhw: So did your God preprogramme your march 3.8 billion years ago? Or did he pop in to give you marching lessons?

DAVID: If I was trained to act like ants, the ant instinct could give the same result. You wouldn't want to bump into other people.

dhw: I can’t follow this.

Of course you can. I was trained in high school and the Army to march. While in formation I acted just like the ants marched.

dhw: If you were trained to act like ants, your behaviour would be the same as that of ants. But you think you have an autonomous intelligence and they don’t. We’re back to the same point made on the “Dennett” thread. If we can’t tell from the outside whether their behaviour is preprogrammed or autonomous, the same applies to our own. So please answer my question: since you firmly believe that your God preprogrammed the ant march 3.8 billion years ago, or popped in to give them marching lessons, do you believe he did the same for you? If not, how can you tell the difference?

If you now understand my marching point, my point, I know I differ from the ant on being automatic, like him marching , but, unlike him, i introspectively understand what I am doing as a result of training.

Biological complexity: managing cellular oxygen levels

by dhw, Monday, October 28, 2019, 10:30 (1614 days ago) @ David Turell

DAVID: I was trained in high school and the Army to march. While in formation I acted just like the ants marched.

dhw: If you were trained to act like ants, your behaviour would be the same as that of ants. But you think you have an autonomous intelligence and they don’t. We’re back to the same point made on the “Dennett” thread. If we can’t tell from the outside whether their behaviour is preprogrammed or autonomous, the same applies to our own. So please answer my question: since you firmly believe that your God preprogrammed the ant march 3.8 billion years ago, or popped in to give them marching lessons, do you believe he did the same for you? If not, how can you tell the difference?

DAVID: If you now understand my marching point, my point, I know I differ from the ant on being automatic, like him marching, but, unlike him, i introspectively understand what I am doing as a result of training.

We are not talking about introspection, which of course I acknowledge as a major difference between ants and us. We are talking about the origin of ant marching (which, incidentally, is totally different from human marching). You assume that ants did not devise their own way of marching – and, incidentally, of training, since we know that ants teach their fellow ants – but your God preprogrammed it 3.8 billion years ago or himself popped in to show them the way. I propose that they worked it out for themselves and passed on the instructions, just as someone or the other devised a way of marching to be passed on to your high school and army trainers, and from them to you. Now please explain how you can tell that their march was preprogrammed and yours was not.

Biological complexity: managing cellular oxygen levels

by David Turell @, Monday, October 28, 2019, 14:05 (1614 days ago) @ dhw

DAVID: I was trained in high school and the Army to march. While in formation I acted just like the ants marched.

dhw: If you were trained to act like ants, your behaviour would be the same as that of ants. But you think you have an autonomous intelligence and they don’t. We’re back to the same point made on the “Dennett” thread. If we can’t tell from the outside whether their behaviour is preprogrammed or autonomous, the same applies to our own. So please answer my question: since you firmly believe that your God preprogrammed the ant march 3.8 billion years ago, or popped in to give them marching lessons, do you believe he did the same for you? If not, how can you tell the difference?

DAVID: If you now understand my marching point, my point, I know I differ from the ant on being automatic, like him marching, but, unlike him, i introspectively understand what I am doing as a result of training.

dhw: We are not talking about introspection, which of course I acknowledge as a major difference between ants and us. We are talking about the origin of ant marching (which, incidentally, is totally different from human marching).

I love how you quibble. Have you ever marched? In marching we are all automatons, ants or humans.

dhw: You assume that ants did not devise their own way of marching – and, incidentally, of training, since we know that ants teach their fellow ants –

Remember in the ant bridge study each ant did its individual role, all ants the same. All automatons

dhw: but your God preprogrammed it 3.8 billion years ago or himself popped in to show them the way. I propose that they worked it out for themselves and passed on the instructions, just as someone or the other devised a way of marching to be passed on to your high school and army trainers, and from them to you. Now please explain how you can tell that their march was preprogrammed and yours was not.

I was trained, ants were programmed.

Biological complexity: managing cellular oxygen levels

by dhw, Tuesday, October 29, 2019, 10:42 (1613 days ago) @ David Turell

DAVID: If you now understand my marching point, my point, I know I differ from the ant on being automatic, like him marching, but, unlike him, i introspectively understand what I am doing as a result of training.

dhw: We are not talking about introspection, which of course I acknowledge as a major difference between ants and us. We are talking about the origin of ant marching (which, incidentally, is totally different from human marching).

DAVID: I love how you quibble. Have you ever marched? In marching we are all automatons, ants or humans.

So why do you think your God preprogrammed the ant march but intelligent humans worked out the human march?

dhw: You assume that ants did not devise their own way of marching – and, incidentally, of training, since we know that ants teach their fellow ants – but your God preprogrammed it 3.8 billion years ago…

DAVID: Remember in the ant bridge study each ant did its individual role, all ants the same. All automatons

You persist in ignoring the fact that this strategy must have had a beginning. Once it was established, the ants would have known (or been taught) their individual roles.

dhw: You assume that ants did not devise their own way of marching [...] but your God preprogrammed it 3.8 billion years ago or himself popped in to show them the way. I propose that they worked it out for themselves and passed on the instructions, just as someone or the other devised a way of marching to be passed on to your high school and army trainers, and from them to you. Now please explain how you can tell that their march was preprogrammed and yours was not.

DAVID: I was trained, ants were programmed.

And that is the nub of the matter. You keep repeating your fixed belief as if it were a fact. So 3.8 billion years ago, your God preprogrammed not only the life form of the ant, but also every single strategy that ants would use to increase their prospects of survival, and indeed the role that each individual ant would play in the strategy. Multiply this by the billions of other life forms, lifestyles and natural wonders which according to you were also preprogrammed in those first living cells, or alternatively imagine your God having to give courses to all the ants that ever existed, not to mention every other organism, including bacteria and the weaverbird...And you talk of just-so stories! How about the possibility that (assuming he exists) he gave all these organisms the wherewithal to figure out their own strategies? Wouldn’t that be almost infinitely simpler, and wouldn’t that explain the huge diversity of life forms, natural wonders etc. which we know constitutes the history of life? Too humanly logical for you?

Biological complexity: managing cellular oxygen levels

by David Turell @, Tuesday, October 29, 2019, 13:55 (1613 days ago) @ dhw

DAVID: If you now understand my marching point, my point, I know I differ from the ant on being automatic, like him marching, but, unlike him, i introspectively understand what I am doing as a result of training.

dhw: We are not talking about introspection, which of course I acknowledge as a major difference between ants and us. We are talking about the origin of ant marching (which, incidentally, is totally different from human marching).

DAVID: I love how you quibble. Have you ever marched? In marching we are all automatons, ants or humans.

dhw: So why do you think your God preprogrammed the ant march but intelligent humans worked out the human march?

Because we can plan a lesson in marching. Yes elder ants can teach a path to follow.


dhw: You assume that ants did not devise their own way of marching – and, incidentally, of training, since we know that ants teach their fellow ants – but your God preprogrammed it 3.8 billion years ago…

DAVID: Remember in the ant bridge study each ant did its individual role, all ants the same. All automatons

dhw: You persist in ignoring the fact that this strategy must have had a beginning. Once it was established, the ants would have known (or been taught) their individual roles.

dhw: You assume that ants did not devise their own way of marching [...] but your God preprogrammed it 3.8 billion years ago or himself popped in to show them the way. I propose that they worked it out for themselves and passed on the instructions, just as someone or the other devised a way of marching to be passed on to your high school and army trainers, and from them to you. Now please explain how you can tell that their march was preprogrammed and yours was not.

DAVID: I was trained, ants were programmed.

dhw: And that is the nub of the matter. You keep repeating your fixed belief as if it were a fact. So 3.8 billion years ago, your God preprogrammed not only the life form of the ant, but also every single strategy that ants would use to increase their prospects of survival, and indeed the role that each individual ant would play in the strategy. Multiply this by the billions of other life forms, lifestyles and natural wonders which according to you were also preprogrammed in those first living cells, or alternatively imagine your God having to give courses to all the ants that ever existed, not to mention every other organism, including bacteria and the weaverbird...And you talk of just-so stories! How about the possibility that (assuming he exists) he gave all these organisms the wherewithal to figure out their own strategies? Wouldn’t that be almost infinitely simpler, and wouldn’t that explain the huge diversity of life forms, natural wonders etc. which we know constitutes the history of life? Too humanly logical for you?

Your guess that He taught ants to think for themselves is not supported by the bridge study. why do you keep ignoring that study? Because it won't support your ant thought theory.

Biological complexity: managing cellular oxygen levels

by dhw, Wednesday, October 30, 2019, 11:40 (1612 days ago) @ David Turell

Amazing how far we have digressed from “managing cellular oxygen levels”, but it actually comes back to the same subject, because I use ant behaviour as an analogy to the way cells autonomously organize themselves, respond to new situations, communicate and take decisions.

dhw: So why do you think your God preprogrammed the ant march but intelligent humans worked out the human march?

DAVID: Because we can plan a lesson in marching. Yes elder ants can teach a path to follow.

And what makes you so sure that the ant march was not originally worked out by intelligent creatures who passed on their “invention” to succeeding generations?

DAVID: I was trained, ants were programmed.

dhw: And that is the nub of the matter. You keep repeating your fixed belief as if it were a fact. So 3.8 billion years ago, your God preprogrammed not only the life form of the ant, but also every single strategy that ants would use to increase their prospects of survival, and indeed the role that each individual ant would play in the strategy. Multiply this by the billions of other life forms, lifestyles and natural wonders which according to you were also preprogrammed in those first living cells[…] And you talk of just-so stories! How about the possibility that (assuming he exists) he gave all these organisms the wherewithal to figure out their own strategies? Wouldn’t that be almost infinitely simpler, and wouldn’t that explain the huge diversity of life forms, natural wonders etc. which we know constitutes the history of life? Too humanly logical for you?

DAVID: Your guess that He taught ants to think for themselves is not supported by the bridge study. why do you keep ignoring that study? Because it won't support your ant thought theory.

I have not ignored that study at all, but have constantly pointed out to you that the bridge strategy, just like all strategies, must have had an ORIGIN. When confronted with a problem, ants – like every other organism – must either work out a solution or they perish. Once they have worked it out, it is passed on and automatically re-used by subsequent generations. And that is the basis of all evolutionary development: whatever works survives. (Yes, that is Darwinian, and perfectly logical.) In the meantime, you totally ignore the sheer incredibility of the above theory that your God provided the first living cells with absolutely every undabbled new organ etc., all in order to “cover the time” before dabbling or switching on the only programme he really wanted: H. sapiens. That really takes some believing! Even you accept that it defies human logic.

Biological complexity: managing cellular oxygen levels

by David Turell @, Wednesday, October 30, 2019, 14:35 (1612 days ago) @ dhw

Amazing how far we have digressed from “managing cellular oxygen levels”, but it actually comes back to the same subject, because I use ant behaviour as an analogy to the way cells autonomously organize themselves, respond to new situations, communicate and take decisions.

dhw: So why do you think your God preprogrammed the ant march but intelligent humans worked out the human march?

DAVID: Because we can plan a lesson in marching. Yes elder ants can teach a path to follow.

And what makes you so sure that the ant march was not originally worked out by intelligent creatures who passed on their “invention” to succeeding generations?

DAVID: I was trained, ants were programmed.

dhw: And that is the nub of the matter. You keep repeating your fixed belief as if it were a fact. So 3.8 billion years ago, your God preprogrammed not only the life form of the ant, but also every single strategy that ants would use to increase their prospects of survival, and indeed the role that each individual ant would play in the strategy. Multiply this by the billions of other life forms, lifestyles and natural wonders which according to you were also preprogrammed in those first living cells[…] And you talk of just-so stories! How about the possibility that (assuming he exists) he gave all these organisms the wherewithal to figure out their own strategies? Wouldn’t that be almost infinitely simpler, and wouldn’t that explain the huge diversity of life forms, natural wonders etc. which we know constitutes the history of life? Too humanly logical for you?

DAVID: Your guess that He taught ants to think for themselves is not supported by the bridge study. why do you keep ignoring that study? Because it won't support your ant thought theory.

dhw: I have not ignored that study at all, but have constantly pointed out to you that the bridge strategy, just like all strategies, must have had an ORIGIN. When confronted with a problem, ants – like every other organism – must either work out a solution or they perish. Once they have worked it out, it is passed on and automatically re-used by subsequent generations. And that is the basis of all evolutionary development: whatever works survives. (Yes, that is Darwinian, and perfectly logical.)

Each ant in the bridge study grabs another ant, each in the same way, to pass over a gap. Undoubtedly an instinct for the colony. It is an exact parallel to ants marching, each ant doing exactly the same thing. Humans are taught to march and have introspection about it. Ants march spaced, simply because they 'know' not to touch each other, no thought involved

dhw: In the meantime, you totally ignore the sheer incredibility of the above theory that your God provided the first living cells with absolutely every undabbled new organ etc., all in order to “cover the time” before dabbling or switching on the only programme he really wanted: H. sapiens. That really takes some believing! Even you accept that it defies human logic.

Usual distortion, commented upon elsewhere

Biological complexity: managing cellular oxygen levels

by dhw, Thursday, October 31, 2019, 11:22 (1611 days ago) @ David Turell

DAVID: Your guess that He taught ants to think for themselves is not supported by the bridge study. why do you keep ignoring that study? Because it won't support your ant thought theory.

dhw: I have not ignored that study at all, but have constantly pointed out to you that the bridge strategy, just like all strategies, must have had an ORIGIN. When confronted with a problem, ants – like every other organism – must either work out a solution or they perish. Once they have worked it out, it is passed on and automatically re-used by subsequent generations. And that is the basis of all evolutionary development: whatever works survives. (Yes, that is Darwinian, and perfectly logical.)

DAVID: Each ant in the bridge study grabs another ant, each in the same way, to pass over a gap. Undoubtedly an instinct for the colony. It is an exact parallel to ants marching, each ant doing exactly the same thing.

Why do you persistently ignore the fact that each strategy must have had an origin? According to you, your God planned every single one 3.8 billion years ago, and the programme automatically switched itself on when the ants were first confronted by the problem (bridging a gap or having to avoid bumping into one another). I suggest that they worked out for themselves how to bridge the gap and how not to bump into one another.

DAVID: Humans are taught to march and have introspection about it. Ants march spaced, simply because they 'know' not to touch each other, no thought involved.

I am not claiming that ants have introspection, which we have agreed may well be unique to humans. I suggest that both ants and humans “know” from experience that bumping into one another is not a good idea, and both species have therefore knowingly devised a method to avoid bumping. This method has been passed down to succeeding generations. Since you acknowledge the impossibility of judging from the outside whether behaviour has been preprogrammed or is the result of autonomous thought, the very least you can offer my suggestion is a 50/50 chance of being right.

Biological complexity: managing cellular oxygen levels

by David Turell @, Thursday, October 31, 2019, 18:54 (1611 days ago) @ dhw

DAVID: Your guess that He taught ants to think for themselves is not supported by the bridge study. why do you keep ignoring that study? Because it won't support your ant thought theory.

dhw: I have not ignored that study at all, but have constantly pointed out to you that the bridge strategy, just like all strategies, must have had an ORIGIN. When confronted with a problem, ants – like every other organism – must either work out a solution or they perish. Once they have worked it out, it is passed on and automatically re-used by subsequent generations. And that is the basis of all evolutionary development: whatever works survives. (Yes, that is Darwinian, and perfectly logical.)

DAVID: Each ant in the bridge study grabs another ant, each in the same way, to pass over a gap. Undoubtedly an instinct for the colony. It is an exact parallel to ants marching, each ant doing exactly the same thing.

Why do you persistently ignore the fact that each strategy must have had an origin? According to you, your God planned every single one 3.8 billion years ago, and the programme automatically switched itself on when the ants were first confronted by the problem (bridging a gap or having to avoid bumping into one another). I suggest that they worked out for themselves how to bridge the gap and how not to bump into one another.

DAVID: Humans are taught to march and have introspection about it. Ants march spaced, simply because they 'know' not to touch each other, no thought involved.

dhw: I am not claiming that ants have introspection, which we have agreed may well be unique to humans. I suggest that both ants and humans “know” from experience that bumping into one another is not a good idea, and both species have therefore knowingly devised a method to avoid bumping. This method has been passed down to succeeding generations. Since you acknowledge the impossibility of judging from the outside whether behaviour has been preprogrammed or is the result of autonomous thought, the very least you can offer my suggestion is a 50/50 chance of being right.

Sorry. I was taught to march. it required understanding and responding to teaching instructions. Ants don't like to bump into each other. They simply follow the leader with spacing.

Biological complexity: managing cellular oxygen levels

by dhw, Friday, November 01, 2019, 10:34 (1610 days ago) @ David Turell

DAVID: Humans are taught to march and have introspection about it. Ants march spaced, simply because they 'know' not to touch each other, no thought involved.

dhw: I am not claiming that ants have introspection, which we have agreed may well be unique to humans. I suggest that both ants and humans “know” from experience that bumping into one another is not a good idea, and both species have therefore knowingly devised a method to avoid bumping. This method has been passed down to succeeding generations. Since you acknowledge the impossibility of judging from the outside whether behaviour has been preprogrammed or is the result of autonomous thought, the very least you can offer my suggestion is a 50/50 chance of being right.

DAVID: Sorry. I was taught to march. it required understanding and responding to teaching instructions. Ants don't like to bump into each other. They simply follow the leader with spacing[

Humans don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Ants don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Humans follow the leader with spacing. Ants follow the leader with spacing. You believe that 3.8 billion years ago, your God provided the first cells with a programme for the creation of ants (plus millions of other life forms) and for the strategies of marching and bridge-building (plus billions of other strategies, lifestyles and natural wonders for all the other life forms) which ants would automatically and unconsciously switch on when needed. Humans, on the other hand, were given the ability to devise the same strategies without any such programme. My purely subjective opinion is that a 3.8-billion-year-old programme for ant-marching and bridge-building and every other life form, strategy etc. in the history of life is more than a teeny bit harder to believe in than the ability of ants and other life forms to work out their own strategies. But of course you are entitled to believe whatever you want.;-)

Biological complexity: managing cellular oxygen levels

by David Turell @, Friday, November 01, 2019, 20:11 (1610 days ago) @ dhw

DAVID: Humans are taught to march and have introspection about it. Ants march spaced, simply because they 'know' not to touch each other, no thought involved.

dhw: I am not claiming that ants have introspection, which we have agreed may well be unique to humans. I suggest that both ants and humans “know” from experience that bumping into one another is not a good idea, and both species have therefore knowingly devised a method to avoid bumping. This method has been passed down to succeeding generations. Since you acknowledge the impossibility of judging from the outside whether behaviour has been preprogrammed or is the result of autonomous thought, the very least you can offer my suggestion is a 50/50 chance of being right.

DAVID: Sorry. I was taught to march. it required understanding and responding to teaching instructions. Ants don't like to bump into each other. They simply follow the leader with spacing[

dhw: Humans don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Ants don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Humans follow the leader with spacing. Ants follow the leader with spacing. You believe that 3.8 billion years ago, your God provided the first cells with a programme for the creation of ants (plus millions of other life forms) and for the strategies of marching and bridge-building (plus billions of other strategies, lifestyles and natural wonders for all the other life forms) which ants would automatically and unconsciously switch on when needed. Humans, on the other hand, were given the ability to devise the same strategies without any such programme. My purely subjective opinion is that a 3.8-billion-year-old programme for ant-marching and bridge-building and every other life form, strategy etc. in the history of life is more than a teeny bit harder to believe in than the ability of ants and other life forms to work out their own strategies. But of course you are entitled to believe whatever you want.;-)

Well, we each have a version. We at least agree they don't have our introspection .

Biological complexity: managing cellular oxygen levels

by dhw, Saturday, November 02, 2019, 12:14 (1609 days ago) @ David Turell

DAVID: Sorry. I was taught to march. it required understanding and responding to teaching instructions. Ants don't like to bump into each other. They simply follow the leader with spacing[

dhw: Humans don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Ants don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Humans follow the leader with spacing. Ants follow the leader with spacing. You believe that 3.8 billion years ago, your God provided the first cells with a programme for the creation of ants (plus millions of other life forms) and for the strategies of marching and bridge-building (plus billions of other strategies, lifestyles and natural wonders for all the other life forms) which ants would automatically and unconsciously switch on when needed. Humans, on the other hand, were given the ability to devise the same strategies without any such programme. My purely subjective opinion is that a 3.8-billion-year-old programme for ant-marching and bridge-building and every other life form, strategy etc. in the history of life is more than a teeny bit harder to believe in than the ability of ants and other life forms to work out their own strategies. But of course you are entitled to believe whatever you want. ;-)

DAVID: Well, we each have a version. We at least agree they don't have our introspection.

At least you have not accused me of distorting your beliefs. Your book The Atheist Delusion is subtitled Science IS Finding God and you make brilliant use of science to argue the case for design and hence for a designer. In my view, this argument should be taken with the utmost seriousness by the scientific world. But I shudder to think what the scientific world would make of the theory I have summarized above!:-(

Biological complexity: managing cellular oxygen levels

by David Turell @, Saturday, November 02, 2019, 19:09 (1609 days ago) @ dhw

DAVID: Sorry. I was taught to march. it required understanding and responding to teaching instructions. Ants don't like to bump into each other. They simply follow the leader with spacing[

dhw: Humans don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Ants don’t like to bump into each other. They therefore devised a system of marching to prevent bumping, and passed on the method to later generations. Humans follow the leader with spacing. Ants follow the leader with spacing. You believe that 3.8 billion years ago, your God provided the first cells with a programme for the creation of ants (plus millions of other life forms) and for the strategies of marching and bridge-building (plus billions of other strategies, lifestyles and natural wonders for all the other life forms) which ants would automatically and unconsciously switch on when needed. Humans, on the other hand, were given the ability to devise the same strategies without any such programme. My purely subjective opinion is that a 3.8-billion-year-old programme for ant-marching and bridge-building and every other life form, strategy etc. in the history of life is more than a teeny bit harder to believe in than the ability of ants and other life forms to work out their own strategies. But of course you are entitled to believe whatever you want. ;-)

DAVID: Well, we each have a version. We at least agree they don't have our introspection.

dhw: At least you have not accused me of distorting your beliefs. Your book The Atheist Delusion is subtitled Science IS Finding God and you make brilliant use of science to argue the case for design and hence for a designer. In my view, this argument should be taken with the utmost seriousness by the scientific world. But I shudder to think what the scientific world would make of the theory I have summarized above!:-(

I didn't bother with my usual response, since you do not understand how irrational your objection seems to me.

Biological complexity: cells manage mitochondrial stress

by David Turell @, Friday, October 18, 2019, 21:26 (1624 days ago) @ dhw

Special factors control mitochondrial stress:

https://www.sciencedaily.com/releases/2019/10/191018125506.htm

"Cells need powerhouses known as mitochondria to utilize the energy stored in our food. Most of the proteins required for this powerhouse function are encoded in the nucleus and transported into the mitochondria after they have been synthesized in the cytosol. Signal sequences are needed to allow the protein to enter the mitochondria. Once the protein has arrived there, the signal sequences are, however, removed.....Dr. Nora Vögtle of the Institute of Biochemistry and Molecular Biology of the University of Freiburg has discovered that errors in the removal of signal sequences lead to an aggregation of these proteins so that they clump together inside the mitochondria.

***

"The aggregation observed by the researchers could cause the cell powerhouses to stop working, but all organisms require this activity for survival. To counteract these defects the cells execute what the researchers call a protective stress response, which enables mitochondria to maintain their key functions.

***

"'Only through this mechanism could the mitochondria ensure cell survival by maintaining generation of energy under these stressful conditions. This completely novel principle in the stress response of cells, explains Vögtle, is probably the earliest reaction that has been detected up until now. She says, "That's the cell's first line of defense when stress appears in its powerhouses.'" (my bold)

From the paper:

"Summary
The mitochondrial proteome is built mainly by import of nuclear-encoded precursors, which are targeted mostly by cleavable presequences. Presequence processing upon import is essential for proteostasis and survival, but the consequences of dysfunctional protein maturation are unknown. We find that impaired presequence processing causes accumulation of precursors inside mitochondria that form aggregates, which escape degradation and unexpectedly do not cause cell death. Instead, cells survive via activation of a mitochondrial unfolded protein response (mtUPR)-like pathway that is triggered very early after precursor accumulation. In contrast to classical stress pathways, this immediate response maintains mitochondrial protein import, membrane potential, and translation through translocation of the nuclear HMG-box transcription factor Rox1 to mitochondria. Rox1 binds mtDNA and performs a TFAM-like function pivotal for transcription and translation. ( Mitochondrial transcription factor A, abbreviated as TFAM or mtTFA, is a protein that in humans is encoded by the TFAM gene.)
Induction of early mtUPR provides a reversible stress model to mechanistically dissect the initial steps in mtUPR pathways with the stressTFAM Rox1 as the first line of defense."

Comment: this complex mechanism had to be in place early to protect the mitochondria. Only design fits

Biological complexity: complex growth factors shown

by David Turell @, Friday, October 11, 2019, 20:16 (1631 days ago) @ dhw

Very skilled demonstration of the enormous complexity of protein molecules controlling growth of cells:

https://phys.org/news/2019-10-master-growth.html

"A team of Whitehead Institute scientists has for the first time revealed the molecular structure of a critical growth regulator bound to its partner proteins, creating a fine-grained view of how they interact to sense nutrient levels and control cell growth. Their findings, described in the October 10th online issue of Science, help answer longstanding questions about how the mTORC1 kinase, and its anchoring complex, Rag-Ragulator, work at a molecular level. Using cryo-electron microscopy, the researchers uncover key structures, including a large coiled region and a small, flexible claw. These discoveries help explain the biology of mTORC1 and also lay the foundation for a new generation of drugs that are more precisely tailored to its distinct molecular makeup.

***

"mTORC1 is a massive protein complex that enables cells to respond appropriately when food is either abundant or scarce, and has been implicated in a wide range of human diseases, including cancer, diabetes, and neurodegenerative disease. It operates within tiny compartments known as lysosomes—miniature recycling stations of the cell. In order to sense nutrient levels in the lysosome, and become active, mTORC1 must first dock at the lysosomal surface, where it meets up with its anchoring protein (called Rag-Ragulator).

"However, this docking is an exquisitely complicated affair. It is regulated by a handful of proteins: an mTORC1 subunit (called Raptor) and the Rag GTPases, which bind Raptor as a non-identical pair and act like a control switch. This switch has four settings: one, which is used when nutrients are high, allows mTORC1 to dock at the lysosome and become active; the other three are used in times of hunger to push the complex away from the lysosomal surface and thereby deactivate it.

***

"With a detailed protein structure in hand, Rogala and his colleagues were able to discern some key structural elements. One, which they describe for the first time, is a claw-like appendage that interacts with one of the Rag GTPases (known as RagC). The other is a large, coiled structure, shaped like a solenoid, that faces RagA.

"'We think that, together, these two structures are acting as detectors for the Rag GTPases—so, is the switch in the right configuration for docking at the lysosome or not?" says Rogala."

Comment: Be sure to look at the diagram of these molecules. These complex giant molecules have to be designed.

Biological complexity: cellular semi-liquid organelles

by David Turell @, Thursday, October 10, 2019, 22:53 (1632 days ago) @ dhw

This research snows how it works in one instance:

https://phys.org/news/2019-10-scientists-liquid-organelles-cells-coexist.html

"New research may help to explain an intriguing phenomenon inside human cells: how wall-less liquid organelles are able to coexist as separate entities instead of just merging together.

"These structures, called membrane-less organelles (MLOs), are liquid droplets made from proteins and RNA, with each droplet holding both materials. The organelles play a crucial role in organizing the internal contents of cells, and can serve as a center of biochemical activity, recruiting molecules needed to carry out essential cellular reactions.

"But how different droplets stay apart from each other remains a mystery. Why don't they always just combine to form bigger droplets?

"'These organelles don't have any membrane, and hence, common intuition would tell you that they are free to mix," says Priya Banerjee, Ph.D., assistant professor of physics in the University at Buffalo College of Arts and Sciences.

***

"The team found that certain types of RNA and proteins are "stickier" than others, enabling them to form gelatinous droplets that don't fuse easily with other droplets in the same viscoelastic state. Specifically, droplets are more likely to be gel-like when they contain RNA molecules rich in a building block called purine, and proteins rich in an amino acid called arginine.

***

"In addition to providing insight into why MLOs resist mixing (due to enhanced viscoelasticity), the study probed the role of RNA in the formation and dissolution of liquid organelles containing FUS. The research found that for the type of droplet being studied, adding low concentrations of RNA to a solution containing the proteins caused droplets to form. But as more RNA was added, the droplets then dissolved.

"'There's usually a very small window where these droplets exist, but the window is significantly wider for arginine-rich proteins," Banerjee says.

***

"Though the team uses model systems to examine individual properties of the droplets, it's likely that many forces work together in a cell to determine the behavior and function of the organelles, he says. There may be multiple other mechanisms, for example, that cause MLOs to take on a gelatinous state or otherwise refuse to mix.


"'Cells are enormously complex, with many different molecules undergoing different processes that come together at the same time to influence what goes on inside MLOs," Banerjee says. "By using model systems, we are able to better understand how one particular variable may impact the formation and dissolution of these organelles. And we do expect to see these same forces at play in nature, inside cells."

Comment: Single cells are hard working factories, and too many membranes would take up too much space, so this is a convenient designed solution that could not have developed in a step-wise way.

Biological complexity: bacteria harvest electrons for food

by David Turell @, Tuesday, November 05, 2019, 18:36 (1606 days ago) @ David Turell
edited by David Turell, Tuesday, November 05, 2019, 18:45

A very specialized complex protein does the transfer:

https://phys.org/news/2019-11-microbes-harvest-electrons.html

"Bacteria don't have mouths, so they need another way to bring their fuel into their bodies. New research from Washington University in St. Louis reveals how one such bacteria pulls in electrons straight from an electrode source.

***

"'I was excited when we found that these phototrophic bacteria use a novel processing step to regulate the production of key electron transfer protein involved in this process," Gupta said. "This study will aid in designing a bacterial platform where bacteria can feed on electricity and carbon dioxide to produce value-added compounds such as biofuels."

***

"Getting the electricity across the outer layer of the bacteria is the key challenge. This barrier is both nonconductive and impermeable to insoluble iron minerals and/or electrodes.

Bose and her collaborators, including Robert Kranz, professor of biology, showed that the naturally occurring strain of Rhodopseudomonas palustris TIE-1 builds a conduit to accept electrons across its outer membrane. The bacteria relies on an iron-containing helper molecule called a deca-heme cytochrome c. By processing this protein, TIE-1 can form an essential bridge to its electron source.

"Extracellular electron uptake, or EEU, can help microbes to survive under nutrient-scarce conditions."

Comment: The usual question arises. How did a chance evolutionary process find such a useful complex protein? By design.

Biological complexity: feast or famine cell controls

by David Turell @, Wednesday, November 06, 2019, 00:09 (1605 days ago) @ David Turell

A special epigenetic mark on histones controls cells' use of energy supplies:

https://phys.org/news/2019-11-feast-famine-scientists-key-bio.html

"The scientists, in a study published in Molecular Cell, found that a chemical mark on histones—a key protein involved in the function of our DNA—occurs naturally under nutrient-limited conditions as cells change the way they make energy, and serves to repress genes that would otherwise drive cell growth. The chemical mark is called crotonylation, and until now its function has not been well understood.

"'Our findings help explain how a changing nutrient environment outside the cell is able to communicate to the nucleus of the cell in such a way that the appropriate genes are switched on or off," said study co-senior author Brian Strahl,

***

"'We identified mechanisms by which cells can quickly reduce their energy consumption as soon as it becomes limited in the local environment. Expression of growth genes are extremely energy-demanding, and they need to be tightly regulated in nutrient-limited environments in order to ensure survival."

"The finding advances basic science by revealing a key mechanism through which cells alter gene expression programs in order to adapt to low-nutrient conditions

"Crotonyl marks occur on the support proteins called histone proteins around which DNA normally is spooled. Like other chemical marks on histones, crotonyl marks are thought to work by loosening or tightening the local wrapping of DNA so that affected genes can become active or are forced into inactivity. Such histone marks are broadly known as "epigenetic" marks because they effectively help control, or program, which genes are turned on and which are turned off in a cell.

"The precise functions of crotonyl marks have been somewhat mysterious. But Strahl and Morrison's labs found evidence that these marks occur naturally under low-nutrient conditions when the main form of chemical energy in cells, related to glucose, is less available and cells start to scavenge chemical energy from fat-related molecules. Fatty acids are generated as byproducts of this alternate energy production process and soon make their way to the nucleus. There enzymes start attaching one form of these fatty acids, crotonyls, to histones. That forces a change in gene activity that slows growth and otherwise adapts the cell for low-nutrient conditions.

"'It's an elegant way that nature has evolved to control the genome using metabolic events happening in the cell," Strahl said.

"Crotonylation in this context appears to have nearly the opposite function of a better-known histone marking called acetylation, which uses byproducts of normal, glucose-related energy production to keep growth genes switched on."

Comment: For decades medicine has known that human starvation results in the basal metabolism reduced by as much as 300 calories a day to preserve survival for as long as possible. This mechanism has now been found in specialized protein markers, which chance evolution could not have found. This is designed.

Biological complexity: mitochondria respond to oxygen lack

by David Turell @, Thursday, November 07, 2019, 17:59 (1604 days ago) @ David Turell

Mitochondria switch metabolism of glycogen when oxygen is depleted:

https://phys.org/news/2019-11-oxygen-deficiency-rewires-mitochondria.html

"Mitochondria burn oxygen and provide energy for the body. Cells lacking oxygen or nutrients have to change their energy supply quickly in order to keep growing. Scientists from the Max Planck Institute for Biology of Ageing have now shown that mitochondria are reprogrammed under depleted oxygen and nutrients.

***

"Cells adapt to oxygen deficiency by switching their energy supply to glycolysis, in which sugar is fermented without oxygen. This may be necessary in old age, for example, as the cells in the body are often less supplied with oxygen and nutrients. Also, cancer cells can face this problem, because some tumours have poor blood supply and thus little oxygen and nutrients reach the cells.

"'It has been known for some time that cells reduce the number of mitochondria when they lack oxygen and switch to glycolysis. We have now discovered that the remaining mitochondria are additionally reprogrammed to meet the new requirements," explains Max Planck Director Thomas Langer.

"This happens via a newly discovered signaling pathway in the cell: a protease in the membrane of mitochondria is activated during the conversion to glycolysis and then breaks down various proteins in the organelles. As a result, no new mitochondria can be formed and the remaining mitochondria change their metabolism. This process eventually stops on its own, as the protease begins to degrade itself at high activity. "This signaling pathway not only has a built-in timer, but also enables a very rapid response to oxygen deficiency," said Langer."

Comment: A highly designed protection system, as mitochondria are the energy engines for all cells which are in active production. Once cells were in active production, this mechanism had to have been there for protection from sudden unexpected oxygen loss. Requires the thinking a designing brain would have to recognize problems in advance of the design.

Biological complexity: sorting chemicals in the cell

by David Turell @, Saturday, November 16, 2019, 21:42 (1595 days ago) @ David Turell

A newly found complex mechanism:

https://www.sciencedaily.com/releases/2019/11/191115074402.htm

"A recent study by a group of scientists has revealed that a different mechanism is responsible for the formation and maintenance of the cell organelle called endosome that sorts and distributes substances entering a cell. Contrary to current knowledge in the field, the scientists show that the functioning of the Golgi is crucial for this organelle's upkeep.

"The cells in our body are workshops that continuously operate to produce and process substances to keep us going. When a substance enters a cell for processing, it is surrounded by a portion of the cell's outer membrane to form a sac. The sac then buds off into the cell and becomes a vesicle containing the substance. This ingestion of substances by the cell is called endocytosis. The vesicle is then quickly merged with an endosome, an organelle also frequently referred to as a 'sorting station'. From the endosome, the substance is either recycled back to the cell membrane (for exiting the cell) or forwarded to a lysosome -- a cell organelle containing enzymes for the breakdown of substances -- for degradation. The substances entering a cell -- and thereby an endosome -- could be nutrients or signal molecules for processing, or even pathogenic viruses which can cause disease. It is therefore extremely important to fully understand the molecular basis of how endosomes are formed and maintained.

***

"...in a recent study published in Communications Biology, a group of scientists from Japan and Austria, led by Prof Jiro Toshima from the Tokyo University of Science, claims that vesicles transported out of the Golgi -- another crucial cell organelle -- and not those from the cell membrane are more important for the formation and maintenance of endosomes. "We used our research to show that endocytic vesicle internalization is not essential, but that vesicle transport from the trans-Golgi network [TGN; the Golgi] is crucial," the team of scientists says.

***

"Prof Toshima and group saw that certain proteins, which are either resident in the Golgi or recruited to it, are transported from the Golgi to the endosomes where they activate Rab5 and spark the formation of endosomes. Deleting or deactivating the genes crucial to the transport of these proteins from the Golgi ultimately affects endosome formation.

"Thus, considering all of these results together, it appears that endocytosis is not necessary for endosome formation and maintenance, but vesicle transport form the Golgi is. "Our results provide a different view of endosome formation and identify the TGN as a critical location for optimal maintenance and functioning of endosomes," Prof Toshima says.

"Given that endosomes are essential to the functioning of the cell and, by extension, the organism, understanding the mechanism of its upkeep is important. The results of this compelling study reveal but a fraction of this mechanism and much remains to be discovered. Even so, this advancement in the knowledge of one of the core pathways by which cells process substances in the body can lead to enhanced comprehension of the molecular basis of diseases that involve defective endosomes, thereby leading to better treatments for such diseases."

Comment: More cellular complexity. How much exquisite complexity has to be shown before everyone realizes a designer is required

Biological complexity: squid color changes

by David Turell @, Saturday, November 16, 2019, 22:58 (1595 days ago) @ David Turell

It is called a marvelous molecular machine:

https://phys.org/news/2019-11-marvelous-molecular-machine.html

"Researchers in the lab of UC Santa Barbara professor Daniel Morse have long been interested in the optical properties of color-changing animals, and they are particularly intrigued by the opalescent inshore squid. Also known as the California market squid, these animals have evolved the ability to finely and continuously tune their color and sheen to a degree unrivaled in other creatures. This enables them to communicate, as well as hide in plain sight in the bright and often featureless upper ocean.

***

"Like most cephalopods, opalescent inshore squid, practice their sorcery by way of what may be the most sophisticated skin found anywhere in nature. Tiny muscles manipulate the skin texture while pigments and iridescent cells affect its appearance. One group of cells controls their color by expanding and contracting cells in their skin that contain sacks of pigment.

"Behind these pigment cells are a layer of iridescent cells—those iridocytes—that reflect light and contribute to the animals' color across the entire visible spectrum. The squids also have leucophores, which control the reflectance of white light. Together, these layers of pigment-containing and light-reflecting cells give the squids the ability to control the brightness, color and hue of their skin over a remarkably broad palette.

"Unlike the color from pigments, the highly dynamic hues of the opalescent inshore squid result from changing the iridocyte's structure itself. Light bounces between nanometer-sized features about the same size as wavelengths in the visible part of the spectrum, producing colors. As these structures change their dimensions, the colors change. Reflectin proteins are behind these features' ability to shapeshift, and the researchers' task was to figure out how they do the job.

***

"Reflectin, which is contained in closely packed layers of membrane in iridocytes, looks a bit like a series of beads on a string, the researchers found. Normally, the links between the beads are strongly positively charged, so they repel each other, straightening out the proteins like uncooked spaghetti.

"Morse and his team discovered that nerve signals to the reflective cells trigger the addition of phosphate groups to the links. These negatively charged phosphate groups neutralize the links' repulsion, allowing the proteins to fold up. The team was especially excited to discover that this folding exposed new, sticky surfaces on the bead-like portions of the reflectin, allowing them to clump together. Up to four phosphates can bind to each reflectin protein, providing the squid with a precisely tunable process: The more phosphates added, the more the proteins fold up, progressively exposing more of the emergent hydrophobic surfaces, and the larger the clumps grow.

"As these clumps grow, the many, single, small proteins in solution become fewer, larger groups of multiple proteins. This changes the fluid pressure inside the membrane stacks, driving water out—a type of "osmotic motor" that responds to the slightest changes in charge generated by the neurons, to which patches of thousands of leucophores and iridocytes are connected. The resulting dehydration reduces the thickness and spacing of the membrane stacks, which shifts the wavelength of reflected light progressively from red to yellow, then to green and finally blue. The more concentrated solution also has a higher refractive index, which increases the cells' brightness.

"'We had no idea that the mechanism we would discover would turn out to be so remarkably complex yet contained and so elegantly integrated in one multifunctional molecule—the block-copolymeric reflectin—with opposing domains so delicately poised that they act like a metastable machine, continually sensing and responding to neuronal signaling by precisely adjusting the osmotic pressure of an intracellular nanostructure to precisely fine-tune the color and brightness of its reflected light," Morse said.

"What's more, the researchers found, the whole process is reversible and cyclable, enabling the squid to continually fine-tune whatever optical properties its situation calls for."

Comment: An amazingly complex color change system. Since it is also reversible and has so many moving interlocking parts, it cannot have been developed by a series of chance mutations and obviously is irreducibly complex, requiring design.

Biological complexity: sorting chemicals in the cell II

by David Turell @, Saturday, November 16, 2019, 23:06 (1594 days ago) @ David Turell

I would note dhw's favorite Albrecht- Buehler thought the Golgi body was the brains of the cell. Seems like there are other parts also at work automatically.

Biological complexity: how ribosome makes RNA

by David Turell @, Saturday, November 23, 2019, 01:09 (1588 days ago) @ David Turell

It takes lots of different protein molecules to shepherd the assembly:

https://phys.org/news/2019-11-cell-biology-scientists-ribosome-real.html

"'This shows that we now can examine in detail how RNAs fold while they are being synthesized and proteins are assembling on them," says first author Olivier Duss, Ph.D., a postdoctoral research fellow in the Department of Integrative Structural & Computational Biology at Scripps Research. "This has been a very difficult thing to study in biology because it involves several distinct biological processes that are dependent on each other and have to be detected simultaneously."

***

"In a proof-of-principle study published last year, the researchers used their approach to record an early, brief and relatively well-studied stage of ribosome assembly from the bacterium E. coli. This involved the transcription, or copying out from its corresponding gene, of a ribosomal RNA, and initial interactions of this RNA strand with a ribosomal protein.

"In the new study, the team extended this approach by tracking not only the transcription of a ribosomal RNA but also its real-time folding. The work provided a detailed look at a complex, and until-now mysterious, part of E. coli ribosome assembly—the formation of an entire major component, or domain, of the E. coli ribosome, with assistance from eight protein partners that end up incorporated into the structure.

"A key finding was that the ribosomal protein partners guide the folding of the RNA strand through multiple temporary interactions with the strand, well before they nestle into their final places in the folded RNA-protein molecule. The findings, according to the researchers, also hint at the existence of unknown RNA assembly factors, most likely proteins, that were not present in their lab-dish-type imaging experiments but are present in cells and boost the efficiency of RNA folding.

"Our study indicates that in ribosomal RNA-folding, and perhaps more generally in RNA-folding in cells, many proteins help fold RNA though weak, transient and semi-specific interactions with it," Duss says."

Comment: A highly complex vital process that requires precise protein activities to produce the correct product. Not by chance.

Biological complexity: mitochondria detect stress

by David Turell @, Saturday, December 14, 2019, 20:24 (1567 days ago) @ David Turell

Mitochondria are like canaries in the coal mine:

https://phys.org/news/2019-12-mitochondria-canary-coal-cellular-stress.html

"Salk researchers have discovered a new function of mitochondria: they set off molecular alarms when cells are exposed to stress or chemicals that can damage DNA, such as chemotherapy.

***

"'Mitochondria are acting as a first line of defense in sensing DNA stress. The mitochondria tell the rest of the cell, 'Hey, I'm under attack, you better protect yourself,'" says Gerald Shadel, a professor in Salk's Molecular and Cell Biology Laboratory and the Audrey Geisel Chair in Biomedical Science.

"Most of the DNA that a cell needs to function is found inside the cell's nucleus, packaged in chromosomes and inherited from both parents. But mitochondria each contain their own small circles of DNA (called mitochondrial DNA or mtDNA), passed only from a mother to her offspring. And most cells contain hundreds—or even thousands—of mitochondria.

***

"In the new study, Shadel and his colleagues set out to look in more detail at what molecular pathways are activated by the release of damaged mtDNA into the cell's interior. They homed in on a subset of genes known as interferon-stimulated genes, or ISGs, that are typically activated by the presence of viruses. But in this case, the team realized, the genes were a particular subset of ISGs turned on by viruses. And this same subset of ISGs is often found to be activated in cancer cells that have developed resistance to chemotherapy with DNA-damaging agents like doxyrubicin.

"To destroy cancer, doxyrubicin targets the nuclear DNA. But the new study found that the drug also causes the damage and release of mtDNA, which in turn activates ISGs. This subset of ISGs, the group discovered, helps protect nuclear DNA from damage—and, thus, causes increased resistance to the chemotherapy drug. When Shadel and his colleagues induced mitochondrial stress in melanoma cancer cells, the cells became more resistant to doxyrubicin when grown in culture dishes and even in mice, as higher levels of the ISGs were protecting the cell's DNA.

"'Perhaps the fact that mitochondrial DNA is present in so many copies in each cell, and has fewer of its own DNA repair pathways, makes it a very effective sensor of DNA stress," says Shadel."

"Most of the time, he points out, it's probably a good thing that the mtDNA is more prone to damage—it acts like a canary in a coal mine to protect healthy cells."

Comment: Mitochondria do much more than produce energy for the cells. The mitochondria genes sense the attack and automatically activate the necessary protein defenses.

Biological complexity: new structure found in bird retina

by David Turell @, Tuesday, December 17, 2019, 18:50 (1564 days ago) @ David Turell

Flycatchers need to see fast moving prey:

https://phys.org/news/2019-12-newly-retinal-vision-birds.html

"The foundation of avian vision rests on cells called cone and rod photoreceptors. Most birds have four cone photoreceptors for color vision, a fifth cone for non-color-related tasks, and a rod for night vision. Each cone photoreceptor cell contains a spherical structure called an "oil droplet," which filters light before it is converted to electrical signals by the visual pigments, enhancing color discrimination.

"However, the researchers have discovered a never-before-seen type of cone structure in the retina of a group of small songbirds, called flycatchers. Instead of an oil droplet, it contains a high- energy-producing cellular structure called "megamitochondria" surrounded by hundreds of small, orange-colored droplets. The researchers named this novel cellular structure a megamitochondria-small oil droplet complex, or MMOD-complex.

***

"Traditional cones were present throughout the retina of these flycatchers, and their density decreased moving away from the center toward the periphery. However, the MMOD-complex photoreceptors were present only in the central region of the retina, an arrangement that could help birds detect flying insects, said Esteban Fernandez-Juricic, a professor of biological sciences at Purdue.

"'The retina of flycatchers, which are sit-and-wait predatory birds, evolved a novel cellular structure in a photoreceptor that may allow them to detect, track and capture fast-moving prey, like insects," he said."

Comment: Another complex structure requiring design by a designer.

Biological complexity: protein switches in action

by David Turell @, Tuesday, December 24, 2019, 18:46 (1557 days ago) @ David Turell

One protein molecule turning on another to function is an automatic activity that requires no intelligence. In this study automatic cell skeleton formation is triggered by molecular interactions:

https://www.sciencedaily.com/releases/2019/12/191223122857.htm

"The goal was to identify the proteins that attach to those of the Rho family, famous in the cell biology world since the discovery in the early 1990s that they dictate how pieces of the cell skeleton -- the "cytoskeleton" -- are assembled.

"In humans, the 20 members of the Rho family are scattered on the inner surface of cell membranes and act like small switches. When a signal from outside or inside the cell activates them, they stimulate other proteins to force the cytoskeleton to add or remove parts to its framework.

"Out of all these proteins, only three, to date, have been thoroughly studied by researchers: Cdc42, Rac1 and RhoA. Cdc42 acts as the lead protein: it indicates the path that white blood cells must take to find a site of infection. Rac1 activates the engines that drive a non-muscular cell forward. RhoA stimulates the formation of fibres that allow cells to contract or form resistant tissues as they come together to produce, for example, the wall of a blood vessel.

***

"Using 28 two-headed proteins and presenting the GTPases -- a superfamily of enzymes that function as 'molecular switches' and are involved in regulating many cellular processes -- in both active and inactive configurations, the team caught a total of 9,939 proteins. Some were already known to the scientists, including the GTPases' activators and deactivators. But the researchers also discovered hundreds of individual proteins with yet-to-be-defined roles.

"These discoveries include the missing link of the cytoskelton Rho process identified in the early '90s. Back then, researchers noticed that the RhoA protein indirectly activates another protein, ERM, causing it to stabilize the cytoskeleton. But they didn't know the precise mechanism behind this process. On their "fishing expedition," Côté and his team found the answer: what forges the link between RhoA and ERM is a protein called SLK.

"In their study, the IRCM team also looked at other proteins that, until now, were virtually unknown to biologists, namely GARRE and PLEKHG3. The scientists demonstrated that these proteins naturally attach to the active forms of Rac1 and RhoG, respectively. "

Comment: The cells' genome contain information/instructions to initiate these automatic protein molecules to react with each other producing cellular skeletons. No thought involved.

Biological complexity:citric acid (Krebs) cyclical reactions

by David Turell @, Wednesday, December 25, 2019, 18:40 (1556 days ago) @ David Turell
edited by David Turell, Wednesday, December 25, 2019, 18:57

Just look at this entry to see the diagrams of the citric (Krebs) cycle which I was taught in med school, to see why a designer is needed:

https://sandwalk.blogspot.com/2019/12/the-evolution-of-citrate-synthase.html#more

Biological complexity:citric acid (Krebs) cyclical reactions

by dhw, Thursday, December 26, 2019, 08:24 (1555 days ago) @ David Turell

DAVID: Just look at this entry to see the diagrams of the citric (Krebs) cycle which I was taught in med school, to see why a designer is needed:
https://sandwalk.blogspot.com/2019/12/the-evolution-of-citrate-synthase.html#more

QUOTE: I think we should make an attempt to explain to students that humans are the end products of three billion years of evolution and they have adapted to a specialized way of life that relies on ingesting and metabolizing complex organic chemicals. The pathways that we see as "normal" in humans humans reflect this specialization.

I accept the logic of belief in a designer, just as I accept the logic of disbelief in some unknown, unknowable, eternal, infinite, immaterial, sourceless, all-powerful, all-knowing conscious mind. That is why I am left with my agnostic non-belief. As regards the above, I think it is also worth explaining to students that there are lots of organisms that are the end products of three billion years of evolution and have adapted to a specialized way of life that relies on ingesting complex organic chemicals, and there are even organisms that have survived 3.8 billion years by adapting to a vast range of specialized ways of life, each of which relies on ingesting complex organic and even inorganic chemicals.

Biological complexity:citric acid (Krebs) cyclical reactions

by David Turell @, Thursday, December 26, 2019, 15:25 (1555 days ago) @ dhw

DAVID: Just look at this entry to see the diagrams of the citric (Krebs) cycle which I was taught in med school, to see why a designer is needed:
https://sandwalk.blogspot.com/2019/12/the-evolution-of-citrate-synthase.html#more

QUOTE: I think we should make an attempt to explain to students that humans are the end products of three billion years of evolution and they have adapted to a specialized way of life that relies on ingesting and metabolizing complex organic chemicals. The pathways that we see as "normal" in humans humans reflect this specialization.

dhw: I accept the logic of belief in a designer, just as I accept the logic of disbelief in some unknown, unknowable, eternal, infinite, immaterial, sourceless, all-powerful, all-knowing conscious mind. That is why I am left with my agnostic non-belief. As regards the above, I think it is also worth explaining to students that there are lots of organisms that are the end products of three billion years of evolution and have adapted to a specialized way of life that relies on ingesting complex organic chemicals, and there are even organisms that have survived 3.8 billion years by adapting to a vast range of specialized ways of life, each of which relies on ingesting complex organic and even inorganic chemicals.

We know why you are an agnostic with very clear logic.

Biological complexity:citric acid (Krebs) cyclical reactions

by David Turell @, Friday, July 01, 2022, 19:09 (637 days ago) @ David Turell

DAVID: Just look at this entry to see the diagrams of the citric (Krebs) cycle which I was taught in med school, to see why a designer is needed:

https://sandwalk.blogspot.com/2019/12/the-evolution-of-citrate-synthase.html#more

This is now the subject of a book explaining the biochemistry of life:

https://www.sciencemagazinedigital.org/sciencemagazine/01_july_2022/MobilePagedArticle....

"The incredible scientific advances centered around DNA, RNA, and proteins have left many people with the impression that the essence of life is found in genetic information. Yet a cell that died seconds ago contains the same genes that it did moments earlier, suggesting that there are other processes at play that bring the inanimate to life. In his latest book, Transformer, biochemist Nick Lane reminds readers in accessible prose that it is life’s dynamic chemistry, its metabolism, that draws inanimate matter into the living state and back again. As Lane puts it, metabolism is not just “what keeps us alive—it is what being alive is.”

"The main hero of the book is the Krebs cycle, a sequence of chemical reactions that most of us were taught releases energy from molecules obtained from the breakdown of sugars or fats, expelling CO2 as a waste product. However, Lane points out that this perspective obscures this vital process’s place at the heart of all biology and life itself.

"Few laypeople know that the Krebs cycle can run in reverse, fixing CO2 and hydrogen gas to produce all the key building blocks of biochemistry—a process as natural and thermodynamically favored as water flowing downhill. Some versions of this reverse Krebs cycle contain a feedback loop that amplifies the quantity of its own chemical constituents. Rather than simply being an engine for the synthesis of the molecules of life, it may thus be more accurate to say that life is what one can make from the Krebs cycle. (my bold)

***

"Lane and others, such as Jack Corliss, Günter Wächtershäuser, Mike Russell, and Bill Martin, speculate that deep-sea hydrothermal vents were life’s birthplace. Some of these researchers argue that a primitive form of the Krebs cycle led to the first living systems and that the cycle may have initially run in the reverse direction. The proton gradients between the inorganic membranes found within these vents may have been key to promoting the chemistry of life, argues Lane."

Comment: I've been long convinced that deep-sea vents were involved in the origin of life. The Kreb's cycle is at the heart of living biochemistry. That is runs backward and forward is a strong indication of a designer at work. How could that have happened by chance? I haven't read this book, but it obviously would help anyone to understand how to look at life through its biochemistry.

Biological complexity: cell division DNA controls

by David Turell @, Friday, December 27, 2019, 18:17 (1554 days ago) @ dhw

The division must be evenly split into new cells for cellular DNA, Controls are very tight:

https://phys.org/news/2019-12-insight-cells-dna.html

"During cell division our chromosomes, containing a duplicated set of DNA, must be split equally between the newly created daughter cells. To ensure this equal segregation of DNA, chromosomes must be correctly attached to microscopic rope-like structures, known as microtubules, which pull them apart.

***

"'We discovered that Astrin arrives at the attachment site with an enzyme called PP1 when proper attachments have been made. Together these proteins rapidly secure attachments so the attachment site is able to resist pulling forces, which are separating the DNA apart. This protein complex only acts on correct attachments, which helps make sure cells end up with the right number of chromosomes after cell division."

"Dr. Duccio Conti, postdoctoral researcher at Queen Mary and first author of the paper, added, "Whilst we originally thought Astrin would be important to cement attachments, we were surprised to find that it actually works as a dynamic lock, ensuring attachments are not stabilised prematurely."

***

"Professor Richard Pickersgill, professor of structural biology and head of the School of Biological and Chemical Sciences at Queen Mary, said: "Right now our cells are dividing to replace lost and damaged cells; it's a wonderful process essential for life but also incredibly complex—over 100 proteins are involved in orchestrating the organisation and segregation of chromosomes alone. There is much still to discover about the detailed mechanism of chromosome segregation, but this work, which explains the role of Astrin in strengthening microtubule attachments, is an important milestone along the way.'" (my bold)

Comment: Note my bold. Over 100 specific proteins are involved. Not a chance development if that many specific proteins are involved. Designed.

Biological complexity: cell division DNA controls

by David Turell @, Friday, December 27, 2019, 18:33 (1554 days ago) @ David Turell

Another set of controls:

https://phys.org/news/2019-12-scientists-reveal-function-histone-variant.html


"DNA replication is a tightly regulated process that ensures the precise duplication of the genome during cell proliferation. Replication origins determine where replication starts on the genome and regulate the whole genome replication program. The human genome contains tens of thousands of origins; however, only about 10 percent of them are used in each cell cycle. So how are origins selected?

"In research published in Nature on Dec. 25th, 2019, Dr. LI Guohong and Dr. ZHU Mingzhao from the Institute of Biophysics of the Chinese Academy of Sciences have demonstrated that the histone variant H2A.Z facilitates the licensing and activation of early DNA replication origins.

"In eukaryotes, DNA wraps around histone octamers to form chromatin in the nucleus. The licensing and activation of replication origins are regulated by both the DNA sequence and chromatin features. However, chromatin-based regulatory mechanisms remain largely uncharacterized.

"In this study, the scientists first found that knocking down H2AFZ genes in HeLa cells results in cell growth defects. Through mass spectrometry, many subunits of prereplication complex were enriched on H2A.Z mono-nucleosomes, indicating that H2A.Z may be involved in the licensing of DNA replication origins.

"To find the mechanism of interaction between H2A.Z and the prereplication complex, the scientists then performed in vitro biochemical analysis and found that H2A.Z-containing nucleosomes bind directly to the histone lysine methyltransferase enzyme SUV420H1. This process promotes H4K20me2 deposition, which further recruits origins recognition complex 1 (ORC1) to help accomplish the licensing of DNA replication origins.

"Furthermore, the scientists generated CD4CreH2A.Zf/f mice to study the function of H2A.Z-regulated replication in a more physiological context. Using these mice, they conditionally knocked out (CKO) H2az1/H2az2 in T cells. They then found that in H2A.Z CKO mic the activated T cells have defects in cell proliferation and DNA replication.

"This study describes a novel epigenetic regulation mechanism for DNA replication origin selection and offers a new way of understanding DNA replication regulation in eukaryotes."

Comment: Another example of the complexity involved in the division of DNA during cell division. Only design fits.

Biological complexity: how seeds germinate

by David Turell @, Friday, December 27, 2019, 18:43 (1554 days ago) @ David Turell

They may remain dry for years and then with rain water will suddenly germinate through an automatic process:

https://www.sciencedaily.com/releases/2019/12/191227104940.htm

"Plant seeds may strike the casual observer as unspectacular -- but they have properties that are nothing short of superpowers. In a dry state they can store their energy for years and then suddenly release it for germination when environmental conditions are favourable. One striking example is the "super bloom" in the Death Valley National Park, when seeds that have endured the dry and hot desert for decades suddenly germinate at rainfall followed by a rare and spectacular desert bloom several months later. Seeds conserve a fully formed embryo, which only continues growing when conditions are right for it to do so. This may be the case only years -- or in more extreme cases even centuries -- later.

***

"The researchers discovered that when the seeds came into contact with water, energy metabolism was established in a matter of minutes, and the plant cells' "power stations" -- known as mitochondria -- activated their respiration. The researchers also found out which molecular switches are activated to enable energy to be released efficiently -- with the so-called thiol-redox switches playing a central role."

Comment: This process is under total information control. Cannot be created by chance, as the mechanism may lie fallow for years and dos not allow hunt and peck or trial events..

Biological complexity: cell cytoplasm can self-organize

by David Turell @, Thursday, January 02, 2020, 18:39 (1548 days ago) @ David Turell

It is built into protein molecules to organize and position themselves:

https://www.quantamagazine.org/unscrambled-eggs-self-organization-restores-cells-order-...

"If simply left alone, the liquid innards of a cell — its cytoplasm — have a surprising capacity to reassemble, even without components that appeared essential to some scientists. Experiments recently described in Science revealed the unanticipated extent of this talent and delved into its mechanics. They vividly illustrated how well equipped cells are to restore themselves to order after chaos intrudes,

***

"Self-organization occurs at many levels in living systems. String the right sequence of amino acids together and a long peptide chain will fold itself into a working protein. Cells within an early embryo arrange themselves to generate tissues to build a human.

***

"Cheng and Ferrell are the first to get the entire cytoplasm to arrange itself as if inside a whole cell, said Rebecca Heald, a cell biologist at the University of California, Berkeley.
“It’s an amazing demonstration of the properties of the cytoplasm and its ability to self-organize,” she said. “Visually, it’s incredibly striking that you can have this kind of organization happen spontaneously after homogenizing these eggs.”

"Seeing the compartments emerge made Cheng and Ferrell want to know how it happened...However, they quickly zeroed in on another suspect: a star-shaped organelle called an aster derived from the sperm.

"Seeing the compartments emerge made Cheng and Ferrell want to know how it happened. They knew at the outset that the DNA contained in the sperm was not responsible, since self-organization wouldn’t require the expression of genes. However, they quickly zeroed in on another suspect: a star-shaped organelle called an aster derived from the sperm.

***

"These asters, constructed of hollow rods called microtubules, sprout from a structure known as the centrosome, which organizes the microtubules. When cells rest between divisions, microtubule asters organize the cell’s contents. Frog eggs lack usable centrosomes, so when Cheng added the sperm, he gave the cytoplasm a powerful organizational tool.

***

“'That doesn’t surprise me, but I am sure it surprised other people,” Heald said. Her own research, along with that of others, has shown that it’s possible to create microtubule structures without centrosomes. The key lies with microtubules themselves. “Biology is full of redundancy, because when a process is very important, you want to have multiple mechanisms supporting it,” she said. (my bold)

"Like magnets, microtubules are polarized. With their plus ends growing outward and minus ends attached to the centrosome, which is often near the nucleus, they form what Heald describes as a compass within the cell. Motor proteins, such as dynein, ferry cargo along the microtubules, guided by their polarity.

***

"The self-organized compartments lack one major component of cells: membranes. The membrane surrounding a cell defines it and its relationship with the outside world.

***

"Like the nuclei within the developing fruit fly embryo, the compartments that contained sperm in Cheng and Farrell’s experiments divided to produce more of themselves — a “completely unexpected” result to Heald. Normally, membranes would delineate this process, but instead voids surrounding the compartments became the boundaries. “Unless you have a boundary, you can’t see a division happening,” she said. “This spontaneously made a boundary.'”

Comment: The key issue is to understand that proteins do all of this as if they come with a programmed agenda. Well perhaps they do and were designed to act this way from the beginning of organic chemistry as it appeared on Earth. God the designer fits better than assuming nature did it by chance.

Biological complexity: coiling DNA in chromosomes

by David Turell @, Saturday, January 04, 2020, 00:13 (1546 days ago) @ David Turell

Protein snake-like cords seem to do the job:

https://phys.org/news/2020-01-snake-like-proteins-wrangle-dna.html

"Members of Rice's Center for Theoretical Biological Physics (CTBP) are taking a deep dive into the dynamics of essential proteins that help DNA fold into its compact, functional form in chromosomes. They found a key protein's "coiled coils" also braid around each other and writhe like snakes as they form bigger loops in the DNA.

"The loops, in turn, bring together sites on DNA that regulate the transcription of genetic messages. While the loops and their functions are becoming better understood, until now nobody has been able to take a close look at the condensin and cohesin proteins that wrangle the DNA into shape.

***

"...structural maintenance of chromosomes (SMC) proteins may actively manage DNA through a novel mechanism.

"They found these proteins have ring-shaped lassos that consist of two 35-nanometer long protein coiled coils. These terminate on one end in a pair of "head unit" motors that bind to DNA coils, and on the other in "hinges" thought to open and close to entrap the strands.
The lab's simulations showed these coiled coils are anything but limp lariats.

"'We already knew the coiled coils have some sort of structural importance, but what we saw is that these long coils are quite active," Krepel said. "We're still investigating to what extent, but as we ran the simulations, we saw that the coils want to come together, kind of like headphones that get all twisted when you put them in your bag. We saw the twist right away."

"'Braiding is the word we use," Wolynes added. "People thought the coiled coils were simply hanging out, but they didn't think they'd coil again on top of each other in an organized fashion.

"'One of the key ideas of DNA physics is that DNA operates by changing its degree of coiling and its topology," he said. "Well, braiding is a topological feature. We think we see that the topology of the protein can interact with the topology of the DNA much as threads entwine with each other on a spinning wheel."

"Krepel noted the SMC proteins are positively charged, and DNA is negatively charged. "We're looking at how these positive and negative charges potentially play together," she said. "It seems clear the coils would almost certainly braid themselves around the DNA using these charge patterns," Wolynes said.

***

"The models further suggested that the ATPase motors that bind DNA can twirl the braids.

"'We're still guessing at the details, but we think when the two motors are both twisting to extrude DNA into loops, one untwisting and the other uptwisting, the lassos could transfer twisting of the coils into twisting around the DNA," Wolynes said. "The coils aren't just passively hanging there. They're much more involved in the process than we thought.'"

Comment: Yet again we see protein molecules that act like they know what they are doing. They are controlled by the way they automatically fold and the way they are attracted by electrical charges, among other attributes. Protein molecules cannot think. And this is the key to understanding how cells work through automatically reacting molecules.

Biological complexity: touch and pressure sensing

by David Turell @, Thursday, January 09, 2020, 18:44 (1541 days ago) @ David Turell

It requires huge complex ion pore proteins:

https://www.nature.com/articles/d41586-019-03955-w?utm_source=Nature+Briefing&utm_c...

"The discovery of Piezo2 and a related protein, Piezo1, was a high point in a decades-long search for the mechanisms that control the sense of touch. The Piezos are ion channels — gates in the cell membrane that allow ions to pass through — that are sensitive to tension. “We’ve learned a lot about how cells communicate, and it’s almost always been about chemical signalling,” says Ardem Patapoutian, a molecular neurobiologist at Scripps Research in La Jolla, California, whose group identified the Piezos. “What we’re realizing now is that mechanical sensation, this physical force, is also a signalling mechanism, and very little is known about it.”

***

"Touch underlies the functioning of almost every tissue and cell type, says Patapoutian. Organisms interpret forces to understand their world, to enjoy a caress and to avoid painful stimuli. In the body, cells sense blood flowing past, air inflating the lungs and the fullness of the stomach or bladder. Hearing is based on cells in the inner ear detecting the force of sound waves.

***

"One of the biggest questions is how the proteins, situated in the cell membrane, sense and respond to force. Using cryo-electron microscopy (cryo-EM), scientists have made progress in unravelling the Piezo channels’ bizarre, three-bladed structure, but a complete mechanism has been elusive.

***

"Researchers were abuzz with the result, Goodman recalls, particularly because the Piezo proteins were so large and complex. Made of more than 2,500 amino acids and weighing a hefty 300 kilodaltons, Piezo1’s structure crosses the cell membrane a record-breaking 38 times. (For comparison, mammalian proteins typically contain closer to 500 amino acids.)

***

"Fortunately, as Xiao was setting up his lab in 2013, another option for obtaining high-resolution structures was coming online: cryo-EM. His group used the method to report4 the first structure of Piezo1 in 2015, and since then, several higher-resolution versions have followed from Xiao’s group, MacKinnon’s, and Patapoutian’s. Last September, Xiao followed up with a picture of Piezo2, which is similar to Piezo1 in size and shape. Xiao’s picture of Piezo2 was the clearest view yet of the ends of the three blades, which move around and so are hard to capture5.

"The images were striking. Three Piezo proteins come together in a trimer that straddles the plasma membrane (see ‘Pressure sensors’). From the central pore, three arms spiral out like the blades on a propeller. They curve up and out, creating a deep divot in the surface of the cell.

****

Comment: At this point please see the complexity of the diagrams

***

“'The discovery of Piezos was a huge step forward for the whole field,” says Kate Poole, a biologist at the University of New South Wales in Sydney, Australia, but “it is also clear that the story is not just Piezos.”

***

"Patapoutian’s team, meanwhile, is looking for entirely new channel families. In 2018, he, Murthy and Scripps structural biologist Andrew Ward reported what they think could be the largest group of mechanically activated channels. They knew of a protein family that helps plants to sense osmotic pressure — the OSCA proteins — and reasoned that they might sense force more generally. In human kidney cells, OSCAs did indeed respond to Murthy’s stretching of the cell membrane.

"The researchers also knew from previous studies that the OSCA proteins were closely related to another family of proteins in mammals, the TMEM63 proteins. TMEM63 channels from mice, humans and even fruit flies responded to stretch in Murthy’s assays, too, so OSCA and TMEM63 proteins make up a large family of force sensors that is common to many living things.

"The channels discovered so far cannot explain all instances of cellular mechano-sensitivity, says Murthy, now a biophysicist and neuroscientist at Oregon Health & Science University in Portland. More mechanosensors must be out there."

Comment: How much complexity must be demonstrated before it is fully accepted a designing brain is required to exist? And don't tell me infinity can do it. This universe is not infinitely old.

Biological complexity: touch and pressure sensing

by dhw, Friday, January 10, 2020, 10:08 (1540 days ago) @ David Turell

DAVID: How much complexity must be demonstrated before it is fully accepted a designing brain is required to exist? And don't tell me infinity can do it. This universe is not infinitely old.

But you ARE telling us that infinity and eternity can do it – in the form of “pure energy” which has…not a brain, which of course is material, but some kind of immaterial consciousness that has no limits and no source. By giving it a name like “God”, you simply give it an identity, as if that somehow made the concept graspable. I totally accept the logic of your design argument, but I find your concept of non-finite, eternally conscious energy just as incredible as that of unconscious, infinite and eternal energy coming up with the goods. Once again, I would say that belief in either requires a leap of faith.

Biological complexity: touch and pressure sensing

by David Turell @, Friday, January 10, 2020, 14:47 (1540 days ago) @ dhw

DAVID: How much complexity must be demonstrated before it is fully accepted a designing brain is required to exist? And don't tell me infinity can do it. This universe is not infinitely old.

dhw: But you ARE telling us that infinity and eternity can do it – in the form of “pure energy” which has…not a brain, which of course is material, but some kind of immaterial consciousness that has no limits and no source. By giving it a name like “God”, you simply give it an identity, as if that somehow made the concept graspable. I totally accept the logic of your design argument, but I find your concept of non-finite, eternally conscious energy just as incredible as that of unconscious, infinite and eternal energy coming up with the goods. Once again, I would say that belief in either requires a leap of faith.

I would repeat , logic requires a planing mind, which God has. How does your unconscious energy think? Since something cannot come from nothing, something has always existed. You do not address all the evidence, which most be considered..

Biological complexity: watch as cellular elements move

by David Turell @, Friday, January 17, 2020, 01:20 (1533 days ago) @ David Turell

Amazing videos looking at the elements of cells move about as they work:

https://phys.org/news/2020-01-microscopy-technique-reveals-cells-d.html

"Light microscopy makes it simple to identify specific cellular structures by tagging them with easy-to-see fluorescent molecules. With the development of super-resolution (SR) fluorescence microscopy, these structures can be viewed with even greater clarity. But fluorescence can reveal only a few of the more than 10,000 proteins in a cell at a given time, making it difficult to understand how these few relate to everything else. Electron microscopy (EM), on the other hand, reveals all cellular structures in high-resolution pictures—but delineating one feature from all others by EM alone can be difficult because the space inside of cells is so crowded.

"Combining the two techniques gives scientists a clear picture of how specific cellular features relate to their surroundings, says Harald Hess, a senior group leader at the Howard Hughes Medical Institute's Janelia Research Campus. "This is a very powerful method.'"

Comment: Nothing more to abstract except the videos, which I could move here, but its easier to look at the original site. These units act as if they know what they are doing. They don't. Be amazed at how living cells look at work. Never by chance.

Biological complexity: cell surface molecular activity

by David Turell @, Friday, January 17, 2020, 18:11 (1533 days ago) @ David Turell

20 different proteins are active on a neuron's surface:

https://phys.org/news/2020-01-surveying-proteins-neuron-surface.html

"Cell surfaces are incredibly dynamic places, especially for cellular communication, says Luo, a neurobiologist at Stanford University. In the nervous system, proteins on the surfaces of nerve cells help the cells find each other and link up. Luo's team wanted a complete view of the proteins that direct connections in the developing fly brain. The researchers focused on proteins involved in forming olfactory networks, which control a fly's sense of smell.

***

"Luo's team added a new twist to the technique. They made the enzyme target proteins on fruit fly olfactory neurons at a particular point in brain development: when neurons are making decisions about which connections to form. The team compared the proteins present in adult cells with those present in the developing brain. "The difference is actually very striking," Luo says.

"The team identified 20 proteins that were more abundant on the surfaces of developing neurons and knocked them down one by one to see if their absence had an effect on brain wiring. Surprising even to the researchers, all 20 were involved in wiring the fly olfactory network. What's more, many of the proteins they found hadn't even been known to play a role in neural development."

Comment: in embryology so much is iong on at teh saame time it demands the recognition of design, and a designer.

Biological complexity: cell competition

by David Turell @, Friday, January 24, 2020, 00:53 (1526 days ago) @ David Turell

Normal cells act to remove unfit and aberrant cells:

https://www.scientificamerican.com/article/survival-of-the-fittest-cells/?utm_source=ne...

"an explosion of similar discoveries has revealed squabbles, fights and all-out wars playing out on the cellular level. Known as cell competition, it works a bit like natural selection between species, in that fitter cells win out over their less-fit neighbours. The phenomenon can act as quality control during an organism’s development, as a defence against precancerous cells and as a key part of maintaining organs such as the skin, intestine and heart. Cells use a variety of ways to eliminate their rivals, from kicking them out of a tissue to inducing cell suicide or even engulfing them and cannibalizing their components. The observations reveal that the development and maintenance of tissues are much more chaotic processes than previously thought. “This is a radical departure from development as a preprogrammed set of rules that run like clockwork,” says Thomas Zwaka, a stem-cell biologist at the Icahn School of Medicine at Mount Sinai in New York City.

"But questions abound as to how individual cells recognize and act on weaknesses in their neighbours. Labs have been diligently hunting for—and squabbling over—the potential markers for fitness and how they trigger competitive behaviours.

***

"Myc acts as a master controller of cell growth, and Minute encodes a key component needed for synthesizing proteins—so it’s not surprising that reduced expression of those proteins makes cells less fit. But the next finding took people by surprise. A pair of papers by Johnston and Moreno showed that cells with an extra copy of normal dMyc outcompeted wild-type cells. These fitter-than-wild-type cells came to be called “supercompetitors”.

"The discovery of supercompetition emphasized that cell competition is about the relative fitness of a group of cells, says Zwaka. If one cell is falling behind, the entire group of neighbours could decide it has to go. But on the flipside, they can also sense that certain cells are better and should survive.

"Cell competition wasn’t simply about getting rid of defects; it was about survival of the fittest, with the less-fit ‘loser’ cells dying and the ‘winners’ proliferating. Importantly, competition was seen only when there was a mixture of genetically different cells, a phenomenon known as mosaicism. In this way, cell competition acts like a quality-control system, booting out undesirable cells during development.

***

"But Torres’s team, led by then-postdoc Cristina Clavería, also made the striking observation that Myc expression varied naturally in mouse ESCs. Cells in the embryo with approximately half the amount of the protein compared with their neighbours were dying by apoptosis. This was one of the first studies that strongly pointed to naturally arising cell competition.

***

"One big puzzle is how cells in a group sense fitness. “Maybe cells are recognizing chemical differences, or physical differences, or differences in cell-membrane composition,” says Fujita, who adds that labs have found evidence for all three.

"His filament-poking kidney-cell experiments suggest that cell–cell contact is needed. Others have seen chemical-fitness signals that seem to be short-range, travelling up to eight cell diameters. Exactly which molecules are responsible for this signalling—either secreted chemicals or physical tags—is the subject of intense debate and investigation.

"Both Johnston and Zwaka have turned up signals associated with immune surveillance. Johnston’s group identified molecules that typically call immune cells to swarm in and engulf foreign invaders and that were driving death in losers. Normal cells express low levels of these death signals at all times. But in a competitive mix, winners flooded their loser neighbours with the signal, which pushed them to kill themselves.

"Zwaka proposes that cells might assess each other’s health by sniffing out the general signals or debris that cells shed. It’s akin to smelling the steaks that your neighbour is grilling for dinner and concluding that they must be doing well.

"Or it could be as simple as seeing which flag your neighbour is flying. Moreno heads his own group now at the Champalimaud Centre for the Unknown in Lisbon, Portugal, which discovered a membrane-spanning protein called Flower. In humans, the protein can take four forms, each displaying its own characteristic structure on the outer cell surface. Two signal ‘I’m a winner’ and the other two signal ‘I’m a loser’ to nearby cells, says Moreno."

Comment: Much of this cell competition helps explain embryological formation. And I think the comments about how this works is through molecular sensing is a correct view. In the embryo much of has got to be automatic to follow the blue print in the DNA.

Biological complexity: cells need acidic lysosomes

by David Turell @, Friday, January 24, 2020, 02:05 (1526 days ago) @ David Turell

Special organelles in cells have many duties including utilizing iron:

https://phys.org/news/2020-01-cells-acidic-lysosomes.html

"Just like the body contains lungs, liver, and lymph nodes, so does each of the body's cells contain tiny specialized organs. Perhaps most peculiar among them are lysosomes—bubble-like sacks that act as part recycling bin, part stomach.

"Among other things, a lysosome devours cellular debris—and, like a stomach, it needs to be acidic to do its job. In fact, without acidic lysosomes, cells in culture stop dividing and eventually die off.

"'We asked a very simple question: Why?" says Kivanç Birsoy, Chapman Perelman Assistant Professor at The Rockefeller University. Experiments in his lab uncovered an equally simple answer: Iron. It turns out that a cell can no longer access this essential nutrient when the pH within its lysosomes rises.

***

"...scientists learned that lysosomes carry out multiple jobs inside cells—from engulfing all sorts of cellular garbage and breaking it down for reuse, to relaying biochemical signal and processing nutrients.

"In spite of their complex functions, however, most functions of lysosomes are dispensable. When they don't function properly, "the cell somehow finds ways to compensate," Birsoy says.
The critical exception, as shown by the lab's recent findings, is converting iron into its nutrient form. "Processing iron seems to be the one thing cells cannot accomplish without lysosomes," he says.

"Ross Weber, a graduate student in Birsoy's lab, made the discovery after he reduced cells' lysosomal acidity enough to stress the cells, but not kill them. In responding to this challenge, the cells activated genes involved in the use of iron, while their iron levels dramatically dropped.

"Cells don't cope for long without iron, which is needed to make DNA and other essential molecules. When a rise in pH causes iron depletion, cells stop dividing and eventually die. The scientists think this happens because lysosomes free iron from the molecules that transport it, something they do best at a pH of 4 to 5, the approximate acidity of a tomato."

Comment: Additional complexity as to how cells operate. Not by chance.

Biological complexity: how cells can repair broken DNA

by David Turell @, Sunday, February 09, 2020, 16:05 (1510 days ago) @ David Turell

Using filaments in a special mechanism:

https://www.sciencedaily.com/releases/2020/02/200205132349.htm

"An elaborate system of filaments, liquid droplet dynamics and protein connectors enables the repair of some damaged DNA in the nuclei of cells, researchers have found. The findings further challenge the belief that broken DNA floats aimlessly -- and highlight the value of cross-disciplinary research in biology and physics.

***

"DNA repair helps ensure genome stability, which in turn allows cells to function and promotes health in all organisms. Double-strand DNA breaks are especially toxic to cells, and researchers had assumed for decades that these breaks floated inside cell nuclei without direction, until they trigger other cellular changes or happen on a fixer mechanism.

"That thinking began to change in 2015, when Karim Mekhail and his lab showed that damaged DNA can be intentionally transported by motor protein 'ambulances' to DNA 'hospitals,' areas enriched with certain repair factors in the nuclei. The researchers later worked with U of T aerospace engineers to show that after a single double-strand break, DNA travels for repair via long 'autobahns' of thread-like microtubules, which are also moving.

***

"'The liquid droplets work with intranuclear microtubules to promote the clustering of damaged DNA sites," says Mekhail, an associate professor of laboratory medicine and pathobiology at U of T. "Repair proteins at these different sites assemble in droplets that fuse into a larger repair-centre droplet, through the action of the shorter nuclear microtubules."

"This larger oil-like droplet then behaves like a spider, says Mekhail, shooting out a web of star-shaped filaments that tether to the longer autobahns along which damaged DNA can be transported to the DNA hospitals.

***

"After months of talks and experiments, computer simulations repeatedly predicted that the shorter filaments would move like pistons, lowering pressure in the nucleoplasm and creating a suction effect that leads to the fusion of droplets. Mekhail and his team confirmed that finding in their lab.

***

"The most surprising finding came after several cycles of droplet fusion, the researchers found. "It was very bizarre and totally unexpected, I still remember the day," Mekhail says. Oshidari observed that the larger droplets initiate an internal concentration of filament building blocks, forcing creation of a kind of self-interlocking brick road, which together with the spidery webs allow DNA to hook onto the longer autobahn filaments."

Comment: In analyzing very complex systems of this sort, which are so protective in maintaining vital functioning structures, we could ask, "which came first, chicken or egg?". Answer: "both". DNA cannot be placed in charge unless its protections are also put in place at the same time. Simultaneous appearance requires design and its designer's mental activity.

This is why the so-called RNA world start to life is ludicrous. Part of a cell is not life. Life requires wholly active intact cells with all their parts. Initial real life was cells.

So is life a stupendous natural miracle, or a creation by a designer? The answer is obvious.

Biological complexity: plants two fiber guidance systems

by David Turell @, Monday, February 10, 2020, 15:22 (1509 days ago) @ David Turell

Cellulose fibers are guided in two ways in plants:

https://www.sciencedaily.com/releases/2020/02/200206132325.htm

"Organised cellulose fibres allow plants to grow, support themselves and store fixed carbon from the atmosphere.

***

"Previous studies have shown that microtubules -- hollow tubes with a diameter one thousandth of a human hair -- play a key role in organising cellulose synthesis. They do this by guiding cellulose synthase complexes (CSCs) -- nanomachines that spin cellulose fibres out while travelling along the cell membrane.

"But when microtubules are removed by drugs, CSCs continue to journey in an organised way, suggesting another mechanism is at play.

***

"By slowing down microtubules inside growing leaves, spacing them apart and removing them altogether in some experiments, they reveal a system that can independently guide CSCs.

"In this system CSCs interact with the cellulose trails left by other complexes, like ants following the chemical trails left by other ants.

"Further investigation reveals this autonomous system can be overridden by microtubule guidance, allowing the 'ant columns' to be redirected in response to environmental and developmental cues.

"Together the findings reveal that plants have a dual guidance system to organise their cellulose fibres.

"The study concludes that having a dual guidance may provide a general mechanism to ensure both strong coherence and flexibility of response to environmental and developmental cues, allowing effective regulation of the growth and strength of cell walls.

"'The mechanism we discovered was not predicted," says lead author Dr Jordi Chan."

Comment: Having a backup system shows good planning. Why should any natural process have two systems as Dr. Chan's surprise shows? He is with Darwin think, but it easily explained if one accepts a thinking designer planned the mechanisms.

Biological complexity: control of bacteria dividing

by David Turell @, Monday, February 10, 2020, 22:11 (1509 days ago) @ David Turell

A specialize protein is in charge:

https://www.sciencedaily.com/releases/2020/02/200210112324.htm

"The ability of pathogens to multiply in the host is crucial for the spread of infections. The speed of bacterial division greatly depends on the environmental conditions. Under unfavorable conditions, such as nutrient deficiency, bacteria tend to pause after division and reproduce more slowly. But how do bacteria know, when it is time to enter the next round of cell division?

"A team at the Biozentrum of the University of Basel, led by Prof. Urs Jenal has now identified a central switch for reproduction in the model bacterium Caulobacter crescentus: the signaling molecule c-di-GMP. In their current study, published in the journal Nature Communications, they report that this molecule initiates a "clock-like" mechanism, which determines whether individual bacteria reproduce.

"How long a cell pauses after division and how it then decides to engage in the next round of division is still poorly understood. The signaling molecule c-di-GMP plays a key role in this process. "The rise in the c-di-GMP level sets the individual cogwheels of the cell's clock into action, one after the other," explains Jenal. "These cogwheels are enzymes called kinases. They prepare the transition of the cell from the resting to the division phase."

"Under favorable living conditions, newborn bacteria begin to produce the signaling molecule -- this starts the clock ticking. The initially low c-di-GMP level activates a first kinase. This activates the expression of over 100 genes, which drive the cell towards division and boost the production of c-di-GMP.

"The resulting peak levels of c-di-GMP finally stimulate the last wheel of the machinery, also a kinase. "With this step, the cell ultimately decides to replicate its DNA and to trigger cell division," explains Jenal. "Simultaneously the over 100 genes are switched off again, as these are only important for the transition phase but obstruct later stages of proliferation."

"In a parallel study, recently been published in PNAS, a team led by Prof. Tilman Schirmer, also at the Biozentrum of the University of Basel, describes how c-di-GMP activates the first cogwheel of the newly discovered clock at the atomic level.

"The researchers have revealed that the mobile domains of the kinase are initially locked in a fixed position. The binding of c-di-GMP liberates the domains, thereby activating the kinase for gene expression. "In our study, we have discovered a new mode of c-di-GMP mediated activation," says Schirmer. "Once again, we are fascinated by the diverse ?strategies? of this small molecule to regulate biochemical processes."

"The c-di-GMP regulated timing of the bacterial cell cycle by this signaling molecule seems to be a universal mechanism. The researchers assume that this mechanism enables bacteria to precisely coordinate growth and development. "

Comment: It starts a precise cascade of specialized enzymes. Enzymes are huge very specialized proteins. Chance evolution cannot find these precise molecules. Design is required.

Biological complexity: maintaining cell shape

by David Turell @, Monday, February 17, 2020, 19:13 (1502 days ago) @ David Turell

Expansion and contraction forces have to be balanced to maintain cell shape:

https://phys.org/news/2020-02-protein-function-protrusive-contractile-cell.html

"In a healthy cell, there is a fine balance between the protrusive structures that make the cell more migratory, and the contractile structures that maintain the cell's shape and its association with the environment. A disturbance in this balance leads to several diseases, such as invasive cancers.

"The most important component of both protrusive and contractile machineries is a protein called actin. This means that the proper distribution of actin between these structures is essential for the normal function of the cell. Nevertheless, the mechanisms that ensure that actin is distributed correctly between the protrusive and contractile machineries have remained elusive.

"Researchers at the University of Helsinki, Finland, and the University of Pennsylvania, Philadelphia, U.S., have now identified a protein called tropomodulin as a key player that maintains the balance between the protrusive and contractile actin-filament machineries within a cell.

***

"'We have now revealed that tropomodulins stabilise the actin filaments of the contractile structures in non-muscle cells through interacting with specific proteins within these actin filament bundles. The depletion of tropomodulins led to a loss of contractile structures, accompanied by an excess of protrusive structures, and thus to severe problems in a cell's shape and force production," says Academy Professor Pekka Lappalainen from the HiLiFE—Institute of Biotechnology, University of Helsinki.

"Researchers were surprised to see that the depletion of one protein can have such drastic effects on the balance of the actin machinery.

"'Another exciting and unexpected finding of this study was the notion that the same protein can have a different function depending on the tissue or cell type."

Comment: I don't know why the research team is surprised at a single protein showing differing protein functions in different cells, when differing cells have differing DNA code expressions. This system requires careful balances to work correctly. Life is a symphony of balanced protein reactions. It cannot have come together by chance.

Biological complexity: clearing misfolded proteins

by David Turell @, Tuesday, February 18, 2020, 20:16 (1501 days ago) @ David Turell

In extracellular fluid a new found clearing mechanism:

https://phys.org/news/2020-02-cells-misfolded-proteins-tissues.html

" A number of diseases are believed to be caused by the gradual buildup of misfolded proteins that can aggregate together and damage neurons and other cells in the body. To help prevent this damage, cells have developed numerous quality control systems that recognize misfolded proteins within the cell and either fold them back into their correct shape or else degrade them before they start to aggregate.

"'However, approximately 11% of human proteins exist outside of the cell, where they are subjected to even more stresses that may cause them to misfold," says Eisuke Itakura, an assistant professor in the Department of Biology at Chiba University in Japan.

***

"A protein called Clusterin can bind to misfolded extracellular proteins and prevent them from aggregating. In the new study, Itakura and colleagues discovered that Clusterin can escort misfolded proteins into the cell and deliver them to the cell's garbage-disposal units—the lysosomes—where they can be degraded. The researchers also discovered that, after binding to misfolded proteins, Clusterin enters cells by binding to proteins known as heparan sulfate proteoglycans, which are present on the surface of almost all human cells.

"Itakura and colleagues found that, together, Clusterin and heparan sulfate proteoglycans allow many different cell types to internalize and degrade a wide variety of misfolded extracellular proteins. "We therefore think that this pathway is a general extracellular protein quality control system responsible for the clearance of misfolded proteins from diverse tissues and body fluids," Itakura says.

"Intriguingly, the researchers also found that Clusterin and heparan sulfate proteoglycans can import amyloid β into cells for degradation. Mutations in the gene encoding Clusterin have been linked to an increased risk of developing Alzheimer's disease, and experiments in rats have shown that injecting Clusterin into the brain can prevent amyloid β-induced neurodegeneration. '"

Comment: Miss-folded protein molecules cannot perform the proper functions of a properly folded protein. It is the folding that creates the functional ability. Obviously life cannot continue without this correction process, which must have been present when Life started. Design is required.

Biological complexity: control of cell skeletal structure

by David Turell @, Thursday, February 20, 2020, 23:23 (1498 days ago) @ David Turell

One of the jobs of centrosomes and its parts, centrioles:

https://phys.org/news/2020-02-scaffold-center-cellular-skeleton.html

"All animal cells have an organelle called a centrosome, which is essential to the organization of their cell skeleton. The centrosome plays fundamental roles, especially during cell division, where it allows equal sharing of genetic information between two daughter cells. When the cells stop dividing, the centrioles, cylindrical structures composed of microtubules at the base of the centrosome, migrate to the plasma membrane and allow the formation of primary and mobile cilia, which are used respectively for the transfer of information and the genesis of movement. While performing these crucial biological functions, centrioles are therefore subjected to many physical forces, which they must resist. Scientists from the University of Geneva (UNIGE) have discovered an internal structure at the center of these nano-cylinders, a real cellular scaffolding that maintains the physical integrity of this organelle. This study, published in the journal Science Advances, will provide a better understanding of the functions of the centriole and the pathologies associated with its dysfunction. (my bold)

" The centrioles, cylindrical nano-structures, form the centrosome, the main microtubule organizing center of the cell skeleton, and the cilia, real cellular antennas. Defects in the assembly or functioning of the centriole can lead to pathologies in humans, such as ciliopathies—retinal disorders that can cause loss of vision.

"Centrioles, formed by microtubules, are components of the cell skeleton. "They have a canonical organization defined by nine triplets of microtubules that must be maintained as a structural unit in order to resist the various forces they face during their cellular functions," explains Paul Guichard, Professor in the Department of Cell Biology of the Faculty of Science at UNIGE.

"The group of Paul Guichard and Virginie Hamel, a researcher at the Department of Cell Biology and co-leader of the study, discovered an internal scaffolding for this organelle using high-powered electron microscopes, ..."This study allowed to analyze centrioles of four different species and to demonstrate that this inner scaffold is present systematically," reports Maeva Le Guennec, a UNIGE researcher.

"We then investigated which centriolar proteins were located in this new structure," says Virginie Hamel. To do this, the UNIGE researchers used an innovative super-resolution method, called expansion microscopy, which makes it possible to inflate cells without deforming them in order to observe their internal organization. Thus, they were able to identify four proteins that are located at the level of this inner scaffold."

Comment: Cells are highly complex protein structures with builtin processes to maintain proper shape and function. By the way, the centrosome and centrioles are part of the Albrecht-Buehler discussion about cell intelligence. A=B does not agree with most researchers theories:

"Yet, the vast majority of today's biologists devote their efforts to prove the opposite, namely that specific molecular interactions create the cellular functions"

http://www.basic.northwestern.edu/g-buehler/FRAME.HTM

This study discussion is structure, but the controls must originate in the genome instructions. Note the bold in first paragraph above. I wonder what A-B thinks now since his research dates from 25-50 years ago.

Biological complexity: control of cell clean up

by David Turell @, Thursday, February 20, 2020, 23:38 (1498 days ago) @ David Turell

With all the protein reactions in active cells as RNA's deliver messages and then are degraded, there is an efficient cleanup mechanism:

https://www.sciencedaily.com/releases/2020/02/200220101115.htm

"Cells are small factories that constantly produce protein and RNA molecules by decoding the genetic information stored in the DNA of their chromosomes. The first phase of this decoding, the transcription process, "transcribes" the DNA code into RNA molecules. In humans, and most other organisms, all cells of the body carry the full genetic information of the entire organism, with each individual cell requiring only a small subset of its DNA decoded. Even so, the first decoding phase (transcription) is pervasive and produces a large amount of surplus RNAs.

"These extraneous RNAs do, however, not accumulate, as they are degraded shortly after their production. This prevents deleterious accumulation of non-functional transcripts that would otherwise be detrimental to cell health. Most of this RNA decay is carried out by the nuclear RNA exosome complex, an RNA 3'-5' exonuclease, which is recruited to RNA by specific adapters, like the so-called NEXT complex and the PAXT connection. The laboratory of Torben Heick Jensen previously found that NEXT and PAXT aid in decay of different kinds of nuclear RNAs, but how specificity is achieved remained enigmatic.

"With their new publication, the research team now reveals that NEXT substrates contain 'naked' 3'ends, whereas PAXT substrates harbor so-called poly(A)-tailed 3'ends. Despite this clear division, the study also reveal that the decay systems can co-operate, which helps cells to degrade NEXT substrates, even in the potentially hazardous situation when NEXT activity is decreased. In this case, NEXT targets (which are normally produced without a poly(A) tail and swiftly removed) acquire poly(A) tails -- a hallmark of PAXT targets -- which subject them to PAXT-mediated decay. In conjunction, this provides a two-layered targeting mechanism for the efficient nuclear sorting of the human transcriptome."

Comment: In such high speed production, there will be residual garbage, which must be promptly cleared or the cell will break down. In initial creation of such a system both sides must be in place, production and garbage removal. Only design can accomplish this result.

Biological complexity: how mitochondria call for help:

by David Turell @, Thursday, March 05, 2020, 22:01 (1485 days ago) @ David Turell

They always need help from the whole cell:

https://phys.org/news/2020-03-mitochondrial-distress-pathway-revealed.html

"This unbiased genome-wide screening procedure revealed two mitochondrial key factors that are essential for the ability of the mitochondria to activate the cellular stress response. One of these is the enzyme OMA1, which can cleave target proteins, and the other is a barely studied protein called DELE1," Jae explains.

When mitochondria are exposed to stress, OMA1 becomes activated and induces the cleavage of the DELE1 protein into a shorter fragment. This fragment is then redistributed to the cytosol, where it binds to another enzyme called HRI, which in turn triggers the ISR. "HRI was thus far believed to be primarily required for the formation of red blood cells," says Jae. "Our study has now shown that it can also be activated by DELE1 in the context of mitochondrial perturbation."

Comment: As usual the reaction involves very specialized proteins and complex enzymes. Could not have developed by chance.

Biological complexity: diurnal rhythms

by David Turell @, Thursday, March 12, 2020, 14:24 (1478 days ago) @ David Turell

Controlled by specific molecular reactions:

http://nautil.us/issue/83/intelligence/how-your-body-knows-what-time-it-is?utm_source=N...

"Many organisms perform best at certain hours of the day. The slug species Arion subfuscus, living in almost total darkness, knowing nothing about the Gregorian calendar, lays its eggs between the last week of August and the first week of September.1 Bees forage for nectar, knowing the best times to visit the best fields and the exact timing of nectar secretions for individual species of flowers.

"In the mid-20th century, the Austrian Nobel laureate Karl von Frisch provided enormous insights on honeybee communication and foraging time. He discovered that bees have internal clocks that tell them not only where the nectar is to be found but also precisely when that food will be ready. “I know of no other living creature,” he wrote in his book on bee language, “that learns so easily as the bee when, according to its ‘internal clock,’ to come to the table.”

***

"So, without getting into the full description of the differences between protein functions of humans and flies, we can interpret the Drosophila model of the circadian clock as simply a feedback loop that operates by a specific gene expression with a relatively short half-life. In essence and in generality, the loop simply behaves like this: The quantity of A molecules increases, reaching a threshold that creates B molecules (with a relatively short half-life), which in turn shut down production of the A molecules.

"Unlike fruit flies, humans have strong temperaments and wills that permit defiance of their weaker, yet persistent, biochemical controls. The model circadian rhythm for a person who rises at roughly 6 a.m. and runs through each day with a regularity tuned to the sun is broadly illustrated here.

Go tp site to see diagram


"All living things learn to manage daily environmental changes, especially the atmospheric lightness and darkness caused by the 24-hour cycle of earth rotation. A human’s hereditary information includes the biochemical mechanisms of proteins gotten from the routines of his or her ancestral life. And although millions of cells in a person’s body have specialized functions, every one of them contains the same code of hereditary information.

"This led to the idea that a circadian gene’s instructions are responsible for per mRNA cycling following a feedback loop with return response instructions. The magic here is that the per gene located on the X chromosome of the fly cell contains the information for the mRNA (that has a relatively short half-life), which instructs the ribosomes to produce proteins connected with the per gene (called PER molecules, capitalized to avoid confusion with the per gene) that effectively travel back to the cell nucleus to turn off the activity of the per gene. Morning light would then destroy PER molecules. With PER molecules gone, the per gene would renew the process of encoding mRNA to complete a 24-hour feedback loop. In effect, it is the fruit fly’s molecular clock hand encapsulated in a single cell; moreover, it has since been discovered that the biological clock in most mammals works by the same feedback loop, though in mammals it takes a whole group of per genes for the process to continue. It could be that this Drosophila melanogaster per gene model is the result of organic evolutionary adaptation of the Earth’s circadian environment to maximize survival and well-being on a planet where life existence is governed by the alternation of light and darkness.

***

"Here is how the circadian oscillator of Drosophila melanogaster works. The per gene in the nucleus of the cell transcribes mRNA molecules that migrate to the cytoplasm to give information and green light for ribosomes (the protein workshop) to build both stable and unstable protein molecules. The stable protein accumulates in the cytoplasm. As night goes on, protein levels accumulate to reach a threshold by roughly the middle of the night, when they enter the nucleus and begin to repress transcription from per gene instructions and soon after completely turn protein building off. In the morning, as the sun rises, the proteins decay and after several hours vanish. With all protein gone from the nucleus, the per gene turns on to restart transcription, and so the approximate 24-hour-cycle loop begins again. On and on it goes, indefinitely.

***

"... the full body-clock system involves both the SCN in the brain and the trillions of peripheral clocks embedded in almost every cell of the body. We are a bundle of clocks that are synchronized to the environment by zeitgebers, of which changes in light and darkness are but just one.

"With exception to cells in the eye, mammalian cells have no photoreceptors, so only the SCN
[suprachiasmatic nucleus in the brain ] can indirectly sense light by way of neural tract signals coming from the retina, and therefore, we tend to be awake mostly when light signals tell us to be."

Comment: this system is controlled by light and depends on specific molecular feedback loops. Only design can create this system.

Biological complexity: diurnal rhythms

by dhw, Friday, March 13, 2020, 17:32 (1477 days ago) @ David Turell

QUOTES: We are a bundle of clocks that are synchronized to the environment by zeitgebers, of which changes in light and darkness are but just one.

"[…] we tend to be awake mostly when light signals tell us to be."

DAVID: this system is controlled by light and depends on specific molecular feedback loops. Only design can create this system.

The whole article clearly describes how organisms respond and adapt to the environment. If they didn’t, they would not survive. According to you, every single response by every single organism has been specially designed by your God and geared to the creation of H. sapiens. There is nothing in this article that can be used to exclude the possibility that the cell communities of each organism have adjusted themselves to the conditions – which for a theist would mean that God designed the autonomous mechanism enabling each organism to work out its own “specific molecular feedback loops”.

Biological complexity: diurnal rhythms

by David Turell @, Friday, March 13, 2020, 17:59 (1477 days ago) @ dhw

QUOTES: We are a bundle of clocks that are synchronized to the environment by zeitgebers, of which changes in light and darkness are but just one.

"[…] we tend to be awake mostly when light signals tell us to be."

DAVID: this system is controlled by light and depends on specific molecular feedback loops. Only design can create this system.

dhw: The whole article clearly describes how organisms respond and adapt to the environment. If they didn’t, they would not survive. According to you, every single response by every single organism has been specially designed by your God and geared to the creation of H. sapiens. There is nothing in this article that can be used to exclude the possibility that the cell communities of each organism have adjusted themselves to the conditions – which for a theist would mean that God designed the autonomous mechanism enabling each organism to work out its own “specific molecular feedback loops”.

This theist disagrees. Feedback oops are critically designed t o control all the metabolic functions of life. They are automatically in place in a ll of us from birth .

Biological complexity: 'hero' proteins protect others

by David Turell @, Friday, March 20, 2020, 18:03 (1470 days ago) @ David Turell

A new type of cellular protein is found:

https://www.the-scientist.com/news-opinion/hero-proteins-may-shield-other-proteins-from...

"Flexible proteins appear to protect molecules from becoming denatured in extreme conditions such as heat and from clumping up, as happens in some neurodegenerative diseases.

"Researchers at RIKEN and the University of Tokyo report the existence of a new class of proteins in Drosophila and human cell extracts that may serve as shields that protect other proteins from becoming damaged and causing disease. An excess of the proteins, known as Hero proteins, was associated with a 30 percent increase in the lifespan of Drosophila, according to the study,

***

"Iwasaki called the new type of protein a Heat-resistant obscure (Hero) protein—not because of their ability to rescue Argonaute from destruction, but because in Japan, the term “hero” means “weak or not rigid,” and Hero proteins don’t have stiff 3-D structures like other proteins do. But recognition of a more widespread role for Hero proteins in protecting other molecules in the cell gives the name new meaning.

***

"Hero proteins can survive these biologically challenging conditions. Heat-resistant proteins have been found in extremophiles—organisms known to live in extreme environments—but were thought to be rare in other organisms. In the new study, Tsuboyama and his team boiled lysates from Drosophila and human cell lines, identifying hundreds of Hero proteins that withstood the temperature.

"The researchers selected six of these proteins and mixed them with “client” proteins—other functional proteins that on their own would be denatured by extreme conditions—before exposing them to high temperatures, drying, chemicals, and other harsh treatments. The Hero proteins prevented certain clients from losing their shape and function.

***

"The authors emphasized that there is a lot left to learn about the proteins. Each Hero protein seems able to protect some client proteins, but not all of them. Moreover, amino acid sequences differ considerably between Hero proteins, making it difficult to predict their functions. The researchers write in the study that they hope future studies will help them identify which clients each Hero might work with.

"Whatever discoveries future work might hold, Tsuboyama says, the scientific community’s reaction to the team’s new study has been consistent: “Almost everyone says that Hero proteins are interesting but mysterious.'”

Comment: It is not surprising that protection against stressing proteins is present. A designer would think to provide such protections

Biological complexity: apoptosis cellular controls

by David Turell @, Sunday, April 05, 2020, 19:03 (1454 days ago) @ David Turell

Cell death is carefully controlled by specific cellular proteins. We turn over our cells with new ones constantly, which means the body you see in a mirror is you but it is not the same as the body from a previous time:

https://medicalxpress.com/news/2020-04-protein-to-protein-couples-cell-survival-prolife...

"Human cells respond to stresses like DNA damage, metabolic imbalance and starvation by first trying to repair the problem. If that does not work, the cells then induce programmed cell death, called apoptosis. Apoptosis is a highly regulated cell fate decision that removes about 50 billion to 70 billion cells each day in adults.

"The regulators of apoptosis watch over cell functions, especially cell replication and the decision to enter the cell cycle. This portion of the life of a cell requires accurate DNA replication and error-free chromosome separation. At multiple checkpoints during this process, pathways exist to induce apoptosis as needed.

"William Placzek, Ph.D., and Robert Whitaker have found a direct link between the protein MCL1—a member of the large BCL2 protein family known as the gatekeepers of apoptosis—and a cell-cycle checkpoint protein called P18. Through this link, they show the first demonstration that MCL1, which functions in the decision between either cell survival or programmed death, can also directly initiate cell proliferation, via the CDK4/6-RB pathway.

***

"The BCL2 family includes pro-apoptotic proteins and anti-apoptotic proteins that compete via direct protein-to-protein binding to determine cell fate. These detailed interactions have significance in human health because the anti-apoptotic BCL2-family proteins turn out to be key regulators of cancer tumorigenesis and/or anti-cancer therapeutic responses. Upregulation of the proteins is a common event in various types of cancer. In particular, overexpression of the anti-apoptotic BCL2-family protein MCL1 is a mechanism used by solid tumors to evade some standard cancer chemotherapies.

"Besides its role in cancer, Placzek said, "we expect this communication between the BCL2 family and the CDK4/6-RB pathway exists and will have significant impact in normal cellular proliferation, in stem cell growth and in differentiation. Of particular interest is how this interaction impacts hematopoietic and neuronal progenitor cell speciation, where MCL1 has been identified as a key mediator of differentiation."

"Nine years ago, Placzek and colleagues at the Sanford-Burnham Medical Research Institute identified a novel protein motif that could bind to the mouse version of MCL1. A protein structural motif is a secondary structure on the protein that can interact with a secondary structure on another protein, akin to a space capsule docking to the International Space Station. The novel motif found by Placzek and colleagues was a reversal of the known binding motif BH3, so they called it reverse BH3, or rBH3.

"Search of the human genome DNA sequence identified several proteins that putatively had an rBH3 motif, including P18, a regulator acting at the G1/S stage of the mammalian cell cycle.
The current study shows biological significance for the rBH3 motif.

"We have demonstrated that the rBH3 motif is more than a unique peptide sequence," Placzek said. "It is a natural protein motif that is able to mediate direct protein-to-protein interactions between MCL1 and an rBH3-containing protein."

***

"They showed that the two proteins bind together in vitro and endogenously inside cells of two solid tumor cell lines; they also showed that the rBH3 motif on P18 was necessary and sufficient to mediate that binding. In the two solid tumor cell lines, they showed that overexpression of MCL1 induced a loss of P18 through a transcriptionally independent cysteine-protease degradation process. That overexpression of MCL1 also affected the cell cycle, as shown by a decrease in the G1 cell population and corresponding increases in the S and G2/M populations, and those changes are RB1-dependent. Finally, they showed that those changes occur because of increased cell proliferation, rather than the alternate possibility, a G2/M block."

Comment: Here again we see specific specialized proteins controlling increased cell division and old cell death. This must be precisely controlled, and it obviously works because our bodies are exactly reduplicated. Chance can't create this carefully designed system. Only a designer can.

Biological complexity: Size of body protein reactions

by David Turell @, Wednesday, April 08, 2020, 19:12 (1451 days ago) @ David Turell

Only two to eleven percent of reactions described:

https://phys.org/news/2020-04-world-largest-protein-clues-health.html

"The human body is composed of billions of cells, each of which is made and maintained through countless interactions among its molecular parts. But which interactions sustain health and which ones can cause disease when they go awry? The human genome project has provided us with a "parts list" for the cell, but only if we can understand how these parts go together, or interact, can we really begin to understand how the cell works and what goes wrong in disease.

"To answer these questions, scientists needed a reference map of interactions—an interactome— between gene-encoded proteins, which make up cells and do most of the work in them.

***

"Humans have about 20,000 protein-coding genes but scientists still know remarkably little about most of the proteins they encode. Fortunately, this information can be gleaned from interaction data thanks to the "guilt by association" principle, according to which two proteins that have similar interacting partners are likely involved in similar biological processes.

"'We can use our human interactome map to predict protein function," says Roth, who is also Senior Scientist at the Sinai Health System's Lunenfeld-Tanenbaum Research Institute. "People can look up their favourite protein and get clues about its function from the proteins it interacts with."

***

"The team tested all possible pairwise combinations among 17,500 proteins for their ability to interact with each other in three separate versions of a yeast-based assay, each done in triplicate, amounting to a staggering three billion separate tests. The results yielded ~53,000 high-confidence binary interactions between more than 8,000 proteins, which were verified by other methods. The majority of interactions had never been detected before.

"Although the largest map of its kind to date, the map remains incomplete, representing between 2-11 per cent of all human protein interactions. Roth said that one reason why many interactions were missed is probably because yeast cells lack certain human-specific molecular factors that are needed for proper protein function."

Comment: this shows how little we know about how life emerges from the mass of protein molecule reactions, all coordinated with each other. Some of the processes are simply maintenance (think producing urine, or oxygen CO2 exchange) At the same time the amounts of protein product produced is under tight controls by feedback loops of molecules. Most protein molecules are quite large, and required enzymes which must be present to speed all biochemical reactions, because they basically cannot otherwise occur/be completed at anywhere near the speed needed. No question design is required. The only debate is what or who is the designer. Any sensible thought realizes it is a mental giant!

Biological complexity: control of actin in cells

by David Turell @, Thursday, April 09, 2020, 01:50 (1450 days ago) @ David Turell

One of the most prevalent of all molecules in cells. it forms the fibers that support the tra nsport of protein products i n cells:

https://phys.org/news/2020-04-advance-actin-cell-function.html

"The research shows how actin is modified, and should accelerate further research on how actin works and is regulated in cells. The researchers used X-ray crystallography and other advanced techniques to reveal the atomic-scale structure of actin as it is being modified by a partner enzyme during the attachment of a cluster of atoms, called an acetyl group, at the start of the chain of amino acids that forms the protein. The modification, called N-terminal acetylation, can occur on the vast majority of human proteins and is thought to have important biological functions. However, in the case of actin those functions have not been entirely clear.

***

"Actin's importance is underscored by the fact that in mammalian cells it is the most abundant protein in the cytoplasm, the space outside the nucleus. It is best known for forming cable-like structures called filaments, which make up much of the supportive "skeleton" of cells, and also play key roles in cell division and in cells' ability to move about in tissues.

"N-terminal acetylation can occur on actin, as it does on more than 80 percent of human proteins, and appears to help regulate actin's ability to form filaments. However, the precise functions of this modification have never been clear, and scientists—a team led by Dominguez and a team of collaborators at the University of Bergen in Norway led by Dr. Thomas Arnesen—discovered the enzyme that catalyzes actin N-terminal acetylation only in 2018.

***

"One of their key findings was that NAA80 does not recognize and acetylate actin when the protein is assembled into filaments. It does acetylate actin when it exists as a separate molecule, called a monomer. However, the most efficient N-terminal acetylation occurs when actin is bound to another protein called profilin—a known partner of actin, and one that is closely involved in actin's formation of filaments and like actin is also very abundant in the cell.

"'It was a surprise to us to find that this protein, NAA80, appears to have evolved to recognize not actin alone but the profilin-actin complex," Dominguez says. "It suggests that profilin has a role as a 'chaperone' that allows actin to be N-terminally acetylated prior to filament formation."

"One of their key findings was that NAA80 does not recognize and acetylate actin when the protein is assembled into filaments. It does acetylate actin when it exists as a separate molecule, called a monomer. However, the most efficient N-terminal acetylation occurs when actin is bound to another protein called profilin—a known partner of actin, and one that is closely involved in actin's formation of filaments and like actin is also very abundant in the cell.

"'It was a surprise to us to find that this protein, NAA80, appears to have evolved to recognize not actin alone but the profilin-actin complex," Dominguez says. "It suggests that profilin has a role as a 'chaperone' that allows actin to be N-terminally acetylated prior to filament formation.'"

Comment: Such a highly irreducibly complex system requiring specific enzymes must have been designed. It puts actin under precise formation control. There must be a designer

Biological complexity: nanotechnology explores complexity

by David Turell @, Thursday, April 09, 2020, 19:13 (1450 days ago) @ David Turell

Study of the nanotechnology of life teaches us how to understand the intricacies of protein formation and integration as life emerges from these multiple highly controlled integrated reactions:

https://aeon.co/essays/the-future-is-nano-and-it-will-revolutionise-medical-science?utm...

"Clever scientists with broad visions started to realise that a new kind of technology, prophesied by Richard Feynman in the 1950s, was finally materialising, as researchers achieved the capacity to visualise, fabricate and manipulate matter at the nanometre scale.

***

"From the start, nanotechnologists have been involved with and inspired by biology, primarily because the molecular players and the main drug targets in medicine – proteins, DNA and other biomolecules – are nanosized. But we physicists were also fascinated by the capacity of biology to produce materials that adapt, evolve, survive and even think – materials that surpass human technological abilities in every possible way.

***

"Far from being the static entities featured in traditional biochemistry books, proteins have been observed performing complex yet surprisingly familiar movements that sometimes bear an uncanny resemblance to macroscopic human-made machines. Some work as nanomotors that rotate to maximise the efficiency of chemical reactions; others can ‘walk’ on molecular tracks with a processive ‘hand-over-hand’ movement that allows them to transport cargos around the cell.

***

"At the same time, progress in genetics and biochemistry led to a greater understanding of the chemical activity of proteins and their relation to the information stored in cellular DNA" (my bold)
***

"Bacteria and cancers are teaching us the same lesson that we are learning in other aspects of our relationship with nature: namely, that life resists reductionist approaches and bounces back with complex behaviours that thwart our optimistic strategies to dominate it.

***

"In nature, they result from the careful and deterministic folding of molecular strings (polymers) consisting of combinations of 20 different units (amino acids). They can take on any imaginable shape and function at the nanoscale. In fact, we still don’t know how many different proteins are in our bodies (perhaps it is unknowable), since our cells could have the capacity to create and modify proteins as and when they are needed.... No human-made artificial nanotechnology can dream of such capacities, but we can try to learn how life does it. (my bold)

***

"This realisation came from the discovery made at Harvard by Chris Sander and Debora Marks of structural ‘staples’ (formed by amino acids sticking to each other) that hold a protein molecule together. Sanders and Marks looked at information contained in the genomic DNA of organisms that have proteins related to each other via a shared evolutionary history. When the staples are inserted into the computer model, it’s possible to explore how the protein folds within those constraints.

***

"What’s interesting here is that the story has not unfolded quite as the pioneers of nanotechnology imagined, or as early visions of ‘nanorobots’ predicted, because this nanotechnology no longer emerges from a reductionist standpoint that envisages wholly artificial nanomachines deployed inside living cells. Instead, it utilises nature itself, harnessing its complexity and evolutionary history to create nanostructures.

***

"What the new nanotechnology seems to point toward is an inexorable dimming of the boundaries between the sciences. Though still in an embryonic state, the new transmaterial science of producing artificial materials inspired by biology is already being used to create new medicines, develop new strategies for regenerating tissues and organs, and improve the responses of the immune system. In parallel, hybrid bioinorganic devices that mimic biological processes will soon be used in new computers and electronic devices. By increasingly refining our ability to learn biology using the methods of physics, nanotechnologists are throwing off the yolk of reductionism, and learning how to distil the recipes of the Universe in order to fabricate and assemble matter from the nanometre scale up."

Comment: The startling degree of complexity, and the fact that we still do not know how many different proteins are in our bodies tells us how little we still know about the biochemistry of life. we are determining some of the information that life uses in shaping the proteins of life's processes. It also tells us a designer is required. I've only culled out one side of the info. The article discusses the successes of nanotechnology production of necessary results and should be read completely.

Biological complexity: how big is the bush of life?

by David Turell @, Sunday, April 12, 2020, 20:00 (1447 days ago) @ David Turell

Everywhere we look we find new species. We have no idea how big it is until we explore everywhere on Earth, and certainly do not know God's reasons for this massive diversity:

https://phys.org/news/2020-04-species-exploration-abyssal-deep-sea.html

"An estimated 150-foot siphonophore— seemingly the longest animal ever recorded was discovered during a month-long scientific expedition exploring the submarine canyons near Ningaloo. Additionally, up to 30 new underwater species were made by researchers from the Western Australian Museum aboard Schmidt Ocean Institute's research vessel Falkor.

"The discovery of the massive gelatinous string siphonophore—a floating colony of tiny individual zooids that clone themselves thousands of times into specialized bodies that string together to work as a team—was just one of the unique finds among some of the deepest fish and marine invertebrates ever recorded for Western Australia.

***

"During the expedition, scientists collected the first giant hydroids in Australia, discovered large communities of glass sponges in Cape Range Canyon, and observed for the first time in Western Australia the bioluminescent Taning's octopus squid, long-tailed sea cucumber, and a number of other molluscs, barnacle and squat lobster species. Some of the species collected will be exhibited at the Western Australian Museum.

"The team also found the largest specimen of the giant siphonophore Apolemia ever recorded—video of which was posted on Schmidt Ocean Institute's Twitter account. "We suspected these deep sea areas would be diverse but we have been blown away by the significance of what we have seen," Wilson said. (my bold)

***

"'There is so much we don't know about the deep sea, and there are countless species never before seen," said Wendy Schmidt, co-founder of Schmidt Ocean Institute. "Our planet is deeply interconnected—what happens in the deep sea impacts life on land—and vice versa. This research is vital to advance our understanding of that connection—and the importance of protecting these fragile ecosystems. The Ningaloo Canyons are just one of many vast underwater wonders we are about to discover that can help us better understand our planet."
(my bold)

Comment: My first bold is a notice of my surprise at their surprise. of course their is endless diversity to find in our bush of life. The second bold is right on point: the interconnectedness is vital as I constantly point out about the balance of econiches, and the necessary supply of food for all, no matter how diverse. All of this diversity comes from evolution from bacteria. Its presence in this size advertises its importance. Let us not hear about God enjoying spectacle or whatever humanistic weirdness can be imagined. If it is God's creation, it is highly purposeful for a real reason.

Biological complexity: how big is the bush of life?

by dhw, Monday, April 13, 2020, 13:41 (1446 days ago) @ David Turell

QUOTE: "We suspected these deep sea areas would be diverse but we have been blown away by the significance of what we have seen," Wilson said. (David's bold)

DAVID: My first bold is a notice of my surprise at their surprise. of course their is endless diversity to find in our bush of life.

Why of course? According to you, your God’s one and only purpose was to produce humans. In that case, why did he need “endless” diversity? Elementary logic suggests that if he had only wanted humans, he would only have needed to provide enough diversity to feed humans. But “of course” endless variety would be the result of his creating a mechanism which gave free rein to organisms to work out their own ways of coping with or exploiting all the different forms of environment.

Quote: "Our planet is deeply interconnected—what happens in the deep sea impacts life on land—and vice versa. This research is vital to advance our understanding of that connection—and the importance of protecting these fragile ecosystems. The Ningaloo Canyons are just one of many vast underwater wonders we are about to discover that can help us better understand our planet." (David's bold)

DAVID: The second bold is right on point: the interconnectedness is vital as I constantly point out about the balance of econiches, and the necessary supply of food for all, no matter how diverse. All of this diversity comes from evolution from bacteria. Its presence in this size advertises its importance. Let us not hear about God enjoying spectacle or whatever humanistic weirdness can be imagined. If it is God's creation, it is highly purposeful for a real reason.

You already quoted this a couple of days ago, and ignored my response:
"I would not question the article’s statement that our planet is deeply interconnected. It always has been, long before humans arrived. And when connections break, we get new connections and new econiches. That does not mean your God specially designed 3.X billion years’ worth of non-human econiches for the sake of humans who were not even there!" Please stop stating the blindingly obvious fact that all organisms need food, as if somehow that provided a logical explanation for your theory. It doesn’t.

QUOTE: “The discovery of the massive gelatinous string siphonophore—a floating colony of tiny individual zooids that clone themselves thousands of times into specialized bodies that string together to work as a team—was just one of the unique finds among some of the deepest fish and marine invertebrates ever recorded for Western Australia.

Now this really is worth a new comment. You could hardly have a better description of how multicellularity works. All multicellular bodies are collections of cells that clone themselves thousands of times into specialized bodies that string together to work as a team. I have called them cell communities. My pet analogy has always been ant colonies, but maybe the siphonofore is even better. Thank you for this intriguing article.

Biological complexity: circadian clock root controls

by David Turell @, Monday, April 13, 2020, 19:20 (1446 days ago) @ dhw

As usual a complex protein system:

https://phys.org/news/2020-04-small-protein-synchronizes-circadian-clocks.html

"Five years ago, researchers from the Centre for Research in Agricultural Genomics (CRAG) led by the CSIC Research Professor Paloma Mas made the breakthrough discovery that the circadian clocks in the growing tip of the plant shoot function in a similar way to the clocks in the mammalian brain, which in both cases are able to synchronize the daily rhythms of the cells in distal organs. From that seminal finding, plant researchers have been eager to discover the messenger molecule that could travel from the shoot to the root to orchestrate the rhythms...They have identified a small essential clock protein called ELF4 as the required messenger. Furthermore, through a series of ingenious experiments, the researchers discovered that the movement of this molecule is sensitive to the ambient temperature.

***

"In plants, this circadian biological clock is crucial to set up the time for germination, growth and flowering, among other processes. The circadian clock is built of a set of cellular proteins whose amount and activity oscillate daily.

***

"The researchers designed grafting experiments with the model plant Arabidopsis thaliana, connecting different shoots into several roots in which the clock was not working properly. These experiments allowed them to identify the clock protein ELF4, an acronym that accounts for "EARLY FLOWERING 4" as the messenger that moves from shoots to roots to convey circadian information.

"Anyone who has ever experienced jet lag, knows that the circadian biological clock is able to reset itself by environmental light cues, allowing the body to adapt to the new time zone within few days. In the same way that the circadian clock can synchronize to environmental light, it can also integrate information about ambient temperature.

***

"They discovered that at lower temperatures (12C), ELF4 mobility from shoots to roots was favoured, resulting in a slow-paced root clock. Instead, when the experiments were performed at higher temperatures (28C), they observed less ELF4 movement, which lead to a faster root clock. This newly described mechanism could provide an advantage for optimal root responsiveness to temperature variations."

Comment: A marvelous system that is carefully controlled for both light availability and temperature levels. I would assume, as in all biochemistry of life, there is an sideline feedback loop not yet identified. This complex system must be originally designed or from the beginning plant roots would not have responded properly.

Biological complexity: some bacteria have circadian rhythm

by David Turell @, Friday, February 12, 2021, 05:12 (1141 days ago) @ David Turell

In the gut:

https://bigthink.com/surprising-science/gut-bacteria-circadian-rhythm?rebelltitem=1#reb...

"...a new study, published in Science Advances, that found the bacterium Bacillus subtilis is run by its own circadian rhythms.

"Also known as "grass bacillus," B. subtilis thrives in the gastrointestinal tracts of humans as well as grass-feeding ruminants. You can easily and cheaply purchase bottles of this bacterium as a probiotic due to its supposed immune system-boosting properties. The strain is found in soil, though you probably want to secure it by other means, making it a favorite of supplement companies.

***

"For this study, the European research team chose B. subtilis thanks to previous observations that, like humans, it seems to follow a 24-hour circadian clock. It also responds to red and blue lights (again, like humans), causing the researchers to believe that it entrains to environmental conditions. The team discovered this by enzymatically inducing bioluminescence in order to stare into this mysterious world.

***

"'We've found for the first time that non-photosynthetic bacteria can tell the time. They adapt their molecular workings to the time of day by reading the cycles in the light or in the temperature environment."

***

"Rather than only responding to light and dark, B. subtilis takes cues from temperature drops, hinting at a circadian rhythm.

"Although bacteria comprise 15 percent of all living matter, the team notes that circadian clocks have not been identified in nonphotosynthetic bacteria—until now. They note that bacterium such as Rhodospirillum rubrum displays rhythmic processes such as enzymatic activity yet has no apparent circadian clock.

***

"'Our study opens doors to investigate circadian rhythms across bacteria. Now that we have established that bacteria can tell the time we need to find out the processes that cause these rhythms to occur and understand why having a rhythm provides bacteria with an advantage."

"Understanding the survival methods of bacterium clues us in on the long, slow process of evolution. While this new discovery does not state the purpose of the circadian clock in B. subtilis, it opens up a new line of research for one of the most perplexing components of human biology: our guts."

Comment: Hopefully we will find a purpose for this. Night and day on Earth sets up this requirement but why in the darkness of the gut?

Biological complexity: how big is the bush of life?

by David Turell @, Monday, April 13, 2020, 20:42 (1446 days ago) @ dhw

DAVID: My first bold is a notice of my surprise at their surprise. of course their is endless diversity to find in our bush of life.

dhw: Why of course? According to you, your God’s one and only purpose was to produce humans. In that case, why did he need “endless” diversity? Elementary logic suggests that if he had only wanted humans, he would only have needed to provide enough diversity to feed humans. But “of course” endless variety would be the result of his creating a mechanism which gave free rein to organisms to work out their own ways of coping with or exploiting all the different forms of environment.

Quote: "Our planet is deeply interconnected—what happens in the deep sea impacts life on land—and vice versa. This research is vital to advance our understanding of that connection—and the importance of protecting these fragile ecosystems. The Ningaloo Canyons are just one of many vast underwater wonders we are about to discover that can help us better understand our planet." (David's bold)

DAVID: The second bold is right on point: the interconnectedness is vital as I constantly point out about the balance of econiches, and the necessary supply of food for all, no matter how diverse. All of this diversity comes from evolution from bacteria. Its presence in this size advertises its importance. Let us not hear about God enjoying spectacle or whatever humanistic weirdness can be imagined. If it is God's creation, it is highly purposeful for a real reason.

dhw: You already quoted this a couple of days ago, and ignored my response:
"I would not question the article’s statement that our planet is deeply interconnected. It always has been, long before humans arrived. And when connections break, we get new connections and new econiches. That does not mean your God specially designed 3.X billion years’ worth of non-human econiches for the sake of humans who were not even there!"

Your whole series of comments about God's activities resembles a discontent spectator at a sports match. From your unhappy viewpoint, the manager and/or the team captain really have very little idea of what they are planning or how to conduct the action for the best result. You don't really know the persons involved, or how they reasonably think from their vast knowledge of the game, but in your opinion they are not doing what you think is correct. Your very weak image of your god leads you very astray from what real theists think.

God started the universe knowing that humans were His final goal. His methodology was fully thought out in advance. He had no need to experiment or create spectacles. Everything we know about are His deliberate creations. We theists don't second guess Him like you do. No wonder you are floundering around in a morass of your own human criticisms of a god which you describe, not realizing how much you are debating, from your strange viewpoint, with a humanized version. Note I do not capitalize your god versions.

QUOTE: “The discovery of the massive gelatinous string siphonophore—a floating colony of tiny individual zooids that clone themselves thousands of times into specialized bodies that string together to work as a team—was just one of the unique finds among some of the deepest fish and marine invertebrates ever recorded for Western Australia.

dhw: Now this really is worth a new comment. You could hardly have a better description of how multicellularity works. All multicellular bodies are collections of cells that clone themselves thousands of times into specialized bodies that string together to work as a team. I have called them cell communities. My pet analogy has always been ant colonies, but maybe the siphonofore is even better. Thank you for this intriguing article.

These are simply single celled organisms clumped together, which again you have again exaggerated into one of your woolly hopes about out individual cell intelligence. Stromatolite mats are exactly the same, examples of a degree of simple cell cooperation for simple tasks.

Biological complexity: how big is the bush of life?

by dhw, Tuesday, April 14, 2020, 16:01 (1445 days ago) @ David Turell

QUOTE: “The discovery of the massive gelatinous string siphonophore—a floating colony of tiny individual zooids that clone themselves thousands of times into specialized bodies that string together to work as a team—was just one of the unique finds among some of the deepest fish and marine invertebrates ever recorded for Western Australia.”

dhw: Now this really is worth a new comment. You could hardly have a better description of how multicellularity works. All multicellular bodies are collections of cells that clone themselves thousands of times into specialized bodies that string together to work as a team. I have called them cell communities. My pet analogy has always been ant colonies, but maybe the siphonofore is even better. Thank you for this intriguing article.

DAVID: These are simply single celled organisms clumped together, which again you have again exaggerated into one of your woolly hopes about out individual cell intelligence. Stromatolite mats are exactly the same, examples of a degree of simple cell cooperation for simple tasks.

Do you deny that our own body consists of single cells clumped together into specialized groups which cooperate as teams?

Biological complexity: how big is the bush of life?

by David Turell @, Tuesday, April 14, 2020, 19:18 (1445 days ago) @ dhw

QUOTE: “The discovery of the massive gelatinous string siphonophore—a floating colony of tiny individual zooids that clone themselves thousands of times into specialized bodies that string together to work as a team—was just one of the unique finds among some of the deepest fish and marine invertebrates ever recorded for Western Australia.”

dhw: Now this really is worth a new comment. You could hardly have a better description of how multicellularity works. All multicellular bodies are collections of cells that clone themselves thousands of times into specialized bodies that string together to work as a team. I have called them cell communities. My pet analogy has always been ant colonies, but maybe the siphonofore is even better. Thank you for this intriguing article.

DAVID: These are simply single celled organisms clumped together, which again you have again exaggerated into one of your woolly hopes about out individual cell intelligence. Stromatolite mats are exactly the same, examples of a degree of simple cell cooperation for simple tasks.

dhw: Do you deny that our own body consists of single cells clumped together into specialized groups which cooperate as teams?

Not your view. Our cells are highly specialized for their complex tasks. See the new entry on siphonosphores. They have some interesting specializations as individuals in contributing to the whole.

Biological complexity: more on siphonosphores

by David Turell @, Tuesday, April 14, 2020, 19:37 (1445 days ago) @ David Turell

There is more complexity in this report:

https://www.newsweek.com/otherworldly-150-foot-long-string-like-organism-deep-sea-milli...

"Resembling a long piece of string, siphonophores—a group of creatures related to jellyfish and corals—may look like one organism, but they are actually made up of many thousands of individual, specialized clones that come together to form a single entity.

"The crew is estimating it to be more than 120 meters in total length—possibly over 390 feet long," Logan Mock-Bunting, a spokesperson for the Schmidt Ocean Institute, told Newsweek. "We are in the process of outside confirmation of these measurements."

"Siphonophores like this one are deep-sea predators that lie in wait for unfortunate animals to come into contact with the stinging cells found on some of the specialized clones.

"'This animal is a kind of jelly, called a siphonophore. It's made of millions of interconnected clones, like if the Borg and the Clone Wars had a baby together. There are about a dozen different jobs a clone can do in the colony, and each clone is specialized to a particular task," Rebecca Helm, an assistant professor at the University of North Carolina Asheville who saw the SOI video, wrote in a Twitter thread.

"'I've gone on numerous expeditions and have never, EVER, seen anything like this. Let me tell you what this is and why it is blowing my mind," she said. "Most of the siphonophore colonies I've seen are maybe 20 centimeters long, maybe a meter. But THIS animal is massive. AND not just massive, the colony is exhibiting a stunning behavior: it's hunting."

"According to Helm, some of the clones that make up the siphonophore specialize in catching prey with the help of the aforementioned stinging cells.

"'Their slender bodies hang with a single long tentacle dangling like a hook-studded fishing line," Helm said. "A siphonophore colony in a line creates a curtain of deadly tentacles in the open ocean, but in THIS case, the animal is hunting in a galaxy-like spiral, the long wisp-like tentacles draped below. And the colony does not need to move to feed."

"'Once a clone captures its prey—a fish or crustacean—it will reel it to the colony & other clones that work as mouths will surround it. Often many swallowing it at once. Once they prey is digested, they'll send the nutrients through a long digestive tract that travels down the whole colony, so that every other clone can use the nutrients. In this way, this siphonophore may remain still and feed for a long time, and I mean LONG," she said.

"While it is difficult to determine how old a siphonophore colony is, Helm suggests that the animal in the video could be tens or possibly hundreds of years old.

"'Everything in the deep sea grows incredibly slowly. It's only a few degrees above freezing, life takes time to grow," she said.

"'This is one of the largest and most stunning and pristine siphonophores that I've ever seen. And to think, there are millions, probably billions of underwater siphonophore galaxies out there just like this one. Siphonophores are not rare, just fragile and remote. As we explore the ocean's more, who knows what other creatures we will see.'"

Comment: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

Biological complexity: more on siphonosphores

by dhw, Wednesday, April 15, 2020, 13:39 (1444 days ago) @ David Turell

dhw: You could hardly have a better description of how multicellularity works. All multicellular bodies are collections of cells that clone themselves thousands of times into specialized bodies that string together to work as a team. I have called them cell communities. My pet analogy has always been ant colonies, but maybe the siphonofore is even better. Thank you for this intriguing article.

DAVID: These are simply single celled organisms clumped together, which again you have again exaggerated into one of your woolly hopes about out individual cell intelligence. Stromatolite mats are exactly the same, examples of a degree of simple cell cooperation for simple tasks.

dhw: Do you deny that our own body consists of single cells clumped together into specialized groups which cooperate as teams?

DAVID: Not your view. Our cells are highly specialized for their complex tasks. See the new entry on siphonosphores. They have some interesting specializations as individuals in contributing to the whole.

What is not my view? The new entry confirms what I wrote above:

QUOTE: "Resembling a long piece of string, siphonophores—a group of creatures related to jellyfish and corals—may look like one organism, but they are actually made up of many thousands of individual, specialized clones that come together to form a single entity. […]There are about a dozen different jobs a clone can do in the colony, and each clone is specialized to a particular task…"

DAVID: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

So do you or do you not agree that this guy’s body works in the same way as our own bodies: communities of cells with different functions working as a team?

Biological complexity: more on siphonosphores

by David Turell @, Wednesday, April 15, 2020, 19:41 (1444 days ago) @ dhw

dhw: You could hardly have a better description of how multicellularity works. All multicellular bodies are collections of cells that clone themselves thousands of times into specialized bodies that string together to work as a team. I have called them cell communities. My pet analogy has always been ant colonies, but maybe the siphonofore is even better. Thank you for this intriguing article.

DAVID: These are simply single celled organisms clumped together, which again you have again exaggerated into one of your woolly hopes about out individual cell intelligence. Stromatolite mats are exactly the same, examples of a degree of simple cell cooperation for simple tasks.

dhw: Do you deny that our own body consists of single cells clumped together into specialized groups which cooperate as teams?

DAVID: Not your view. Our cells are highly specialized for their complex tasks. See the new entry on siphonosphores. They have some interesting specializations as individuals in contributing to the whole.

What is not my view? The new entry confirms what I wrote above:

QUOTE: "Resembling a long piece of string, siphonophores—a group of creatures related to jellyfish and corals—may look like one organism, but they are actually made up of many thousands of individual, specialized clones that come together to form a single entity. […]There are about a dozen different jobs a clone can do in the colony, and each clone is specialized to a particular task…"

DAVID: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

dhw: So do you or do you not agree that this guy’s body works in the same way as our own bodies: communities of cells with different functions working as a team?

It seems to be an early experimentation in simple multicellularity, by having different organisms work cooperatively. Each individual must reproduce itself slowly over time to continue its contribution.

Biological complexity: more on siphonosphores

by dhw, Thursday, April 16, 2020, 11:35 (1443 days ago) @ David Turell

dhw: The new entry confirms what I wrote above:

QUOTE: "Resembling a long piece of string, siphonophores—a group of creatures related to jellyfish and corals—may look like one organism, but they are actually made up of many thousands of individual, specialized clones that come together to form a single entity. […]There are about a dozen different jobs a clone can do in the colony, and each clone is specialized to a particular task…"

DAVID: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

dhw: So do you or do you not agree that this guy’s body works in the same way as our own bodies: communities of cells with different functions working as a team?

DAVID: It seems to be an early experimentation in simple multicellularity, by having different organisms work cooperatively. Each individual must reproduce itself slowly over time to continue its contribution.

I will take that as an agreement that this guy’s body works in the same way as ours, but you can’t bring yourself to say so.

Under “Immunity system complexity”:
DAVID: A fantastic system, designed for great protection. Yes, designed, not by chance. The author is wrong about how IGG was used. I was one of several senior medical students in the summer before school started up again, who worked for the N.Y. State Health Department and gave hundreds of well kids the IGG by injections in the butt. Hard to do. My hand was sore each day from pushing ice cold thick liquid into the kids. They did n't enjoy it either, but it broke the epidemic in the areas we visited over weekends, being bused from our regular jobs in Syracuse, N.Y.

The system, really is fantastic, and brings to mind my own pet analogy of the ant colony, though this is vastly more complex. It’s always the same story: individuals working together in a team, and the team working together with other teams. The mind boggles, and once again you present the strongest possible case for design. I love the autobiographical piece as well! Thank you.

Biological complexity: more on siphonosphores

by David Turell @, Thursday, April 16, 2020, 20:04 (1443 days ago) @ dhw

DAVID: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

dhw: So do you or do you not agree that this guy’s body works in the same way as our own bodies: communities of cells with different functions working as a team?

DAVID: It seems to be an early experimentation in simple multicellularity, by having different organisms work cooperatively. Each individual must reproduce itself slowly over time to continue its contribution.

dhw: I will take that as an agreement that this guy’s body works in the same way as ours, but you can’t bring yourself to say so.

I stand by what I said. In a tiny way like us. What is your point?


Under “Immunity system complexity”:

DAVID: A fantastic system, designed for great protection. Yes, designed, not by chance. The author is wrong about how IGG was used. I was one of several senior medical students in the summer before school started up again, who worked for the N.Y. State Health Department and gave hundreds of well kids the IGG by injections in the butt. Hard to do. My hand was sore each day from pushing ice cold thick liquid into the kids. They didn't enjoy it either, but it broke the epidemic in the areas we visited over weekends, being bused from our regular jobs in Syracuse, N.Y.

dhw: The system, really is fantastic, and brings to mind my own pet analogy of the ant colony, though this is vastly more complex. It’s always the same story: individuals working together in a team, and the team working together with other teams. The mind boggles, and once again you present the strongest possible case for design. I love the autobiographical piece as well! Thank you.

Thank you. The author's mistake pushed me to reveal it.

Biological complexity: more on siphonosphores

by dhw, Friday, April 17, 2020, 10:50 (1442 days ago) @ David Turell

DAVID: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

dhw: So do you or do you not agree that this guy’s body works in the same way as our own bodies: communities of cells with different functions working as a team?

DAVID: It seems to be an early experimentation in simple multicellularity, by having different organisms work cooperatively. Each individual must reproduce itself slowly over time to continue its contribution.

dhw: I will take that as an agreement that this guy’s body works in the same way as ours, but you can’t bring yourself to say so.

DAVID: I stand by what I said. In a tiny way like us. What is your point?

The discussion started when I pointed out that my new friend the siphonosphore provided a wonderful illustration of how all multicellular bodies function – including ours: through the cooperation of cellular communities. Instead of accepting the analogy, you proceeded to challenge it. I really don’t know why, since you keep confirming everything I said. Perhaps just arguing for the sake of arguing?

Biological complexity: more on siphonosphores

by David Turell @, Friday, April 17, 2020, 18:44 (1442 days ago) @ dhw

DAVID: I've changed my view. More research and this guy is much more of a multicellular organism than bacterial mats, as I first suggested. Another example of an econiche system with strange participants. I accept it as another God-design example.

dhw: So do you or do you not agree that this guy’s body works in the same way as our own bodies: communities of cells with different functions working as a team?

DAVID: It seems to be an early experimentation in simple multicellularity, by having different organisms work cooperatively. Each individual must reproduce itself slowly over time to continue its contribution.

dhw: I will take that as an agreement that this guy’s body works in the same way as ours, but you can’t bring yourself to say so.

DAVID: I stand by what I said. In a tiny way like us. What is your point?

dhw: The discussion started when I pointed out that my new friend the siphonosphore provided a wonderful illustration of how all multicellular bodies function – including ours: through the cooperation of cellular communities. Instead of accepting the analogy, you proceeded to challenge it. I really don’t know why, since you keep confirming everything I said. Perhaps just arguing for the sake of arguing?

This is not really multicellularity. Your complaint is reminiscent of your cell committees brilliance theorizing. Frankly I don't dare give you an inch. You always want to take a yard about real intelligence popping up everywhere.

Biological complexity: more on siphonosphores

by dhw, Saturday, April 18, 2020, 13:08 (1441 days ago) @ David Turell

dhw: The discussion started when I pointed out that my new friend the siphonosphore provided a wonderful illustration of how all multicellular bodies function – including ours: through the cooperation of cellular communities. Instead of accepting the analogy, you proceeded to challenge it. I really don’t know why, since you keep confirming everything I said. Perhaps just arguing for the sake of arguing?

DAVID: This is not really multicellularity.

DAVID (14th April): this guy is much more of a multicellular organism than bacterial mats, as I first suggested.

DAVID: Your complaint is reminiscent of your cell committees brilliance theorizing. Frankly I don't dare give you an inch. You always want to take a yard about real intelligence popping up everywhere.

I’m only complaining about your pointless rejection of the analogy. Do you or do you not agree that “this guy” illustrates the way in which all multicellular bodies function – through cooperation between cellular communities?

Biological complexity: more on siphonosphores

by David Turell @, Saturday, April 18, 2020, 20:33 (1441 days ago) @ dhw

dhw: The discussion started when I pointed out that my new friend the siphonosphore provided a wonderful illustration of how all multicellular bodies function – including ours: through the cooperation of cellular communities. Instead of accepting the analogy, you proceeded to challenge it. I really don’t know why, since you keep confirming everything I said. Perhaps just arguing for the sake of arguing?

DAVID: This is not really multicellularity.

DAVID (14th April): this guy is much more of a multicellular organism than bacterial mats, as I first suggested.

DAVID: Your complaint is reminiscent of your cell committees brilliance theorizing. Frankly I don't dare give you an inch. You always want to take a yard about real intelligence popping up everywhere.

dhw: I’m only complaining about your pointless rejection of the analogy. Do you or do you not agree that “this guy” illustrates the way in which all multicellular bodies function – through cooperation between cellular communities?

I'll give you it is a slim imitation. All it is is individuals who cooperate.

Biological complexity: bacterial controlled clumps

by David Turell @, Thursday, August 13, 2020, 01:14 (1324 days ago) @ David Turell

A very strange bacterial multicellular activity:

https://www.sciencedaily.com/releases/2020/08/200812094849.htm

"Research has revealed that multicellular physiology in the social bacterium Myxococcus xanthus--a bacterium that can actively reorganize its community according to the environment in which it is found -- is modulated by the secretion of two natural sugar polymers in separate zones of a swarm.

***

"Professor Salim Timo Islam has been carrying out research in bacterial physiology for four years, focusing on the interactions of bacterial cells with each other, as well as with underlying surfaces. Along with his PhD student Fares Saïdi, they are investigating the origins of multicellularity. More precisely, their work revolves around the factors that allow cells to multiply, specialize, communicate, interact, and move. These behaviours are all associated with multicellularity as they promote the expansion of a community of cells and the formation of complex structures.

"Their research has characterized two compounds contributing to multicellularity and the distinct areas of production, for each, within a community. Exopolysaccharide (EPS) is produced more by cells at the periphery of the swarm. Production of the second sugar polymer, a novel biosurfactant (BPS), is enriched toward the centre of the swarm. "Since the factors contributing to the development of bacterial communities remain poorly understood, it is very exciting to have identified another," mentions Professor Islam, a specialist in microbial biochemistry and co-first author of the study along with his PhD student Fares Saïdi.

"Multicellularity is typically associated with organisms such as fungi, plants, and animals. As part of this study, the researchers studied the basis for this evolutionary transition on a smaller scale: the bacterium Myxococcus xanthus. This organism has the distinction of being able to reorganize the structure of its population, allowing it to react to different environmental signals and even eat other bacteria.

"In response to a hostile environment, such as in instances of nutrient deficiency, this bacterium directs its homogenous population to specialize into three subtypes of cells. These communities thus form 3-dimensional structures, visible to the naked eye. It is thanks to this multicellular lifestyle that they ensure the survival of their community."

Comment: multicellularity had to start somehow. This is group action. Amoeba also have similar activities. Designed by God?

Biological complexity: digestive complexity

by David Turell @, Friday, August 14, 2020, 19:16 (1323 days ago) @ David Turell

How small intestine villi handle fats:

https://medicalxpress.com/news/2020-08-newly-gut-cells-nurture-lymph.html

"After approximately eight hours [ from eating], food molecules reach your small intestine, where specialized lymph capillaries, called lacteals, absorb fat nutrients. Lacteals are different from other lymphatics, as they continue to regenerate during adulthood, with a slow, but steady pace. Their unique renewal capacity is still poorly understood.

"A team of scientists led by Koh Gou Young at the Center for Vascular Research, within the Institute for Basic Science (IBS, South Korea) have identified new subsets of gut connective cells, which are crucial for lymphatic growth.

***

"The walls of the small intestine are covered with fingerlike projections, called villi. Lining these villi, heterogeneous populations of epithelial, immune, vascular, connective and even neural cells co-exist and help the digestive process. Lacteals and blood capillaries run inside the villi and take in different food molecules. The gut environment needs to cope with water secretion and reabsorption (osmotic stress), as well as the repetitive muscular activity that moves food through the intestine. How all these complex mechanisms are harmonized is still a mystery.

"The research team was able to place a new piece towards completing this mysterious puzzle. The researchers found that the regulatory proteins YAP/TAZ in villi's connective cells, the intestinal stromal cells, play a role in the growth of nearby lacteals. In mice with an abnormal hyperactivation of YAP/TAZ, the team observed atypical sprouting of lacteals and impaired dietary fat uptake.

***

"The researchers took a step further and discovered that intestinal stromal cells belong to several subtypes, with distinct gene expression and localizations within the villi. Among these subsets, three newly identified populations secrete VEGF-C—an essential molecule for lymphatic growth—upon YAP/TAZ activation. Yang Myung Jin, first co-author of this study, explains, "We were very surprised to see such heterogeneity in a cell population that was considered homogeneous."

"Lastly, researchers showed that mechanical force and osmotic stress regulate YAP/TAZ activity in stromal cells. In summary, mechanical stimulation activates YAP/TAZ in the intestinal stromal cells, which in turn release VEGF-C and can account for lacteal growth. Cho Hyunsoo, first co-author of this study notes, "This result implies a crucial link between the physiology of intestinal environment and biological interactions between cell types.'"

Comment: Real GI tracts appeared in the Cambrian animals. We can assume the beginnings of this ability to digest various food forms stated then. Since animals need constant intake of food energy, it is apparent, this had to be designed in place as the animals appeared.

Biological complexity: more bacterial mat complexity

by David Turell @, Thursday, January 06, 2022, 18:03 (813 days ago) @ David Turell

New layers defined:

https://www.newscientist.com/article/2303605-bacteria-form-complex-structures-like-thos...

"Biofilms, slimy clumps of microorganisms like bacteria and fungi, were long thought to be biologically simple, with no more than a primitive level of structural organisation. This contrasts with many multicellular organisms, including animals, in which cells can grow into different forms at different times and places during the body’s development to produce complex and varied biological structures.

"Now, Gürol Süel at the University of California, San Diego, and his colleagues have discovered that bacterial biofilms are less simple than we had thought. The researchers found that the biofilms form ring-like structures as they grow and consume the nutrients in their environment. As the nutrient supply diminishes, certain cells essentially become frozen in time in terms of the way they function, as a wave of nutrient depletion washes over them. This is known as a “clock and wavefront”, and has previously been seen only in animals and plants.

“'If we just think of [biofilms] as globs of bacterial cells, even if they’re from one species, we’re mistaken,” says Süel. “They’re highly organised, and they’re organised in a very non-trivial way. This organisation seems to be reminiscent of what vertebrates and plants did during development, so there must be a connection there.”

"Though the research was focused only on observing the patterns, Süel proposes that the patterning could be the biofilm diversifying its resilient cells to try to increase its chances of survival.

"While biofilms have been shown to be more complicated in recent years, being capable of forms of memory and long-distance communication, the discovery of complex structures could challenge the assumed divide between simple, unicellular organisms and complex, multicellular ones.

“'That debate will be rekindled by this study,” says Tanmay Bharat at the University of Oxford. “From an evolutionary cell biology perspective, it would be interesting to study where the differences lie. What defines a true multicellular organism?'”

Comment: As usual I have to reinterpret this in ID terms. The designer preplans for the next stage in complexity and a giant step was multicellularity with sexual reproduction.

Biological complexity: more bacterial mat complexity

by David Turell @, Friday, March 24, 2023, 23:33 (370 days ago) @ David Turell

A careful complete description:

https://www.scientificamerican.com/article/bacteria-gang-together-in-killer-biofilms-bu...

"Although individual bacteria are not visible to the naked eye, in this slime they form easily seen communities referred to as microbial mats, or “biofilms.” Through a microscope these films show remarkable three-dimensional structure, with microbes glued onto one another to form many levels of filaments, winding pathways and features resembling tiny towers. To me, they look like cities of slime, a pulsing metropolis with blocks and skyscrapers and streets that are busier than major avenues in Tokyo or New York.

***

"There were early clues that bacteria within biofilms become fundamentally different from single cells. In 1998 researchers George A. O’Toole and Roberto Kolter demonstrated that biofilm formation by the soil bacterium Pseudomonas fluorescens required the synthesis of new proteins as well as the presence of 24 genes. Most of the genes were of unknown function, although some encoded proteins used for surface attachment, such as adhesins. The mystery genes suggested that becoming an attached cell meant taking on a novel bacterial physiology. Then, in 2002, my colleagues and I demonstrated that bacteria not only change on surface contact but keep transforming and adapting as the biofilm develops from just a few attached cells into a 3-D community, producing different sets of proteins at each stage. Further work showed that the proteins enable the transition from one biofilm stage to the next in a set sequence.

"These findings suggested that biofilms, like cities, are built brick by brick, with their construction following a master plan, one building phase and one city block at a time. Knowing how biofilms are built means that we have started to understand how to interfere with the master plan. In the laboratory, by adding chemicals that inhibit or enhance some of these proteins, we can stop biofilms at a particular developmental stage or even remodel them, making them revert to earlier stages. And some strategies are making their way to the clinic."

Comment: the article goes on to describe how to medical treat biofilm problems. My point is to show another example of bacterial actions. In this case banding together and supporting each other with new proteins helps them survive. Only bacteria have this capacity with the distinct ability to edit DNA as necessary. Living alone one-celled organisms must be ready and able to help themselves. Shapiro has shown this.

Biological complexity: metabolons in cells

by David Turell @, Friday, April 17, 2020, 22:11 (1442 days ago) @ dhw

Enzyme groups long hypothesized as active in cells:

https://www.sciencedaily.com/releases/2020/04/200416151734.htm

"For more than 40 years, scientists have hypothesized the existence of enzyme clusters, or "metabolons," in facilitating various processes within cells. Using a novel imaging technology combined with mass spectrometry, researchers at Penn State, for the first time, have directly observed functional metabolons involved in generating purines, the most abundant cellular metabolites.

***

"'Our study suggests that enzymes are not haphazardly located throughout cells, but instead occur in discrete clusters, or metabolons, that carry out specific metabolic pathways," said Stephen Benkovic, Evan Pugh University Professor and Eberly Chair in Chemistry. "Not only did we find proof that metabolons exist, but we also found that this metabolon occurs near mitochondria in cancer cells."

***

"In the study, the team searched for a specific kind of metabolon, called a "purinosome," that was thought to carry out "de novo purine biosynthesis," the process by which new purines -- building blocks of DNA and RNA -- are synthesized. The researchers investigated these purinosomes within HeLa cells, a cervical cancer cell line commonly used in scientific research.

"'We have shown that the de novo purine biosynthetic [DNPB] pathway is carried out by purinosomes consisting of at least nine enzymes acting together synergistically to increase their overall activity by at least by seven-fold," said Vidhi Pareek, assistant research professor, Department of Chemistry and the Huck Institutes of Life Sciences.

***

"Importantly, the team found that the DNPB pathway occurs in a channeled manner and the juxtaposition of purinosomes to the mitochondria facilitates uptake of substrates generated by the mitochondria for utilization in the pathway. Channeling occurs when enzymes are located close together so that the molecules produced are quickly transferred and processed along the enzymatic pathway, restricting equilibration with the bulk cytosol.

"'Our experiment allowed us to show that the efficiency of the de novo purine biosynthetic pathway is increased by channeling and that the proximity of purinosomes near mitochondria is consequential for the pathway," said Benkovic.'"

Comment: this is an irreducibly complex designed system that God has provided to improve cellular productive efficiency, since the processes work at such high speed.

Biological complexity: more mitochondrial controls found

by David Turell @, Friday, April 17, 2020, 22:21 (1442 days ago) @ David Turell

"16 'short open reading frame-encoded peptides' (SEPs) whose genetic code is translated in the nucleus, but which are then imported into mitochondria, the power-generating structures of cells":

https://www.sciencedaily.com/releases/2020/04/200416135841.htm

"SEPs have been fascinating the scientific community for several years now, as they represent a mini-proteome that has never been explored; a repository of new gene functions," said Dr Ho. "But there haven't been systematic studies to validate their functions and biological relevance. We found that the mitochondria are a hotspot for their functions, for reasons we don't completely yet understand."

The scientists singled out one of the 16 mitochondrial SEPs they discovered for further analysis. Knocking out the gene that codes for the SEP, which they named BRAWNIN, in zebrafish led to extreme growth retardation and lactic acid accumulation in cells. Further tests revealed that BRAWNIN was essential for the assembly of a group of molecules in the mitochondria called respiratory chain complex III. This molecular complex is essential for all life forms that use oxygen for energy generation, according to Dr Ho.

***

Dr Ho also noted there are 15 more mitochondrial SEPs to investigate. "We are actively looking for collaborators who are interested in studying them," she added.

Comment: the fact that these are integrated with the cell nucleus indicates the degree of complex design that has cells doing their jobs. Designer required.

Biological complexity: what capsases do

by David Turell @, Thursday, April 16, 2020, 05:45 (1443 days ago) @ dhw

Poorly understood enzyme now gives up it secrets:

https://medicalxpress.com/news/2020-04-secrets-enigmatic-caspase-.html

"The findings show that caspase-6 is a key regulator of innate immunity, inflammasome activation and host defense. Modulation of caspase-6 could be beneficial for treating viral diseases like influenza and other inflammatory diseases including cancer.

***

"Caspases are a family of enzymes that regulate programmed cell death (how a cell self-destructs), inflammation and other biological functions. Caspase-6 has previously been characterized as an executioner caspase in a non-inflammatory form of cell death called apoptosis. Caspase-6 has also been linked to neurological disorders like Alzheimer's disease and Huntington disease. However, the full range of the enzyme's function was not well understood. Now, researchers have discovered for the first time how caspase-6 regulates the ZBP1-NLRP3 inflammasome.

***

"'Caspase-6 has essential functions in innate immunity, inflammation and in driving PANoptosis."

"The Kanneganti laboratory previously was first to identify ZNA-binding protein 1 (ZBP1) as an innate immune sensor of influenza, an RNA virus. Their work also revealed that ZBP1 triggers inflammatory cell death in the form of pyroptosis, apoptosis and necroptosis, which together are known as PANoptosis.

"PANoptosis is an inflammatory death pathway regulated by components of a structure termed the PANoptosome, which mediates cell death that cannot be assigned to any of the single cell death pathways described previously. In this study, the scientists found that caspase-6 played a critical role in this process.

"The researchers found that caspase-6 interacts with RIPK3 to facilitate the recruitment of RIPK3 to the ZBP1-PANoptosome. This makes caspase-6 crucial for assembly of this ZBP1-mediated inflammatory cell death-inducing complex. In line with these findings, the researchers demonstrated that caspase-6 is required for ZBP1-mediated PANoptosis during viral infection.

"'Caspase-6 deficiency in mice leads to increased susceptibility to influenza virus infection and higher levels of viral replication in the lungs," said first author Min Zheng, Ph.D., of the St. Jude Department of Immunology. "It is likely that the caspase-6-mediated inflammatory cell death pathway is essential to fighting other viruses that activate similar innate immunepathways, potentially including other respiratory viruses.'"

Comment: Another very complex set of actions by a giant enzyme molecule that helps kill cells that need to be removed, an also fights virus infections. A strange mix of activities. An oher example of a system that is so complex, it must be designed.

Biological complexity: cell sugar, fat traffic control

by David Turell @, Friday, April 24, 2020, 22:37 (1435 days ago) @ David Turell

Controls what happens with too much or too little to eat:

https://medicalxpress.com/news/2020-04-traffic-officer-protein-sugarfat-conversion.html

"Scientists in Texas and Pennsylvania have identified a protein sensor that restricts how much sugar and fat our cells convert into energy during periods of starvation.

***

"'We want to offer, in the future, a solution to the metabolic crisis faced by millions of people across the world," Dr. Muniswamy said. "Millions of people consume too much food, while millions of others are in poverty and subsist on too little food. We are studying what happens at the molecular level in both situations with a goal of developing a drug to intervene."

"Our bodies continuously move things from cell to cell with what are sort of like roadways and cars. The vehicle required for fat and sugar conversion is called the mitochondrial calcium uniporter, or MCU. Like traffic moving people to destinations, the speed at which the MCU moves the energy is essential. If it is too slow, conditions such as obesity appear. If it is too fast, malnourishment results.

***

"In the Science Signaling article, Dr. Muniswamy and colleagues describe another key component that, like a traffic police officer, regulates this roadway activity.

"'We identified a mitochondrial protein called MICU1 that functions as a gatekeeper of this roadway," Dr. Muniswamy said.

"When nutrient levels are low, MICU1 clamps down on the channel activity to prevent excess energy transaction. "When you're starving, you want to live longer, you don't want to burn all the sugar and the fat you have, so MICU1 slows down the activity," Dr. Muniswamy said.
The opposite is also true—if the roadway traffic is driving too slowly, MICU1 can rev it up."

Comment: In the distant past, we suffered from feast and famine. Obviously there had to be mechanisms to mitigate the extremes. Medical education tells us there is an average 300 calorie switch in metabolism in either direction. This complexity requires design, as chance cannot develop a back and forth system like this one.

Biological complexity: how eyes get cleaned

by David Turell @, Monday, April 27, 2020, 23:12 (1432 days ago) @ David Turell

Turns out same way as the brain with a very specialized system:

https://medicalxpress.com/news/2020-04-discovery-scientists-eyes-cellular-debris.html

"Like the brain, the eyes lack the classic lymphatic vessels responsible for the circulation of fluids and removal of waste products, as is common in peripheral organs. In recent years, it was discovered that the brain possesses a unique "glymphatic" system, a privileged brain-only method of draining and disposing of molecular wastes. This transport system, when healthy, involves shuttling neurotoxic proteins such as amyloid-β out of the brain.

***

"The new findings explain how a glymphatic system maintains eye health and underscores that impairment—clogging—of this vital waste pathway can lead to glaucoma, a major worldwide cause of blindness. Nedergaard has defined "glymphatic" as an amalgam of the words glial and lymphatic. Glial cells are the primary cellular components that support neurons—nerve cells. The glymphatic pathway substitutes for a lymphatic system, which exists in neither the brain nor the eye.

***

"Intriguingly, the team found the lymphatic vessels are connected to the same pathways that dispose wastes from the brain. The discovery is a scientific first and opens a new window into understanding how the eyes clear metabolic and cellular debris. The findings also shed new light on how the eyes and brain share critical pathways.

"Even though the finding is new, the waste clearance system in the brain was first defined by Nedergaard in 2012. The pathway involves a labyrinth of intricate perivascular tunnels that are formed by glial cells, which underlie the efficient elimination of soluble metabolites from the central nervous system. In addition to waste disposal, Nedergaard and colleagues also have found that the pathways support the distribution of critical nutrients and compounds throughout the brain, substances that include glucose, amino acids, growth factors and lipids."

Comment: Another highly complex system that has to be designed.

Biological complexity: bacterial memory

by David Turell @, Tuesday, April 28, 2020, 01:21 (1431 days ago) @ David Turell

Using light the membrane potential is changed in bacteria and they remember the stimulation some hours later:

https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30116-2

Summary:

"Cellular membrane potential plays a key role in the formation and retrieval of memories in the metazoan brain, but it remains unclear whether such memory can also be encoded in simpler organisms like bacteria. Here, we show that single-cell-level memory patterns can be imprinted in bacterial biofilms by light-induced changes in the membrane potential. We demonstrate that transient optical perturbations generate a persistent and robust potassium-channel-mediated change in the membrane potential of bacteria within the biofilm. The light-exposed cells respond in an anti-phase manner, relative to unexposed cells, to both natural and induced oscillations in extracellular ion concentrations. This anti-phase response, which persists for hours following the transient optical stimulus, enables a direct single-cell resolution visualization of spatial memory patterns within the biofilm. The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria. "

A science report about this finding:

https://cosmosmagazine.com/biology/bacteria-with-robust-memories?utm_source=Cosmos+-+Ma...

"Previous research by Süel and others has shown that bacteria use ion channels to communicate and suggested they might also have the ability to store information about their past states.

"In the new study, the researchers were able to encode complex memory patterns in bacterial biofilms with light-induced changes in the cell membrane potential of Bacillus subtilis bacteria.

"The optical imprints, they found, lasted for hours after the initial stimulus, leading to a direct, controllable single-cell resolution depiction of memory.

"'When we perturbed these bacteria with light they remembered and responded differently from that point on," says Süel. "So for the first time we can directly visualise which cells have the memory. That's something we can't visualise in the human brain.'"

Comment: What is shown is ion channel perturbations which last for some period of time. It is not magical bacterial mentation, but a demonstration of how light affects bacterial membranes.

Biological complexity: bacterial memory

by dhw, Tuesday, April 28, 2020, 10:53 (1431 days ago) @ David Turell

QUOTES: “The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria."

"Previous research by Süel and others has shown that bacteria use ion channels to communicate and suggested they might also have the ability to store information about their past states.

"'When we perturbed these bacteria with light they remembered and responded differently from that point on.'"

DAVID: What is shown is ion channel perturbations which last for some period of time. It is not magical bacterial mentation, but a demonstration of how light affects bacterial membranes.

What is shown is that bacteria have memory, store information, communicate, and change their behaviour according to the conditions. All of these are attributes we would normally associate with intelligence.

Biological complexity: bacterial memory

by David Turell @, Tuesday, April 28, 2020, 20:23 (1431 days ago) @ dhw

QUOTES: “The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria."

"Previous research by Süel and others has shown that bacteria use ion channels to communicate and suggested they might also have the ability to store information about their past states.

"'When we perturbed these bacteria with light they remembered and responded differently from that point on.'"

DAVID: What is shown is ion channel perturbations which last for some period of time. It is not magical bacterial mentation, but a demonstration of how light affects bacterial membranes.

dhw: What is shown is that bacteria have memory, store information, communicate, and change their behaviour according to the conditions. All of these are attributes we would normally associate with intelligence.

Usual twist. The article shows exactly what happens physically in the ant membranes, a form of
chemical memory, nothing more.

Biological complexity: bacterial memory

by dhw, Wednesday, April 29, 2020, 15:53 (1430 days ago) @ David Turell

QUOTES: “The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria."

"Previous research by Süel and others has shown that bacteria use ion channels to communicate and suggested they might also have the ability to store information about their past states.

"'When we perturbed these bacteria with light they remembered and responded differently from that point on.'"

DAVID: What is shown is ion channel perturbations which last for some period of time. It is not magical bacterial mentation, but a demonstration of how light affects bacterial membranes

dhw: What is shown is that bacteria have memory, store information, communicate, and change their behaviour according to the conditions. All of these are attributes we would normally associate with intelligence.

DAVID: Usual twist. The article shows exactly what happens physically in the ant membranes, a form of chemical memory, nothing more.

There are only two ways you can study any living being: 1) the material workings, and 2) the behavioural. How do you know that human memory, storage of information, communication, ability to change behaviour are not “nothing more” than chemical?

Biological complexity: bacterial memory

by David Turell @, Wednesday, April 29, 2020, 20:54 (1430 days ago) @ dhw

QUOTES: “The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria."

"Previous research by Süel and others has shown that bacteria use ion channels to communicate and suggested they might also have the ability to store information about their past states.

"'When we perturbed these bacteria with light they remembered and responded differently from that point on.'"

DAVID: What is shown is ion channel perturbations which last for some period of time. It is not magical bacterial mentation, but a demonstration of how light affects bacterial membranes

dhw: What is shown is that bacteria have memory, store information, communicate, and change their behaviour according to the conditions. All of these are attributes we would normally associate with intelligence.

DAVID: Usual twist. The article shows exactly what happens physically in the ant membranes, a form of chemical memory, nothing more.

dhw: There are only two ways you can study any living being: 1) the material workings, and 2) the behavioural. How do you know that human memory, storage of information, communication, ability to change behaviour are not “nothing more” than chemical?

At the basis they are chemical also, but the use of charged ions is directed into complex networks of axons and changeable dendrites to create human n=mental capacities. The bacterial memory is extremely simple arrangement of ions.

Biological complexity: how gecko toes cling

by David Turell @, Saturday, May 09, 2020, 05:01 (1420 days ago) @ David Turell

Clinging to vertical surfaces it takes soft hairy toes:

https://phys.org/news/2020-05-robot-heed-adjustable-hairy-toes.html

"As his previous research showed, geckos' toes can stick to the smoothest surfaces through the use of intermolecular forces, and uncurl and peel in milliseconds. Their toes have up to 15,000 hairs per foot, and each hair has "an awful case of split ends, with as many as a thousand nano-sized tips that allow close surface contact," he said.

***

"One puzzle, he said, is that gecko toes only stick in one direction. They grab when pulled in one direction, but release when peeled in the opposite direction. Yet, geckos move agilely in any orientation.

***

"To the researcher's surprise, geckos ran sideways just as fast as they climbed upward, easily and quickly realigning their toes against gravity. The toes of the front and hind top feet during sideways wall-running shifted upward and acted just like toes of the front feet during climbing.

***

"'Toes allowed agile locomotion by distributing control among multiple, compliant, redundant structures that mitigate the risks of moving on challenging terrain," Full said. "Distributed control shows how biological adhesion can be deployed more effectively and offers design ideas for new robot feet, novel grippers and unique manipulators.'"

Comment: How did this develop by trial and error? constant climbing and falling is not the answer. Only design fits.

Biological complexity: glycan layers add to c ell complex it

by David Turell @, Sunday, May 10, 2020, 20:30 (1419 days ago) @ David Turell

Glycans, sugar complexes attached to proteins on cell membranes add defenses as well as control of protein traffic in and out:

https://www.quantamagazine.org/sugars-on-coronavirus-spike-protein-offer-vaccine-clues-...

"the surface of a cell is adorned with a forest canopy of sugars, intricate and diverse clusters of carbohydrates that extend like branches and leaves from protein tree trunks. And because that canopy is the face that a cell shows to the world, these complex carbohydrates, or glycans, play a critical role in its encounters and interactions with other cells or molecules.

***

"The sheer complexity of sugars makes them more difficult to study. DNA, RNA and proteins are linear molecules built according to defined sets of rules, and scientists have the tools to sequence, analyze and manipulate them. But glycans are branching structures that assemble without a known template. The same site on two identical proteins might be occupied by very different glycans, for instance. Glycans also have exponentially more potential configurations than DNA or proteins: Three different nucleotides can make six distinct DNA sequences; three amino acids can make six unique peptides; three glycan building blocks can form more than a thousand structures. Glycans are flexible, wobbly and variable; intricate, dynamic and somewhat unpredictable.

***

“'The sugars aren’t just Christmas lights there to make things happy,” said Victor Nizet, a researcher in pediatric medicine at the University of California, San Diego who specializes in host-microbe interactions and infectious disease. “They’re a critical element of the structure of the house.”

"Glycans help to stabilize proteins and to ensure that they get folded properly. As receptors on the surfaces of cells, they regulate cell function and movement. They’re involved in processes ranging from growth factor signaling to the binding of sperm and egg. They determine a person’s blood type.

***

“'They really play an enormous diversity of roles in the body, and we’re kind of just starting to understand the composition of these glycans and where they reside,” said Andrew Ward, a computational biologist at the Scripps Research Institute in California.

"Without taking sugars into account, we can’t fully understand how proteins and cells interact and function. “Imagine a world in which each of us knew only a fraction of the alphabet,” wrote Jamey Marth,"

Comment: The remainder of the article describes how viruses and bacteria use glycans to fool cell defenses. Another intensely complex set of molecules that demand the recognition of the need for design and a designer.

Biological complexity: diurnal rhythms

by David Turell @, Tuesday, February 02, 2021, 20:43 (1151 days ago) @ David Turell

Single celled ocean organisms have it:

https://www.sciencedaily.com/releases/2021/02/210201200019.htm

"Single-celled organisms in the open ocean use a diverse array of genetic tools to detect light, even in tiny amounts, and respond, according to a study published Feb. 1 in the Proceedings of the National Academy of Sciences.

***

"Though invisible to the human eye, ocean microbes support all marine life, from sardines to whales. Knowing these communities' inner workings could reveal how they will fare under changing ocean conditions.

"'Just like rainforests generate oxygen and take up carbon dioxide, ocean organisms do the same thing in the world's oceans. People probably don't realize this, but these unicellular organisms are about as important as rainforests for our planet's functioning," Coesel said.

"By analyzing RNA filtered out of seawater samples collected throughout the day and night, the study identifies four main groups of photoreceptors, many of them new. This genetic activity uses light to trigger changes in the metabolism, growth, cell division, movements and death of marine organisms.

***

"The researchers collected water samples far from shore and looked at all genetic activity from protists: single-celled organisms with a nucleus. They filtered the water to select organisms measuring between 200 nanometers to one-tenth of a millimeter across. These included photosynthetic organisms, like algae, which absorb light for energy, as well as other single-celled plankton that gain energy by consuming other organisms.

***

"While the sun is up, these organisms gain energy and grow in size, and at night, when the ultraviolet light is less damaging to their DNA, they undergo cell division.

"'Daylight is important for ocean organisms, we know that, we take it for granted. But to see the rhythm of genetic activity during these four days, and the beautiful synchronicity, you realize just how powerful light is," Armbrust said."

Comment: Not surprising, and it shows the importance of a rotating Earth with day and night periods. Undoubtedly all organisms follow that rhythm.

Biological complexity: neural controls over mitochondria

by David Turell @, Wednesday, February 03, 2021, 18:26 (1150 days ago) @ David Turell

The transfer of a key enzyme is under neural controls:

https://phys.org/news/2021-02-neural-mitochondrial-rna-nucleus.html

"...researchers show that mitochondria translocate their key RNA methyltransferase enzyme, TRMT1, into host cell nuclei in response to neural activity. This subcellular relocalization of key RNA modifiers suggests a new understanding of how neurons plastically reconfigure their nuclei as network dynamics change.

"While epigenetic processes involving DNA methylation and histone modifications are known to be critical in learning and memory, the role of RNA modifications in cognitive function has been less well characterized.

***

"The researchers found that depolarization of neurons using KCL caused the relocation of TRMT1 from mitochondria and cytosol, as well as the relocation of TRMT1L from the nucleolus, into small punctate compartments of the nucleus. Although short depolarization bursts with KCL has been used to mimic long-term potentiation (LTP) via induction of immediate early genes, it is not a perfect simulator of real neural activity. In order to do that, fast electrical stimulation should be used to generate individual spike trains from individual neurons.

***

"An important question in all this is how mitochondria know that the neuron is firing, and furthermore, how they send TRMT1 to the nucleus. While it is known that mitochondria can rapidly respond to the influx of calcium that occurs during depolarization of tiny pre- or postsynaptic structures, these signals would likely wash out, temporally, near the nucleus inside of a large neuron.

***

"As far as the second question, the transfer of molecules from mitochondria to nucleus is a nice trick that cells regularly employ to control genes and epigenetic structure. For example, ATFS-1 (activating transcription factor associated with stress), which mediates the mitochondrial uncoupling response, is often translocated into the nucleus to modify gene expression. Similarly, PDC (pyruvate decarboxylase) can enter the nucleus under certain conditions to generate acetyl-CoA for histone acetylation.

"For the case of TRMT1, the presence of a strong MLS peptide overrides the weak NLS and the protein is initially targeted to mitochondrial transporters upon being synthesized. After entry, various proteases immediately cleave the signal sequence and activate the protein. Later on, contingent upon sufficient depolarization or other presumptive mitoflash events, the protein can exit the mitochondria. This time, lacking the MLS, the weak NLS eventually brings the protein back home to the nucleus."

Comment: a highly technical article with many processes and molecules described. It is another example of the intense complexity that dictates neuron activity with their mitochondria, and demands that one accept design as the source.

Biological complexity: gut biome may affect brain

by David Turell @, Thursday, February 04, 2021, 14:34 (1149 days ago) @ David Turell

The research is suggestive:

https://www.nature.com/articles/d41586-021-00260-3?WT.ec_id=NATURE-20210204&utm_sou...

"Thousands of publications over the past decade have revealed that the trillions of bacteria in the gut could have profound effects on the brain, and might be tied to a whole host of disorders. Funders such as the US National Institutes of Health are investing millions of dollars in exploring the connection.

"But along with that explosion of interest has come hype. Some gut–brain researchers claim or imply causal relationships when many studies show only correlations, and shaky ones at that, says Maureen O’Malley, a philosopher at the University of Sydney in Australia who studies the field of microbiome research. “Have you found an actual cause, or have you found just another effect?”

"In recent years, however, the field has made significant strides, O’Malley says. Rather than talking about the microbiome as a whole, some research teams have begun drilling down to identify specific microbes, mapping out the complex and sometimes surprising pathways that connect them to the brain. “That is what allows causal attributions to be made,” she says. Studies in mice — and preliminary work in humans — suggest that microbes can trigger or alter the course of conditions such as Parkinson’s disease, autism spectrum disorder and more (see ‘Possible pathways to the brain’). Therapies aimed at tweaking the microbiome could help to prevent or treat these diseases, an idea that some researchers and companies are already testing in human clinical trials.

***

"It’s not yet clear how that signal in the gut reaches the brain, but one likely conduit is the vagus nerve. The vagus connects the brainstem to many organs, including the colon, making it the longest of the twelve cranial nerves that carry signals between the brain and the rest of the body. “It’s really a highway,” Cryan says. And research in humans and animals suggests that it has a crucial role in ferrying at least some messages between the gut and the brain.

***

"In each of these diseases, many mechanistic questions remain. Researchers in the field acknowledge that they have yet to flesh out the pathways from microbe to brain. And the trickiest step will be validating these animal findings in humans and moving into trials. “These are extraordinary claims, which should require extraordinary evidence,” says Mitchell."

Comment: This is early in discovery. When I was in practice many years ago H. pylori was found by two Australian pathologists related to duodenal ulcer. Their report was laughed at by American GI specialists. But the bug was easily treatable. I was one of many Docs who tried an antibiotic cure. Worked beautifully!!! This new research is pointing at a similar result. Bacteria started life and are still modifying more complex living forms. Bacteria
have been allowed to survive while 99% of all species disappeared because they were meant to continue to have these roles as God designed.

Biological complexity: bacteria have complex organelles

by David Turell @, Sunday, May 17, 2020, 22:36 (1412 days ago) @ David Turell

Another view of this advanced degree of complexity in bacteria:

https://www.quantamagazine.org/bacterial-organelles-revise-ideas-about-which-came-first...

"In contrast to eukaryotes, which all have a suite of organelles in common, different groups of prokaryotes showcase their own specialized compartments. One kind of bacterial organelle, discovered in 1979, is essentially a little magnet wrapped in a lipid package; another hosts a series of reactions crucial for energy metabolism; still others serve as small storage units for nutrients.

***

"The very existence of organelles in these bacteria, coupled with intriguing parallels to the more familiar ones that characterize eukaryotes, has prompted scientists to revise how they think about the evolution of cellular complexity — all while offering new ways to probe the basic principles that underlie it.

***

"Among the best studied of the bacterial organelles are the magnetosomes, round structures that build magnetic particles within their lipid bilayer membranes. The organelles allow aquatic “magnetotactic” bacteria to navigate vertically along the Earth’s magnetic fields toward the low-oxygen depths in which they thrive.

***

"Some species of planctomycetes contain a membrane-bound organelle called an anammoxosome, which sequesters a chemical reaction that produces nitrogen along with toxic intermediaries. Anammoxosomes act like energy factories for the bacteria, much as mitochondria do in eukaryotes, though anammoxosomes do not seem to be remnants of symbionts as mitochondria are.

***

"Those results have been called into question — imaging seems to indicate that the compartment isn’t entirely closed, meaning it does not satisfy the definition of an organelle — but experts remain excited about these bacteria. They have the most complex internal membrane system seen in prokaryotes to date, and they contain proteins that structurally resemble those that shape and maintain eukaryotic membranes. They also seem capable of processes that were thought to be unique to eukaryotes, such as digesting nutrients inside their cells and synthesizing molecules called sterols.

***

"Bacteria also seem to have a wide variety of enclosed structures that are bound not by a lipid membrane but by a protein coat. Take carboxysomes, which evolved in bacteria twice, independently, to fix carbon. They and smaller, self-assembling nanocompartments have a polyhedral structure that looks shockingly like a viral capsid, the protein shell that encloses viral genomic material.

"The catalog keeps getting longer: Komeili and his colleagues recently discovered a new lipid-bound organelle that accumulates iron, which they’ve dubbed the ferrosome.

***

"No one knows whether the structures seen in bacteria represent primitive, intermediate steps in the evolution of eukaryotic organelles, or separate innovations that evolved independently of those of eukaryotes. It’s possible that the answer varies with each organelle. But even if the bacterial and eukaryotic organelles did evolve completely independently, the prokaryotic structures may be useful for understanding the eukaryotic ones. (my bold)

***

"This work not only suggests that compartmentalization is more prevalent among the various branches of the tree of life than people thought; it also indicates that this kind of complexity was not the critical innovation needed to trigger eukaryotic evolution.

***

"Rather, eukaryotic characteristics likely emerged as part of a long, gradual trend, just as Rout’s work on the nuclear pore complex demonstrated. “It’s showing us that stepwise evolution is possible,” Devos said, “as opposed to a big explosive change from nothing to everything.”

***

"Given that all of life is connected, whether in the deep evolutionary past, this new understanding of evolutionary history can give us more clues about where we came from. At the very least, “people are recognizing that there’s more diversity out there in the environment,” Dacks said, “and that the nice clean stories just don’t cut it anymore.'”

Comment: My bold represents the key point: the evolutionary jump to eukaryote cells may have been much smaller than previously thought, and therefore original bacteria at/after the start of life may have been much more complex than previously realized, implying even more the necessity that a designer was/is required.

Biological complexity: cellular delivery systems

by David Turell @, Wednesday, May 20, 2020, 15:19 (1409 days ago) @ David Turell

Must require design:

https://evolutionnews.org/2020/05/just-in-time-delivery-in-living-cells/

"A cell is a large place, like a city to the molecules inside; it is inefficient to store needed cargoes far from their work sites. Within the cell, highways of microtubules grow in the directions that cargo carriers like kinesins need them. Some new discoveries show that additional mechanisms supplement those well-known processes to provide just-in-time delivery.

***

"At the cellular level, a protein called LPL (lipoprotein lipase) is there to help regulate triglycerides. Lipases are enzymes necessary for the proper distribution and utilization of lipids in the human body, but some of these enzymes can be dangerous if not handled carefully.

***

"Upon translation in the ribosomes, LPLs in adipocytes are sent to the Golgi apparatus for maturation and proper folding. When ready, they are accompanied by another enzyme, SDC1 (syndecan-1), for sequestration into vesicles. There, a third enzyme named HSPG stabilizes them, rendering them inactive, as two strands of LPL wind into a helical shape. When they get the call for action, they emerge from their vesicles like firefighters at a station, unwind from their helical shape, separate, and hang onto HSPGs on the cell surface.

***

"A new cellular biology study, published last month in the journal Structure by scientists at Vanderbilt, reports a shape-shifting structure in the human body which plays an important role in the timely delivery of fats and proteins.

"Led by Lauren Jackson, assistant professor of biological sciences and biochemistry at Vanderbilt, the work is the first to visualize this structure — a type of protein complex found in human cells known as retromer — and report its unique ability to transfigure itself into a variety of different architectures and structures.

***

"Our data suggest the metazoan retromer is an adaptable and plastic scaffold that accommodates interactions with different sorting nexins to sort multiple cargoes from endosomes their final destinations... The retromers can take on a variety of forms, joining in complexes.

“'This flexible scaffold structure plays a key role in the sorting and delivery process,” said Jackson. “These structures reveal how one complex alone is able to sort and deliver cellular ‘cargo’ to different destinations.”

***

"Proteins are molecular work horses in the cell that perform specific tasks, but it is essential that the timing of protein activities is exquisitely controlled. When proteins have fulfilled their tasks, degradation of these proteins will end processes that are unneeded or detrimental. To control timing, a label — called “ubiquitin” — is attached to unwanted proteins, marking the protein for degradation. Although complex molecular machineries were known to attach ubiquitin, how these machines carry out the labeling process was unknown.

***

"Sperm can be up to 20 times smaller than a normal cell in the body. And while sperm carry only half as much genetic material as a regular cell, it needs to be folded and packaged in a special way in order to fit. One way nature does this is by replacing histones — proteins around which DNA is wound, like beads on a necklace — with a different type of protein called protamines.

"Thankfully, the fertilized egg knows how to get to the precious genes that helped make you.
Researchers at University of California San Diego School of Medicine have discovered that the enzyme SPRK1 leads the first step in untangling a sperm’s genome, kicking out special packing proteins, which opens up the paternal DNA and allows for major reorganization — all in a matter of hours."

Comment: Same old story. Complexity beyond belief which requires design.

Biological complexity: cell division controls in humans

by David Turell @, Tuesday, March 23, 2021, 22:32 (1102 days ago) @ David Turell

New research on different molecular controllers:

https://phys.org/news/2021-03-human-cells-dna-replication.html

"Bruce Stillman has been dissecting DNA replication, a critical step in cell division, since the 1980s. His lab studies how Origin Recognition Complexes—ORCs—coordinate DNA duplication. They discovered how our cells assemble and disassemble ORCs during the cell division cycle. One ORC protein is sequestered into small liquid droplets, keeping it apart until the right time to recruit other proteins and initiate DNA replication.

"The ORC recognizes where to initiate replication at numerous locations along the long, linear stretches of DNA in our cells' chromosomes. Fully assembled ORCs recruit other proteins to make precise copies of the chromosomes. This mechanism is necessary to inherit DNA accurately without errors that can lead to disorders such as cancer.

"...humans have a variety of cells that divide at different times. To choreograph this, the researchers found that one human ORC protein, ORC1, has certain regions that yeast ORC1 lacks. When ORC binds to DNA, ORC1 recruits CDC6, a protein that assembles other DNA replication proteins. Some of the human-specific regions of ORC1 and CDC6 bind other proteins that regulate DNA replication. Manzar Hossain, a research investigator in Stillman's lab, says:

"'We found that ORC1 and CDC6 interact in a very tangential manner. We found a very short time period which allows them to interact."

"DNA-bound ORC1 is sequestered into liquid droplets that briefly change shape, then brings in CDC6. Kuhulika Bhalla, a postdoc in Stillman's lab, explains:

"'So if you can imagine a lava lamp, like you've got liquid, but you've got other colored liquid within it. And they still managed to stay separated."

"Throughout most of the cell division cycle, ORC1 and CDC6 amounts oscillate in the cell. Stillman explains that "both high and low amounts of ORC1 lead to severe consequences for cell viability. So, you have to have just the right amount" of each protein throughout the cell cycle. Stillman and his colleagues have shown that CDC6 recruits other regulatory proteins that control the activity and levels of ORC1 in both space and time."

Comment: having two molecules that cooperate together requires carefully designed controls. Two complex molecules working together did not happen by chance.

Biological complexity:cell division controls of mitochondria

by David Turell @, Thursday, March 25, 2021, 14:33 (1100 days ago) @ David Turell

Amazing action within the cell as it divides mitochondria:

https://www.nature.com/articles/d41586-021-00511-3?WT.ec_id=NATURE-20210325&utm_sou...

"Using cutting-edge light-microscopy technology, the authors report evidence that these actin waves have a role in mitochondrial partitioning during mitosis of human cells. Like chromosomal partitioning, mitochondrial inheritance depends on dynamic processes orchestrated by the cytoskeleton — yet it turns out that these partitioning events occur in a completely different way.

"The authors describe three modes of interaction between mitochondria and actin during mitosis. Previous work5 suggested that the myosin motor protein Myo19 dynamically tethers mitochondria to an actin network and maintains the distribution of mitochondria throughout the cytoplasm. First, Moore and colleagues observed this process in greater detail than had been reported previously, and found that it is independent of the presence of actin waves. Second, within a wave, mitochondria are encased by what looks like clouds of actin filaments that seem to immobilize the organelles. And third, sometimes these clouds ‘opened’, to be followed by an astonishing burst of mitochondrial movement. The organelles were propelled by the rapid growth (polymerization) of actin filaments. This generated what looks like a comet tail made of actin. These mitochondrial movements were rapid, randomly oriented, and covered substantial distances in the cell.

***

"The authors present stunning images of twin actin tails emanating from the front of mitochondria and extending behind the organelle, similar to the contrails left in the sky by twin-engine aircraft. The comet tails that Moore and colleagues observed were often slightly twisted.

***

"The authors fed their experimental data into computer models, and the results suggest that the actin waves trigger bursts of movement driven by comet tails that randomly distribute mitochondria during cell division. This activity promotes organelle dispersion, and ensures that the burden of damaged mitochondria is evenly split between the two daughter cells of the mitotic division.

***

"A previous study reported that revolving actin waves regulate the balance between the division and fusion of mitochondria during the interphase stage of the cell cycle, which precedes mitosis. It will be important to discover whether mitochondrial movement, interconnectivity and dispersion are processes that mutually affect each other.

"Certain types of cell divide asymmetrically and generate daughter cells with different fates. During the division of a stem cell, the older mitochondria in the dividing cell are preferentially partitioned to the daughter cell that is destined to differentiate, whereas the younger and ‘fitter’ mitochondria are apportioned to the daughter cell that maintains stem-cell properties. One can predict, therefore, that mitochondria mixing is suppressed in these cells and that other, as yet unknown, mechanisms ensure the asymmetric inheritance of mitochondria. Clearly, mitochondrial research will yield many more surprises in the future.

Comment: As the complexity is explored at sub-microscopic levels the evidence for a required designer grows. View the article to see the figures of the processes.

Biological complexity: mitochondrial splitting, repair

by David Turell @, Thursday, May 06, 2021, 15:31 (1058 days ago) @ David Turell

Two different systems for simple cell division and removing damaged parts:

https://www.nature.com/articles/d41586-021-01173-x?WT.ec_id=NATURE-202105&sap-outbo...

"During mitophagy, damaged portions of mitochondria separate from healthy portions through mitochondrial division6. However, damage is not the only reason for mitochondrial division. It also occurs during cell growth and cell division. In this scenario, the new cellular property generated by cell division is furnished using mitochondria generated by division. In contrast to damage-associated division, mitochondrial division during cell growth is a sign that times are good.

"It stands to reason that different mechanisms control mitochondrial division for mitophagy and for cell growth. Although there have been hints of specific types of division, clear evidence has been lacking until now. The protein DRP1 is required for the vast majority of cases of mitochondrial division6. DRP1 can be activated in different ways to drive such division in mammals. These include: interaction with mitochondrial DRP1 receptors (MFF, MID49, MID51 and FIS1); DRP1 modification (post-translational alterations); interaction with the actin cytoskeleton (filaments of actin protein) or the mitochondrial lipid cardiolipin; and contact with various organelles, including the endoplasmic reticulum (ER), lysosomes and the Golgi (in the form of Golgi-derived vesicles). It has been unclear whether these factors contribute to a single division pathway or to different pathways.

***

"The authors demonstrate that peripheral and midzone divisions have substantially different properties. Midzone division occurs in organelles with hallmarks of healthy mitochondria — they do not display signs of abnormalities, such as a reduction of membrane polarization or a change in the level of reactive oxygen species (ROS). By contrast, peripheral division occurs when the tip of the organelle has developed a decrease in membrane potential and an increase in ROS, with a noticeable lack of these alterations in the other portion of the organelle. In addition, this smaller product of a peripheral division often lacks replicating DNA — which is a sign of an unhealthy mitochondrion. (my bold)

"These findings suggest that peripheral division occurs when mitochondria are damaged, and is a precursor to mitophagy. Indeed, the authors report that peripheral divisions increased on exposure to various cellular stresses, and were associated with the accumulation of markers of mitophagy. By contrast, midzone division increased after stimulation of cell proliferation.

***

"Kleele and colleagues’ careful work is valuable, because it clearly demonstrates that there is more than one type of mitochondrial division, thus enabling a more nuanced analysis of division factors based on the reason for division. Moreover, this work is a reminder that we need to walk before we can run when trying to map complicated biological processes such as mitophagy. Otherwise, our understanding of them might be hampered by an incomplete grasp of the earlier processes that lead up to them."

Comment: Exciting new research into the mysterious mitochondria in normal cell division and in controlling damage. Mitochondria supply energy by the process of oxidation, handling dangerous reactive oxygen species (ROS). As in a fire, oxygen burns. The deeper we go the more complex it gets in the creators designs. This is a review paper on early research and much of it asks probing questions.

Biological complexity:tiny enzyme changes, huge new function

by David Turell @, Friday, May 07, 2021, 21:42 (1057 days ago) @ David Turell

Changing a few amino acids and enzymes functional ability is dramatically altered:

https://phys.org/news/2021-05-tiny-amino-acid-differences-enzymes.html

"Just a few changes to an enzyme's amino acids can be enough to dramatically change its function, enabling microbes to inhabit wildly different environments.

"University of Queensland microbiologist Associate Professor Ulrike Kappler, led by an international team of researchers, made this discovery when investigating how Haemophilus influenzae bacteria colonize the human respiratory system.

"'This disease-causing bacterium is supremely adapted to living in humans, so much so that they cannot survive anywhere else," Dr. Kappler said.

"'It turns out that one enzyme, MtsZ, is the key player in this adaptation.

"'But, surprisingly, close relatives of this protein, which promotes Haemophilus survival exclusively inside humans, help other species of bacteria to survive exclusively in lakes.

"'How could closely related enzymes help one bacterial species live exclusively in humans and another to live only in lakes?

"'The answer is a matter of minute amino acid changes."

"The research shows that a sequence difference of just three amino acids, a difference of less than 0.25 percent of the MtsZ enzyme sequence, changes the functionality of the enzyme between bacteria living in lakes compared with those living in humans.

***

"'The slight changes in this enzyme enable the lake-dwelling bacteria to live on decaying algae and generate energy.

"'Contrast this with Haemophilus, which uses MtsZ to scavenge amino acids from the human body and use them for bacterial growth and replication."

Comment: In the biochemistry of life God designed a system that is easily altered. Just change a proteins fold and results in a different function appear.

Biological complexity: how hemoglobin appeared

by David Turell @, Wednesday, May 20, 2020, 19:47 (1409 days ago) @ David Turell

Without hemoglobin present in red blood cells, we would not be here:

https://phys.org/news/2020-05-reveal-complex-hemoglobin-resurrecting-ancient.html

The group identified the evolutionary "missing link" through which hemoglobin—the essential four-part protein complex that transports oxygen in the blood of virtually all vertebrate animals—evolved from simple precursors. And they found that it took just two mutations more than 400 million years ago to trigger the emergence of modern hemoglobin's structure and function.

***

Each hemoglobin molecule is a four-part protein complex made up of two copies each of two different proteins, but the proteins to which they are most closely related do not form complexes at all. The team's strategy, pioneered in Thornton's lab over the last two decades, was a kind of molecular time travel: use statistical and biochemical methods to reconstruct and experimentally characterize ancient proteins before, during and after the evolution of the earliest forms of hemoglobin. This allowed them to identify the missing link during hemoglobin evolution—a two-part complex, consisting of two copies of a single protein, which existed before the last common ancestor of humans and sharks. This ancient two-part complex did not yet possess any of modern hemoglobin's critical properties that allow it to bind oxygen in the lungs and deliver it to distant cells in the brain, muscles and other tissues.

By introducing into this missing link protein various mutations that occurred during the next historical interval, they found that just two mutations on the protein's surface triggered formation of the four-part complex and imparted the critical changes in its oxygen-binding function.

***

Analysis of the ancient proteins' atomic structures showed how the two mutations took advantage of even more ancient features to assemble the intermediate two-part complex into the four-part complex. The mutations introduced two changes on the protein surface that allowed it to bind tightly to the surface of the other protein, which remained unchanged as it was recruited into the new interaction. Other ancient parts of the two surfaces also stuck together simply by chance, adding further strength to the interaction that was triggered by the two new mutations. Those older elements, Thornton pointed out, and even the two-part complex itself, must have existed then by chance, rather than because they enhanced the protein's final structure or function, because they evolved before those properties came into being. (my bold)

Perhaps the most surprising result was that the two critical mutations, by inducing formation of the four-part structure, also triggered the critical changes in the complex's oxygen-binding functions. Hemoglobin can perform its physiological function because its affinity for oxygen is high enough to bind oxygen in the lungs, but low enough to release it in the tissues elsewhere in the body. It also binds oxygen cooperatively: When one of the four components takes up a molecule of oxygen, the other components tend to do the same—and this happens in the reverse direction, as well—so the whole complex becomes even more effective at recruiting oxygen and releasing it in the right places.

Hemoglobin's ancient precursors—including the missing link two-part complex—bound oxygen too tightly and were not cooperative, so they could not have effectively performed the oxygen-exchange function. The researchers found that the two key mutations not only conferred the four-part structure but also imparted hemoglobin's critical oxygen-binding properties.

***

"Imagine if those two mutations never occurred, or if the structural features that they took advantage of weren't in place at the time," Thornton said. "Hemoglobin as we know it would not have evolved, and neither would many of the subsequent innovations that depend on efficient oxygen transport, like rapid metabolism and the ability to grow much larger and move much faster than our ancient marine ancestors." (my bold)

Comment: Note my bolds. This is a Darwinist piece of research reporting where all must occur by chance. What are the odds for that? Instead I see God's purpose in the events knowing what is to come in the future. What is also important is hemoglobin carries CO2 out to the lungs and releases it faster than it picks up oxygen. We know we are short of breath from CO2 levels, not O2 levels. And another side gain is the development of myoglobin in muscles where oxygen is handled faster than other organs to allow rapid muscle use. It is easy to see the purpose. Why see chance?

Biological complexity: making a ribosome isn't easy

by David Turell @, Saturday, May 23, 2020, 01:36 (1406 days ago) @ David Turell

In life the ribosome constructs itself before going to work. It took seven years for humans to do it!:

https://www.sciencedaily.com/releases/2020/05/200521102052.htm

As the cell's protein factory, the ribosome is the only natural machine that manufactures its own parts. That is why understanding how the machine, itself, is made, could unlock the door to everything from understanding how life develops to designing new methods of drug production.

***

The core is a long strand of RNA, and 20 different proteins must be attached to the strand. These get organized by the weak chemical forces between the protein molecules and the RNA -- repelling at some points and attracting in others -- and the whole structure thus relies on the proper manufacture and organization of each component. Add to that another six proteins that are not part of the structure, but act as chaperones to assist in the assembly. That makes at total of a least 27 different genes -- one to encode each component or chaperone -- that must work together to make the subunit.

***

The tiny chips in Bar-Ziv's lab are based on densely-packed DNA strands attached at one end to the surface. In the beginning, the team used all 27 genes needed to reproduce the 30S subunit of a ribosome from an E coli bacterium. The components were caught in "molecular traps" placed near their genes, and this improved the efficiency of the process and enabled the scientists to observe the production process in real time. Then they took a step back, allowing the various parts to autonomously assemble themselves into the ribosomal units, without outside direction or interference. (my bold)

***

In the beginning, Bar-Ziv and Shulman Daube found they could make the components, but getting them to self-assemble, as the natural structures do, was a challenging hurdle. Over the course of the next seven years and hundreds of trials, the scientists tracked down the proper placement of the genes on the chips. Something like the organization of genes in the chromosome, the genes on the chip had to be positioned in the right locations, and in the proper relative quantities. This, it turned out, was crucial to the overall orchestration of the complex assembly process. Each time, the scientists would attach a different constellation of genes to the chips, narrowing down the possibilities until they had a composition that could mimic that natural process of subunit production as well as self-assembly. In nature, subunit assembly is a hierarchal process. In the course of their experiments, the scientists were able to break down the assembly to the individual steps to prove that the end result was a self-assembled subunit, and to observe the roles of the chaperones in this process. (my bold)

Comment: Note the first bold. One major step was using life's own process rather than humans doing it. And many folks deny it was all designed!

Biological complexity: how muscle cells fuse into fibers

by David Turell @, Wednesday, May 27, 2020, 00:18 (1402 days ago) @ David Turell

It is an orchestrated dance:

https://phys.org/news/2020-05-urge-merge-cells-fuse.html

"Scientists have known for a decade that cells that fuse with others to perform their essential functions—such as muscle cells that join together to make fibers—form long projections that invade the territory of their fusion partners. But how the thin and floppy polymers involved in this process propel mechanically stiff protrusions has been unknown.

"In a new study published online today in Nature Cell Biology, UT Southwestern scientists outline the mechanisms behind the formation of these projections, focusing on the interaction between two proteins known as actin and dynamin. The findings, they say, offer insight on a key cellular process that's essential for the conception, development, regeneration, and physiology of multicellular organisms

***

"First, adhesion molecules draw cell membranes together, but leave a gap between cells; next, one cell extends fingerlike projections that invade the other cell; finally, so-called fusogenic proteins bring the cells' membranes even closer to touch and merge.

"For that middle step, Chen says, research from her lab and others has shown that a protein called actin plays a key role in forming projections. However, actin forms floppy and thin polymers, known as actin filaments, each with a diameter of only 7 nanometers. How these thin filaments become mechanically rigid enough to push out projections that invade other cells was unclear.

***

"To solve it, Chen and her colleagues studied actin's interaction with dynamin, a protein that can release energy from specific chemical bonds found throughout cells. One of dynamin's roles is to pinch off newly formed vesicles that bring cargo into cells, by forming a structure around the "neck" of the vesicles protruding in from the cell membrane. Although previous studies have shown that dynamin and actin were associated with each other in many cellular structures, how they work together has remained a mystery for two decades.

"Using fruit fly muscle cells as a model system, Chen and her team started by observing muscle cell fusion in embryos genetically engineered to not make any functional dynamin. They found that without dynamin function, not only could these cells no longer merge, they also couldn't form the normal projections, suggesting that dynamin plays a key role in this step of the process.

***

"Although this experiment shows that dynamin has the capacity to capture and hold multiple actin filaments into stronger bundles, Chen says, fully occupied dynamin helices are unlikely to last long in cells, where ample energy sources that can cause these dynamin structures to dissolve into individual units is abundant. Sure enough, when the researchers added energy sources to the dynamin-actin mix, the dynamin helices did come apart, but not in a synchronized fashion. While fully assembled helices broke apart, others remained—keeping the actin bundles together while allowing new filaments to emanate from areas unbound by dynamin. Such a dynamic process ultimately leads to the formation of multiple interconnected parallel actin bundles, hence further increasing the mechanical strength of the actin network, says Chen. Experiments in cells showed that the dynamic actin bundling process was critical for cells to form projections and fuse with other cells."

Comment: this type of cellular coordination is designed into the cells various activities as the embryo is formed. Not learned cooperation, but designed cooperation. If cells had to learn how to do this, no embryo would ever form.

Biological complexity: cleaning up worn out muscle cells

by David Turell @, Thursday, May 28, 2020, 20:12 (1401 days ago) @ David Turell

The process involves attaching ubiquitin to the cells to destroy them:

https://www.sciencedaily.com/releases/2020/05/200528082552.htm

"Researchers at the University of Copenhagen's Department of Nutrition, Exercise and Sports have demonstrated that physical activity prompts a clean-up of muscles as the protein Ubiquitin tags onto worn-out proteins, causing them to be degraded. This prevents the accumulation of damaged proteins and helps keep muscles healthy.

***

"Maintaining muscular function is essential. Part of our ability to do so depends upon proteins -- the building blocks of muscles -- being degraded when worn-out and eliminated in a kind of clean up process that allows them to be replaced by freshly synthesized proteins.

***

"'One of these methods is when Ubiquitin, "the death-marker," tags a protein in question. Ubiquitin itself is a small protein. It attaches itself to the amino acid Lysine on worn-out proteins, after which the protein is transported to a Proteasome, which is a structure that gobbles up proteins and spits them out as amino acids. These amino acids can then be reused in the synthesis of new proteins. As such, Ubiquitin contributes to a very sustainable circulation of the body's proteins.'"

Comment: A neatly designed process which reuses amino acids for new muscle proteins. This could not develop by chance.

Biological complexity: magic molecular reactions

by David Turell @, Sunday, June 07, 2020, 19:32 (1391 days ago) @ David Turell

It depends on enzymatic help, as previously described but also on molecular surface actions most of which involve two molecular reactikons:

https://www.quantamagazine.org/new-machine-learning-system-decodes-how-proteins-interac...

"Correia’s system, called MaSIF (short for molecular surface interaction fingerprinting), avoids the inherent complexity of a protein’s 3D shape by ignoring the molecules’ internal structure. Instead, the system scans the protein’s 2D surface for what the researchers call interaction fingerprints: features learned by a neural network that indicate that another protein could bind there. “The idea [is that when] any two molecules come together, what they’re essentially presenting to one another is that surface. So that’s all you need,” said Mohammed AlQuraishi, a protein researcher at Harvard Medical School who also uses deep learning. “It’s very, very innovative.”

***

"One version of the system, called MaSIF-site, can examine the whole surface of a protein and predict where another protein is most likely to bind, an approach similar to painting a target on a curved canvas. “It’s what we like to call the one-body problem,” Correia said. “You can think about this as a way to understand where the functional sites on a particular protein are.” MaSIF-site performed roughly 25% better at this task than two leading site-interaction predictors.

"Another version of the system, called MaSIF-search, tackles what Correia calls the many-to-many problem: Instead of predicting how one protein will fit together with one target molecule (as typically happens in docking simulations), the system compares the interaction fingerprints of many proteins to many others, looking for fits. (“In a cell you have 10,000 proteins, and many of them are bumping into each other all the time,” explained Correia.) On this task, MaSIF didn’t outperform a leading molecular-docking predictor; it found roughly half as many potential fits within a random set of 100 proteins. But the docking predictor needed nearly 100 days’ worth of computing time to perform its search. MaSIF took four minutes.

"That massive speedup “opens interesting possibilities” for basic research, said Bronstein. After all, in the human body, proteins form functional networks comprising tens of thousands of interactions. “Constructing these graphs takes a lot of time,” Bronstein said. “With methods [like MaSIF], it may only be an approximation, but it allows you to at least build some rough version of these protein-to-protein networks for any organism.”

"AlQuraishi noted that while MaSIF’s skin-deep approach to predicting protein interactions made sense, it wasn’t able to capture a phenomenon called induced fit: the way molecular surfaces change shape (and chemistry) when they get close to each other. In other words, the surfaces of two proteins may not exhibit complementary fingerprints until they’re already almost touching — a factor MaSIF will miss, since induced fit depends on the structure beneath a protein’s surface. “What evolution is probably optimizing for is precisely this induced fit,” said AlQuraishi. “What’s surprising about [MaSIF] is that even with this caveat, it still works pretty well.” (my bold)

"Incorporating induced fit and other surface dynamics into MaSIF is something Correia plans to explore. “To me it’s the last frontier of understanding [protein] function,” he said. “That’s probably how I’m going to be spending my next 10 years.'”

Comment: This article discusses new techniques in studying protein molecule functions in order to react together. What I have picked out are the actual molecular actions and reactions that occur constantly in cellular production of biologic products. Note my bold. These molecules have built-in automatic reactions. They do not think, but innately are built to produce what they have to do. What should be carefully remembered is these are molecule on molecule reactions. Most reactions require enormous enzyme molecules to force reactions that otherwise might take centuries to happen. None of this can develop by chance.

Biological complexity: electric spark of life

by David Turell @, Saturday, July 04, 2020, 19:02 (1364 days ago) @ David Turell

Electrons are a vital part of biological processes:

http://nautil.us/issue/86/energy/uncovering-the-spark-of-life

"...humans didn’t invent electricity, no matter how much we’d like to think so. It precedes us, and life itself, as an inanimate physical process. It is also at the core of how organisms access the motivating force for life—energy.

***

"Energy is a measure of the ability to do work, and cells, the fundamental unit of life as we know it, have much work to do. They construct proteins, copy themselves, and move against the ubiquitous pull of gravity. In the biosphere we’re familiar with, organisms depend upon the sun to bankroll their work—either directly through photosynthesis, or by consuming its organic products. Both of these processes are fundamentally electrical. So is the metabolism of the deep biosphere, a parallel world beneath our feet1 that thrives in the dark. Thousands of meters down, scientists have found bacteria that electrify themselves by eating and breathing simple geofuels.

***

"On Earth’s surface, many organisms produce electricity by shuttling charge from glucose to oxygen. Underground, they can use hydrogen and carbon dioxide. But the operation that generates electricity in both cases is the same—an equilibration of charge between two compatible compounds. After all, electricity is nothing more than energy derived from either static or dynamic charge. But what exactly is charge, and how does life use electricity to do work?

***

"The difference in charge between the two terminals is known as voltage, and the flow of current between them can be used productively. On Earth, more ancient, deep biosphere bacteria utilize low voltage circuits, while the more complex surface-dwelling organisms depend upon higher voltages.

***

"All cells that have been studied bridge the charge difference between what is eaten and what is breathed with a biological wire known as the electron transport chain (ETC). The universality of the ETC suggests it was an early innovation in the evolution of life on Earth

***

"All kinds of compounds, everything from hydrogen gas to sulfate—can serve as the terminals of a metabolic circuit. Despite this flexibility, the depth of structural and functional similarity in the ETC across a multitude of life forms suggests only a few degrees of freedom during the system’s evolution.

***

"Annette Rowe is head of the Electromicrobiology Laboratory at the University of Cincinnati, where she studies the often unusual ways that organisms power their metabolic circuits. Some of her research has focused on bacteria capable of breathing current carried by electrodes.2 Reached by phone, Rowe points out that while the metabolic systems of two organisms may “have protein architecture that looks really similar, most of them are uniquely derived, evolutionarily speaking.” This means that the same solution to the problem of distributing the electric harvest throughout the cell has appeared over and over again throughout history. The name of that solution? Adenosine triphosphate.

"Adenosine triphosphate, ATP for short, is one of those incredible pieces of biology that appears to be universal. There is no exception to the rule that to live is to work, and no exception to the rule that all known cells use electrochemical gradients to do work. But most internal cellular processes do not access electricity directly. Instead, they channel the electric power into a mobile intermediary—ATP—for much the same reason that we prefer wireless technology. Dragging a cord about is prohibitively restrictive. Internal cellular processes like active transport, polymerization, and locomotion occur far from metabolic machinery. Instead of depending on a tangle of wires, cells use diffusible ATP to provide the necessary kick. “ATP is a fundamental currency to life as we know it,”

Comment: Extracted from an essay on how to find life on Mars. It appears that are strict rules in evolution to handle the energy electrons provide with ATP used everywhere. Electrons play an integral role in photosynthesis (2020-06-16, 22:31) These are highly complex processes that must be designed

Biological complexity: Backup corrections for broken DNA

by David Turell @, Monday, July 06, 2020, 23:05 (1362 days ago) @ David Turell

Yes, dhw, errors do occur in DNA replication, but God inserted backup repair mechanisms:

https://phys.org/news/2020-07-great-specificity-action-enzymes-double-strand.html

"Dr. Daley is first author of research, published June 18 in the journal Nature Communications, that sheds light on a double-strand break repair process called homologous recombination. Joined by senior authors Patrick Sung, DPhil, and Sandeep Burma, Ph.D., and other collaborators, Dr. Daley found that among an array of mechanisms that initiate homologous recombination, each one is quite different. Homologous recombination is initiated by a process called DNA end resection where one of the two strands of DNA at a break is chewed back

***

"'For a decade we have known that resection enzymes are at the forefront of homologous recombination. What we didn't know is why so many of these enzymes are involved, and why we need three or four different enzymes that seem to accomplish the same task in repairing double-strand breaks."

***

"'It's like an engine mechanic who has a set of tools at his disposal," Dr. Sung said. "The tool he uses depends on the issue that needs to be repaired. In like fashion, each DNA repair tool in our cells is designed to repair a distinctive type of break in our DNA."

"The research team studied complex breaks that featured double-strand breaks with other kinds of DNA damage nearby—such complex breaks are more relevant physiologically, Dr. Daley said. Studies in the field of DNA repair usually tend to look at simpler versions of double-strand breaks, he said. Dr. Daley found that each resection enzyme is tailored to deal with a specific type of complex break, which explains why a diverse toolkit of resection enzymes has evolved over millennia." (my bold)

Comment: No surprise. Enough repair tools to cover all types of DNA tears. It seems God recognized errors would occur and provided all the necessary tools for perfect reproduction. Makes logical sense recognizing no biological living system can operate at high speed perfectly. This discussion about errors has begun years after the start of this website. I have't hidden it. Courses in biochemistry describe it as an obvious problem, and point out all the corrective mechanisms required. We would not have evolved without them.

Biological complexity: problem, define an individual

by David Turell @, Saturday, July 18, 2020, 23:33 (1350 days ago) @ David Turell

Apparently not easy as a part of biological philosophy:

https://www.quantamagazine.org/what-is-an-individual-biology-seeks-clues-in-information...

"At the core of that working definition was the idea that an individual should not be considered in spatial terms but in temporal ones: as something that persists stably but dynamically through time. “It’s a different way of thinking about individuals,” said Mitchell, who was not involved in the work. “As kind of a verb, instead of a noun.”

***

"Many philosophers and biologists have taken up this “process view,” in which organisms and other biological systems exist not as fixed objects or materials but as flowing patterns and relationships in a river of flux.

***

"Unfortunately, “once gene theory took over, it became a biology of things,” said Scott Gilbert, a developmental biologist at Swarthmore College. But now that’s starting to change again. “Twentieth-century biology was a biology of things,” he said. “Twenty-first-century biology is a biology of processes.”

***

"Their formalism, which they published in Theory in Biosciences in March, is based on three axioms. One is that individuality can exist at any level of biological organization, from the subcellular to the social. A second is that individuality can be nested — one individual can exist inside another. The most novel (and perhaps most counterintuitive) axiom, though, is that individuality exists on a continuum, and entities can have quantifiable degrees of it.

***

“'Think about building a kind of microscope which would allow me to see information being propagated forward in time,” Krakauer said. They described a mathematical framework that breaks information flows down into parts and evaluates individuality based on how different combinations of environmental influences and internal dynamics can predict a system’s future states.

"Based on these gradients of information flow, the Santa Fe team distinguishes three types of individuality. The first is the organismal individual, an entity that is shaped by environmental factors but is strongly self-organizing. Nearly all of the information that defines such an individual is internal and based on its own prior states. “This is a lens that, if you wore it, would allow you to see humans and mammals and birds,” Krakauer said.

"The second type of individuality is the colonial form, which involves a more complicated relationship between internal and external factors. Individuals in this category might include an ant colony or a spiderweb — distributed systems that are “partially scaffolded” by their environment but still maintain some structure on their own.

"The third type is driven almost entirely by the environment. “If you remove the scaffolding, the [entity] would fall apart,” Krakauer said. It’s like a tornado, which dissipates under the wrong temperature and moisture conditions. The very first life to arise on Earth was probably like this, Krakauer added.
way to think about biological units.

"Within this theory, individuals can be cells, tissues, organisms, colonies, companies, political institutions, online groups, artificial intelligence or cities — even ideas or theories, according to Krakauer. “What we’re trying to do is discover a whole zoo of life forms that extend far beyond what we have conventionally called living,” he said.

***

"As an alternative, Ramstead is collaborating with Karl Friston, a renowned neuroscientist at University College London, to build a theory around Friston’s “free-energy principle” of biological self-organization.

***

"The free-energy principle asserts that any self-organizing system will look as if it generates predictions about its environment and seeks to minimize the error of those predictions. For organisms, that means in part that they are constantly measuring their sensory and perceptual experiences against their expectations.

***

"...attempts to use information flows, in theory or practice, to carve nature at its joints are “the beginning of sketching out ideas and concepts that could be potentially foundational for new areas of biology,” Hoyal Cuthill said.

"Laubichler agreed. “For the life sciences or biology to grow up as a scientific discipline,” he said, “it needs to do something like this.'”

Comment: I view this as over-analysis. Biology does not lend itself to physics, but the information biology uses runs biology.

Biological complexity: problem, define an individual

by dhw, Sunday, July 19, 2020, 13:18 (1349 days ago) @ David Turell

QUOTE: “'Think about building a kind of microscope which would allow me to see information being propagated forward in time,” Krakauer said. They described a mathematical framework that breaks information flows down into parts and evaluates individuality based on how different combinations of environmental influences and internal dynamics can predict a system’s future states.

As if any mathematical framework can predict changing environmental influences! Even internal dynamics can be changed by those influences! And not even we as individuals can predict how our internal dynamics will function when faced with unknown environmental influences!

QUOTE: "Within this theory, individuals can be cells, tissues, organisms, colonies, companies, political institutions, online groups, artificial intelligence or cities — even ideas or theories, according to Krakauer. “What we’re trying to do is discover a whole zoo of life forms that extend far beyond what we have conventionally called living,” he said.

What they are trying to do is change the definition of “individual” and predict the unpredictable. Extending the “zoo of life forms” etc. means nothing more than the obvious fact that it is not just living organisms that evolve. I predict that many more such projects will be unveiled as professors urgently seek more funding.

DAVID: I view this as over-analysis. Biology does not lend itself to physics, but the information biology uses runs biology.

I would say individuality does not lend itself to mathematical formulas.

Biological complexity: problem, define an individual

by David Turell @, Sunday, July 19, 2020, 21:37 (1349 days ago) @ dhw

QUOTE: “'Think about building a kind of microscope which would allow me to see information being propagated forward in time,” Krakauer said. They described a mathematical framework that breaks information flows down into parts and evaluates individuality based on how different combinations of environmental influences and internal dynamics can predict a system’s future states.

dhw: As if any mathematical framework can predict changing environmental influences! Even internal dynamics can be changed by those influences! And not even we as individuals can predict how our internal dynamics will function when faced with unknown environmental influences!

QUOTE: "Within this theory, individuals can be cells, tissues, organisms, colonies, companies, political institutions, online groups, artificial intelligence or cities — even ideas or theories, according to Krakauer. “What we’re trying to do is discover a whole zoo of life forms that extend far beyond what we have conventionally called living,” he said.

dhw: What they are trying to do is change the definition of “individual” and predict the unpredictable. Extending the “zoo of life forms” etc. means nothing more than the obvious fact that it is not just living organisms that evolve. I predict that many more such projects will be unveiled as professors urgently seek more funding.

DAVID: I view this as over-analysis. Biology does not lend itself to physics, but the information biology uses runs biology.

dhw: I would say individuality does not lend itself to mathematical formulas.

It is nice to fully agree.

Biological complexity: weird manganese eating bacteria

by David Turell @, Tuesday, July 21, 2020, 19:01 (1347 days ago) @ David Turell

Found recently in a lab sink:

https://www.sciencenews.org/article/scientists-stumbled-across-first-known-manganese-fu...

"Scientists have discovered the first bacteria known to use the metal manganese to grow. And the researchers had to look only as far as the office sink.

***

"When bacteria do borrow electrons from manganese, they convert the metal to a dark material called manganese oxide. Manganese oxide is found all over the planet — from deposits in Earth’s crust to the seafloor to drinking water. And, as it turned out, in Leadbetter’s glass jar.

***

"Leadbetter and Yu first identified about 70 bacterial species in the jar, which likely came from the tap water. The pair then isolated two bacterial species that, when present together, generate manganese oxide. Given manganese carbonate, these bacteria multiplied exponentially. As the bacterial population size increased, the rate of manganese oxide production increased along with it, suggesting that the bacteria were using manganese as fuel.

"The team dubbed the newly identified species ‘Candidatus Manganitrophus noduliformans’ and Ramlibacter lithotrophicus. The researchers don’t yet know the exact role of each species. Both might be integral in generating energy from the manganese or one could be the main driver.

"The findings could help researchers manage manganese oxide that pollutes drinking water, says Amy Pruden, an environmental scientist at Virginia Tech in Blacksburg who was not involved in the study. “Now that we have an idea of who the manganese oxidizers are, we can start looking for them in drinking water systems and maybe we can find better controls.”

"Leadbetter suspects that similar bacteria may also be responsible for grapefruit-sized balls of manganese oxide on the ocean floor, first spotted in the 1870s, that have puzzled scientists. He wants to search there and other places for more examples of bacteria that use manganese for energy.

“'Let’s see if we can find these organisms in other environments,” Leadbetter says. “Not just my sink.'”

Comment: I've described electron-eating bacteria before. Not unusual.

Biological complexity: how cells move molecules

by David Turell @, Friday, July 24, 2020, 00:28 (1344 days ago) @ David Turell

In very special packages:

https://phys.org/news/2020-07-biologists-cells-resources.html

"Florida State University researchers have new insight into the tiny packages that cells use to move molecules, a structure that is key to cellular metabolism, drug delivery and more.

***

"Scientists have previously observed cells create vesicles—fluid-filled sacks that move materials within a cell or from one cell to another. They have also observed a protein called clathrin form a cage-like arrangement that made up the outside structure of vesicles.

"But there were still questions about how exactly clathrin forms those structures and what determines the shapes it can take.

***

"Using high-powered microscopes, the FSU researchers discovered that another protein, known as an adaptor protein, ties multiple clathrin molecules together in a way that allows those structures to take on different sizes.

"They also showed that the clathrin coat could make a so-called "basket" shape, and one that scientists had thought the protein could not form, showing that clathrin assembly is more complicated than previously thought.

***

"'This shows that there are things we don't understand about how clathrin coat assembly is regulated and progresses in cells," Stagg said. "Our hypothesis is that the cargo that vesicles carry has a role in dictating how the coats are made and that explains why we see different structures."

"The ability for cells to form vesicles is essential. It is the main route by which molecules like hormones, proteins and viruses enter cells and move within them. If it stops working, cells can die, or disease can take hold in an organism. (my bold)

"Understanding cellular transport is also important because the process is often hijacked by viruses like influenza or the virus that causes COVID-19 to gain entry to the cell.

"'Understanding the molecular mechanisms of clathrin-based transport is important because it is such a fundamental process," Stagg said. "It touches on so many cellular processes. The better we understand it, the more likely it is that we can manipulate it to do things like stop virus entry, enhance drug delivery inside cells or modulate neurotransmitter levels in the brain, just to mention a few. It's a really exciting time for clathrin research.'"

Comment: Another very complex mechanism to transport molecular product. Note my bold. All biochemists know mistakes happen. None of life's processes are fail-safe despite many safeguard systems in place.

Biological complexity: cell 'water wires' pass info

by David Turell @, Wednesday, July 29, 2020, 23:59 (1339 days ago) @ David Turell

One molecule wide channels pass ions:

https://evolutionnews.org/2020/07/biophysicists-find-water-wires-are-biological-informa...

"Water conducts electricity; it can also conduct energy and information. Biophysicists are finding that “water wires” at the nanoscale fine-tune enzymatic actions — indeed, can be indispensable for function.

***

"Cells need to both attract the right molecules to go through the channel and authenticate them through the “selectivity filter.” Water can assist this process via electricity. Since H2O is bipolar, single water molecules in a chain, held together by hydrogen bonds, become a sort of “wire” through which ions can pass. Additionally, the fact that some amino acids are hydrophilic allows biological channels to attract water molecules to the exact positions inside the channel where they can assist the selectivity filter.

***

"Water wires are critical for the functioning of many membrane proteins, as in channels that conduct water, protons, and other ions. Here, in liquid crystalline lipid bilayers under symmetric environmental conditions, the selective hydrogen bonding interactions between eight waters comprising a water wire and a subset of 26 carbonyl oxygens lining the antiparallel dimeric gramicidin A channel are characterized by 17O NMR spectroscopy at 35.2 T … and computational studies.

***

"The results reveal that selective pore-lining carbonyl oxygens form remarkably stable hydrogen bonds with waters in the wire, such that the water wire does not change its orientation on the millisecond NMR timescale. The stable orientation of the water-wire dipole also provides a simple explanation for the low affinity of the second cation binding site in this dimeric channel, despite a separation of ∼24 Å from the first binding site at the opposite end of the pore.

***

"The water wire itself has a stability gradient from the negative end of the electric dipole to the positive end, based on optimal hydrogen bonding of the waters at the negative end of the electric dipole. The water interactions at this end of the dipole over the first three waters of the water wire are particularly stable.

"Is there a reason why the hydrogen bonds need to be stable? Yes; the timing of passage of cations requires that the binding sites not flip too quickly.

"Water wires are critical biological assemblies supported by membrane proteins for the purposes of transporting charge and ions across membranes.

***

"In short, the spacing of all the amino acids and water molecules is optimized for function. The first ion is sucked in, forming its stable hydrogen bonds with the water, so that the second ion entering the channel doesn’t flip the dipole over and break the flow. That requires precision foresight both positionally and temporally. And this is one of the simplest examples found in a bacterium! It is fair to expect even more optimization will be found in future studies of water wires in more complex membrane channels.

***

"The profound influence of the water wire in this model system and the stable water–carbonyl interactions illustrate the significance and functionality for such wires in many channels and materials. In particular, the stability of the water wire and its electric dipole suggests that its influence in many other systems could be more significant than generally recognized. To achieve such an understanding, unique 17O spectroscopy as reported here at a field strength of 35.2 T demonstrates the exquisite sensitivity to the chemical environs surrounding oxygen sites where so much of biological chemistry takes place."

Comment: This is why water must be present for life to appear. An amazingly designed system, not by chance. The source article is extremely complex:

https://www.pnas.org/content/117/22/11908.full

The abstract first sentence: "Water wires are critical for the functioning of many membrane proteins, as in channels that conduct water, protons, and other ions. Here, in liquid crystalline lipid bilayers under symmetric environmental conditions, the selective hydrogen bonding interactions between eight waters comprising a water wire and a subset of 26 carbonyl oxygens lining the antiparallel dimeric gramicidin A channel are characterized by 17O NMR spectroscopy at 35.2 T (or 1,500 MHz for 1H) and computational studies." "Nuff said.

Biological complexity: how cells fight dehydration

by David Turell @, Wednesday, August 05, 2020, 00:08 (1332 days ago) @ David Turell

Their structure can only survive so much dehydration:

https://phys.org/news/2020-08-protein-adverse-impact-loss-cells.html

"A researcher has found how a protein inside the body reduces the adverse effects of hypertonicity, an imbalance of water and solutes inside cells. Hypertonicity causes cell shrinkage and eventual cell death. The findings could have implications for a wide range of illnesses including edema from brain tumors, autoimmune diseases and kidney damage.

"'We have found a mechanism for how the protein, called Nuclear Factor of Activated T cells 5 (NFAT 5), works to regulate tonicity particularly in response to hypertonicity," said Raj Kumar, clinical professor of biochemistry, UH College of Medicine. Kumar is reporting his findings in the journal Proceedings of the National Academy of Sciences. NFAT5 plays a crucial role protecting cells against harmful effects of stress in tissues, such as the kidneys, that experience large fluctuations in fluid volume. When NFAT5 is activated, it expresses protective osmolytes, small solutes that impact the balance of fluids and help maintain the integrity of cells. Kumar found that the work of osmolytes doesn't stop there. In a symbiotic process, they also may activate NFAT5.

"'NFAT5 makes osmolytes and osmolytes act on NFAT 5 to give it structure so it can activate genes," said Kumar. The first 200 amino acids in the genetic sequence of NFAT5 are intrinsically ordered, unstructured with no defined shape. Kumar found that osmolytes increase the structure in the region and once structured, NFAT5 interacts with other proteins, some critical to maintain cellular function.

***

"If you've ever owned a plant, you know how important water is to its lifeblood. Not surprisingly, water plays the same role with humans, making up about 70% of cell mass. For all 70 trillion cells in the human body, each one needs the balance of water and solutes to carry out its mission, assuring the body, its organs and tissues, all work properly.

"But that delicate balance is sometimes disturbed and, just as when water leeches out of plant cells causing the plant to die, when water leeches out of human cells, via osmosis, cell death begins as the cells start shrinking.

"'Mammalian cells have adaptive responses that enhance survival during various forms of stress," said Kumar. "Cells adapt to hypertonic stress by accumulating organic osmolytes, which are known to compensate for the cell volume reduction induced by the hyperosmotic environment by allowing for the osmotic influx of water into cells."

"The findings raise the possibility that increased intracellular ionic strength and elevated osmolytes caused by hypertonicity activate and stabilize NFAT5."

Comment: Organisms must appear armed with this complex defense mechanism, or the would not survive severe dehydration. Only design fits

Biological complexity: bacterial double wall

by David Turell @, Thursday, August 13, 2020, 18:35 (1324 days ago) @ David Turell

How it works is a feedback loop with complex lipoproteins:

https://www.nature.com/articles/d41586-020-02256-x?WT.ec_id=NATURE-202008&sap-outbo...

"Feedback inhibition occurs when the product of a metabolic pathway diminishes its own production by triggering a decrease in the activity of a key enzyme in the pathway. Such inhibition controls the production of lipopolysaccharide (LPS) molecules, which are an integral part of the outer membrane of some bacteria. It has long been suspected that the feedback signal responsible for regulating LPS biosynthesis is either LPS itself, or one of its precursors1. But, writing in Nature, Clairfeuille et al.2 add to a flurry of recent work3–5 showing that the membrane protein PbgA is the long-sought LPS signal transducer in the bacterium Escherichia coli. The current study extends our understanding of PbgA by providing a high-resolution structure of the protein bound to LPS.

***

"Investigations published this year of how this pathway is regulated have produced a model in which PbgA on the inner membrane modulates the activity of LpxC by interacting with LapB — a protein that guides the enzyme FtsH to degrade LpxC1. So when levels of LPS are low, PbgA inhibits the interaction between LapB and FtsH in the inner membrane, stabilizing LpxC and promoting LPS biosynthesis. When the number of LPS molecules exceeds a threshold in the outer membrane, LPS transport across the bridge ceases. LPS accumulates on the external surface of the inner membrane, which can cause the formation of potentially lethal irregular membrane structures3. By sensing the accumulated LPS, PbgA can relax its inhibition of LapB–FtsH. LpxC can be degraded, thus diminishing LPS biosynthesis and restoring the phospholipid–LPS balance

***

"Clairfeuille and co-workers’ structure reveals that PbgA binds the lipid A moiety through a linker domain, using an amino-acid sequence that has not been reported in any other LPS-binding protein. Mutations in this LPS-binding motif compromised PbgA function. In a final set of experiments, the authors demonstrated that a synthetic peptide based on this sequence could bind LPS and inhibit bacterial growth. Through rational design, they improved the peptide’s antibiotic spectrum and potency.

"The polymyxins bind lipid A by interacting with both of its phosphorylated sugars18, but PbgA binds to just one. The polymyxin antibiotic colistin is used as a last resort for treatment of infections in the clinic, but it can also increase outer membrane permeability, thereby sensitizing bacteria to more-effective antibiotics. Clairfeuille and co-workers’ show that the PbgA-derived peptide also sensitizes bacteria to other antibiotics, acts in synergy with colistin, and is not hampered by the LPS modifications catalysed by EptA."

Comment: Feedback loops are complex. This article shows are highly complex they can be. There is no way they c an appear as a complete mechanism by chance. They have to be designed all at once at the beginning of the organism. Only a diagram can explain all this complexity to you.

Biological complexity: protecting cell DNA from auto-attack

by David Turell @, Thursday, August 13, 2020, 22:12 (1324 days ago) @ David Turell

DNA loose from the nucleus will be attacked by cellular defense mechanisms unless a backup defense steps in:

https://phys.org/news/2020-08-protein-cells-dna.html

"Viruses multiply by injecting their DNA into a host cell. Once it enters the intracellular fluid, this foreign material triggers a defense mechanism known as the cGAS-STING pathway. The protein cyclic GMP-AMP Synthase (cGAS), which is also found inside the fluid, binds to the invading DNA to create a new molecule. This, in turn, binds to another protein called Stimulator of Interferon Genes (STING), which induces an inflammatory immune response.


"Sometimes, the material contained inside the fluid—and in contact with the cGAS protein—comes not from a virus but from the cell itself, for instance after the nucleus has accidentally ruptured. When this happens, the cGAS-STING pathway isn't activated. Scientists at EPFL have demonstrated how cells are able to respond differently to their own DNA and to genetic material from a pathogen—and avoid attacking the wrong target. Their discovery, published in a paper in the journal Science, sheds new light on the complex processes at work in the body's inflammatory response.

"The team, led by Prof. Andrea Ablasser and working with colleagues from the laboratories of Prof. Beat Fierz and Prof. Selman Sakar, uncovered new insights into the key role of a small protein known as Barrier-to-Autointegration Factor (BAF). They showed that, by binding to the inoffensive DNA, BAF prevents the cGAS protein from doing the same, thereby stopping the cGAS-STING pathway in its tracks.

***

"There are various ways to cause a nucleus to rupture, such as by applying mechanical pressure. But according to Baptiste Guey, one of the paper's lead authors, only one of these methods—removing the BAF protein—induces an immune response. "We can therefore conclude that BAF plays a key role in preventing the cell from attacking its own DNA," says Guey.

"The protein's inhibitor role is vitally important: Although the cGAS-STING pathway helps the body fight off infections, it also needs to be kept in check. "Nuclei do occasionally rupture, but cells are able to repair the damage," says Marilena Wischnewski, another lead author of the paper. "If cGAS bound to the DNA every time that happened, the consequences would be more serious."

***

"The protein is found in varying quantities in different types of cells. The team is planning to dig deeper into these variations as they seek to understand how different tissue types respond to infection and inflammation."

Comment: this is another protective mechanism that had to be designed and in place when when organisms appeared in evolution. Too complex for chance development.

Biological complexity: controlling intercellular signalling

by David Turell @, Tuesday, August 25, 2020, 20:36 (1312 days ago) @ David Turell

The cells have a method of constricting molecular movement to allow proper interpretation:

https://phys.org/news/2020-08-enzyme-prisons-cell-molecule.html

"There are up to a hundred different receptors on the surface of each cell in the human body. The cell uses these receptors to receive extracellular signals, which it then transmits to its interior. Such signals arrive at the cell in various forms, including as sensory perceptions, neurotransmitters like dopamine, or hormones like insulin.

"One of the most important signaling molecules the cell uses to transmit such stimuli to its interior, which then triggers the corresponding signaling pathways, is a small molecule called cAMP. This so-called second messenger was discovered in the 1950s. Until now, experimental observations have assumed that cAMP diffuses freely—i.e., that its concentration is basically the same throughout the cell—and that one signal should therefore encompass the entire cell.

***

"The team now reports in Cell that, contrary to previous assumptions, the majority of cAMP molecules cannot move around freely in the cell, but are actually bound to certain proteins—particularly protein kinases. In addition to the three scientists and Professor Martin Falcke from the MDC, the research project involved other Berlin researchers as well as scientists from Würzburg and Minneapolis.

"'Due to this protein binding, the concentration of free cAMP in the cell is actually very low," says Professor Martin Lohse, who is last author of the study and former head of the group. "This gives the rather slow cAMP-degrading enzymes, the phosphodiesterases (PDEs), enough time to form nanometer-sized compartments around themselves that are almost free of cAMP." The signaling molecule is then regulated separately in each of these tiny compartments. "This enables cells to process different receptor signals simultaneously in many such compartments," explains Lohse. The researchers were able to demonstrate this using the example of the cAMP-dependent protein kinase A (PKA), the activation of which in different compartments required different amounts of cAMP.

***

"The team's measurements showed that most compartments are actually smaller than 10 nanometers—i.e., 10 millionths of a millimeter. This way, the cell is able to create thousands of distinct cellular domains in which it can regulate cAMP separately and thus protect itself from the signaling molecule's unintended effects. "We were able to show that a specific signaling pathway was initially interrupted in a hole that was virtually cAMP-free," said Annibale. "But when we inhibited the PDEs that create these holes, the pathway continued on unobstructed."

"'This means the cell does not act like a single on/off switch, but rather like an entire chip containing thousands of such switches," explains Lohse, summarizing the findings of the research. "The mistake made in past experiments was to use cAMP concentrations that were far too high, thus enabling a large amount of the signaling molecule to diffuse freely in the cell because all binding sites were occupied.'"

Comment: this complex design shows how molecules are carefully controlled to avoid error and create clear signals.

Biological complexity: differing cell responses

by David Turell @, Tuesday, September 01, 2020, 17:45 (1305 days ago) @ David Turell

This article expresses surprise at cells variable responses. I don't know why. Any biologist knows feedback loops control output. Why shouldn't muscle cells vary in their output also, tailored to need?:

https://phys.org/news/2020-09-responses-individual-cells-muscles.html

"Minute differences in individual muscle cell contractions allow the entire muscle to flex with greater control and accuracy. Long dismissed as "noise" or error, experts now suspect that biological systems may have evolved to include unavoidable variation as a form of information in their communication channels.

"'The differences between cells' responses to stimulation is actually another form of information," said Professor Shinya Kuroda

***

"Reliable and accurate responses to all levels of stimulation ensure that cells' differences remain consistent and therefore meaningful, rather than unpredictable and chaotic. The variation between cells means that, as a whole, the muscle tissue can detect a wider range of stimulation intensities and can respond with a corresponding wider range of control. If all cells responded identically, the whole muscle tissue could only perform on/off binary responses.

***

"This concept of individual cell variability communicating essential information through biological systems may also be relevant to other processes where life requires a wide spectrum of responses, like hormone secretion. For example, the pancreas may be able to release different amounts of insulin hormone due to individual beta cells of the pancreas responding differently to blood sugar levels."

Comment: The bold is something I was taught in Med school!!! What was known as an old idea is now new!

Biological complexity: molecules fold, interpret information

by David Turell @, Wednesday, September 02, 2020, 23:14 (1304 days ago) @ David Turell

How information and sensations are transmitted by molecules:

https://evolutionnews.org/2020/08/research-reveals-biological-design-in-the-sensing-and...

"A paper in PNAS on describes the properties of talin, “an adaptor protein that transduces mechanical signals into biochemical cues by recruiting a network of protein ligands in a force-dependent way.” This example complements our earlier article about mechanotransduction. Once again, fine tuning of forces and materials is found, but this time at a scale that is orders of magnitude smaller.

"These force cues have a complex nature, oscillate in time with different frequency components, and are often embedded in noise. However, most assays to explore the mechanics of force-sensing proteins rely on simple perturbations, such as constant or ramped forces. Here, we use our magnetic tweezers design to subject single talin domains to oscillatory forces and external mechanical noise. We show that talin ignores random external fluctuations but synchronizes its folding dynamics with force oscillations in a frequency-dependent way. We hypothesize that this finely tuned response could underpin talin force-sensing properties.

"Talin’s job as an “exquisite force sensor” is to grab and hold parts together inside the cell.

"Talin is a mechanosensing hub protein in focal adhesions, which cross-links transmembrane integrins with the active F-actin filaments and recruits several binding proteins to control the function and fate of this organelle. For example, vinculin binds to cryptic helices in mechanically unfolded talin domains, subsequently recruiting actin filaments that reinforce the cellular junction. Hence, talin transduces mechanical forces through its folding dynamics.

"This enzyme senses motions of neighboring cells or the extracellular matrix. Somehow, talin deconvolves this noisy signals of motion into recognizable oscillations at particular frequencies and knows how to respond. Its spring-like domains unfold so that other molecules can attach, and then it binds them together. It is a truly remarkable reaction that differs from other types of mechanosensing, opening the door for more discoveries in biophysics at the molecular scale:

"Although initially formulated in the context of nonlinear physics, stochastic resonance has been demonstrated in a broad range of biological systems, with particular emphasis as a sensory mechanism in mechanoreceptors, like the crayfish hair cells, the cricket cercal system, or the vestibular and auditory system. Interestingly, in all of these examples, signal transduction involves the activation of gated ion channels, which convert mechanical perturbations into electrophysiological signals. However, mechanotransduction also involves biochemical signaling, where force stimuli trigger downstream signaling pathways through a complex network of interacting proteins. In this sense, it remains to be explored whether stochastic resonance could also play a role in mechanotransduction pathways that involve ligand binding to force-bearing proteins instead of gating of mechanosensitive channels.

"In the case of talin, the implications for design are clear:

"Mechanical signal transduction relies on the robust and finely tuned response of molecular force sensors.Mechanical information is encoded in both the amplitude of the signal and its time-dependent evolution. Hence, both components must be accurately deciphered and interpreted by cellular force sensors.

"The only evolution spoken of in the paper is the “time-dependent evolution” (unfolding) of the vibrations that talin senses: i.e., the behavior of the oscillations from initiation to damping. That ability implies even more design than a simple response to a vibration. It implies that talin can recognize encoded information both in the signal strength and in its behavior in time, and respond accordingly by unfolding the appropriate domain for binding to other protein parts. The three authors from Columbia University describe the actions of this enzyme as a “tuning fork of cellular mechanotransduction.”

"No Miracles Here

"These examples of biological mastery of force are not miracles; they are subject to the laws of physics and obey the laws of physics. But wow, do they know how to take advantage of the laws of physics! From the mightiest dinosaur, to the largest birds, to the tiniest spider, to molecules in the cell, biological designs show how to push the limits of the possible. Such exceptional applications of materials and forces rightly excite our wonder and admiration."

Comment: Another entry from the ID website showing the necessity for a designer.

Biological complexity: G.I. neuron network controls

by David Turell @, Friday, September 04, 2020, 20:46 (1302 days ago) @ David Turell

Neuron network is difficult to study but new techniques have shown partially how it works:

https://medicalxpress.com/news/2020-09-single-cell-atlas-nerve-cells-gut.html

"Embedded throughout the gastrointestinal system is an extensive array of neurons that coordinates nearly all activities involved in digestion, gut motility, and response to noxious stimuli. These cells make up the enteric nervous system (ENS) and transmit signals from the gut to the brain, but are rare and fragile, making them difficult to isolate and study.

"A team led by researchers at the Broad Institute of MIT and Harvard and Massachusetts General Hospital has now overcome these challenges with new methods that they developed to generate a single-cell map of the ENS in humans and mice.

"By analyzing gene activity in these individual neurons, the scientists infer that neurons in the gut are communicating with a variety of other cell types, including immune cells. They also found that key genes associated with disease are expressed in these cells.

"The findings suggest that the ENS is a central hub linking the intestinal, immune, and central nervous systems, and plays an important role in allergic, inflammatory, and motility disorders of the gut, as well as diseases affecting the brain.

"The team's analysis revealed dozens of distinct subsets of neurons in the enteric nervous system and showed that the composition of the cells and their gene expression varied by anatomical region of the gut, age, and even time of day when the sample was taken.

"The data also suggest multiple new circuits between different subtypes of neurons and surrounding cells. The connections found between the enteric neurons and the immune system could help guide future study of how the nervous system might be involved in gastrointestinal disease, and why certain diseases of the central nervous system, such as autism spectrum disorder and Parkinson's disease, have gut dysfunction as an early symptom.

"Xavier says studying these enteric neurons could yield new insight into irritable bowel syndrome, allergic disorders of the gut, and unexplained enteric neuropathy (impairment or degradation of the nerves in the digestive system).

"'In many ways, the enteric neurons could be compared to the conductor of an orchestra," said Xavier. "For example, patients with food allergies often develop abdominal pain, nausea, vomiting, and diarrhea, all in a very short time, suggesting that the enteric neurons have sensed something wrong and activated an early warning system. Targeting these cells could potentially be a way to lessen allergic responses to food and other allergens.'"

Comment: This system of nerves and neurons controls the propulsion of the food along the intestinal cavity by a series of coordinated muscle series of contractions, that conducts the contents at exactly the right speed to allow for complete absorption of the nutrients. This has to have been designed. Chance cannot create this complex mechanism.

Biological complexity: controls of plant root absorption

by David Turell @, Friday, September 04, 2020, 20:58 (1302 days ago) @ David Turell

Carefully and complexly controlled to allow absorption of water, minerals and nutrients:

https://www.cell.com/current-biology/fulltext/S0960-9822(20)31154-4?_returnURL=https%3A...

"Casparian strips (CSs) are cell wall modifications of vascular plants restricting extracellular free diffusion into and out of the vascular system [1]. This barrier plays a critical role in controlling the acquisition of nutrients and water necessary for normal plant development. CSs are formed by the precise deposition of a band of lignin approximately 2 μm wide and 150 nm thick spanning the apoplastic space between adjacent endodermal cells. Here, we identified a copper-containing protein, Uclacyanin1 (UCC1), that is sub-compartmentalized within the CS. UCC1 forms a central CS nanodomain in comparison with other CS-located proteins that are found to be mainly accumulated at the periphery of the CS. We found that loss-of-function of two uclacyanins (UCC1 and UCC2) reduces lignification specifically in this central CS nanodomain, revealing a nano-compartmentalized machinery for lignin polymerization. This loss of lignification leads to increased endodermal permeability and, consequently, to a loss of mineral nutrient homeostasis.

***

"In conclusion, this study reveals the first loss-of-function phenotype for members of the plant-specific blue copper protein family of phytocyanins. Several studies suggested their implication in lignin polymerization, but this has never previously been shown. Our analysis indicates a role for the uclacyanins in the deposition of lignin in a newly discovered nanoscale domain within the CS. Further, the subcellular localization of UCC1, and the phenotype of the ucc(s) mutants, reveals a sub-compartmentalization of the machinery required for lignin polymerization at the CS."

Comment: A highly definitive study of proteins and gene controls of root absorption which is precisely controlled. Too complex for any process of origination except by design.

Biological complexity: removing cellular garbage

by David Turell @, Friday, September 04, 2020, 21:10 (1302 days ago) @ David Turell
edited by David Turell, Friday, September 04, 2020, 21:46

This is part of the error control system as it removes from the cells waste and improperly formed protein molecules:

https://phys.org/news/2020-09-scientists-reveal-key-formation-recycling.html

"Autophagy, from the Greek for "self-eating," is an essential process that isolates and recycles cellular components under conditions of stress or when resources are limited. Cargoes such as misfolded proteins or damaged organelles are captured in a double membrane-bound compartment called the autophagosome and targeted for degradation. A fundamental question concerns precisely how these "garbage bags" form in the cell. Scientists have now reconstructed the first steps in the formation of autophagosomes. They show that tiny vesicles loaded with the pro-tein Atg9 act as the seed from which the autophagosome emerges.

"Autophagosomes first form as cup-shaped membranes in the cell, which then grow to engulf the cellular material designated for destruction. The formation of these membranes is catalyzed by a complex machinery of proteins.

***

"One of the factors is Atg9, a protein whose importance in the process was known, but whose role was not clear. Atg9 is found in small intracellular vesi-cles. Researchers Justyna Sawa-Makarska, Verena Baumann and Nicolas Coudevylle from the Martens lab now show that they form a platform on which the autophagy machinery can assemble to build the autophagosome. "Atg9 vesicles are abundant in the cell, which means they can be rapidly recruited when autophagosomes are needed," explains group leader Sascha Martens.

"Cells encapsulate cargo in vesicles, so that they can be correctly transported and degraded in a chemical environment that is different to the one normally found in cells. Autophagosomes therefore consist of a double membrane made of phospholipids. This greasy envelope creates a waterproof package that separates material from the aqueous surroundings of the cell and marks it for degradation. However, Atg9 vesicles do not supply the bulk of the lipids to the growing autophagosome.

"The biogenesis of autophagosome involves numerous proteins. By isolating and characterizing 21 of these components, the scientists have been able to rebuild parts of the autophagy machinery in the "test tube" – an arduous process that took Sascha Martens and his team almost ten years. "With this approach we could reconstitute the early steps of autophagosome biogenesis in a controlled manner," he says. With the elaborate toolkit the Martens lab has developed, the scientists now aim to unravel the next steps in the biogenesis of the autophagosome."

Comment: This study describes a series of precise protein molecular steps. The system had to be in place with the appearance of the first cells, for continuous garbage accumulation would lead to cell death. Only design fits. This thought applies to origin of life. The very first cells that lived had to have a garbage system as an integral part of the cell. And obviously this is a very important part of God's error control editing system

Biological complexity: ATP rotor design shown

by David Turell @, Wednesday, September 16, 2020, 19:40 (1290 days ago) @ David Turell

ATP is used all through life to provide an energy supply. Its complex structure is now known:

https://www.sciencedaily.com/releases/2020/09/200914114134.htm

"ATP synthase is also referred to as complex V of the respiratory chain, a series of protein complexes in the membrane of mitochondria. This respiratory chain creates a proton gradient, which the ATP synthase uses to make ATP. Previously, Sazanov was the first to solve the protein structure of bacterial complex I, and the first to solve the structure of a mammalian complex I. In the new study, Sazanov and lab members Gergely Pinke and Long Zhou turned to mammalian complex V, the final unsolved structure in the mammalian respiratory chain. "F1Fo-ATP synthase is one of the most important enzymes on Earth. It provides energy for most life forms, including us humans, but until now, we didn't know fully how it works," explains Sazanov.

***

"In their high-resolution structure of Fo, the researchers found that the c-ring is plugged by two lipids, one from each side of the membrane. While the top (facing F1) lipid rotates along with the shaft, the bottom lipid does not rotate, as it is likely connected to the Fo domain via a "hook apparatus."

"This newly uncovered structure sheds light on a controversy in biology: how and where the so-called permeability transition pore opens. This pore is linked with cell death, and opens for example during strokes and heart attacks. So far, it was known that the pore forms in mitochondria in response to high levels of Calcium, but the pore's exact location remained unknown. Now, using the fully solved structure of F1Fo, Sazanov and his group can describe how the pore forms in F1Fo-ATP synthase: When Calcium binds in the F1 subunit, a large conformational change is induced. The complex has to accommodate this change, and in doing so, pulls on the hook apparatus. The apparatus in turn pulls out the lipid plug on the bottom side of the Fo, initiating pore opening. "When the pore is open for a longer period of time, the c-ring is destabilized and pore formation becomes irreversible," explains Sazanov. "This model is consistent with all available data from mutants. To be fully sure that this is how the permeability transition pore forms, one would need to solve the structure of ATP synthase during Calcium-induced transitions, which we are doing now.'"

Comment: Highly complex. Obviously designed.

Biological complexity: forming ribosomes

by David Turell @, Friday, September 18, 2020, 14:20 (1288 days ago) @ David Turell

Still only partially understood:

https://science.sciencemag.org/content/369/6510/1470

"How ribosomes are made
The formation of eukaryotic ribosomes is a complex process that starts with transcription of a large precursor RNA that assembles into a large 90S preribosome, which matures to finally give the 40S small subunit of the ribosome. Cheng et al. and Du et al. give insight into this process, using cryo–electron microscopy to look at intermediates along the pathway. Together, these studies reveal how a cast of molecular players act to coordinate the compositional and structural changes that transform the 90S preribosome into a pre-40S subunit.

"Abstract
Production of small ribosomal subunits initially requires the formation of a 90S precursor followed by an enigmatic process of restructuring into the primordial pre-40S subunit. We elucidate this process by biochemical and cryo–electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90S pre-ribosome, followed by Utp24 endonuclease–driven RNA cleavage at site A1, thereby separating the 5′-external transcribed spacer (ETS) from 18S ribosomal RNA. Next, the 5′-ETS and 90S assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40S emerges, still retaining some 90S factors including Dhr1, now ready to unwind the final small nucleolar U3–18S RNA hybrid. Our data shed light on the elusive 90S to pre-40S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins."

Comment: This is the core of protein production. Not by chance.

Biological complexity: how cells know what to do

by David Turell @, Monday, September 28, 2020, 18:47 (1278 days ago) @ David Turell

Very advanced new research:

https://phys.org/news/2020-09-reveals-wounds.html

Many cells in our bodies are on the move and somehow seem to 'know' where to go. But how do they learn the location of their destination? This question is key to understanding phenomena such as the renewal of cells in our body, the migration of cancer cells, and especially how wounds heal.

***

The researchers built a mathematical model to describe the interactions within a layer of cells on a substrate, similar to a layer of skin. These cells contain chemical signalers—proteins—that allow them to sense other cells around them, so whether they are pushed or pulled, and to control their own movement. What the scientists found is that the intricate interplay of cell movement, sensing of the environment, and states of protein activation within the cells combine to create coupled mechanical and chemical traveling waves in which directional information is encoded.

The mechanical wave appears as denser and sparser regions of cells alternating in space and time. The chemical wave appears as protein activity and is triggered by cell movement and mechanical feedback. The cells' chemistry in turn drives cell shape changes and movement closing a feedback loop with cell mechanics. In this coupled system these mechanical and chemical waves arise spontaneously due to feedback and amplification.

In a normal unwounded layer of cells, these waves propagate without a preferred direction, but when an artificial wound is introduced on one side, waves re-orient to propagate exclusively away from the wound. The researchers thus hypothesized that the waves could be a communication tool, allowing cells very far from the wound—and thus not directly "seeing" it—to sense which way to go.

A density wave makes the neighbors of a cell push and pull on it along the direction in which the wave is traveling. Since the forces exerted on the cell are equal and opposite between the crests and troughs of each wave, the result is that the cell just moves small distances back and forth without any net motion. In effect, the cell has no way of knowing the direction the wave came from and thus has no information about the location of the wound.

This is where the second wave of protein activity comes in. It hits the cell slightly after the density wave due to the delay that it takes for proteins to activate. And because protein activity controls the speed at which the cells move, a delay between the two waves allows for cells to move quickly when being pulled in the direction of the wound, and slowly when being pushed away. In this way, cells can break symmetry and start to move in the preferred direction towards the wound.

The researchers at Kyoto University observed this out-of-equilibrium behavior of wound healing during in vitro experiments with real cells on a substrate. They used a novel microscopy technique to allow them to measures protein activity within each cell: the protein was modified so that it lit up when activated thus revealing waves of protein activation propagating throughout the cell layer. The researchers were able to quantitatively predict the wave patterns, which they then also observed experimentally. More strikingly, they also found that the delay between the two waves was close to the theoretically predicted optimum for allowing cells to extract maximum information from the waves.

This mechanism of self-organization is remarkable for allowing robust and spontaneous communication of direction over large distances within cell layers. It demonstrates one way in which coordinated behavior can arise in our bodies helping them to heal and grow.

Comment: The cells are programmed to follow mechanical and chemical signals. The bold exhibits exquisite design.

Biological complexity: cell plasticity alters functions

by David Turell @, Monday, September 28, 2020, 18:58 (1278 days ago) @ David Turell

This is present in embryology and in immune systems which require altering cell functions:

https://phys.org/news/2020-09-method-cell-plasticity.html

"Cell plasticity is a property by which a cell can take on different and reversible identities. Cell plasticity is also essential for embryo development and for the correct function of the immune system. This property is also crucial in cancer as many cancer cells use it to gain resistance to chemotherapy and invade and colonize distant parts of the body.

***

"'The identity of each cell type is defined by a particular gene expression program. What makes plastic cells special is that, in addition to their identity genes, they can express at low levels genes belonging to other cell identities. This sort of "background noise" is what allows them to change identity at a given time, and what was once "background noise" becomes the dominant genetic program," explains Serrano.

***

"'We have observed that CDK8 inhibition strengthens the expression of genes that determine cell identity, and this occures at the expense of switching off the "background noise" of alternative identities. So the cells are fixed in a specific identity and they lose their plasticity," says Cian J Lynch, first author of the study and postdoctoral fellow in the same laboratory."

Comment: CDK8 is a very specific protein with very strong influence on how a cell develops its form and function. How did chance evolution find this specific molecule? Not ,likely. Design fits.

Biological complexity: protection from nasty enzymes

by David Turell @, Monday, September 28, 2020, 19:08 (1278 days ago) @ David Turell

Enzymes that destroy cellular garbage can severely damage good tissue if the get loose:

https://phys.org/news/2020-09-lipids-lysosomes-autophagy-keys-kidney.html

Lysosomes are cellular waste disposal organelles containing potent enzymes. These enzymes can cause cellular damage if they leak out of ruptured lysosomes. In a recent study led by Osaka University, researchers found that several distinct pathways involved in the repair or elimination of damaged lysosomes work together in response to lysosomal damage. The proper activation and function of these pathways was essential for preventing kidney injury in a mouse model of oxalate crystal-induced kidney damage.

Human cells need to work like well-oiled machines to keep our bodies running as they should. Waste products such as misfolded proteins, damaged cellular components, and carbohydrates get in the way and must be quickly disposed of. Dealing with this cellular "trash" are spherical, membrane-bound organelles called lysosomes filled with a mixture of potent enzymes. In a process called autophagy, waste products are contained within a double-membraned vesicle, called an autophagosome, that fuses with a lysosome. The lysosomal enzymes then get to work breaking down the waste into components that can be recycled.

The problem with lysosomes is that if they are ruptured, their contents can leak out and cause serious damage to the cell. Calcium oxalate crystal-induced kidney injury, which is linked to the progression of chronic kidney disease, is actually the result of lysosomal damage caused by the crystals. It is not surprising then that cells have several pathways to repair or quickly eliminate damaged lysosomes. Yet the exact steps in these pathways and how they interact during the lysosomal damage response are not entirely clear.

***

"A protein called TFEB turns on genes necessary for autophagy and the production of new lysosomes in response to lysosomal damage," explains lead author Shuhei Nakamura. "By inhibiting TFEB function in HeLa cells and then inducing lysosome damage, we confirmed that TFEB is activated upon lysosomal damage and is necessary for the removal of damaged lysosomes."

Attachment of lipids to a protein called LC3 is an essential step in the formation of the autophagosome. To their surprise, the researchers also found that lipidated LC3 was necessary for the activation of TFEB during the lysosomal damage response, but there was no clear link between the systems.

"Calcium is a known activator of TFEB," says senior author Tamotsu Yoshimori. "To identify how the TFEB and LC3 systems overlapped, we investigated lysosomal calcium channel TRPML1. We found that lipidated LC3 was recruited by lysosomes in response to damage, and that the lipidated protein interacted with TRPML1, causing increased calcium efflux from the lysosome, which activated TFEB."

The physiological importance of this interaction was then confirmed using a mouse model of oxalate crystal-induced kidney damage. Mice lacking TFEB had more severe kidney damage compared with control animals. Understanding how these pathways interact is the first step in preventing lysosomal damage-associated diseases.

Comment: A highly sophisticated protection system which could not develop stepwise in evolution. It had to be a designed protection system from the beginning, or life would not have ever survived.

Biological complexity: molecular machines seen clearly

by David Turell @, Friday, October 02, 2020, 19:12 (1274 days ago) @ David Turell

The molecules act in more precise and amazing ways than previously imagined:

https://evolutionnews.org/2020/09/new-research-finds-molecular-machines-are-even-more-a...

"Images of the molecular machines that Michael Behe brought to public attention 21 years ago were dim and fuzzy at the time but were convincing enough then to make a strong case for irreducible complexity. Now, new imaging techniques such as cryo-electron microscopy allow scientists to look at individual parts of the machines at near-atomic resolution.

***

"In 1997, John E. Walker shared the Nobel Prize in Chemistry with Paul Boyer and Jens Skou for discovering that ATP was synthesized in cells by a rotary engine.

***

"The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. [Emphasis added.]

"A “Grotthus mechanism” is a hand-off series something like a bucket brigade. The protons that power the rotor do not just flow by themselves; they are passed along to the inlet by a bucket brigade of water molecules, which take in each proton and hand it off to the next water molecule.

***

"Since 1997, researchers also found that ATP synthase machines come in pairs (dimers). The dimers, further, are mounted in rows on folds of the cristae (the membranes within mitochondria). The precise angle between the two dimerized motors and the spacing between them maximizes proton intake. The new paper says that the angle between the dimers flexes a bit, damping vibrations even more, thanks to specific molecules at the pivot of the wedge that allow some flexing, but not too much:

"Our structure of bovine dimers has a wedge made of small proteins and specific lipids in the membrane domain of each monomer that imposes a range of acute angles on the central axes of the monomers, and a pivot between the wedges accommodates rocking motions of the machine accompanying catalysis and other movements that happen independently. It also throws light on how the membrane rotor is made to turn."

***

"Publishing in Nature Communications,3 Al-Otaibi and six others in the UK used cryo-electron microscopy to study the “structure of the bacterial flagellum cap complex” that “suggests a molecular mechanism for filament elongation.”

"The pentagonal cap, looking somewhat like a stool, is composed of FliD proteins. This cap is first extruded in pieces through the central channel of the hook. Its subunits self-assemble at the end, while forming “an extensive set of contacts across several subunits, that contribute to FliD oligomerization.” The cap then guides individual flagellin proteins coming up through the channel into their positions in the growing filament, as shown in the animation. This is a well-controlled process, they found, dependent on the precise arrangement of amino acids in each protein, so that contacts work as intended."

"Once outside of FliD, we propose that exposed hydrophobic residues act as a chaperone, and promote flagellin folding in its insertion site. In order to accommodate the next flagellin subunit, conformational changes need to occur to open an adjacent binding pocket. We propose that the folding of the new flagellin protomer leads to dislodging of the cap complex, that rotates by ~65°, thus positioning an adjacent cavity of the cap complex close to the next flagellin insertion site (Fig. 5). This hypothesis agrees with previously proposed mechanisms of flagellar elongation."

Comment: The best way to appreciate this degree of complexity is to view some of the videos on the internet. There are rare mistakes that are edited out. This is an older (2014) video from Facebook which takes sometime to download and does not show these newest findings. This can happen only through exact design. How much detail of these machines must be shown before a designer is accepted?

Biological complexity: molecular machines seen clearly

by David Turell @, Thursday, October 08, 2020, 04:46 (1268 days ago) @ David Turell

More on rotary proton pumps:

https://www.sciencedaily.com/releases/2020/10/201007145304.htm

"All cells with nuclei, from yeast to humans, are organized like cities, with a variety of small compartments -- organelles -- that serve as factories where various types of work are done. Some of those factories, like the ones that break down and recycle molecules, need to continually pump in protons -- hydrogen atoms with their electrons stripped off -- to maintain the acidic environment they need to do their job. For this they rely on molecular Ferris wheels.

"Embedded in the organelle's fatty outer membrane, these microscopic machines have rotors that spin 100 times per second, picking up protons from outside the organelle and dropping them off on the inside.

***

"'Malfunctions in these molecular machines contribute to diseases such as osteoporosis, neurodegeneration, diabetes, cancer and AIDS, so understanding them is important for human health."

***

"No human cell can function without proton pumps, which among other things help organelles intercept viruses and other pathogens and divert them to cellular trash bins.

***

"The simulations, which incorporated cryo-EM structures derived from images of the yeast Ferris wheel captured at two different points in its rotation, confirmed the experimentally observed water molecules lining up to form "wires" at the proton drop-off point. These wires convey protons from their seats on the Ferris wheel to landing spots inside the organelle, like a fire brigade passing buckets hand to hand, bridging a gap they couldn't navigate on their own."

Comment: Very precisely designed pumps. These irreducibly complex mechanisms cannot appear by chance. A designer is required.

Biological complexity: heart muscle precise design

by David Turell @, Wednesday, October 14, 2020, 20:13 (1262 days ago) @ David Turell

The muscle fibers are specifically tailored at the same length for proper contractions:

https://phys.org/news/2020-10-molecular-heart.html

"Filament-like proteins in heart muscle cells have to be exactly the same length so that they can coordinate perfectly to make the heart beat.

"Another protein decides when the filament is the right size and puts a wee little cap on it. But, if that protein makes a mistake and puts the cap on too early, another protein, leiomodin, comes along and knocks the cap out of the way.

"This little dance at the molecular scale might sound insignificant, but it plays a critical role in the development of healthy heart and other muscles. Reporting in the journal, Plos Biology, a WSU research team has proven for the first time how the mechanism works.

***

"Heart muscle is made of tiny thick and thin filaments of proteins. With the help of electrical signals, the rope-like filaments bind and unbind in an intricate and precise architecture, allowing heart muscle to contract and beat.

"The thin filaments are made of actin, the most abundant protein in the human body. Tropomysin, another protein, wraps itself around the actin filaments. Tropomyosin together with two other proteins, tropomodulin and leiomodin, at the end of the actin filaments act as a sort of cap and determine the filament length.

"'It's beautifully designed," said Kostyukova, whose research is focused on understanding protein structures.

"And, tightly regulated.

"To keep heart muscle healthy, the actin filaments, which are about a micron long, all have to be the exact same length. In families with cardiomyopathy, genetic mutations result in formation of filaments that are either too short or too long. Those affected can have significant heart problems that cause disability, illness and death."

Comment: I don't have to comment about the marvels of the design, as the authors have done it.

Biological complexity: kidney filtration barely understood

by David Turell @, Friday, October 16, 2020, 14:42 (1260 days ago) @ David Turell

Finding another small step in the process:

https://science.sciencemag.org/content/370/6514/305.1?utm_campaign=twis_sci_2020-10-15

"When the kidneys filter the blood through structures called glomeruli, circulating proteins such as albumin are reabsorbed to limit proteinuria (protein in the urine) and prevent damage to kidney cells. Gualdani et al. found that mechanosensing induced by fluid flow through the kidneys activated the cation channel TRPV4 to promote the endocytosis of albumin by kidney cells. Experimental manipulations that impair glomerular filtration exacerbated proteinuria in mice lacking TRPV4. Thus, defects in TRPV4-mediated endocytosis may underlie proteinuria, a symptom of many kidney diseases."

Comment: The kidneys are constantly at work maintaining fluid and mineral balance in the body. We still hardly understand it. This is one new small step. Thre is no way to deny design when studying this.

Biological complexity: Driving the production of ATP energy

by David Turell @, Thursday, October 29, 2020, 20:52 (1247 days ago) @ David Turell

Mammalian respiratory complex I is a huge enzyme whose structure in now more understood:

https://science.sciencemag.org/content/370/6516/eabc4209?utm_campaign=toc_sci-mag_2020-...

"Secrets of a proton pumping machine:
Mitochondrial complex I serves as a primary entry point for electrons from the tricarboxylic acid cycle into the mitochondrial electron transport chain. This massive, membrane-embedded protein complex must couple quinone reduction to conformational changes across more than 150 angstroms within four separate proton pumps. Kampjut et al. determined five structures of complex I in states along the catalytic cycle, a deactive conformation, and one with the inhibitor rotenone bound. The resolution of some structures was sufficient to see water molecules and to trace putative paths for proton transfer within the proton-pumping membrane domain. The structures add valuable details that provide a basis for generating mechanistic hypotheses for this crucial complex.

***

"We showed that opening and closing movements of the peripheral and membrane arms of complex I are critical for catalysis. Opening and closing is accompanied by coordinated conformational changes at the junction between the two arms, around the quinone binding cavity. These changes involve five conserved protein loops and are initiated by the reduction of quinone, the resulting negative charge in its cavity, and decylubiquinone (DQ) movement between the deep and the shallow binding sites. The bulky inhibitor rotenone also binds at these two sites and, unexpectedly, also within ND4—one of the three antiporter-like subunits. The deactive state is defined by a notable relocation of the entire ND6 transmembrane (TM) helix 4, arresting the enzyme in the open conformation.

***

"A key role in this process is played by electrostatic interactions between the conserved charged residues, forming the highly hydrated “central axis” of the membrane arm. The distribution of the observed water molecules also suggests that links to the matrix and intermembrane space (IMS) sides in the distal subunit ND5 are much more hydrated than in other antiporters, and we propose the possibility that all four protons per cycle are ejected into the IMS via this subunit, rather than one per each antiporter (dashed arrows in the figure).

***

"Abstract
Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo–electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions."

Comment: Read the entire site and the complexity of their findings will make your eyes roll. Mine did. Remember this sx a giant enzyme which could not have developed by chance.

Biological complexity: how parasitic plants attack

by David Turell @, Wednesday, November 04, 2020, 19:04 (1241 days ago) @ David Turell

The molecule ethylene is driven genetically:

https://phys.org/news/2020-11-parasitic-ethylene-host-invasion.html

"Researchers at Nara Institute of Science and Technology in Japan report in a new study in Science Advances that parasitic plants use the plant hormone ethylene as a signal to invade the roots of host plants.

"To develop a successful parasitic relationship, parasitic plants form a specialized structure, the haustorium which attaches to and invades the host plant. The formation of haustoria is regulated by signal molecules derived from the host plant and allows the parasitic plant to absorb water, nutrients, and small materials from the host plant.

"'To understand the genetic programs for haustorium development, we identified mutants that displayed haustorial defects on host invasion," says lead author of the study Songkui Cui. "Genome sequencing showed that these mutants have defective ethylene signaling, and it turned out that ethylene signaling genes are crucial for the parasitic plant to infect its host plant."

"Ethylene is a gaseous plant hormone that is involved in fruit ripening, aging of leaves, and the formation of root nodules. Ethylene is also widely involved in plant interactions with viruses and numerous organisms, such as insects and bacteria, lending either resistance or susceptibility to plants depending on the types of pathogens.

"'Our results indicate that ethylene mediates host recognition in parasitic plants for host invasion," explains project leader Satoko Yoshida. "This is the first time that the mediation of host invasion by parasitic plant genes has been identified via forward genetics. Our findings offer a new understanding of how a parasitic plant uses the ethylene molecule to tweak haustorium development and host invasion."

***

"'Our results suggest that parasitic plants have taken over ethylene signaling for parasitism at multiple stages of their life cycle, such as germination, haustorium growth termination, and host invasion."

Comment: Another very complex mechanism that must be considered as designed.

Biological complexity: more molecular complexity

by David Turell @, Thursday, November 05, 2020, 19:04 (1240 days ago) @ David Turell

Protein function is not only from folding molecules but also changes in bonds:

https://phys.org/news/2020-11-proteins.html


"A ground-breaking discovery by Centenary Institute scientists has provided new understanding as to the nature of proteins and how they exist and operate in the human body.

"The key finding—the changing state of a protein's structural bonds—

***

" Proteins are responsible for all of life's processes and had previously been considered to exist in an intact single state when mature. The new study however has found two human proteins involved in blood clotting and immunity existing in different and changing states.

"'The most sophisticated molecules made in nature are proteins which consist of unique sequences of amino acids," said Dr. Diego Butera from the ACRF Centenary Cancer Research Centre and lead author of the study. "Disulphide bonds link the amino acid chains together and were thought to just stabilize protein structure."

"Previously it has been believed that these disulphide bonds were fully formed in the mature and functional protein. In this study however, the researchers found that the proteins are being produced in multiple disulphide-bonded states.

"'We were able to precisely measure whether the disulphide bonds in the blood proteins were formed or broken. Remarkably, we saw that the proteins were made in multiple, possibly thousands, of different disulphide-bonded states," said Dr. Butera.

"Professor Philip Hogg, Head of the ACRF Centenary Cancer Research Centre and senior author of the study believes that their research will change how proteins are viewed and targeted in future drug and medical experiments.

"'It's very likely that we will find many other proteins that exist in multiple states. Crucially, a drug may bind more or less preferentially to different states, impacting the effectiveness of the drug."

"'In experimental settings, differing states of a protein should now be considered as part of the investigative medical research process," Professor Hogg said.

Comment: A very valuable finding. Protein molecules in life act in much more complex ways than we knew, which also shows again the immensity of the error problem and the necessity of all the editing mechanisms God designed.

Biological complexity: how cells remove garbage

by David Turell @, Saturday, November 07, 2020, 19:52 (1238 days ago) @ David Turell

Not fully understood but highly complex:

https://phys.org/news/2020-11-cell-dump-proteins.html

"In a new paper with results that senior author Eric Strieter at the University of Massachusetts Amherst calls "incredibly surprising," he and his chemistry lab group report that they have discovered how an enzyme known as UCH37 regulates a cell's waste management system.

"As he explains, a very large protease called a proteasome is responsible for degrading the vast majority of proteins in a cell; it may be made up of as many as 40 proteins. It has been known for more than 20 years that UCH37 is one of the regulatory enzymes that associates with the proteasome, he adds, "but no one understood what it was doing."

"It turns out that the crux of the whole process, he adds, is how complicated modifications in a small protein called ubiquitin can be. "In addition to modifying other proteins, ubiquitin modifies itself resulting in a wide array of chains. Some of these chains can have extensive branching. We found that UCH37 removes branchpoints from chains, allowing degradation to proceed.'" (my bold)

***

"This technique led to one more surprise. "Instead of acting as expected and opposing the degradation process, it turned out that UCH37 was removing branchpoints from ubiquitin chains to help degrade proteins," Strieter says. "You would think that by removing the signal for degradation that degradation would be impaired," he adds, "but it didn't work that way."

"In future experiments, Strieter and colleagues hope to further explore the degradation process and learn in more detail how UCH37 manages to regulate cellular function."

Comment: More evidence about how living protein molecules must work together perfectly at extremely high speed in nanoseconds or even shorter for life to function. This process involves very complex alteration of molecular sections. Note my bold

Biological complexity: intracellular organization

by David Turell @, Tuesday, November 24, 2020, 23:44 (1220 days ago) @ David Turell

Amazing details are appearing, but not yet complete:

https://knowablemagazine.org/article/living-world/2020/what-is-liquid-liquid-phase-sepa...

Biologists have studied these cellular processes for decades.

***

"But at the crucial in-between scale, a big question mark remains: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?

"The latter appears to be true, according to recent research at the intersection of physics and biology. Over the last decade, cell biologists have come to appreciate what many believe to be a whole new way that cells shape their internal landscape. Like blobs merging, then dispersing, in a lava lamp, or a salad dressing that separates into bubbles of oil and vinegar, groups of proteins can sometimes congeal into distinct droplets. One key way these droplets form is through a process called liquid-liquid phase separation.

***

"Liquid-liquid phase separation is a relatively new concept for cell biologists, notwithstanding a few observations of liquid droplets in cells over the years, including one from more than a century ago. But in the physics world it’s old news — which is handy. “The power of this is that it sits on almost 100 years of condensed matter physics,” says biophysicist Alex Holehouse of Washington University in St. Louis,

***

"Structurally, the proteins within a condensate are a bit like a tangle of cooked spaghetti, if you can imagine spaghetti strands made of weak Velcro. They bind lightly to many parts of the other proteins in the condensate, in no particular orientation. (Contrast that with the key-in-a-lock kind of binding that occurs when an enzyme attaches to a target or a chemical sticks to a receptor.) Many of the proteins or protein regions that make these weak connections are what biochemists call disordered, meaning they don’t take on a firm three-dimensional shape like most proteins do. The sum of all those weak forces holds the droplet together.

***

"...a team led by biophysicist Michael Rosen at the University of Texas Southwestern Medical Center reported that proteins in a test tube could undergo phase separation to form droplets. The study showed that this phenomenon, which physicists and chemists have observed in many different molecules, occurs in proteins that can bind many targets.

***

"The biggest, broadest hypothesis for the function of these droplets is that they concentrate specific sets of proteins and other molecules so as to house, kick-start or speed up the reactions the proteins engage in.

"For example, concentrating certain proteins in droplets near the cell membrane intensifies signals to assemble the cell’s cytoskeleton, the mesh of filaments that gives a cell its 3-D shape, as Rosen’s team reported in 2019. The phase separation may rev up a molecular process that normally ticks over barely above idle, the researchers proposed.

"And work from geneticist Richard Young’s lab at the Massachusetts Institute of Technology suggests that phase separation concentrates droplets of proteins needed to turn on the activity of genes or prod a chromosome to start copying itself at the correct places on the DNA strand. Rather than relying on chance for the right proteins to appear where they are needed, the droplets form what Young calls “a goody bag” of all the components that are necessary for these processes to occur.

***

“'I think there’s no doubt that phase separation plays a very important role for cells,” she says. Researchers so far have identified at least 20 different types of phase-separated droplets, each consisting of different proteins and other molecules and emerging under different circumstances.

"Some condensates, like P granules, are long-standing characters in the cell, newly identified as products of phase separation. Others are just emerging. The diversity is not surprising, says Lee: Just like cell organelles that are bounded by membranes all have different functions, membraneless ones probably do too."

Comment: Cells are manufacturing factories and they have to be organized just like production lines, but they don't appear that way to the naked eye; just sloppy soups. I had a course in physical chemistry in 1953!! Why has biology research just beginning to catch up? Try to tell me this was not designed!!!!

Biological complexity: AI predicts protein folds

by David Turell @, Tuesday, December 01, 2020, 22:51 (1214 days ago) @ David Turell

Life exists based on precisely folded proteins in which is their shape produces a precise functional mode:

https://www.newscientist.com/article/2261156-deepminds-ai-biologist-can-decipher-secret...

"An AI system developed by UK-based company DeepMind has achieved the long-sought-after goal of accurately predicting the shape of proteins from their sequence alone, a key part of understanding how the machinery of life works. In a competition, AlphaFold was able to match two-thirds of the results achieved by humans doing expensive and time-consuming lab experiments.

***

"Proteins are vital for life. Cells are full of machines – from turbines that generate energy to transporters that walk along tracks pulling cargo – that are built from proteins, and the shapes of these machines are crucial. For instance, the coronavirus can enter and infect cells because the spike protein on its surface fits into a receptor on human cells, like a key into a lock.


"These shapes depend on the sequence of 20 different amino acids that are chained together to make proteins. It is easy to work out the sequence of any protein because this is determined by the DNA that codes for it. But despite half a century of efforts, biologists hadn’t previously been able to work out the shape of a protein from its sequence alone.

"Instead, they have had to rely on experimental methods such as X-ray crystallography, which involves analysing the diffraction pattern formed when an X-ray beam is fired through a protein crystal.

***

"For each target protein, groups including DeepMind’s look for variants found in related species and feed their sequence and structure into the AI system, along with the sequence of the target protein. The idea is that the system learns to work out the shape of the target protein by looking at patterns linking sequence and structure.

"Predicted shapes are scored out of 100 based on how close each amino acid is to the position determined by experiment. A score above 90 is considered to be on a par with results obtained by experiments.

"In the 2016 competition, the best team got a median score of around 40 in the hardest category. In 2018, the first version of AlphaFold got a median score of nearly 60 in this category. This year, a redesigned AlphaFold got a median score of 87 in the hardest category. Across all categories, it scored above 90 for two-thirds of the proteins.

"DeepMind found an AI learning technique also works in human brains
While this result is amazing, there were some clear failures, says Moult. For instance, AlphaFold didn’t do well with a protein whose structure is influenced by interactions with other proteins that surround it."

Comment: The shape and folding is based on amino acid sequences, attritive and repulsive electrical forces and also the influence of neighboring molecules. The latter creates a problem as indicated.

Biological complexity: A pore is made in vitro

by David Turell @, Monday, December 21, 2020, 19:18 (1194 days ago) @ David Turell

Its complex shape is now known:

https://phys.org/news/2020-12-scientists-gamma-tubulin-complex-vitro.html

"Researchers from the Microtubule Organization lab,... have achieved the first in vitro reconstitution of the human -tubulin ring complex (γTuRC), responsible for initiating microtubule formation. In addition, they revealed its 3-D structure by cryo-electron microscopy. The key to their success lies in the identification of the RUVBL protein complex as an essential γTuRC assembly helper.

***

"Microtubules are a component of the cytoskeleton, which is essential for intracellular transport processes and cell division. Microtubules cannot form spontaneously in cells but require nucleation by the γTuRC. Mutations in γTuRC subunits cause neurodevelopmental defects such as microcephaly and have also been linked to defects in the retina.

"Although the γTuRC was discovered 25 years ago, the field had not been successful in producing it recombinantly in vitro," says co-corresponding author Jens Lüders, "this new achievement opens the door to studies aimed at elucidating the microtubule nucleation mechanism and how it is regulated".

***

"'Our group has been exploring the function of RUVBL in the assembly of large macromolecular structures relevant to cancer for years. Discovering that RUVBL is also essential for the formation of γTuRC opens new avenues of research to understand how cells build complex functional structures," says co-corresponding author Oscar Llorca.

"' γTuRC is a very large structure built by multiple and interconnected subunits. Determining its 3-D architecture has been an immense challenge, made possible by advances in cryo-electron microscopy methods that allowed us to observe individual molecules of this complex with extremely high detail ", explains co-first author Marina Serna."

Comment: Look at the video in the article and tell me with honesty chance did this.

Biological complexity: protein double folding

by David Turell @, Friday, January 01, 2021, 15:06 (1183 days ago) @ David Turell

Two functions, two folds in some proteins:

https://science.sciencemag.org/content/371/6524/86

"One sequence encoding two structures
Most proteins have stable, folded structures, but there are rare examples of metamorphic proteins that can switch between two different folds that may each have a different function. Dishman et al. investigated the evolution of XCL1, which is a member of the chemokine family that interconverts between the chemokine fold and a second, noncanonical fold that forms dimers. The authors used nuclear magnetic resonance spectroscopy to investigate the structures of inferred evolutionary ancestral sequences. Their results suggest that XCL1 evolved from an ancestor with the chemokine fold and then transitioned to prefer the noncanonical fold before reaching the modern-day metamorphic protein."

Abstract
"Metamorphic proteins switch between different folds, defying the protein folding paradigm. It is unclear how fold switching arises during evolution. With ancestral reconstruction and nuclear magnetic resonance, we studied the evolution of the metamorphic human protein XCL1, which has two distinct folds with different functions, making it an unusual member of the chemokine family, whose members generally adopt one conserved fold. XCL1 evolved from an ancestor with the chemokine fold. Evolution of a dimer interface, changes in structural constraints and molecular strain, and alteration of intramolecular protein contacts drove the evolution of metamorphosis. Then, XCL1 likely evolved to preferentially populate the noncanonical fold before reaching its modern-day near-equal population of folds. These discoveries illuminate how one sequence has evolved to encode multiple structures, revealing principles for protein design and engineering."

Comment: The chemical details are not important to the point this makes. This is a protein which in two different shapes performs tweo different functions. This is obviously pure design, not any form of natural evolution .

Biological complexity: cellular manufacturing controls:

by David Turell @, Thursday, January 07, 2021, 19:07 (1177 days ago) @ David Turell

How to coordinate protein enzyme reactions in packed cells:

https://www.quantamagazine.org/molecular-condensates-in-cells-may-hold-keys-to-lifes-re...

"Imagine packing all the people in the world into the Great Salt Lake in Utah — all of us jammed shoulder to shoulder, yet also charging past one another at insanely high speeds. That gives you some idea of how densely crowded the 5 billion proteins in a typical cell are, said Anthony Hyman, a British cell biologist and a director of the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden.

"Somehow in that bustling cytoplasm, enzymes need to find their substrates, and signaling molecules need to find their receptors, so the cell can carry out the work of growing, dividing and surviving. If cells were sloshing bags of evenly mixed cytoplasm, that would be difficult to achieve. But they are not. Membrane-bounded organelles help to organize some of the contents, usefully compartmentalizing sets of materials and providing surfaces that enable important processes, such as the production of ATP, the biochemical fuel of cells. But, as scientists are still only beginning to appreciate, they are only one source of order.

"Recent experiments reveal that some proteins spontaneously gather into transient assemblies called condensates, in response to molecular forces that precisely balance transitions between the formation and dissolution of droplets inside the cell. Condensates, sometimes referred to as membraneless organelles, can sequester specific proteins from the rest of the cytoplasm, preventing unwanted biochemical reactions and greatly increasing the efficiency of useful ones. These discoveries are changing our fundamental understanding of how cells work.

"For instance, condensates may explain the speed of many cellular processes. “The key thing about a condensate — it’s not like a factory; it’s more like a flash mob. You turn on the radio, and everyone comes together, and then you turn it off and everyone disappears,” Hyman said.

***

"These condensates aren’t just novel but thought-provoking: The idea that their functions emerge from the collective behaviors of the molecules has become the central concept in condensate biology, and it contrasts sharply with the classic picture of pairs of biochemical agents and their targets fitting together like locks and keys. Researchers are still figuring out how to probe the functionality of these emergent properties; that will require the development of new techniques to measure and manipulate the viscosity and other properties of tiny droplets in a cell.

***

"These condensates aren’t just novel but thought-provoking: The idea that their functions emerge from the collective behaviors of the molecules has become the central concept in condensate biology, and it contrasts sharply with the classic picture of pairs of biochemical agents and their targets fitting together like locks and keys. Researchers are still figuring out how to probe the functionality of these emergent properties; that will require the development of new techniques to measure and manipulate the viscosity and other properties of tiny droplets in a cell.

***

"Ribosomes are cells’ protein-making factories, and the number of them in a cell often limits its rate of growth. Work by Brangwynne and others suggests that fast-growing cells might get some help from the biggest condensate in the nucleus: the nucleolus. The nucleolus facilitates the rapid transcription of ribosomal RNAs by gathering up all of the required transcription machinery, including the specific enzyme (RNA polymerase I) that makes them.

***

"The ATP was preventing protein aggregation at the concentrations found in living cells.

***

"The chemist noted that in industrial processes, additives called hydrotropes are used to increase the solubility of hydrophobic molecules. Returning to his lab, Hyman and his colleagues found that ATP worked exceptionally well as a hydrotrope.

"Intriguingly, ATP is a very abundant metabolite in cells, with a typical concentration of 3-5 millimolar. Most enzymes that use ATP operate efficiently with concentrations three orders of magnitude lower. Why, then, is ATP so concentrated inside cells, if it isn’t needed to drive metabolic reactions?

"One candidate explanation, Hyman suggests, is that ATP doesn’t act as a hydrotrope below 3-5 millimolar. “One possibility is that in the origin of life, ATP might have evolved as a biological hydrotrope to keep biomolecules soluble in high concentration and was later co-opted as energy,” he said.

***

"Protein aggregates can also solve problems that require very quick physiological responses, like stopping bleeding after injury."

Comment: To understand the point of this article with which I have just given a skimmed view, reread the introduction. In a lab a human controls each substance added one by one in any reaction. A cell is organized soup with multiple side-by-side reaction The design of the complex processes is extremely detailed. Never by chance. The article is at the lay reader level. Read it.

Biological complexity: nuclear pore mechanics

by David Turell @, Thursday, January 07, 2021, 19:53 (1177 days ago) @ David Turell

Finally visualized at the molecular level:

https://phys.org/news/2021-01-scientists-capture-portal-cell-nucleus.html

"The nucleus of a cell is well-shielded by a double membrane to protect its most sensitive possession—its DNA. Anything that enters or exits must pass through the nuclear pores, cylindrical structures made of hundreds of proteins. Scientists have made great advances in figuring out the architecture of the pore by reconstructing each of its parts in the lab. But they have struggled to understand how those parts work together—whether the pore is a passive drain or a dynamic, flexible structure.

***

"Their findings, published in eLife, suggest the proteins forming the pore's inner ring constantly change their orientation as they let cargo through, changing the whole conformation of the channel.

"It suggests it may be working like a finger trap toy," Simon says.

***

"For the study, the researchers embedded fluorescent chemicals in the nuclear pore proteins. These markers brighten up only when light is shone onto them at an angle parallel to their direction, so by monitoring the light they give off, the researchers can infer the precise orientation of a protein, or even subdomains of a protein.

"The team then manipulated the amount of cargo transport through the pore and monitored the motion of the proteins. While most compartments of the nuclear pore were static, the inner ring proteins flip-flopped rapidly between two orientations. "If we shut down transport, they would stay in one orientation. If we started it up, they would switch," Simon says."

Comment: It is obvious protein function as dependent on folding. This result is what would be expected. A designer required. Without the pores working from the start along with all the
processes functioning life couldn't work.

Biological complexity: protein folding creates life

by David Turell @, Saturday, January 30, 2021, 19:37 (1154 days ago) @ David Turell

Without the ability of proteins to fold and create different functions life could not exist:

http://backreaction.blogspot.com/2021/01/has-protein-folding-been-solved.html

"Understanding how proteins fold is important because the function of a protein depends on its shape. Some mutations can lead to a change in the amino acid sequence of a protein which causes the protein to fold the wrong way. It can then no longer fulfil its function and the result can be severe illness. There are many diseases which are caused by improperly folded proteins, for example, type two diabetes, Alzheimer’s, Parkinson’s, and also ALS, that’s the disease that Stephen Hawking had. (my bold)

"So, understanding how proteins fold is essential to figuring out how these diseases come about, and how to maybe cure them. But the benefit of understanding protein folding goes beyond that. If we knew how proteins fold, it would generally be much easier to synthetically produce proteins with a desired function.

"But protein folding is a hideously difficult problem. What makes it so difficult is that there’s a huge number of ways proteins can fold. The amino acid chains are long and they can fold in many different directions, so the possibilities increase exponentially with the length of the chain.

"Cyrus Levinthal estimated in the nineteen-sixties that a typical protein could fold in more than ten to the one-hundred-forty ways. Don’t take this number too seriously though. The number of possible foldings actually depends on the size of the protein. Small proteins may have as “few” as ten to the fifty, while some large ones can have and a mind-blowing ten to the three-hundred possible foldings. That’s almost as many vacua as there are in string theory!

"So, just trying out all possible foldings is clearly not feasible. We’d never figure out which one is the most stable one.

"The problem is so difficult, you may think it’s unsolvable. But not all is bad. Scientists found out in the nineteen-fifties that when proteins fold under controlled conditions, for example in a test tube, then the shape into which they fold is pretty much determined by the sequence of amino acids. And even in a natural environment, rather than a test tube, this is usually still the case.

"Indeed, the Nobel Prize for Chemistry was awarded for this in 1972. Before that, one could have been worried that proteins have a large numbers of stable shapes, but that doesn’t seem to be the case. This is probably because natural selection preferentially made use of large molecules which reliably fold the same way.

"There are some exceptions to this. For example prions, like the ones that are responsible for mad cow disease, have several stable shapes. And proteins can change shape if their environment changes, for instance when they encounter certain substances inside a cell. But mostly, the amino acid sequence determines the shape of the protein.

Comment: this article goes own to explain how we are learning about the folding process and predicting how a protein might fold. The point I'm raising is that without this folding process life cannot exist, based on the biochemistry we know. God had to create this roulette game of chance knowing that molecules must be allowed to fold on their own to achieve the speed needed. He was able to create a great many good editing systems, but those systems rely on the same protein folding process, so errors are at times maintained but somehow the errors are insignificant enough that we humans were successfully evolved from bacteria. dhw ignores all of this. Perhaps it is from the lack of understanding the biochemistry of life.

Biological complexity: protein folding creates life

by David Turell @, Monday, February 01, 2021, 19:07 (1152 days ago) @ David Turell

More studies in miss-folding causes and controls:

https://www.sciencedaily.com/releases/2021/02/210201101531.htm

"It's commonly accepted that protein folding/misfolding are alternative reactions of unfolded proteins but the principles governing this remain unknown. Here, researchers describe a general concept that links protein folding and misfolding: protein folding and amyloid formation are separated by the supersaturation barrier of a denatured protein. Breakdown of this supersaturation barrier is required to shift the protein to the amyloid pathway, linking Anfinsen's intramolecular folding universe with the 'outer' intermolecular misfolding universe.

***

"Summarizing their motivation for this work, senior author Masahiro Noji explains: "The thermodynamic hypothesis of protein folding, known as the 'Anfinsen's dogma' describes that the native structure of a protein represents a free energy minimum determined by the amino acid sequence. However, this is not consistent with the misfolding of globular proteins to form amyloid fibrils." Therefore, Yuji Goto and colleagues set out to explore the link between protein folding and misfolding.

"Although proteins perform their functions by folding to their native structures, as represented by Anfinsen's dogma, proteins often misfold to form amyloid fibrils, leading to amyloidosis. In their paper, the research team from Osaka University describe a general concept for the link between protein folding and misfolding.

"'The supersaturation barrier of a denatured protein separates protein folding and amyloid formation, and misfolding occurs when this barrier breaks down" corresponding author Yuji Goto says. "Our results show a clear link between correct protein folding, as defined by Anfinsen's dogma, and protein misfolding."

"Supersaturation can be observed throughout nature in the formation of crystals, including those involved in ice formation. Here, the team at Osaka University show that supersaturation is fundamental to correct protein folding. The supersaturation barrier represents a novel concept that will advance the field of protein folding and contribute to the development of therapeutic strategies to prevent and treat amyloidosis, including those involved in neurodegenerative diseases."

Comment: We are still learning about folding of proteins which is so crucial to maintaining life.

Biological complexity: protein folding creates life

by David Turell @, Wednesday, February 03, 2021, 17:55 (1150 days ago) @ David Turell

Some proteins have more than one shape to perform different functions:

https://www.quantamagazine.org/metamorphic-proteins-change-their-folds-for-different-jo...

"Proteins are molecular origami at its finest. Classically, a protein is imagined as a chain of amino acids that folds into a single stable configuration, one that evolution has selected over the ages for a particular function. But in the last few years, biophysicists have learned how numerous and extraordinary the exceptions to that rule are — including some two-faced proteins that can refold as needed in an instant.

"First came the discovery of a special class of fold-switching proteins that have more than one stable conformation and can perform two different functions. Such proteins might seem unlikely to evolve because natural selection for the first shape and function could easily be detrimental to the second, and vice versa. Yet fold-switching proteins, of which about 100 are currently known, have evolved in all kingdoms of life and perform more than 30 types of biological functions. (my bold)

***

"Researchers at the Medical College of Wisconsin have now reconstructed the evolutionary history of a metamorphic human protein called XCL1. In one shape, it acts as a signaling molecule called a chemokine, binding to receptors on white blood cells and recruiting them to fight infections. But it can easily switch to a second shape that kills bacterial invaders as an antibiotic.

***

"The fact that the ancestors exhibited the two folds unevenly while the modern XCL1 exhibits both in equal proportion strongly suggests that the switching property “is not an accident or an artifact. It’s something that must have been beneficial and improved the fitness of the organism, because it appeared to be selected for,” said Brian Volkman, a biophysicist and senior author of the study, which appeared in Science on January 1. (Comment here: pure Darwin. Design fits also)

***

"But why would metamorphosis be better than having two specialized proteins? The scientists theorize in their paper about a couple of linked possibilities. If a single protein can do double duty, it spares the cell from transcribing, translating and maintaining more than one gene. But the more compelling advantage may be that the protein’s ability to transform may give the body a more dynamic way to control its defenses against bacteria.

"Because XCL1 can adopt its two folded forms with equal probability, it can switch between them faster than once per second. But changes in the temperature or salt concentration or the introduction of binding partners can change that equilibrium. For example, around microbial pathogens, more of the XCL1 proteins get stuck in the conformation that interacts with the microbial membranes, shifting the balance toward that fold. Elsewhere in the body, the protein can adopt the other fold more often and bind to the receptors on white blood cells to mobilize them. (my bold)

***

"Metamorphic fold-switching also enables the body to eliminate an unwanted function simply by flipping the protein’s structure to the other conformation, rather than having to wait for the protein to be degraded. “This has the elegance of simplicity,” Volkman said.

"The arguments for these apparent advantages can seem so convincing that they raise the question of why XCL1 is the only chemokine that evolved metamorphic folding. The researchers acknowledge that this is still a mystery."

Comment: Once again note high speed requirements, while the free floating molecules can make mistakes..

Biological complexity: protein folding creates life

by David Turell @, Sunday, July 17, 2022, 16:22 (621 days ago) @ David Turell

a new study of protein folding and form change creating a new function:

https://www.sciencedaily.com/releases/2022/07/220715142146.htm

"Though it has long been known that proteins wiggle and move, scientists have debated the significance of this "dancing" act, says Dominique Frueh, Ph.D., associate professor of biophysics and biophysical chemistry at the Johns Hopkins University School of Medicine. "The way proteins engage with the right partner at the right time -- essentially, how they communicate -- is very important for understanding their function," he says, "and we have found that protein wiggles are critical for this communication."

"In a bid to further such understanding, Frueh's team studied the wiggling action of the HMWP2 protein, a type of enzyme called nonribosomal peptide synthetases. These enzymes are made of several domains, or distinct regions, that work together like an assembly line to make complex natural products from small chemicals.

***

"'We found that the two domains would only bind to one another as the second domain gets modified, which means they would only engage as needed for making the product and avoid wasting time together when the second domain is not modified," says Frueh. "Somehow, the first domain is able to sense when the second domain is modified, and we sought to investigate whether motions played a role in this recognition process."

"They also found changes in motion across the entire domain flagged with carbon-13c, not only where it binds to the second domain but also at a second, remote binding site used by a third domain.

"On an atomic level, Frueh says these two sites on HMWP2 could be considered "far" apart -- about 40 billionths of a meter. And how they interact, despite their distance, was particularly intriguing to the scientists.

***

"'We found that the protein domain was structurally stable, but all of its movement was hindered," says Frueh. The mutated protein's lack of movement damaged its ability to bind with other domains even when they were modified, according to the researchers, demonstrating that the motions within the protein were necessary for the domains to work together."

Comment: we know that protein folding creates new functions, but how the proteins 'know' how to relate is still the very complex black box of functional proteins creating life. Only a designer mind can have created this.

Biological complexity: intracellular organization

by David Turell @, Monday, February 08, 2021, 16:29 (1145 days ago) @ David Turell

Cell proteins form membraneless droplets:

https://phys.org/news/2021-02-membraneless-organelles.html

"In cells, numerous important biochemical functions take place within spherical chambers made from proteins and RNA.

"These compartments are akin to specialized rooms inside a house, but their architecture is radically different: They don't have walls. Instead, they take the form of liquid droplets that don't have a membrane, forming spontaneously, similar to oil droplets in water. Sometimes, the droplets are found alone. Other times, one droplet can be found nested inside of another. And these varying assemblies can regulate the functions the droplets perform.

***

"The research lays out physical rules controlling the arrangement of various types of synthetic MLOs created using just three kinds of building materials: RNA and two different proteins, a prion-like polypeptide (PLP) and an arginine-rich polypeptide (RRP).

***

"'Different condensates can coexist inside the cells," says first author Taranpreet Kaur, a Ph.D. student in physics in the UB College of Arts and Sciences. "They can be detached, attached to another condensate, or completely embedded within one another. So how is the cell controlling this? We found two different mechanisms that allowed us to control the architecture of synthetic membraneless organelles formed inside a test tube. First, the amount of RNA in the mixture helps to regulate the morphology of the organelles. The other factor is the amino acid sequence of the proteins involved."

"'These two factors impact how sticky the surfaces of the condensates are, changing how they interact with other droplets," says Priya Banerjee, Ph.D., UB assistant professor of physics, and one of two senior authors of the paper. "In all, we have shown using a simple system of three components that we can create different kinds of organelles and control their arrangement in a predictive manner. We suspect that such mechanisms may be employed by cells to arrange different MLOs for optimizing their functional output.'"

Comment: We've seen that phase transitions are one physico-electrochemical method, stickiness is now another to corral free-floating molecules into usable networks. Still not hard-wire control which allows for errors, but obviously the required mechanism.

Biological complexity: structure of a mitochondrial ribosome

by David Turell @, Tuesday, February 16, 2021, 18:31 (1137 days ago) @ David Turell

Involves 22 associated factors:

https://phys.org/news/2021-02-glimpse-formation-mitoribosome.html

"SciLifeLab Fellow Alexey Amunts and his team together with researchers from the Czech Academy of Sciences report an assembly intermediate of the ribosome in mitochondria. It reveals 22 associated factors that cooperatively organize the biogenesis process.

"The mitochondrial ribosome is an intricate machine that translates the organellar genome into functional proteins. The formation of the mitochondrial ribosome is a hierarchical process involving dozens of different components.

***

"The resulting structure revealed that the assembly factors form a network that spans a distance of 18 nanometres shielding the sensitive ribosomal core that is made of less-stable nucleic acids. The network is designed to connect all the functional regions on the mitoribosomal large subunit for their correlated maturation.

"A phylogenetic analysis further showed that most of the newly identified assembly factors also exist in human, and therefore the derived characteristics represent general principles. However, an unexpected finding is that some of those factors appeared to loose their activity. Despite being deactivated, they still contribute as structural mediators for a stabilization of the functionally active partners on the mitoribosomal core. The preservation of the deactivated factors implies a mechanism of the evolutionary conservation of the sequential assembly."

Comment: Such purposeful complexity is not a result of chance organization

Biological complexity: structure of a mitochondrial ribosome

by David Turell @, Thursday, February 18, 2021, 21:38 (1135 days ago) @ David Turell

Another article on structure and function:

https://phys.org/news/2021-02-mitochondria-genesis-body-powerhouses.html

"The bulk of energy production in mitochondria takes place in naturally evolved nano-factories incorporated in specialised membranes. These nano-factories consist of proteins cooperatively transporting ions and electrons to generate the chemical energy currency of our bodies which have to be constantly maintained, replaced and duplicated during cell division. To address this, mitochondria have their own protein making machine called the mitoribosome. The first fundamental understanding of how the mitoribosome looks was achieved in 2014.

***

"'...this first glimpse into the architecture revealed only a partial picture of a static model. Yet the mitoribosome is a flexible molecular machine that requires the motion of its parts relative to each other in order to work. Therefore, in the current study, the team used the high throughput cryo-EM data acquisition at the electron Bio-Imaging Centre (eBIC) at Diamond to obtain 30 times more data allowing the team to describe conformational changes during the process of protein synthesis and association with the membrane adaptor. eBIC has been a strategic investment from the Wellcome Trust, UKRI's BBSRC and MRC. Being embedded at Diamond, eBIC benefits from amongst other things the well-established user support in place.

***

"'Our study exposed the dynamic molecular mechanism that explains how the mitoribosome actually works to form the cellular powerhouse and reveals that the mitoribosome is much more flexible and active than previously thought. The discovery of intrinsic conformational changes represents a gating mechanism of the mitoribosome without similarity in bacterial and cytosolic systems. Together, the data offer a molecular insight into how proteins are synthesized in human mitochondria," adds Alexey Amunts.

***

"The most important aspect of Alexey's work is the interaction between mitoribosome and OXA1L and the associated flexibility. The fact that mitoribosome is flexible as such is not novel, but the particular flexibility associated with OXA1L interaction is. This is important for synthesis of membrane proteins, including respiratory chain proteins. Overall, this work significantly widens our understanding how mitoribosome functions. The work by Alexey Amunts lab resolves another mystery about basic biological processes necessary for creating life as we know it."

"The sequencing of the human mitochondrial genome 40 years ago was a turning point in mitochondrial research, postulating a putative specialized mechanism for the synthesis of the mitochondrial transmembrane proteins. Indeed, the discovered gating mechanism of the human mitoribosome represents a unique occurrence. Therefore, the structural data offer a fundamental understanding into how bioenergetic proteins are synthesized in our body".


Comment: The real point to me is that the mitochondria are so complex new study techniques have to be invented just to study them. Designed, not by chance development .

Biological complexity: how proteins congregate

by David Turell @, Monday, March 29, 2021, 20:07 (1096 days ago) @ David Turell

Large protein molecules are drawn together by their electrical charges:

https://phys.org/news/2021-03-proteins-complex-simple-explanation.html

"Reporting in the journal eLife, the Spartan team led by Michael Feig and Lisa Lapidus showed that relatively simple characteristics help RNA and proteins organize themselves. Researchers believe that when these biomolecules congregate, or condense, it can help speed up or enhance a range of cellular functions. "The main consequence of such condensates is that it may bring functionally related biomolecules closer together," said Feig, a professor in the Department of Biochemistry and Molecular Biology in the MSU College of Natural Science.

"'Having them condensed could speed up the process because you don't have to wait for a molecule to show up from far away," said Lapidus, a professor in the Department of Physics and Astronomy.

"Although more research is needed to reveal the exact workings of condensates, the MSU team has revealed that relatively basic traits of the biomolecules involved can spur what's known as phase separation.

"Specifically, when RNA and proteins are large enough and have sufficiently strong and opposite electric charges, they can form a condensed phase that's biologically distinct from a more diffuse phase of biomolecules.

"These remarkably simple drivers suggest that the phenomenon could be widespread in biology.

***

"'Phase separation is a key mechanism for forming membrane-less organelles, which are responsible for a number of functions in cells," Dutagaci said, including metabolism and DNA replication. "These are the processes that help cells live.'"

Comment: This process is well known, but how easily it happened was not realized. Obviously crowding together speeds reactions. The maintenance of life requires the high speed.

Biological complexity: how cells get anchored

by David Turell @, Monday, March 29, 2021, 20:25 (1096 days ago) @ David Turell

As usual a specialized protein:

https://www.sciencedaily.com/releases/2021/03/210329085946.htm

"Each human being is made of billions of cells. In order to ensure his survival, cells must coordinate with each other and attach in the right place to perform their tasks. Scientists from the University of Geneva (UNIGE), Switzerland, in collaboration with the University of Tampere in Finland, have highlighted the key role of a protein called paxillin, which enables cells to perceive their environment and anchor at the right place with the help of cellular "crampons." Indeed, without functional paxillin, the cell is unable to attach properly and slips continuously.

***

"To ensure our survival, each cell performs specific functions in coordination with their neighbours. In such a dynamic system, the migration of cells and their anchoring at the right place are essential. But how do cells manage to coordinate with each other? Scientists have long believed that cells communicate mainly through chemical signals, such as hormones. However, recent discoveries suggest that mechanical signals play a major role in cell coordination. "This is why we started to study the ability of cells to decipher and respond to their physical environment," explains Bernhard Wehrle-Haller, Professor at the Department of cell physiology and metabolism at UNIGE Faculty of Medicine.

***

"When a cell has to move, it "senses" its environment with the help of proteins on its surface, the integrins. When the cell detects a suitable location, a complex network of proteins, called focal adhesion, is then set up to form cellular crampons that anchor the cell to its environment. "But how is this anchoring mechanism regulated? This is what we wanted to find out," explains Marta Ripamonti, researcher in the laboratory of Prof. Bernhard Wehrle-Haller and first author of the study.

"By studying paxillin, one of the many proteins that make up these crampons, researchers were able to unravel the mystery. "We knew that this protein played a role in the assembly of focal adhesions, but we didn't expect it to be the key regulator," says Prof. Bernhard Wehrle-Haller with enthusiasm. Without functional paxillin, cells are unable to anchor, regardless of the suitability of their environment. In addition, paxillin has also the function of informing the cell that anchoring has taken place correctly, thus transforming a mechanical response into a biological signal that the cell can understand."

Comment: Such precise controls cannot be developed by chance since exact results are required.

Biological complexity: complexity of cell death

by David Turell @, Tuesday, March 30, 2021, 15:48 (1095 days ago) @ David Turell

Older, worn out cells have to be carefully discarded:

https://neurosciencenews.com/phagocyte-apoptosis-18133/

"Scientists at the Institute for Integrated Cell-Material Sciences (iCeMS) and colleagues in Japan have revealed molecular mechanisms involved in eliminating unwanted cells in the body. A nuclear protein fragment released into the cytoplasm activates a plasma membrane protein to display a lipid on the cell surface, signalling other cells to get rid of it.

***

“'Every day, ten billion cells die and are engulfed by blood cells called phagocytes. If this didn’t happen, dead cells would burst, triggering an auto-immune reaction,” explains iCeMS biochemist Jun Suzuki, who led the study. “It is important to understand how dead cells are eliminated as part of our body’s maintenance.” (my bold)

"Scientists already know that dead cells display an ‘eat me’ signal on their surface that is recognized by phagocytes. During this process, lipids are flipped between the inner and outer parts of the cell membrane via a variety of proteins called scramblases. Suzuki and his team have already identified several of these lipid-scrambling proteins, but some of their activation mechanisms have been unclear.

***

“'We found that a nuclear protein fragment activates Xkr4 to display the ‘eat me’ signal to phagocytes,” says iCeMS cell biologist Masahiro Maruoka, the first author of the study.

"Specifically, the scientists found that cell death signals lead to a nuclear protein, called XRCC4, getting cut by an enzyme. A fragment of XRCC4 leaves the nucleus, activating Xkr4, which forms a dimer: the linking of identical pieces into configurations. Both XRCC4 binding and dimer formation are necessary for Xkr4 to ultimately transfer lipids on the cell surface to alert phagocytes.

"Xkr4 is only one of the scrambling proteins. Others are activated much faster during cell death."

Comment: Note my bold. If old cells can trigger severe immune reactions, how does a chance mutation form of evolution recognize the problem? It doesn't. Design required.

Biological complexity: intercellular transport controls

by David Turell @, Wednesday, April 07, 2021, 21:49 (1087 days ago) @ David Turell

Where three cells meet:

https://phys.org/news/2021-04-junctions-cells-gateways-substances.html

"Special connections between neighboring cells ensure that these cellular barriers are, on the one hand, stable and tight—thus protecting the body and organs against pathogens—while, on the other hand, they remain permeable to specific substances or migrating cells. This is how the cells allow dissolved nutrients to be transported into organs, and how cells of the immune system are able to migrate from the blood across the blood vessel wall into inflamed tissue.

***

"The researchers found that, at the points where three cells meet, the epithelial cells loosen their connections in a controlled manner and the yolk proteins are transported to the egg cell through the resulting gaps.

"At places where only two cells connect, the connections are maintained, thus keeping the tissue integrity intact.

***

"The scientists found that the epithelial cells sequentially removed four different adhesion proteins from their membranes. "This process takes several hours, and only when the last protein is gone do the cell junctions open," explains biologist Jone Isasti-Sanchez, who is the first author of the study and a doctoral candidate in the Integrated Research Training Group within the Collaborative Research Center 1348 "Dynamic Cellular Interfaces" at the University of Münster. After the junctions have opened, the uptake of yolk proteins into the egg proceeds over about 16 hours and, subsequently, the process reverses—the intercellular spaces close again.

"The researchers demonstrated that the cells open their contact sites by taking up adhesion proteins from the surface into the cell interior, using a basic cellular process called endocytosis. An important new finding is that endocytosis seems to take place to a greater extent at those points where three cells meet, and, as a result, the cell junctions only open up at these points. Where only two cells meet, the contact is maintained. "The fact that this process occurs selectively at the three-cell contact-points and, moreover, in such an orderly fashion, is probably important for preventing the tissue from falling apart," says Stefan Luschnig. In addition, he adds that the process presumably has to take place in a very controlled manner because the opening of gates in a tissue comes with the risk that pathogens will enter.

"In their experiments, the scientists also genetically increased or reduced the amount of the adhesion protein E-cadherin and were able to show that the amount of this protein determines how wide the intercellular spaces open. In addition, they found that the mechanical tension in the cytoskeleton plays a key role in the process. This tension is generated by a structure consisting of the proteins actin and myosin, which encircles the cell periphery and is able to contract, similar to a rubber band. When the researchers increased the activity of myosin in the cell, the cytoskeleton contracted more, which prevented the cell junctions from opening."

Comment: Another tightly controlled mechanism that can only develop by design.

Biological complexity: how nerve conduction works

by David Turell @, Sunday, April 18, 2021, 19:50 (1076 days ago) @ David Turell

It is done by ionized molecules at very high speed approximating electric wires in your home:

https://phys.org/news/2021-04-fruit-flies-insights-highway-nerve.html

"The nervous system is the internet of the human body and can in the same way transfer signals over long distances very quickly. Some of the most important elements in this signaling are the axons. They are projections of the nerve cells which send signals to other nerve cells or muscles. For instance, axons that jut out from nerve cells in the spinal cord can be over one meter long.

***

"'We have found out, that the protein Rab2 has to be present and functioning properly in order for the nerve cells to send effective signals between the central nervous system and the body. When we remove the protein in fruit flies we can see that the signal molecules are accumulate in the axons like in a traffic jam," explains visiting researchers Viktor Karlovich Lund from the Department of Neuroscience.

***

"Even though one has to be careful drawing conclusions between species, the researchers think that they have good reason to believe that their discovery is also relevant in humans.

"'We share around 75 percent of disease-related genes with fruit flies. Beyond that, we know that the genes coding for Rab2 look alike in many different species—they have a high degree of evolutionary conservation. This makes us quite convinced that the same mechanism or one very similar exists in the human nervous system," says Ole Kjærulff, Associate Professor at the Department of Neuroscience.

"The signaling works by signaling molecules being transferred from one end of the axons to other nerve cells.

"'Some types of signals require that the signal molecules first travel very far in the same cell. They are packaged into small organelles with a membrane around them and then they are transported op to one meter or more. This requires a complex machinery where everything needs to run smoothly," says Ole Kjærulff.

"Inside the axons the 'cargo' is pulled by motor proteins that can be compared to small locomotives.

"'Our best guess is that the Rab2 protein is the link between the motor proteins driving forward and the cargo being pulled. Almost like a molecular glue holding everything together," says Viktor Karlovich Lund."

Comment: The signal cargos are ionized molecules, which because of the electrical charge, can move down an axon at high speed as if it were a copper wire. Think about it. The ability to carry fast noxious signals of possible damaging events protects animals and us from damage, possibly potentially with loss of life. The design had to be present when animals with nerves first appeared to guarantee survival so evolution might continue forward.

Biological complexity: deactivating unwanted enzymes

by David Turell @, Friday, April 30, 2021, 21:56 (1064 days ago) @ David Turell

A new system is discovered:

https://phys.org/news/2021-04-piecing-lancl-puzzle.html

"Bacteria contain enzymes called LanC that are capable of producing small proteins called lanthipeptides, which are characterized by the addition of a thiol group to a modified serine or threonine amino acid. Similar proteins—called LanC-like or LanCL—have been found in different eukaryotic cells for decades, but their function was unknown.

"'LanCLs are found in nearly all higher organisms, including humans. Although scientists have worked on these proteins for over 20 years, we didn't know their function.

***

"The first breakthrough came in 2015, when the Nair lab in the Department of Biochemistry solved the crystal structure of a LanC-containing protein in bacteria. The protein was bound to another enzyme called a kinase, which modifies proteins by adding a phosphate group. Inspired by this discovery, the researchers tested whether LanCL proteins were also binding to kinases in eukaryotic cells. "We saw that they were able to bind to many kinases, including AKT and mTOR, and all of a sudden the pieces of the puzzle started forming a picture," van der Donk said.

"The next piece fell into place in collaboration with Benjamin Davis, a professor of chemistry at the University of Oxford. The Davis group showed that eliminating a particular phosphate group in kinases causes them to become activated. Scientists had assumed that such processed proteins would be inactive. Together, the Illinois and Oxford groups were able to show that LanCL adds glutathione to kinases with eliminated phosphate groups, after which the kinases became deactivated. "We realized that when the LanCL proteins are absent, the cell has a big problem because there are active proteins floating around that need to be turned off," van der Donk said.

***

"The researchers are interested in understanding the role of these proteins and making a complete list of all the possible targets of LanCLs. "When you have abnormal kinases, it can cause all kinds of problems, including cancer. LanCL proteins eliminate these damaged kinases and it is possible that they also affect other proteins that we are not aware of. We need to connect their cellular functions to the results we saw in the mice," Chen said."

Comment: This system had to exist. Used up unwanted molecules had to have a garbage system go keep an active living system functional. Not by chance, but by excellent design.

Biological complexity: deciphering cell surface glycans

by David Turell @, Monday, May 03, 2021, 18:43 (1061 days ago) @ David Turell

A whole new area being decoded:

https://www.quantamagazine.org/researchers-read-the-sugary-language-on-cell-surfaces-20...

"Gagneux pivoted to the study of the glycomolecules, or glycans, in that “rainforest canopy” that shrouds cells. Glycans are a spectacularly diverse group of complex sugars (polysaccharides). They can exist on their own — cellulose is a plant glycan made up of long chains of glucose — or they can be anchored to other biomolecules like proteins and lipids, whose chemical properties they modify. Their structure can be linear (as in cellulose), but they can also be very highly branched, adding to their variety and complexity.

***

"After analyzing a comprehensive data set of glycan structures and their known interactions, researchers at Harvard University and the Massachusetts Institute of Technology found a shared structural “language” that all organisms use when making glycans, like a municipal building code that ensures consistent, compatible architecture. The researchers have released a set of online tools that anyone can use to analyze glycan structures and functions.

***

"...glycans are still one of the greatest enigmas of the biological universe.” They’re “actually so prominent, they’re a major component of biomass on the planet.” In fact, glycans make up most of the organic matter by mass: Cellulose and chitin, the major building material of arthropod exoskeletons and fungal cell walls, are nature’s two most abundant organic polymers. And yet in contrast with the overabundance of glycans, “this whole field has been left behind,” Varki said.

***

"Bojar, who was a postdoctoral fellow at the Wyss Institute and MIT at the time, is the study’s first author. He and his colleagues observed 1,027 unique simple sugars (monosaccharides) and chemical bonds in the glycan sequences. They treated these as “glycoletters” — “the smallest units of an alphabet for a glycan language,” they wrote. They then began looking through the data set for patterns of “glycowords,” defined as sequences five glycoletters long (that is, three monosaccharides linked by two bonds).

***

"In theory, the glycoletters in the data set could have formed nearly 1.2 trillion different glycowords. Yet, surprisingly, the researchers’ results indicated that only 19,866 distinct glycowords were present across all the available sequences. Notwithstanding the immense complexity and diversity of glycans, and the differences in glycans that are characteristic of various species, the evidence suggested that all organisms follow very similar rules in assembling them and use essentially the same biomolecular language to define their structure.

***

"Antibody proteins latch onto specific antigen targets on pathogens. But it is the glycans linked to the proteins that determine how the antibodies interact with the rest of the body’s defenses and help to direct what kind of immune response follows. In the future, Bojar said, the tools might be able to suggest glycans that would improve the performance of antibodies, for example by limiting their side effects or more precisely calibrating their half-life in the body.

"Mahal noted that she is already using the tools to learn more about the specificity of the assays used to identify the glycans on cells. “These new computational technologies combined with high-throughput analysis will revolutionize our understanding of the glycome and its role in disease,” she said."

Comment: It seems every system in living biochemistry is organized in coded procedures. It is to early to fully understand this latest area of research, but it will blossom as DNA research has done. Not designed by chance.

Biological complexity: contingency planning

by David Turell @, Wednesday, May 05, 2021, 22:02 (1059 days ago) @ David Turell

How does 'what if' contingency planning appear in cell function?:

https://evolutionnews.org/2021/05/contingency-planning-in-the-cell-affirms-design/

Collagen is the most abundant protein in the human body. When collagen fibers are assembled, there’s a polysaccharide that usually sits idly by. It is called N-glycan, and its role has remained elusive for decades. Now, scientists have figured out what it’s there for. Rasia C. Li et al., publishing in PNAS, announced that “Collagen’s enigmatic, highly conserved N-glycan has an essential proteostatic function.” The team figured that this member must have a function because it is highly conserved in all domains of life despite the energetic cost of maintaining it. With that knowledge, they searched for its elusive purpose.

By assaying N-glycan function under conditions of impaired collagen folding, we show that, although the N-glycan is dispensable under normal conditions, it is essential for collagen folding and secretion under conditions that challenge proteostasis. Such environments are commonly encountered during development, tissue repair, and disease.

***

A 2017 textbook on the Essentials of Glycosylation spends several pages describing the synthesis of N-glycans. It takes a lot of cellular machinery to construct these players! “The biosynthesis of N-glycans is most complex in mammals,” the three authors say. There are processes to make the nascent molecule, then there are early processing steps, late processing steps and maturation steps. These occur in two cellular compartments: the Golgi and the endoplasmic reticulum.

N-Glycan synthesis begins on a lipid-like polyisoprenoid molecule termed dolichol-phosphate (Dol-P) in eukaryotes. Following synthesis of an oligosaccharide that contains as many as 14 sugars, the N-glycan is transferred “en bloc” to protein. This synthetic pathway is conserved in all metazoa, plants, and yeast…. N-Glycans affect many properties of glycoproteins including their conformation, solubility, antigenicity, activity, and recognition by glycan-binding proteins…. Defects in N-glycan synthesis lead to a variety of human diseases.

Comment: Protective mechanisms of this must be present when the initial system is designed. It cannot be developed from observing mistakes as there would have been a stop to their evolution. Only design fits.

Biological complexity: contingency planning photosynthesis

by David Turell @, Wednesday, May 05, 2021, 22:07 (1059 days ago) @ David Turell

To avoid sunburn plants have quantum tricks:

https://evolutionnews.org/2021/05/contingency-planning-in-the-cell-affirms-design/

"...Jacob S. Higgins et al. describe how “Photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer.” Plants know their QM (quantum mechanics) well enough to employ it like an overflow valve, steering excess energy into the quenching center.

"Photosynthetic light-harvesting antennae transfer energy toward reaction centers with high efficiency, but in high light or oxidative environments, the antennae divert energy to protect the photosynthetic apparatus. For a decade, quantum effects driven by vibronic coupling, where electronic and vibrational states couple, have been suggested to explain the energy transfer efficiency, but questions remain whether quantum effects are merely consequences of molecular systems. Here, we show evidence that biology tunes interpigment vibronic coupling, indicating that the quantum mechanism is operative in the efficient transfer regime and exploited by evolution for photoprotection. Specifically, the Fenna–Matthews–Olson complex uses redox-active cysteine residues to tune the resonance between its excitons and a pigment vibration to steer excess excitation toward a quenching site.

"It’s marvelous that evolution “exploited” this QM capability, isn’t it? How many mutations did it take to get that right?"

Comment: Sure, Designed by random mutations.

Biological complexity: contingency planning DNA repair

by David Turell @, Wednesday, May 05, 2021, 22:12 (1059 days ago) @ David Turell

Several described methods:

https://evolutionnews.org/2021/05/contingency-planning-in-the-cell-affirms-design/

"The chart shows five repair systems that protect DNA from damage. These are contingency planning systems that are ready and waiting to step in, like EMTs, when things go wrong during cell division or transcription. There are five systems they discussed:

"Mismatch repair fixes mutations that insert the wrong base

"Nucleotide excision repair comes to aid when DNA structural damage occurs

"Base excision repair fixes bases that become separated from the strand

"Double-stranded break repair solves the complex situation when both DNA strands become separated

"Interstrand crosslinks repair helps when drugs block replication and transcription

"When these systems work properly, they can prevent cancer and drug resistance. Many life-threatening diseases are prevented by these five pathways. When the pathways themselves fail, though, it can be bad news for the organism. The Chinese team felt that systematizing our knowledge about these pathways and the specific consequences of “pathway damage” can help oncologists know which avenues provide the best therapies for specific cancers."

Comment: When DNA formed these protections had to be designed in place.

Biological complexity: exquisite attack needle design

by David Turell @, Wednesday, May 12, 2021, 23:21 (1052 days ago) @ David Turell

An elegant research paper picking apart a very complex protein attack needle:

https://www.nature.com/articles/s41467-021-21143-1

"Abstract
Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.

Introduction
Many important human pathogens including Salmonella, Shigella, Yersinia, and enteropathogenic Escherichia coli employ a conserved, virulent type III secretion system (T3SS), also commonly referred to as the injectisome, to deliver a pleiotropic arsenal of proteins into target eukaryotic cells. These proteins modulate host cell signal transduction processes to establish a biological niche within the host, making T3SSs crucial virulence determinants. Yet, the precise mechanisms that allow these secretion systems to facilitate unfolded protein transport across the bacterial envelope and into the host cell while maintaining bacterial membrane remain integrity poorly understood. Therefore, visualizing the translocation process at the molecular level is essential for our understanding of host–pathogen biology and the development of novel therapies targeting bacterial infection.

"The injectisome is a large molecular machine, over 3.6 MDa in mass, spanning across the inner and outer bacterial membranes with an extracellular filamentous appendage extending out to target host cells. Chaperones present effector proteins in a non-globular, secretion-competent state to a cytoplasmic sorting platform complex, which sorts and loads effectors into the export apparatus (EA) subcomplex located inside the membrane-bound basal body. Extending from the EA is a long, helical needle filament, capped by a tip complex that contacts the host cell membrane via assembly of a translocon pore. The basal body and the needle filament, collectively termed the needle complex, function as a continuous conduit for effector protein translocation from the prokaryotic to the host cell cytoplasm.

***

"In this work we report cryo-EM structures of an active Salmonella enterica sv. Typhimurium needle complex engaged with a SptP3x-GFP substrate, revealing the complete 800 Å-long secretion conduit and unraveling the critical role of the EA in substrate transport. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent transport, providing a rationale for the heterogeneity and structural disorder of signal sequences in T3SS effector proteins. Above, a methionine gasket formed by five SpaP proteins functions as a gate that dilates to accommodate substrates but prevents leaky pore formation to maintain the physical boundaries of compartments separated by a biological membrane. Above the gate, a moveable SpaR loop first folds up to then support substrate transport through the needle complex channel. Together, these findings establish the molecular basis for substrate translocation through T3SSs, improving our understanding of bacterial pathogenicity and motility of flagellated bacteria, and pave the way for the development of novel concepts combating bacterial infections."

Comment: Read these paragraphs slowly as your eyes roll back. Extreme complexity shown beautifully in the diagrams which should be seen to appreciate this DID NOT happen by natural chance events.

"Researchers in Germany recently examined the T3SS in more detail, finding more complexities of engineering that should arouse the observer’s awe. For instance, these machines can fire effector proteins at the rate of 7 to 60 molecules per second! The machine resembles a dart gun in the bacterial cell wall that is loaded from the cytoplasm and can tunnel into a neighboring cell, probably with the aid of a pioneer translocator that opens a hole in the host membrane."

https://evolutionnews.org/2021/05/closer-look-at-the-t3ss-reveals-design/

It is a wild west shoot 'em out at teh bacterial level.

Biological complexity: controls over red cell manufacture

by David Turell @, Friday, May 14, 2021, 19:48 (1050 days ago) @ David Turell

As usual very complex with specific molecules driving the process:

https://science.sciencemag.org/content/372/6543/716

"Metabolic pathway regulates cell fate
Lineage-specific regulators direct cell fate decisions, but the precise mechanisms are not well known. Using an in vivo chemical suppressor screen of a bloodless zebrafish mutant, Rossmann et al. show that the lineage-specific chromatin factor tif1γ directly regulates mitochondrial genes to drive red blood cell differentiation. Loss of tif1γ reduces coenzyme Q synthesis and function, impeding mitochondrial respiration and leading to epigenetic alterations and repression of erythropoiesis. The loss of blood in the mutant fish can be rescued by the addition of coenzyme Q. This work establishes a mechanism by which a chromatin factor tunes a metabolic pathway in a tissue-specific manner.

"Abstract
Transcription and metabolism both influence cell function, but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. We discovered, using a chemical suppressor screen, that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma (tif1γ). This rescue depends on the functional link of DHODH to mitochondrial respiration. The transcription elongation factor TIF1γ directly controls coenzyme Q (CoQ) synthesis gene expression. Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon’s bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.

"Vertebrate embryos produce circulating red blood cells (RBCs) that are required for oxygen and carbon dioxide transport. During embryonic development, three overlapping hematopoietic waves can be distinguished that all produce RBCs. In mammals, primitive erythroblasts that emerge in the blood islands within the extraembryonic yolk sac give rise to primitive erythrocytes of the first transient wave, and a second wave generates definitive erythroid-myeloid progenitors in the hemogenic endothelium of the yolk sac. Definitive erythrocytes of the third wave arise from multipotent hematopoietic stem cells that are born in the aortic endothelium of the aorta-gonad-mesonephros region and sustain hematopoiesis throughout the lifetime of the animal. Primitive erythrocytes supply the embryo with the oxygen needed for its rapid proliferation. Failure to initiate the first wave of erythropoiesis leads to embryonic lethality. Erythroid lineage differentiation is regulated by key transcription factors, but the cellular mechanisms that allow the generation and differentiation of the first erythroid progenitors remain largely unknown. Stem and descendent progenitor cells differ by their metabolic profiles, but there is little in vivo evidence for a link between transcriptional regulation and metabolic changes during cell fate decisions.

***

"Discussion
Tissue differentiation can be regulated by metabolic activities. It was previously unclear how lineage transcription factors induce distinct changes during cell fate specification and lineage differentiation. Our work demonstrates that the metabolic state of the tissue required for early erythroid lineage differentiation is under the direct transcriptional control of TIF1γ. CoQ is a critical downstream effector of TIF1γ transcriptional activity, regulating the balance between nucleotide synthesis and ETC activity in embryonic erythropoiesis. This highlights a previously unappreciated role of mitochondrial respiration in driving the early commitment of the erythroid lineage. It has been proposed that transcriptional and metabolic processes influence each other. We demonstrate that this is the case in early erythropoiesis, where exogenous CoQ can drive erythroid differentiation in the mon mutant, including the expression of embryonic globin as a late lineage marker."

comment: this highly complex research article describes the surface of the controlling molecules. We see what controls what, but not how the controls are really performed. This is the magic of the unseen, but understood to exist, exotic control systems that controls/creates embryology and all of life. It is only by understanding this hidden layer exists and must be of the highest complexity, everyone should then understand a designing mind has to be the source. Can research get to this level and reveal it? I hope so. But one shouldn't have to wait for explicit descriptions of the process to accept a designing mind.

Biological complexity: controls over cell division

by David Turell @, Thursday, June 10, 2021, 20:01 (1023 days ago) @ David Turell

Division occurs when the cell reaches a certain size. How does the cells know this?:

https://phys.org/news/2021-06-cells.html

"The question of how these building blocks of life regulate their own size, however, has remained a mystery.

"Now we have an explanation for this long-standing biological question. In a study focusing on the growing tip of plants, researchers show that cells use their DNA content as an internal gauge to assess and adjust their size.

***

"The average cell size results from a balance between how much cells grow and how often they split in two. It has long been clear that cells grow to a certain size before they divide. But how can a cell know how much it has grown?

***

"In this study, which appears in Science, John Innes Centre researchers carefully followed the growth and division of meristem cells over time. They found that although cells can start their life with variable sizes, by the time the cells are ready to replicate their DNA (a necessary step before cell division, as each new cell needs its own copy of the DNA), most of the initial variability in cell sizes has been corrected.

'They then monitored a protein called KRP4, whose role is to delay the start of DNA replication, and found that, regardless of their initial size, cells were always born with the same amount of KRP4. This means that when a cell is born too small, it receives a higher concentration of KRP4, which delays its progression to DNA replication, allowing time for the cell to catch up to the same size of the other cells. Conversely, if a cell is born too big, KRP4 is diluted so it can move quickly onto the next stage without growing further. Over time this keeps meristem cells within a narrow size range.

"But what ensures that cells start off with the same amont of KRP4? It turned out that when cells divide, KRP4 "takes a ride" on the DNA, which is given in identical copies to each newborn cell. In this way, the initial amount of KRP4 becomes proportional to the cell's DNA content. To make sure that KRP4 accumulates in the mother cell in proportion to the DNA content, any excess KRP4 not bound to the DNA is destroyed before cell division by another protein called FBL17. Mathematical models and using gene-edited mutants with varying quantities of these genetic components confirmed the mechanism.

"Professor Robert Sablowski, explains this process, "One riddle we had to solve is how a cell can know how much it has grown when most of the components of a cell increase together in number and size so they cannot be used as a fixed ruler to measure size. One exception is DNA which exists in the cell in a discrete amount—its amount precisely doubles before cell division, but it does not vary with cell growth."

"Future experiments will seek to explain exactly how the regulatory protein KRP4 associates, then dissociates from chromosomes during cell division. The researchers also want to understand whether the mechanism is modulated in different cell types to produce different average sizes.

"The findings may explain the relation between genome size and cell size—species with large genomes and, therefore a lot of DNA in their cells, tend to have larger cells. This is particularly important in crop plants, many of which have been selected to contain multiple copies of the genomes present in their wild ancestors, leading to larger cells and often larger fruits and seeds."

Comment: A very clever mechanism, that had to be designed. Haphazard growth is not a logical process, and chance evolution is not logical.

Biological complexity: insect smell receptors

by David Turell @, Monday, June 21, 2021, 20:33 (1012 days ago) @ David Turell

Very complex but partially described:

https://www.quantamagazine.org/secret-workings-of-smell-receptors-revealed-for-first-ti...

"Smell, rather than sight, reigns as the supreme sense for most animals. It allows them to find food, avoid danger and attract mates; it dominates their perceptions and guides their behavior; it dictates how they interpret and respond to the deluge of sensory information all around them.

***

"Yet olfaction might also be the least well understood of our senses, in part because of the complexity of the inputs it must reckon with. What we might label as a single odor — the smell of coffee in the morning, of wet grass after a summer storm, of shampoo or perfume — is often a mixture of hundreds of types of chemicals. For an animal to detect and discriminate between the many scents that are key to its survival, the limited repertoire of receptors on its olfactory sensory neurons must somehow recognize a vast number of compounds. So an individual receptor has to be able to respond to many diverse, seemingly unrelated odor molecules.

***

"In insects, olfactory receptors are ion channels that activate when an odor molecule binds to them. They may be the largest and most divergent family of ion channels in nature, with millions of variants across the world’s insect species. And so they must carefully balance generality against specificity, staying flexible enough to detect an enormous number of potential odors while being selective enough to reliably recognize the important ones, which could differ considerably from one species or environment to another.

***

"A receptor built around a single binding pocket, with a response profile that can be retuned by the smallest of tweaks, could speed up evolution by freeing it to explore a broad spectrum of chemical repertoires.

"The architecture of the receptor also supported this view. Ruta and her colleagues found that it consisted of four protein subunits loosely bound at the channel’s central pore, like the petals of a flower. Only the central region needed to be conserved as the receptor diversified and evolved; the genetic sequences governing the rest of the receptor units were less constrained. This structural organization meant the receptor could accommodate a wide degree of diversification.

"Such light evolutionary constraints at the receptor level probably impose substantial selective pressure downstream on the neural circuits for olfaction: Nervous systems need good mechanisms for decoding the messy patterns of receptor activity. “Effectively, olfactory systems have evolved to take arbitrary patterns of receptor activation and endow them with meaning through learning and experience,” Ruta said. (my bold)

"Intriguingly, though, nervous systems don’t seem to be making the problem easier for themselves. Scientists had widely supposed that all the receptors on an individual olfactory neuron were of the same class, and that neurons for different classes went to segregated processing regions of the brain. In a pair of preprints posted last November, however, researchers reported that in both flies and mosquitoes, individual olfactory neurons express multiple classes of receptors. “Which is really surprising, and would increase the diversity of sensory perception even more,” Barber said.

"The findings from Ruta’s team are far from the last word on how olfactory receptors work. Insects use many other classes of ion channel olfactory receptors, including ones that are much more complex and much more specific than those of the jumping bristletail. In mammals, the olfactory receptor is not even an ion channel; it belongs to an entirely different family of proteins."

Comment: Amazingly complex as suggested. Note my bold. Odors are learned over time. Literally these receptors fondle the shape of the protein molecules they receive and gradually learn to understand what teh odor means and signifies.

Biological complexity: plant cell regulators

by David Turell @, Monday, June 21, 2021, 20:49 (1012 days ago) @ David Turell

Newly defined:

https://phys.org/news/2021-06-universal-mechanism-cells.html

"All plant cells obtain their energy mainly from two organelles they contain—chloroplasts (responsible for photosynthesis) and mitochondria (responsible for the biochemical cycle of respiration that converts sugars into energy). However, a large number of a plant cell's genes in its mitochondria and chloroplasts can develop defects, jeopardizing their function. Nevertheless, plant cells evolved an amazing tool called the RNA editosome (a large protein complex) to repair these kinds of errors. It can modify defective messenger RNA that result from defective DNA by transforming (deamination) of certain mRNA nucleotides.

"Automatic error correction in plants was discovered about 30 years ago by a team headed by plant physiologist Axel Brennicke and two other groups simultaneously. This mechanism converts certain cytidine nucleotides in the messenger RNA into uridine in order to correct errors in the chloroplast DNA or mitochondrial DNA. RNA editing is therefore essential to processes such as photosynthesis and cellular respiration in plants. Years later, further studies showed that a group of proteins referred to as PPR proteins with DYW domains play a central role in plant RNA editing. These PPR proteins with DYW domains are transcribed in the cell nucleus and migrate through the cells to chloroplasts and mitochondria. However, they are inactive on their way to these organelles. Only once they are within the organelles do they become active and execute their function at a specific mRNA site. How this activation works, however, has been a mystery until now.

***

"This three-dimensional architecture has actually provided the crucial clue to the mechanism of DYW domain activation that applies to all plants. It is due to a zinc atom located in the center of the DYW domain that can accelerate the deamination of cytidine to uridine like a catalyst. For this to happen, however, the zinc must be optimally positioned. The activation switch is provided by a very unusual gating domain in the immediate vicinity of the catalytic center—the structural analysis shows that this gating domain can assume two different positions, thereby switching the enzyme on or off. "The movement of the gating domain regulates the extent to which the zinc ion is available for the catalytic reaction," Weber explains.

***

"Now it has become clear why getting DYW-type PPR proteins to react with RNA in the test tube has been difficult until now: These PPR proteins are nominally inactive and require activation. In the plant cells, they are first produced in the cell nucleus and then very likely migrate in an inactivated state to the organelles, where they become activated. "This is ideal, because otherwise these molecules would be active along the way, altering various RNA molecules in an uncontrolled fashion harmful to the cell," says Weber.

"This work is a breakthrough for plant molecular biology because it describes an additional level of sophisticated regulation in chloroplasts and mitochondria."

Comment: We have previously discussed God's error correction mechanisms. What is obvious is that they must be present when the plant is initially evolved. Chance evolution by chance mutation won't do that.

Biological complexity: the vital importance of heme

by David Turell @, Wednesday, June 30, 2021, 23:42 (1003 days ago) @ David Turell

It is the starting point for the manufacturer of hemoglobin and more:

https://evolutionnews.org/2021/06/designed-for-a-purpose-heme-production-defeats-evolut...

"Seven scientists (Galvin Leung et al.) from two UK universities (Leicester, Bristol) explain the significance of heme in their paper, “Unravelling the mechanisms controlling heme supply and demand,” published in PNAS. Their homage to heme is unrestrained, as is their appreciation for how the cell handles this toxic molecule.

"Heme is essential for the survival of virtually all living systems and is involved in many fundamental biological processes. It is also implicated as a signaling/regulatory molecule and must be mobilized in response to cellular demands. This presents a complex logistical problem: heme cannot simply diffuse around cells because it is both insoluble and cytotoxic. We show that the cell exhibits exquisite control over release of heme by limiting its availability to one molecule or less within cellular compartments.

"Heme is essential for the survival of virtually all living systems — from bacteria, fungi, and yeast, through plants to animals. The family of heme proteins is vast, and heme proteins are responsible for a multitude of functions that are essential for the survival of the cell. To meet the needs of supply and demand for heme in cells, most organisms need to synthesize it. Biosynthesis of the heme cofactor is, therefore, one of the most important metabolic processes in biology; it occurs as an eight-step enzymatic pathway, the last three steps of which occur in the mitochondria. (my bold)

"It takes eight steps to synthesize one heme molecule, and virtually all life needs it — even bacteria, among the simplest of organisms. The other enzymes that construct heme had to already exist before heme could do its job. This is a serious chicken-and-egg problem for the origin of life. (my bold)

***

"We suggest an exchange mechanism between protein partners to control supply and demand. Such a mechanism would provide an in-built buffering capacity for heme, enable cells to hoard supplies of heme, and protect the cell against the undesirable effects of heme.

"How about that; cells know the law of supply and demand. Where did they learn that? In protocell economics class? They also know how to “hoard supplies” of heme (actually, how to maintain emergency stockpiles).

***

"A cell cannot maintain a “pool” of heme to draw from, as once thought, because heme is a “nuisance” to cells. It tends form free radicals, which are dangerous, and though hydrophobic, it dimerizes in solution, making it unsuitable for delivery to proteins that only need one heme molecule per binding site.

"A free molecule of heme can therefore only exist transiently, and if a large reserve of heme is present, the heme molecules would presumably need to be exchanged rapidly between binding partners to remain solubilized, in the same way that heme is solubilized within the interior of other well-known heme proteins (e.g., hemoglobin).

***

"heme availability…. The results demonstrate that concentrations are typically limited to one molecule or less within cellular compartments. These miniscule amounts of free heme are consistent with a system that sequesters the heme and is able to buffer changes in heme availability while retaining the capability to mobilize heme when and where it is needed. … This exquisite control, in which heme is made available for transfer one molecule at a time, protects the cellagainst the toxic effect of excess heme and offers a simple mechanism for heme-dependent regulation in single-molecule steps.

"In effect, the cell maintains “an exchangeable (buffered) heme reservoir” that solves the availability problem while simultaneously protecting the cell from heme’s toxic effects. Free heme (the risky kind) was detected only in “a minute fraction of the entire amount of heme present in the cell”

***

"This exquisite control also provides a mechanism for heme-dependent signaling and regulation, as heme can be supplied discretely, leading to the switching on of proteins in single-molecule steps.

***

"To nail the case for design, consider the level of exquisite control...The human body makes around 250 billion red blood cells per day, and each RBC contains 270 million hemoglobin molecules, each constructed with 4 heme groups. That multiplies out to 27 billion trillion hemes per day!

"It’s amazing enough that each cell in the body orchestrates its synthesis and availability of heme. On top of that, the whole body, too, regulates the number of hemoglobin molecules and red blood cells that carry another cytotoxic substance — oxygen — from our lungs to each cell in a safe, regulated, exquisitely controlled manner. Every red-blooded person should take this to heart: we would be walking packages of explosives if it were not for mechanisms “designed for the purpose” of using energy safely for life,..."

Comment: Toxic heme is vital and is tightly controlled as it is a feedstock for many important living processes. Tell me how that happens by chance. There is no answer but a careful designer creating the process: it can only appear in cellular functions with safeguards simultaneously in place. Not to mention eight specific steps orchestrated by giant complex enzymes made up out of thousands of specific amino acids.

Biological complexity: dying c ells protect living ones

by David Turell @, Friday, July 09, 2021, 18:56 (994 days ago) @ David Turell

Cells are constantly dying and being replaced. The continue=to-live cells are protected by a specific mechanism:

https://phys.org/news/2021-07-dying-cells-neighbors-tissue.html

"To enable tissue renewal, human tissues constantly eliminate millions of cells, without jeopardizing tissue integrity, form and connectivity. The mechanisms involved in maintaining this integrity remain unknown. Scientists from the Institut Pasteur and the CNRS today revealed a new process which allows eliminated cells to temporarily protect their neighbors from cell death, thereby maintaining tissue integrity. This protective mechanism is vital, and if disrupted can lead to a temporary loss of connectivity. The scientists observed that when the mechanism is deactivated, the simultaneous elimination of several neighboring cells compromises tissue integrity. This lack of integrity could be responsible for chronic inflammation.

"Human epithelia are tissues found in several parts of the body (such as the epidermis and internal mucosa). They are composed of layers of contiguous cells that serve as a physical and chemical barrier. This role is constantly being put to the test by both the outside environment and their own renewal. Tissue renewal involves the formation of new cells by cell division and the elimination of dead cells. The mechanisms that regulate the ability of epithelia to maintain their integrity in contexts involving large numbers of eliminated cells remain poorly understood, despite the fact that this situation occurs regularly during embryogenesis or the maintenance of adult tissues.

***

"...the research team revealed that when a cell dies, the EGFR-ERK pathway—a cell activation signaling pathway known for its involvement in the regulation of cell survival—is temporarily activated in the neighboring cells. The scientists observed that the activation of the EGFR-ERK pathway protected neighboring cells from cell death for approximately one hour, thereby preventing the simultaneous elimination of a group of cells. "We already knew that this pathway plays a key role in regulating cell survival in epithelial tissue, but we were surprised to observe such protective dynamics between cells," comments Romain Levayer, Head of the Cell Death and Epithelial Homeostasis Unit at the Institut Pasteur and last author of the study.

***

"The scientists' observations confirm that tissues need to develop mechanisms preventing the elimination of neighboring groups of cells. "These observations are important as they illustrate the incredible self-organizing ability of biological tissues, a property that enables them to withstand stressful conditions. So there is no need for a conductor to orchestrate where and when the cells should die; everything is based on highly local communications between neighboring cells," adds Romain Levayer.

"This process seems to have been conserved during evolution. The same protective mechanism based on local EGFR-ERK activation was discovered independently in human cell lines by the research group led by Olivier Pertz at the University of Bern in Switzerland. The results of the other study suggest that the protective mechanism is conserved between species separated by hundreds of millions of years, indicating that it is a relatively universal mechanism." (my bold)

Comment: No surprise in my bold. This protective mechanism had to be designed very early in evolution since cells are replaced constantly to keep tissues up-to-date in active metabolism. I imagine, when this mechanism is picked apart it will look highly designed.

Biological complexity: more photosynthesis complexity

by David Turell @, Wednesday, July 14, 2021, 17:22 (989 days ago) @ David Turell

New components found for low light environments:

https://phys.org/news/2021-07-unique-pigments-photosynthetic-marine-bacterium.html

"Scientists used to believe that photosystem I, the membrane protein complex present in all aerobic organisms, utilized a form of chlorophyll called chlorophyll a for photosynthesis. But that changed when a marine cyanobacterium was discovered in the 1990s that employs a different form of chlorophyll; Acaryochloris marina uses chlorophyll d to harness far-red wavelengths of light, whose energy was previously considered to be too low to be useful for typical organisms.

"'How A. marina uses low-energy light for photosynthesis has been a long-standing question," notes Koji Yonekura, who leads the Biostructural Mechanism Group at the RIKEN SPring-8 Center.

"Now, Tasuku Hamaguchi, Keisuke Kawakami, Yonekura and their colleagues have shed light on this question by analyzing the structure of the photosystem I reaction center—the part of chlorophyll that converts sunlight into a form of chemical energy that can be used by the rest of the photosynthetic machinery—of chlorophyll d in A. marina. They realized this by using cryo-electron microscopy at a higher resolution than has been applied to look at these protein complexes before.

"The researchers' analysis revealed that one of the light-harvesting pigments is pheophytin a, a metal-free chlorin that differs from other type I reaction centers. This exquisite combination of pheophytin a and chlorophyll d helps to explain some ways that the cyanobacterium can efficiently harness the low energy of far-red light for photosynthesis."

Comment: The word 'exquisite' shows how beautifully designed this system appears to be. Not by chance. The more complexity we find, the more a designer must be necessary.

Biological complexity: cell division requires being loose

by David Turell @, Wednesday, July 28, 2021, 20:04 (975 days ago) @ David Turell

The evolving cell must loosen itself from others:

https://www.sciencedaily.com/releases/2021/07/210727171703.htm

"Researchers found that CDK1, the master regulator of the cell cycle binds directly to, and modifies, the core protein talin that is essential to the process of cell adhesion. This interaction represents a coupling of the cell proliferation and adhesion processes. This indicates a unifying mechanism by which the processes of cell division and adhesion are controlled.

***

"Dr Ben Goult, Reader in Biochemistry at the University of Kent and a Principal Investigator of the paper said: 'The potential of this discovery is huge as it provides a new understanding of how cell division is coordinated within the confines of a complex multicellular organism. Cell division needs to be tightly coupled to the cell adhesion to allow our cells to divide without disrupting the integrity of our tissues and organs. This research is vital in our understanding of other cellular diseases and of cancer's ability to spread within the human body.'"

Comment: another example of irreducible complexity. All of this mechanism must have all parts in place all at once to work. It must become loose to start cell division process. Only design fits.

Biological complexity: controls of nucleolus

by David Turell @, Friday, July 30, 2021, 15:14 (973 days ago) @ David Turell

A vital part of a nucleus has no membrane to separate itself, but it totally controlled by a liquid liquid phase transition:

https://science.sciencemag.org/content/373/6554/486

"Intracellular organelles that lack a membrane boundary are often formed through liquid-liquid phase separation. The biophysical properties of such structures are linked to their physiological functions and involvement in diseases. Most of these organelles contain RNA molecules that associate with RNA binding proteins (RBPs) to control intracellular phase separation (1). Specific long noncoding RNAs (lncRNAs) are especially important in the architecture of membraneless organelles (2). On page 547 of this issue, Wu et al. (3) provide a mechanistic understanding of how lncRNAs modulate the biophysical properties of phase-separated nucleolar subdomains of the nucleus, where ribosome biogenesis takes place.

"The nucleolus is the largest membraneless subnuclear organelle and serves as a location for ribosome production, a critical determinant of protein synthesis capacity. It comprises multilayered phase-separated subdomains that possess distinct biophysical properties: fibrillar centers (FCs) that contain the tandemly repeated ribosomal RNA (rRNA) gene cluster [or ribosomal DNA (rDNA)]; the dense fibrillar component (DFC) that surrounds FCs; and the granular component (GC) that includes dozens of FC/DFC units (4). The organized multilayered structure of the nucleolus is thought to ensure efficient ribosome biogenesis. This is initiated by rDNA transcription by RNA polymerase I (Pol I) to generate pre-rRNA at the border between the FC and DFC, subsequent pre-rRNA processing in the DFC, and later events, including ribonucleo-protein (RNP) assembly into the ribosomal subunits in the GC.

"Wu et al. focused on a human-specific nucleolar lncRNA called SLERT (a box H/ACA small nucleolar RNA–ended long noncoding RNA that enhances pre-rRNA transcription) that is located in the DFC. The importance of SLERT was noted by the reduced size and liquidity of the FC/DFC in the absence of the lncRNA (5). SLERT associates with the nucleolar RNA helicase DDX21 (DExD-box helicase 21), which regulates transcription by Pol I. Through in vitro reconstitution and in vivo experiments, Wu et al. demonstrate a role of DDX21 in the architecture and biophysical properties of the FC/DFC and in the regulation of Pol I–mediated transcription. The authors also show how SLERT modulates two distinct DDX21 functions."

Explanatory summary:

https://science.sciencemag.org/content/373/6554/529.15?utm_campaign=twis_sci_2021-07-29...

"The nucleolus is a multilayered, membraneless nuclear condensate in which DNA polymerase I (Pol I)–mediated ribosomal DNA (rDNA) transcription and pre-rRNA processing occur in fibrillar center and dense fibrillar component (FC/DFC) units. How the biophysical properties of the nucleolus are regulated has remained elusive. Wu et al. found that the RNA helicase DDX21 forms a shell coating each FC/DFC unit in the nucleolus (see the Perspective by Yamazaki and Hirose). The authors found that a long noncoding RNA called SLERT facilitates the transition from the open to the closed configuration of the helicase using a chaperonelike mechanism. DDX21 in the closed conformation forms loose clusters that confer the FC/DFC unit sufficient liquidity and space required for Pol I processivity. In addition, DDX21 within the loose clusters cannot approach and wrap rDNA, thus licensing rDNA for transcription."

Comment: One does not need to fully understand the architecture described to recognize the extreme complexity. Note lots of 'junk DNA' is required. Evolution produced a purposeful design in 80% in our genome. There is no evidence of any random or chance development. It must be seen as designed

Biological complexity: how sperm prepares for fertilization

by David Turell @, Friday, August 20, 2021, 21:05 (952 days ago) @ David Turell

Two necessary molecular steps:

https://phys.org/news/2021-08-givgirdin-spatiotemporal-sperm-capacitation.html

"Mammalian sperm cannot fertilize an egg from the get-go. It's an ability acquired only after insemination, during passage through the female reproductive tract, and requires two consecutive, time-sensitive processes to provide sperm with the physical and biochemical traits necessary to complete their fundamental job.

"The first process is called capacitation, which alters the physiology of each spermatozoa, changing the membrane of the head to help it penetrate the hard, outer layer of an egg—the zona pellucida—and chemistry in the tail to generate greater motility, the ability to move and swim.

"The second process is acrosome reaction (AR), a chemical action that involves releasing enzymes in the spermatozoa's head that further boost penetration of the zona pellucida.

"Both processes are essential to successful fertilization of an egg, and AR is time-dependent: It cannot take place too early or too late. Indeed, premature AR has been associated with idiopathic (spontaneous) male infertility.

***

"Specifically, the research team, led by senior author Pradipta Ghosh, MD, professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine, found that GIV—a member of the G protein family that serve as molecular switches inside cells, transmitting and fine-tuning signals—regulates the activity of enzymes that turn on and turn off the processes of capacitation and AR.

"'The findings demonstrate how GIV orchestrates distinct signaling programs in sperm that separated by space and time, effectively supporting capacitation while inhibiting premature AR," said Ghosh. "As a result, GIV plays an essential role in male fertility.'"

Comment: this process which requires two coordinated timed steps demonstrates irreducible complexity which means it had to be designed all at once before being put in place

Biological complexity: function in cells as shape changes

by David Turell @, Thursday, September 09, 2021, 19:03 (932 days ago) @ David Turell

Proteins function according to their folded shapes:

https://phys.org/news/2021-09-method-protein-dynamics-cellular.html

"Cellular processes are regulated through the balance between protein shapes that confer active or inactive functions. In the complexity of cellular regulations, the preferred shape (or conformation) of a protein often depends on the binding of another molecule (called effector), thus implying that the same protein can exert distinct functions depending on the effector it binds to. At the molecular level, protein functions thus translate into protein dynamics, which is key for the development of all cellular processes, from cell division to energy provision and cell fate determination.

"Researchers led by Dr. Modesto Orozco in the Molecular Modelling and Bioinformatics lab at IRB Barcelona have developed a new computational procedure that allows the discovery and quantification of functional protein shapes, thus enabling the molecular details of cellular processes to be revealed. This work focuses on the proteins under allosteric regulation, meaning that the change in their shape happens in a region distant from the binding site of the effector.

"Using this method, the scientists have studied the regulation of adenylate cyclase (AC), a key enzyme involved in the control of a variety of cellular processes, including mediating the effects of a number of hormones and regulating energy metabolism. The work has revealed a surprisingly simple ON/OFF regulation of AC functional dynamics. (my bold)

***

"The newly proposed approach is based on previous work by the Molecular Modelling and Bioinformatics lab focused on co-evolutionary information. Multiple sequence alignment can be used to track the evolutionary history of a protein, and co-evolved amino acid positions can be detected and this information can then be used to fuel the search of native and alternative protein structures.

"'Our work leverages co-evolutionary information to reduce the complexity of all possible shapes available in protein-protein regulations, thereby reducing noise and centering our attention on only few functional shapes, which we can thus quantify," says Dr. Francesco Colizzi, first author of the study."

Comment: These proteins change shape at high speeds, making them difficult to study. Such processes must be designed all at once to work as in the bold above. Stepwise evolution can't do this.

Biological complexity: function of cells shape changes

by David Turell @, Sunday, September 19, 2021, 18:36 (922 days ago) @ David Turell

Molecules "flow":

https://phys.org/news/2021-09-cells-mechanism.html

"This multidisciplinary collaboration combined modeling and experiments to describe a previously-unknown biological process. The teams discovered and characterized a new mechanism that a simple yeast cell uses to acquire its shape. They describe these results in a paper called "Cell patterning by secretion-induced plasma membrane flows" in the latest issue of Science Advances .

"When cells move or grow, they must add new membrane to those growth regions, says Vavylonis. The process of membrane delivery is called exocytosis. Cells also must deliver this membrane to a specific location in order to maintain a sense of direction―called "polarization"―or grow in a coordinated manner.

"'We demonstrated that these processes are coupled: local excess of exocytosis causes some of the proteins attached to the membrane to move ('flow') away from the growth region," says Vavylonis. "These proteins that move away mark the non-growing cell region, thus establishing a self-sustaining pattern, which gives rise to the tubular shape of these yeast cells."

***

"'Our work shows that patterns in biological systems are generally not static," says Rutkowski. "Patterns establish themselves through physical processes involving continuous flow and turnover.'"

Comment: Cell shape changes involve orchestrated molecular reactions, probably programmed.
More complexity in action.

Biological complexity: function of cells shape changes

by David Turell @, Monday, September 20, 2021, 21:33 (921 days ago) @ David Turell

It also involves active actin formation and controls of that growth:

https://www.sciencedaily.com/releases/2021/09/210920121753.htm

"Cells are characterized to be stable yet highly flexible. They constantly modify their shape and even move through tissue. These vital properties are based on a dynamically organized network of branched actin filaments, which generates pushing forces to move the cell membrane. An interdisciplinary team has now revealed a previously unknown mechanism, explaining how stopping the growth of older actin filaments within the network promotes the formation of new ones, thereby maintaining the structure and function of the cytoskeleton, much like proper pruning of hedges in the garden.

***

"Cells grow, divide, change their shape and move. They provide structure for the body and tissues, enter wounds to close them or chase down bacteria in our blood. The mobility of cells is a prerequisite for a variety of essential biological functions and is ensured by the cytoskeleton. This dynamic protein network assembles on the inside of the cell membrane and is responsible for the cell's shape, its mechanical stability and it's ability to move.

"One key component of the cytoskeleton is actin, which can self-assemble into filaments. But where does the pushing force of the cytoskeleton actually originate from? The origin lies in a nucleation process that occurs just beneath the cell membrane. Nucleation of new actin filaments is initiated by a protein complex called Arp2/3, which is activated by membrane-bound nucleation promoting factors (NPF). The Apr2/3 forms the initial seed of a new filament and connects this seed to the side of older filaments. After the initial formation of this actin seed, further actin monomers attach and construct a filament, which grows against the membrane. This growth process generates the pushing force. The resulting structure of the actin network looks like a tree or a hedge, with many connected branches of actin filaments.

"To ensure optimal power transmission to the plasma membrane, the branched actin network requires continuous maintenance. A key player in this process is the capping protein. Its main task is to stop the elongation of filaments before they become too long and to prevent the non-productive elongation of filaments that grow away from the cell membrane. Capping actin filaments thus has a similar effect to trimming a hedge: it keeps the (actin) hedge neat and tidy, much like proper pruning However, it also stimulates the budding production (actin branching) near the plant's edges (membrane) through the Arp2/3 complex. The precise mechanism involved in how the capping protein controls the speed by which Arp2/3 forms new filaments was not previously understood.

***

"A high-resolution structure of the capping protein bound to an actin filament-end produced by co-first author Felipe Merino using electron cryo-microscopy revealed that the capping protein does much more than previously assumed. It not only stops filament growth, but also blocks the end from interacting with other proteins. Most importantly, it blocks the binding of nucleation promoting factors (the Arp2/3 activators) via a tiny "tentacle" extension. Johanna Funk, co-first author of the study, was able to show, that removing this tentacle did not prevent the capping protein from stopping filament growth, but drastically inhibited the network assembly and the efficiency of lamellipodial protrusion required for cell movement when working together with all other proteins required to build branched networks."

Comment: A highly complex system for changing cell structure with stop and go controls, Had to be designed all at once, not by step-by-step evolution.

Biological complexity: how molecules enter cell walls

by David Turell @, Wednesday, October 20, 2021, 19:40 (891 days ago) @ David Turell

Giant ones were doing it in an unknown way until now:

https://phys.org/news/2021-10-magic-proteins-cell-walls.html

"For decades, scientists have wondered how large molecules such as proteins pass through cell walls, also known as plasma membranes, without leaving a trace. That ability is part of what makes certain drugs—including some cancer treatments and the COVID-19 vaccine—work. And it is also how bacterial toxins enter human cells and wreak havoc.

***

"'It is almost like a magic trick, the way the membrane encapsulates these toxins," said Dehua Pei, senior author of the study and a professor of chemistry and biochemistry at The Ohio State University.

***

"While working on the team's other projects, Sahni noticed that some fragments of proteins, known as peptides, cross membranes by pushing against them. The peptides deformed the membrane into small circular buds. The buds then detach as small bubbles, known as vesicles, which eventually "pop," allowing the peptides to be released inside the cell. The team subsequently observed that two structurally different bacterial toxins also employed this same mechanism. This discovery led them to conclude that this budding-and-collapse mechanism is a common mechanism employed by many large biomolecules.

"'This budding-and-collapse phenomenon was previously unknown, but we were able to witness it because we had the equipment, training and experience to know what we were looking at," Sahni said.

"The team witnessed the budding-and-collapse in live cells through confocal microscopy, an imaging technique that allowed them to focus in on what was happening inside the cells, and on the cell membranes, with these specific proteins."

Comment: All of this must be tightly controlled in the general metabolic homeostasis or there would be chaos in the byplay of cells asking for molecules. At the very necessary high speeds it must be automatically guided.

Biological complexity: protecting synapses

by David Turell @, Friday, October 22, 2021, 15:03 (889 days ago) @ David Turell

Another chain of auto-reactions of controlling molecules:

https://www.science.org/doi/10.1126/scisignal.aaz4112

"Another G for GABAB receptor
Activation of GABABR, the G protein–coupled receptor for the inhibitory neurotransmitter GABA, is thought to be neuroprotective through exclusive engagement of Gi/o. However, Wang et al. found that GABABR also engaged G13 to differentially activate the MAPK pathway kinase JNK. In cultured cerebellar granule neurons, this G13-mediated pathway increased the abundance of the postsynaptic scaffolding protein PSD95 and enhanced neuronal survival under low-potassium conditions. The authors further uncovered biological synergy between the two G protein–mediated pathways, with different kinetics in agonist responses. The findings reveal how GABA can mediate neuroprotection through multiple synergistic pathways that depend on distinct G proteins."

"Abstract
G protein–coupled receptors (GPCRs) activate various mitogen-activated protein kinase (MAPK) pathways to regulate critical cell functions. β-Arrestins mediate this mechanism for most GPCRs but not the GABAB receptor (GABABR). When coupled to the G protein Gi/o, GABABR phosphorylates the kinases ERK1 and ERK2. Here, we uncovered a distinct β-arrestin–independent mechanism of MAPK pathway activation by GABABR. We found that GABABR also phosphorylated the kinase JNK downstream of activation of the small guanosine triphosphatases (GTPases) RhoA and Rac1 in primary mouse neurons. However, instead of Gi/o proteins, activation of this RhoA/Rac1-JNK pathway was mediated by G13. This pathway promoted the phosphorylation and accumulation of the postsynaptic scaffolding protein PSD95 and GABABR-mediated neuroprotection in granule neurons. In addition, this pathway synergized with a previously reported GABABR-mediated neuroprotection mediated by a Gi/o-dependent mechanism. GABABR agonists activated G13 with slower kinetics and lower potency than with which they activated Gi/o. Our findings reveal distinct, β-arrestin–independent, context-specific synergistic mechanisms of MAPK activation by G protein–mediated GPCR signaling." (my bold)

Comment: note the use of the word pathway in which one pathway controls or activates another. Pathways are a series of protein reactions working in steps from beginning to end of molecular reactions mediated by enzymes. A perfect example of reactions to present chemical conditions causing new steps. All automatically con trolled.

Biological complexity: secret life of cells

by David Turell @, Friday, October 29, 2021, 15:30 (882 days ago) @ David Turell

The new amazing techniques seeing cell's molecules:

https://www.nature.com/articles/d41586-021-02904-w

"In recent years, imaging techniques such as cryo-ET have started to enable scientists to see biological molecules in their native environments. Unlike older methods that take individual proteins out of their niches to study them, these techniques provide a holistic view of proteins and other molecules together with the cellular landscape. Although they still have limitations — some researchers say that the resolution of cryo-ET, for example, is too low for molecules to be identified with certainty — the techniques are increasing in popularity and sophistication. Researchers who turn to them are not only mesmerized by the beautiful images, but also blown away by some of the secrets that are being revealed — such as the tricks bacteria use to infect cells or how mutated proteins drive neurodegenerative diseases such as Parkinson’s.

"Every peek through the microscope is another chance to explore uncharted cellular terrain, says Grant Jensen, a structural biologist at the California Institute of Technology in Pasadena. “There’s definitely a great joy in being able to see something for the first time,” he says.

***

"Its early proponents sought a technique that could view biological molecules not only in fine detail, but also as they would look inside cells. Like cryo-EM, cryo-ET requires an electron microscope and relies on a sample preparation method known as vitrification: the rapid cooling of the water around a sample so that it freezes into a glass-like state, rather than as ice crystals. Unlike conventional cryo-EM, however, which requires purified samples, investigators can use cryo-ET to capture these molecules in situ.

***

"And this is how proteins live, after all. “Proteins are social — at any given time a protein is in a complex with about ten other proteins,” says Villa. After viewing such interactions with cryo-ET, “I could not stomach the thought of myself studying another protein in isolation,” she adds.

***

"Early demonstrations of cryo-ET from Baumeister’s group included snapshots1 of the cells of Dictyostelium, a bacteria-guzzling amoeba that lives in soil. The team revealed, among other things, previously unseen characteristics of intricate protein networks that make up the amoeba’s cytoskeleton — such as how individual filaments interact with one another and attach to specific structures on the membranes of Dictyostelium cells.

”'You can rarely assign biological functions or cellular functions to an individual molecule — the functions arise from the interaction of all the molecules inhabiting a cellular landscape,” Baumeister says. “That’s where the discovery potential of cryo-ET comes in. Whatever we look at nowadays, there are surprises.”

***

"More recently, scientists have moved on to imaging eukaryotic cells — which are palatial in comparison with prokaryotes. This has been possible largely because of the advent of cryo-FIB milling, which allows researchers to slice cells thinly before placing them under an electron microscope. Baumeister and his colleagues used this mash-up of methods to visualize how molecules were arranged in the vicinity of the nucleus in a human cell3 (see ‘Inside scoop’). Their work revealed how previously unseen, nanometre-thin filaments provided structural support to the nucleus — making it one of the stiffest organelles in animal cells."

Comment: Download this article and see the images. It makes sense of my view that life's processes are entirely automatic reactions and decisions, designed by God at life's first appearance.

Biological complexity: keeping a cell organized

by David Turell @, Sunday, November 21, 2021, 16:24 (859 days ago) @ David Turell

A group of special proteins:

https://www.sciencedaily.com/releases/2021/11/211114201758.htm

"In a study with lab-grown mouse cells, Johns Hopkins Medicine researchers say they have found that a protein that helps form a structural network under the surface of the cell's "command center" -- its nucleus -- is key to ensuring that DNA inside it remains orderly. The new experiments distinguish the role of the protein, called lamin C, revealing its usefulness in diagnostics and treatments for a variety of genetic disorders linked to DNA disorganization, such as the rapid aging disease known as progeria, muscular dystrophy and heart disorders related to mutations in these and related proteins.

***

"Each human cell's nucleus packs about 6 feet of tightly coiled DNA that holds the genetic instructions for every structure and function in the body. To keep the cell working, these threads of DNA must be organized into useable parts. The lamin proteins, which attach to the surface of the nucleus, do that by grabbing onto segments of the DNA, keeping them separate and tidy.

"'Each compartment created by a lamin acts like a kitchen utensil drawer, keeping knives, forks and spoons easy to access, and more rarely used items like serving pieces out of the way until needed," Reddy says.

"In a bid to better understand how lamins influence how the cell uses and organizes its DNA, Reddy and her team used fluorescent dyes to follow three types of lamin proteins -- A, B and C -- through cell division, when DNA from one cell is duplicated then split between two offspring cells.

"While lamin B has been easy to distinguish in previous studies, lamin A and lamin C have historically been treated as duplicate proteins because they are created from the same gene, says Reddy. However, there was growing evidence that A and C type lamins had distinct roles.

***

"Cells without lamin A seemed able to reorganize after cell division as efficiently as normal cells. However, the nuclear DNA organization again fell into disarray in cells without lamin C.

"Reddy says a reason for this distinction was revealed in the behavior of lamin C in dividing cells. Her team found that while lamins A and B quickly bind to the surface of a newly forming nucleus and begin grabbing sections of DNA, lamin C remains dispersed throughout the nucleus and retains a special molecular tag called phosphorylation. The researchers believe this suggests that this modified lamin C helps guide DNA into place during reorganization. Once the DNA is organized, lamin C loses its molecular tag and becomes associated with the rest of the lamins at the edge of the nucleus.

"'There is this exquisite choreography of the different lamin proteins and DNA to get things just as they should be," says Reddy.

***

"The researchers note that these results bring up several new questions, including the role lamins have in organizing and regulating DNA during development. The team hopes to identify how lamin proteins and the genome behave when one specific type of lamin is mutated or disrupted, since there appears to be some cross-talk between the different forms of lamins. They also plan to investigate the cellular pathways that control the lamin proteins, particularly for lamin C, to further distinguish the importance of its role in controlling DNA." (my bold)

Comment: Every aspect of cellular biochemical processes has controls, as in feedback loops previously described. Life based on free-floating protein molecules that must alter folding shapes requires guiding molecule controllers, which as my bold shows, must also have cellular controllers. So we see designed layers of controllers must exist to maintain order in our system of life homeostasis. Only a designing mind can create this.

Biological complexity: keeping a cell organized??

by David Turell @, Monday, November 22, 2021, 15:31 (858 days ago) @ David Turell

Not answered. Missed?

Biological complexity: final cell division controls

by David Turell @, Thursday, December 09, 2021, 21:35 (841 days ago) @ David Turell

Very precise steps:

https://www.science.org/doi/full/10.1126/science.abm7949

Gulluni et al. report that loss of PIK3C2A inhibits abscission, the final stage of cytokinesis, and triggers lens cell senescence and cataract formation in zebrafish, mice, and humans.

"Individual PI phosphates (PIPs) occur within the inner leaflet of cellular membranes, where they form distinct microdomains that recruit specific proteins and thereby regulate diverse cellular processes... Dynamic remodeling of PIPs is a key regulatory mechanism, and multiple studies confirm the importance of PIP remodeling during cytokinesis, notably in the assembly and constriction of the contractile ring that is required before abscission.

"Inhibition of cytokinesis leads to G1 arrest in the next cell cycle, followed by senescence. Gulluni et al. found that senescent multinucleated cells (resulting from defective cytokinesis) accumulate and intercellular bridges (ICBs), the final membranous connection between two daughter cells, persist in cells from PIK3C2A-null patients. These phenotypes suggest a role for PI3K-C2α in late stages of cell division. Indeed, the authors found that PI3K-C2α localizes to ICBs. Direct binding to both PI(4,5)P2 in the plasma membrane and γ-tubulin restricts PI3K-C2α to the ICB central bulge, a structure called the Flemming body. Furthermore, catalytic activity and proper localization of PI3K-C2α are needed for abscission. Gulluni et al. determined that PI3K-C2α at the ICB uses PI(4)P as a substrate to produce a localized pool of PI(3,4)P2, a lipid not previously known to act in cytokinesis.

***

"Recruitment and subsequent release of CHMP4B from the Flemming body must be tightly regulated to ensure that abscission occurs at the correct time and not, for example, while lagging chromosomes persist in the ICB, which would create genomic instability (11). Notably, heterozygous mutations in CHMP4B are linked with early-onset cataracts. However, mice that lack CEP55 develop normally except within the brain. CEP55 is thus not essential for cell division in all cells but is specifically required in neurons, raising the possibility of parallel, cell type–specific pathways to abscission.

***

"Differences in cell type– and tissue-specific cell division pathways could also stem from the need to respond to different regulatory pathways. Abscission is thought to be subject to a checkpoint mechanism, delaying the final step of daughter cell separation until all the chromosomes have left the intercellular bridge. Recent findings suggest that activation of abscission is also susceptible to the state of nuclear envelope reassembly and membrane tension across the ICB (9). Could it be that each of these events feeds into a different arm of the abscission pathway? PI3K-C2α has been found to generate PI(3)P in response to shear stress and increased membrane tension (15). By using independent pathways or those with overlapping function, abscission may have evolved to respond to a variety of events to ensure its correct timing and the maintenance of genome stability."

Comment: there is no need to fully understand all the controlling steps. The point is this final step in cell division is extremely tightly controlled by specific molecular steps, which must have been designed for mistake protections, as possible disease results are noted. We learn the underlying steps by noting errors to begin with.

Biological complexity: final cell division controls

by David Turell @, Monday, December 13, 2021, 15:41 (837 days ago) @ David Turell

Another controlling system found:

https://phys.org/news/2021-12-microtubule-associated-protein-chromosome-segregation.html

"NUS researchers have discovered that a microtubule-associated protein, HMMR, acts as a regulator in controlling chromosome segregation during cell division, an event that is critical for genome stability.

***

"This process is regulated by microtubules, which are polymers that form part of the cytoskeleton, and provide structure and shape to eukaryotic cells. Microtubules are classified into three main subgroups, known as kinetochore-microtubules (kMTs), interpolar microtubules (iMTs) and astral microtubules. Decades of studies have dissected the functions and mechanisms of kMTs in regulating chromosome congression (the process of aligning chromosomes on the spindle) and segregation, but the roles of iMTs and its regulatory mechanism are less understood.

"A research team comprising Prof LIOU Yih-Cherng and his former Ph.D. student, Dr. JIANG Zemin from the Department of Biological Sciences, National University of Singapore found that the microtubule-associated protein HMMR is critical for proper chromosome segregation by regulating the iMTs-formed fibers. When the HMMR protein is depleted, the duplicated chromosomes cannot be equally separated. A a result, the separation is delayed, which causes genome instability in daughter cells. This may induce tumorigenesis, a process in which normal cells acquire malignant properties.

"...the researchers found that the duplicated chromosomes can be distributed to two daughter cells via the force from microtubules sliding within the iMT-formed fibers, even when it is not connected to the spindle pole on one side. However, loss of HMMR drastically reduced this sliding force, and a much slower velocity of sliding apart has been observed. Further investigation shows that this is because the depletion of HMMR greatly impairs the association with a motor protein called HSET and its movement on the spindle pole. This association and movement are critical to HMMR's role in transmitting the force from the bridging iMT fibers to the k-fibers, to drag the chromosomes to the daughter cells.

"Prof Liou said, "This study identified a novel mechanism of how the bridging fibers formed by iMTs is modulated by microtubule-associated proteins during cell division and may provide evidence linking genome instability with human diseases such as cancer.'"

Comment: such precise controls are more evidence of design.

Biological complexity: a cell repair design

by David Turell @, Saturday, December 18, 2021, 14:46 (832 days ago) @ David Turell

Repair of the nucleus membrane specificity:

https://www.science.org/doi/10.1126/science.acz9827?utm_campaign=ec_sci_2021-12-16

"The cell nucleus is surrounded by a double membrane structure known as the nuclear envelope (NE). Ruptures in the NE compromise nuclear-cytoplasmic compartmentalization and contribute to genome instability and pro-inflammatory responses. Resealing of the wounded NE is mediated by the Endosomal Sorting Complex Required for Transport (ESCRT) machinery, a highly conserved membrane-remodeling pathway. During repair, the mechanical strain imposed by the cytoskeleton needs to be relieved to counteract intranuclear pressure. Wallis et al. found that the ESCRT-associated protein BROX regulates the mechanical properties of the NE during repair. BROX bound to the nucleoskeleton-cytoskeleton linker protein Nesprin-2G and promoted its removal from compression sites, which facilitated efficient membrane resealing and protected genetic material from damage."

Comment: This system shows the designer recognized damage could happen and provided a repair system. Design requires understanding the future problems that mistakes will cause. We know this biochemistry of life creates life. We do not know if another system can work. Stating that possibility second-guesses the designer, who probably stuck with this working design as the only one available..

Biological complexity: size control in embryology

by David Turell @, Wednesday, December 22, 2021, 17:38 (828 days ago) @ David Turell

All forms use the same genes, so why tiny and big sizes? Controls found:

https://phys.org/news/2021-12-how-do-our-organs-know.html

"Cells of a developing tissue proliferate and organize themselves under the action of signaling molecules, the morphogens. But how do they know what size is appropriate for the living organism to which they belong?

***

"In previous studies, Marcos Gonzalez-Gaitan's group, in collaboration with the German team, has shown that these concentration gradients of DPP extend over a larger or smaller area depending on the size of the developing tissue. Thus, the smaller a tissue, the smaller the spread of the DPP gradient from its diffusion source. On the other hand, the larger a tissue, the larger the spread of the DPP morphogen gradient. However, the question remained as to how this concentration gradient scales to the growing size of the future tissue/organ.

***

"The scientists collected all this data on DPP in cells belonging to tissues of different sizes in normal flies and in mutants that failed to scale. They found that it is these different individual transport steps that define the extent of the gradient. Thus, in a small tissue, the DPP molecule is mainly spread by diffusion in between cells. Its concentration therefore falls quite rapidly around its source because of degradation, yielding a narrow gradient. On the other hand, in larger tissues, DPP molecules that went inside cells are also highly recycled, making it possible to extend the gradient over a larger area. "We were finally able to propose an unbiased, unified theory of morphogen transport, going down to the key equations of the system and to unravel the mechanism of scaling!" Maria Romanova enthuses."

Comment: what this shows is specific cells of an organ modify DPP to their own purposes with there built in controls in their specifically active DNA genes. This is obviously an irreducibly complex system requiring design all at once to function. It cannot be built stepwise.

Biological complexity: how cells eat and poop

by David Turell @, Sunday, January 02, 2022, 16:31 (817 days ago) @ David Turell

Vesicle formation in cell walls is filmed:

https://phys.org/news/2021-12-high-resolution-lab-cells.html

"The study, published last month in the journal Developmental Cell, found that the intercellular machinery of a cell assembles into a highly curved basket-like structure that eventually grows into a closed cage. Scientists had previously believed that structure began as a flat lattice.

"Membrane curvature is important, Kural said: It controls the formation of the pockets that carry substances into and out of a cell.

"The pockets capture substances around the cell, forming around the extracellular substances, before turning into vesicles—small sacs one-one millionth the size of a red blood cell. Vesicles carry important things for a cell's health—proteins, for example—into the cell. But they can also be hijacked by pathogens that can infect cells.

***

"'Simply put, in contrast to the previous studies, we made high-resolution movies of cells instead of taking snapshots," Kural said. "Our experiments revealed that protein scaffolds start deforming the underlying membrane as soon as they are recruited to the sites of vesicle formation."

"That contrasts with previous hypotheses that the protein scaffolds of a cell had to go through an energy-intensive reorganization in order for the membrane to curve, Kural said.

"The way cells consume and expel vesicles plays a key role for living organisms. The process helps clear bad cholesterol from blood; it also transmits neural signals. The process is known to break down in several diseases, including cancer and Alzheimer's disease."

Comment: Seeing it in action shows it at work, but the underlying biochemistry of dancing molecules still is not known. This process is seen in bacteria so the process is ancient.

Biological complexity: how cells save proteins

by David Turell @, Monday, January 03, 2022, 22:40 (816 days ago) @ David Turell

Another editing system to protect cells:

https://phys.org/news/2022-01-scientists-emergency-pathway-human-cells.html

"Significantly, the researchers discovered that there can be a shift from the tightly controlled process of eliminating proteins in the cells to a less strict mechanism when cells enter an "emergency protocol." This shift can "clear up" the toxic proteins before their toxicity levels get too high.

"Their study was published on 26 October 2021 in Nature Communications. To carry out their study, the researchers investigated several "proteasomes," protein complexes that work by a chemical reaction to degrade unneeded or damaged cell proteins. The researchers found that elevated levels of one type of proteasome, 20S, appears to contribute to cell survival, even for those cells under stress from damaged proteins.

"Human cells—both functional and damaged—are constantly recycled by chemically "tagging" and targeting for removal when they are under stress by the ubiquitin system (2004 Nobel Prize in chemistry). At the same time, a few proteins that are intact and functional can also be dragged into the 20S proteasome "molecular disposal unit" along with the toxic proteins that have be targeted for destruction. Nevertheless, rather than harm cells, this mode of action by 20S proteasome may aid cells in rapidly remove toxic proteins. In their conclusion, the authors raised the interesting speculation that this emergency pathway can help even damaged cells to withstand bouts of stress and allow them to "age gracefully.'"

Comment: more proof of God's error editing processes showing He recognized errors could happen. dhw's complaints are not logical

Biological complexity: light sensing proteins

by David Turell @, Wednesday, January 26, 2022, 19:55 (793 days ago) @ David Turell

Like those in the eye, finding out how they work:

https://phys.org/news/2022-01-illuminating-biological.html

"Light-sensitive proteins drive many crucial processes in biology, ranging from photosynthesis to vision. Much of the science community's understanding of these proteins comes from studies on bacteriorhodopsin, a protein responsible for photosynthesis in certain single-celled organisms. Researchers have previously solved the three-dimensional structure of bacteriorhodopsin and studied its activity in detail, but the limitations of available techniques left puzzling gaps in the resulting models.

"The new study, published Dec. 10 in Nature Communications, describes a technique developed by the investigators, called line-scanning high-speed atomic force microscopy, that captures the motions of bacteriorhodopsin in response to light on a millisecond time scale.

***

"In response to light, bacteriorhodopsin switches between open and closed states. Using their faster imaging technique, the researchers discovered that the transition to the open state and the duration of the open state always happen at the same speed, but the molecule remains in the closed state for longer periods as the intensity of the light decreases. (my bold)

"Optogenetics researchers insert genes for light-sensing molecules in neurons or other cells, enabling them to change the cells' behavior with light pulses. That work has revolutionized neuroscience, and holds potential for treating neurological diseases as well. The more researchers know about light-sensing proteins, the further they'll be able to push optogenetics."

Comment: the molecule is designed to know when to be open and when to be shut based on the amount of light it senses.. Not intelligence but automaticity from a brilliant designer.

Biological complexity: life's required specific metals

by David Turell @, Wednesday, January 26, 2022, 20:23 (793 days ago) @ David Turell

Cobalt is manly discussed:

https://phys.org/news/2022-01-cobalt-essential-life.html

"Cobalt sits in the center of the corrin ring of vitamin B12 and the important cobalamins we derive from it. Perhaps surprisingly, only two of our enzymes bother to use these painfully constructed and meticulously channeled cofactors. Why do our cells go to such great lengths to get a little bit of the cobalt magic, and what catalytic properties might make it so special?

"Other uncommon essential metals, like molybdenum, selenium and iodine, are similarly used only sparingly in cells, and yet we retain the ability to completely synthesize all the useful derivatives for these elements. To tame molybdenum, we construct an elaborate molybdopterin cofactor, while to harness iodine, we assemble thyroxine. To incorporate selenium into the few selenoproteins that require it, the elaborate SECIS machinery shuffles the mRNA code to attract a unique tRNA, upon which its cysteine cargo is transformed into selenocysteine. In each of these cases, researchers understand the special properties of the metals involved that make them indispensable.

"For example, compared to sulfur, selenium is a better nucleophile that will react with reactive oxygen species faster, but its lack of π-bond character means that it can also be more readily reduced. Selenoproteins like GPX4 (glutathione peroxidase) are correspondingly more resistant to both overoxidation and irreversible inactivation. Similarly, the ineluctable requirement for molybdenum, a two-electron redox compound that can shuttle between the +4/+5 and the +5/+6 redox couples, reflects several not-so-common skills. It can perform diverse and energetically challenging redox reactions; it can act as an electron sink or source at low redox potential; and (along with the much rarer tungsten) can effectively transfer oxygen and sulfur atoms during reactions taking place at low potential.

"A noteworthy attempt to divine the essential cobalt character was advanced in a recent commentary in PNAS by geochemist extraordinaire Michael Russell. Poised between Fe and Ni in the periodic table, Russell notes that "the element is particularly 'energy-dense' with paired electrons in the outer orbit. Its occurrence as a metal alloy in serpentinites with a variable valence extending from Co+ through to Co4+, its various spin states, and its contrasting conformations render it unique, with untold contributions to be made to electronics, catalysis and the emergence of life. Indeed, Co–Fe cooperation has just been investigated at the opposite end of the redox spectrum—the electrocatalysis of the O2 evolution reaction. Substitutions of Co are either unfeasible, as in metabolism and in some double-atom catalysis, or they lie in the somewhat remote future."

***

"The form of vitamin B12 used by our methylmalonyl-CoA mutase enzyme located in mitochondria for fatty acid and amino acid breakdown is known as adenosylcobalamin (AdoCbl). The other cobalamin-utilizing enzyme, methionine synthase, acts in the cytosol and uses a methylcobalamin cofactor wherein the adenosyl group is replaced by a methyl group. Land plants and fungi neither synthesize or require cobalamin as they lack methylmalonyl-CoA mutase, and have different kind of methionine synthase that doesn't require B12. When these enzymes are not working properly, their precursor molecules can presumably build up to high levels, causing problems like demyelinating disease and pernicious anemia. (my bold)

"While cobalt's thermal stability and high energy density make it an ideal component for the cathodes of lithium batteries, it's usefulness to life comes from its many other unique properties, some discovered, and some still yet to be found."

Comment: These are metals are vital for our life to exist. Remember massive enzyme molecules are required. They didn't form by chance. Another irreducibly complex system requiring design. I wonder if God designed the periodic table of elements producing in advance these necessary elements. Note: llamas and its relatives in the Andes munching on plants in volcanic soils utilize two to eight milligrams a day of selenium. Selenium is extremely poisonous to us, so we can safely ingest one-two micrograms a day. I suspect when these camelids finally migrated to the Andes from Asia they adapted epigenetically.

Biological complexity: mammalian hibernation metabolism

by David Turell @, Friday, January 28, 2022, 20:56 (791 days ago) @ David Turell

Different processes for different animals:

https://www.sciencemagazinedigital.org/sciencemagazine/28_january_2022/MobilePagedArtic...

Hibernating animals do not eat or drink over a long period of time, often months, when they are inactive and spend most of their time sleeping. During this torpid state, hibernators can drastically reduce their metabolic rates, allowing them to reduce their energy demands. Despite this combination of fasting and inactivity, hibernating animals keep their lean mass relatively stable, with some even gaining muscle mass by the end of hibernation.

To elucidate how squirrels maintain their physiological functions during hibernation, Regan et al. used stable isotope labeling to track the flow of nitrogen and carbon in squirrels during the active phase and hibernation. These experiments revealed that urea, which is produced by the host during protein catabolism, is transported from the blood to the gut lumen in addition to being excreted in the urine.

All animals live in close association with a vast diversity of microorganisms—the microbiota—that contributes to various aspects of host physiology (Display footnote number. Previous research identified that hibernation alters the gut microbiota (Display footnote number, 5). In bears, the microbiota assists in extracting energy from the diet to facilitate prehibernation fattening (Display footnote number. In hibernating frogs, gut microbes encode an increased potential for nitrogen salvage. Using metagenomic sequencing, Regan et al. found that the gut lumen of squirrels contains microorganisms with urease genes, which enable the microorganisms to produce enzymes (i.e., ureases) that metabolize urea into carbon dioxide and ammonium. The ammonium is then used by the same microbiota as a source of nitrogen to produce amino acids, some of which are then absorbed by the host. As a result of this process, nitrogen loss during protein catabolism and urea formation is compensated, which counteracts muscle wasting. Although the process of urea nitrogen salvaging has been known in ruminants such as cattle, goats, and sheep, the identification and molecular delineation of urea nitrogen salvaging in hibernating mammals add another central role for intestinal microorganisms within the coordination of host physiological adaptations.

Comment: Hibernation requires symbiosis with specialized organisms. How does this adaptation work naturally? Not epigenetically since different organisms have to work together. Trial and error would kill if tried suddenly, so it has to be gradual over time and goal directed. How about design?

Biological complexity: microbes making electricity

by David Turell @, Tuesday, February 01, 2022, 19:39 (787 days ago) @ David Turell

From rocks!:

https://phys.org/news/2022-02-microbes-electrical-world-growth-power.html

"In more recent years, scientists have discovered an astonishing new process by which microbes can "breathe" rocks through a process called extracellular electron transfer (EET). With EET microbes are able to "breathe" rocks and other materials that are outside their cell. In other words, microbes literally establish an electrical connection to the outside world, a connection they use to generate the power they need to grow. Researchers have since found groundbreaking uses for EET-capable microbes, such as aiding in toxic waste cleanup and as a source of alternative.

"In a new study in mBio, researchers from Harvard and the University of Minnesota surveyed the tree of life in search of EET and discovered it is far more widespread than previously thought and is spread through horizontal gene transfer. One set of genes that makes EET possible, called mtrCAB, has been especially well-studied in the bacterium Shewanella oneidensis. Shewanella oneidensis was one of the first EET-capable organisms ever discovered. As such, it's had a decades-long head start for the science community to interrogate it in the lab.

***

"'We found these genes in microbes all over the planet from virtually every kind of environment, including the deep sea, salt flats, oil refinery sites, the human gut, and even wastewater contaminated by the Manhattan project," Baker said. Further analysis revealed that the set of genes were horizontally transferred extensively throughout the history of life.

***

"'It's sort of a foregone conclusion that microbes really shape our planet and EET had always been viewed as a niche ability," Girguis said. "But we looked at all of the genomic information from animals, Archaea, and bacteria, and all other forms of life and found it's far more widespread than previously assumed. All of the organisms we identified are capable of plugging directly into the substrates in their environment and changing what's available there."

"'The availability of these different substrates change over time as the Earth continues to evolve, either naturally or from human impact," Baker said. "Understanding how these proteins may have coevolved with the history of oxygen on earth is very important. It could help us understand if this metabolism, or a metabolism like this, helped play a role in one of the massive transformations of our planet's surface that gave rise to the modern world as we know it.'"

Comment: I've presented articles about these guys before and considered them extremeophiles. guess they are too common for that title. Life has all sorts of ways to survive.

Biological complexity: cell division complexity

by David Turell @, Thursday, February 03, 2022, 21:05 (785 days ago) @ David Turell

There is much more than the high school biology pictures and microscopes show:

https://evolutionnews.org/2022/01/dna-packing-one-of-the-supreme-wonders-of-nature/

To pack DNA into chromosome structures molecules work hand over hand:

"Cohesin and condensin are ring-shaped like donuts, leading researchers to propose that chromatin might somehow thread through their middles. But work by chromatin biologist Jan-Michael Peters of the Research Institute of Molecular Pathology in Vienna, and colleagues now shows that, in cohesin’s case at least, the protein complex grabs DNA and pulls it, passing it from one part of itself to another, much like a person hauling rope might pass it hand to hand.

"How does a molecule pass a strand hand to hand without hands or eyes? The Scientist posted an infographic to show what Peters and team found. Cohesin has a “hinge” domain that fastens onto the DNA. The hinge moves toward one of two “head” domains. The other head clamps onto the strand several base pairs down, freeing up the hinge to reset and move down to another position.

"There must certainly be more going on, because this doesn’t explain what happens to the upstream section that was reeled in. The open-access paper in Cell by Bauer et al., “Cohesin mediates DNA loop extrusion by a ‘swing and clamp’ mechanism,” says that each swing of the hinge forms a loop of DNA. Multiple loops parallel to each other begin the process of arranging the DNA for dense packing. Another player called NIPBL associates with cohesin into a cohesin-NIPBL complex during each 50-nm step, spending an ATP on each swing.

"Here, we have analyzed how loop extrusion is mediated by human cohesin-NIPBL complexes, which enable chromatin folding in interphase cells. We have identified DNA binding sites and large-scale conformational changes that are required for loop extrusion and have determined how these are coordinated. Our results suggest that DNA is translocated by a spontaneous 50 nm-swing of cohesin’s hinge, which hands DNA over to the ATPase head of SMC3, where upon binding of ATP, DNA is clamped by NIPBL. During this process, NIPBL “jumps ship” from the hinge toward the SMC3 head and might thereby couple the spontaneous hinge swing to ATP-dependent DNA clamping. These results reveal mechanistic principles of how cohesin-NIPBL and possibly other SMC complexes mediate loop extrusion.

"Remarkable movies made with super-resolution atomic force microscopy show the parts of cohesin undergoing conformational changes. These hand-over-hand motions operate in the dark without eyes, using ATP for energy. They get it right every time!

***

"Researchers at Postech Physics in Korea used a synchrotron, X-rays, and cryo-electron microscopy of intact chromosomes to peer deeper into the resulting package. Their results suggested a different model of organization: a fractal model.

"The packing mechanism that condenses the chromosomes into one-millionth its size without any tanglingand the 3D structure that enables this have puzzled researchers for over a half a century. However, it has been difficult to observe the chromosomes in their native condition. The researchers had to resort to detecting only some components of the chromosomes or infer their condensed state from looking at their uncoiled state….

"Through the study, the research team confirmed that the chromosomes were formed in a fractal structure rather than the hierarchical structure stated in previous studies. In addition, a physical model showing the packing process of chromosomes was presented.

***

"How the DNA strands stay together for the process of mitosis, involving the “puzzling compaction mechanism from a DNA molecule to a chromosome and its error-free unpacking into DNA molecules again” without becoming hopelessly scrambled in the process, must count as one of the supreme wonders of nature. Look how they describe the accuracy of DNA packing despite all the interactions and motions of the adjacent molecules:

"DNA molecules are atomic-scale information storage molecules that promote reliable information transfer via fault-free repetitions of replications and transcriptions. Remarkable accuracy of compacting a few-meters-long DNA into a micrometer-scale object, and the reverse, makes the chromosome one of the most intriguing structures from both physical and biological viewpoints."

Comment: Everything must work together from the beginning, not piece by piece of the structure appearing in some sort of sequence. Irradicably complex by definition. Must be designed.

Biological complexity: calcium pump for muscles

by David Turell @, Tuesday, February 08, 2022, 15:40 (780 days ago) @ David Turell

Irreducibly complex:

https://phys.org/news/2022-02-calcium-motions-captured-action.html

"The pumping action of the calcium pump protein—an intricate molecular machine with several moving parts that helps control muscle contraction—has been detailed with exquisite precision by RIKEN biophysicists. By providing a blueprint of structural changes that occur during operation of the protein, the findings could aid the development of new treatments for skeletal myopathies and heart disease.

"Muscle movement is fundamentally a calcium-driven process. When a muscle cell receives the signal to contract from its associated nerves, it releases a flood of calcium ions from a special intracellular container known as the sarcoplasmic reticulum. Those ions then set the muscle's molecular motors into action, spurring contractions until the calcium is removed.

"That's where the calcium pump comes in. After a frenzied wave of calcium-induced activity, the pump uses energy in the form of adenosine triphosphate (ATP) to return calcium ions to their intracellular storehouse.

***

"Using sophisticated computer models that account for structural changes and energetic profiles, the researchers identified a handful of transition states. They also demonstrated how the rapid exchange of calcium ions for protons at the pump's inner face is critical for releasing calcium into the sarcoplasmic reticulum."

Comment: see the illustration. Pure evidence of design.

Biological complexity: cell death controls

by David Turell @, Monday, February 21, 2022, 16:00 (767 days ago) @ David Turell

Cells must die, but in controlled amounts:

https://www.sciencedaily.com/releases/2022/02/220218100724.htm

"Cell death plays an important role in normal human development and health but requires tightly orchestrated balance to avert disease. Too much can trigger a massive inflammatory immune response that damages tissues and organs. Not enough can interfere with the body's ability to fight infection or lead to cancer.

"Zhigao Wang, PhD, associate professor of cardiovascular sciences at the University of South Florida Health (USF Health) Morsani College of Medicine, studies the complex molecular processes underlying necroptosis, which combines characteristics of apoptosis (regulated or programmed cell death) and necrosis (unregulated cell death).

"During necroptosis dying cells rupture and release their contents. This sends out alarm signals to the immune system, triggering immune cells to fight infection or limit injury. Excessive necroptosis can be a problem in some diseases like stroke or heart attack, when cells die from inadequate blood supply, or in severe COVID-19, when an extreme response to infection causes organ damage or even death.

***

"'Cell death is very complicated process, which requires layers upon layers of brakes to prevent too many cells from dying," said study principal investigator Dr. Wang, a member of the USF Health Heart Institute. "If you want to protect cells from excessive death, then the protein complex we identified in this study is one of many steps you must control."

***

"Receptor-interacting protein kinase (RIPK1) plays a critical role in regulating inflammation and cell death. Many sites on this protein are modified when a phosphate is added (a process known as phosphorylation) to suppress RIPK1's cell death-promoting enzyme activity. How the phosphate is removed from RIPK1 sites (dephosphorylation) to restore cell death is poorly understood. Dr. Wang and colleagues discovered that PPP1R3G recruits phosphatase 1 gamma (PP1γ) to directly remove the inhibitory RIPK1 phosphorylations blocking RIPK1's enzyme activity and cell death, thereby promoting apoptosis and necroptosis.

***

"'In this case, phosphorylation inhibits the cell death function of protein RIPK1, so more cells survive," he said. "Dephosphorylation takes away the inhibition, allowing RIPK1 to activate its cell death function."

"The researchers showed that a specific protein-protein interaction -- that is, PPP1R3G binding to PP1γ -- activates RIPK1 and cell death. Furthermore, using a mouse model for "cytokine storm" in humans, they discovered knockout mice deficient in Ppp1r3g were protected against tumor necrosis factor-induced systemic inflammatory response syndrome. These knockout mice had significantly less tissue damage and a much better survival rate than wildtype mice with the same TNF-induced inflammatory syndrome and all their genes intact."

Comment: the need for such precise controls implies it has to be a designed mechanism, as it is irreducibly complex.

Biological complexity: bone body communications

by David Turell @, Wednesday, March 09, 2022, 19:36 (751 days ago) @ David Turell

Many, many found:

https://www.smithsonianmag.com/science-nature/how-bones-communicate-with-the-rest-of-th...

"Our bones also provide a handy storage site for calcium and phosphorus, minerals essential for nerves and cells to work properly. And each day their spongy interior, the marrow, churns out hundreds of billions of blood cells — which carry oxygen, fight infections and clot the blood in wounds — as well as other cells that make up cartilage and fat.

"Even that’s not all they do. Over the past couple of decades, scientists have discovered that bones are participants in complex chemical conversations with other parts of the body, including the kidneys and the brain; fat and muscle tissue; and even the microbes in our bellies.

***

"Her first finding regarding osteocyte communication with other organs, reported in 2006, was that the cells make a growth factor called FGF23. This molecule then cruises the bloodstream to the kidneys. If the body has too much FGF23 — as happens in an inherited form of rickets — the kidneys release too much phosphorus into urine, and the body starts to run out of the essential mineral. The resulting symptoms include softened bones, weak or stiff muscles, and dental problems.

***

"In a 2000 study, Karsenty investigated whether a hormone called leptin could be a link between these two biological processes. Leptin is produced by fat cells and is best known as a depressor of appetite. It also emerged in evolution around the same time as bone. In experiments with mice, Karsenty found that leptin’s effects in the brain put the brakes on bone remodeling.

***

"...in 2007, Karsenty proposed that bone also has something to say about how the body uses energy. He found that mice lacking a bone-made protein called osteocalcin had trouble regulating their blood sugar levels.

"In further research, Karsenty discovered that osteocalcin also promotes male fertility via its effects on sex hormone production, improves learning and memory by altering neurotransmitter levels in the brain, and boosts muscle function during exercise. He described these messages

***

"For example, skeletal muscle cells make a protein called myostatin that keeps them from growing too large. In experiments with rodents, alongside observations of people, researchers have found that myostatin also keeps bone mass in check.

"During exercise, muscles also make a molecule called beta-aminoisobutyric acid (BAIBA) that influences fat and insulin responses to the increased energy use. Bonewald has found that BAIBA protects osteocytes from dangerous byproducts of cellular metabolism called reactive oxygen species. In young mice that were immobilized — which normally causes atrophy of bone and muscle — providing extra BAIBA kept both bones and muscle healthy.

"In additional studies, Bonewald and colleagues found that another muscle molecule that increases with exercise, irisin, also helps osteocytes to stay alive in culture and promotes bone remodeling in intact animals.

"The conversation isn’t all one-way, either. In return, osteocytes make prostaglandin E2, which promotes muscle growth, on a regular basis. They boost production of this molecular messenger when they experience an increase in the tug from working muscles.

***

"The first hints of a bone-microbiome connection came from a 2012 study of mice raised in a sterile environment, without any microbes at all. These animals had fewer bone-destroying osteoclasts, and thus higher bone mass. Giving the mice a full complement of gut microbes restored bone mass to normal, in the short term.

"But the long-term effects were a bit different. The microbes released molecules called short-chain fatty acids that caused the liver and fat cells to make more of a growth factor called IGF-1, which promoted bone growth.

"Gut microbes also appear to moderate another signal that affects bone: parathyroid hormone (PTH), from the parathyroid glands at the base of the neck. PTH regulates both bone production and breakdown. But PTH can only promote bone growth if mice have a gut full of microbes. Specifically, the microbes make a short-chain fatty acid called butyrate that facilitates this particular conversation. (Incidentally, that FGF23 made by osteocytes also acts on the parathyroid glands, tuning down their secretion of PTH.)

***

"...what’s clear already is that the skeleton is not just a nice set of mechanical supports. Bones constantly remodel themselves in response to the body’s needs, and they’re in constant communication with other parts of the body. Bone is a busy tissue with broad influence, and it’s working behind the scenes during the most basic daily activities."

Comment: a laundry list of how bones are designed to work with all the other parts of the body. A marvelous example of irreducible complexity.

Biological complexity: known cell complexity increases

by David Turell @, Tuesday, March 15, 2022, 15:21 (745 days ago) @ David Turell

New molecular level study:

https://phys.org/news/2022-03-pop-up-factories-beneath-cell-membrane.html

"A living cell is exposed to a variety of stimuli. Countless messengers dock on its surface, where receptors in the cell membrane receive the incoming "orders." Signaling cascades are then triggered inside the cell, which ultimately responds by producing or breaking down substances, or by switching genes on and off in the cell nucleus. So far so clear. But what's exactly going on here? Researchers at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) have now discovered that the processes are far more complex than previously thought.

"There are more than 800 different G protein-coupled receptors (GPCRs), which together make up the most important group of membrane proteins. The surface of a single cell can have up to 100 different GPCRs, each of which responds to very different external signaling molecules. "So you have this very high level of specificity on the outside, but only a handful of molecules inside the cell that respond to activation," Bock says. "And yet they perform multiple and completely different tasks." How exactly this works is something scientists have puzzled over for a long time.

***

"Using a technique known as fluorescence microscopy, researchers examined isolated single cells to find out how cAMP signals from two different receptors are generated and processed simultaneously within a cell. One of the receptors is important for insulin secretion, while the other influences heart and lung function. They discovered that tiny domains with a radius of 30 to 60 nanometers are formed at the site of the activated receptor.

"Bock compares these nanospaces to pop-up factories that form just beneath the cell membrane and get to work the moment an "order" comes in. "When one such nanospace reaches full capacity, the cAMP spills over into the next, and so the signaling cascade travels down into the cell interior," he says.

***

"'The signals that originate at the GPCR initially remain at the local site and only affect the enzymes in their immediate vicinity," she says. "Other regions of the cell are not affected by them, which allows signaling pathways to be turned on and off very precisely."

"Scientists have long regarded the cytosol liquid inside a cell as a large "swimming pool" in which everything floats around freely. But it seems that previously unknown structures—which MDC researchers are now calling "signaling nanoarchitecture"—exist in this liquid and can be switched on as needed. "We can't visualize these nanospaces yet," Bock says. But he suspects that cAMP is kept within the tiny spaces by a gel-like structure. These could be large scaffold proteins, for example, or cAMP-degrading enzymes that use a high concentration of cAMP to create a boundary between the cytosol and the nanodomain.

"It seems, therefore, that a cell is not in fact a switch that can either be "on" or "off." The co-last author and initiator of the project Professor Martin Lohse from ISAR Bioscience in Munich explains that it functions more like a chip that processes many signals simultaneously over a very small area. "This is very important for neurons, for example, as it allows them to process different signals at each of their various protrusions: one site can be activated while another lies dormant and a third is inhibited," he says."

Comment: Please note that all of this complexity is presented as automatic reactions. What always surprises me is that scientists always express surprise when they discover the next layer of complexity exists. There is lots more complexity to be discovered to explain how life works. The design is quite precise.

Biological complexity: known cell complexity increases

by David Turell @, Tuesday, March 15, 2022, 15:34 (745 days ago) @ David Turell

More regulatory cell research:

https://phys.org/news/2022-03-two-part-triggers-key-regulatory-protein.html

"Signaling proteins known as G-protein-coupled receptors (GPCRs) are found in the membranes of cells, and they convert signals from outside a cell into responses within a cell. They are responsible for reacting to signals from hormones, neurotransmitters and sensory signals from the eyes, nose and mouth. The critical role they play in cell biology is highlighted by the fact that roughly half of all drugs on pharmacy shelves target GPCRs.

"There has been much research into how GPCRs activate their scaffolding partners, known as β-arrestins, by binding to them. For a long time, β-arrestins were thought to be activated only by the tail end of GPCRs. But now, Ichio Shimada and Yutaro Shiraishi at the RIKEN Center for Biosystems Dynamics Research and five collaborators have shown how activation of β-arrestin also involves engagement with the GPCR core.

"Using nuclear magnetic resonance spectroscopy, the researchers discovered that β-arrestins bound to the tail of an interacting GPCR are only partially activated—subsequent binding with the core region is needed to push the β-arrestins into full activation mode. This, in turn, triggers downstream signaling cascades involved in everything from sight and smell to immune regulation and neuronal communication.

"'We have demonstrated that β-arrestin activation by GPCR involves two phases," says Shimada. That two-part chain of events helps to stabilize β-arrestins in their fully engaged, activated conformation.

"With an eye to drug development, the researchers also detailed how a drug-like antibody fragment helped to shift the balance in structural conformations to promote more activation-inducing interactions between β-arrestins and GPCRs, even in the absence of core binding.

"That finding highlights a path forward for therapeutically biasing the signaling activities of β-arrestins. "Variants of the antibody may be good candidates to modulate the signal transduction mediated by the GPCR–arrestin complex," says Shiraishi."

Comment: because of the demonstrated automaticity, we can use it to manage therapeutic measures. Cells are designed to work automatically. They just look intelligent.

Biological complexity: vital feedback loops

by David Turell @, Monday, April 04, 2022, 21:36 (725 days ago) @ David Turell

They control what cells do:

https://www.albert.io/blog/positive-negative-feedback-loops-biology/

"Feedback is defined as the information gained about a reaction to a product, which will allow the modification of the product. Feedback loops are therefore the process whereby a change to the system results in an alarm which will trigger a certain result. This result will either increase the change to the system or reduce it to bring the system back to normal. A few questions remain: How do these systems work? What is a positive feedback? What is negative feedback? Where do we find these systems in nature?

"Biological systems operate on a mechanism of inputs and outputs, each caused by and causing a certain event. A feedback loop is a biological occurrence wherein the output of a system amplifies the system (positive feedback) or inhibits the system (negative feedback). Feedback loops are important because they allow living organisms to maintain homeostasis. Homeostasis is the mechanism that enables us to keep our internal environment relatively constant – not too hot, or too cold, not too hungry or tired. The level of energy that an organism needs to maintain homeostasis depends on the type of organism, as well as the environment it inhabits.

"Feedback loops can also occur to a larger degree: at the ecosystem level, a form of homeostasis is maintained. A good example of this is in the cycle of predator and prey populations: a boom in prey population will mean more food for predators, which will increase predator numbers. This will then lead to over predation, and the prey population will again decline. The predator population will decline in response, releasing the pressure on the prey population and allowing it to bounce back. (my bold)

***

"A positive feedback loop occurs in nature when the product of a reaction leads to an increase in that reaction. If we look at a system in homeostasis, a positive feedback loop moves a system further away from the target of equilibrium. It does this by amplifying the effects of a product or event and occurs when something needs to happen quickly.

***

"A negative feedback loop occurs in biology when the product of a reaction leads to a decrease in that reaction. In this way, a negative feedback loop brings a system closer to a target of stability or homeostasis. Negative feedback loops are responsible for the stabilization of a system, and ensure the maintenance of a steady, stable state. The response of the regulating mechanism is opposite to the output of the event.

***

"The key difference between positive and negative feedback is their response to change: positive feedback amplifies change while negative feedback reduces change. This means that positive feedback will result in more of a product: more apples, more contractions, or more clotting platelets. Negative feedback will result in less of a product: less heat, less pressure, or less salt. Positive feedback moves away from a target point while negative feedback moves towards a target.

"Without feedback, homeostasis cannot occur. This means that an organism loses the ability to self-regulate its body. Negative feedback mechanisms are more common in homeostasis, but positive feedback loops are also important. Changes in feedback loops can lead to various issues, including diabetes mellitus. (my bold)

***

"Feedback loops are biological mechanisms whereby homeostasis is maintained. This occurs when the product or output of an event or reaction changes the organism’s response to that reaction. Positive feedback occurs to increase the change or output: the result of a reaction is amplified to make it occur more quickly. Negative feedback occurs to reduce the change or output: the result of a reaction is reduced to bring the system back to a stable state. Some examples of positive feedback are contractions in child birth and the ripening of fruit; negative feedback examples include the regulation of blood glucose levels and osmoregulation."

Comment: our discussions about so-called cell intelligence has bought up feedback loops in the past. Feedback loops are circular protein molecule reactive loops that manage output levels by automatically measuring cell intake or output. What I have left out are explanatory examples which help to understand how they work. Cell intelligent actions cannot cannot be properly discussed unless this set of facts is completely understood. I have not seen evidence of full understanding. They are intelligently designed and work beautifully. This also applies to maintaining ecosystems.

Biological complexity: learning how proteins work

by David Turell @, Wednesday, April 06, 2022, 16:39 (723 days ago) @ David Turell

A study in automaticity of molecules:

https://phys.org/news/2022-04-abundant-secret-doors-human-proteins.html

"A ground-breaking new technique developed by researchers at the Centre for Genomic Regulation (CRG) in Barcelona has revealed the existence of a multitude of previously secret doors that control protein function and which could, in theory, be targeted to dramatically change the course of conditions as varied as dementia, cancer and infectious diseases.

"The method, in which tens of thousands of experiments are performed at the same time, has been used to chart the first ever map of these elusive targets, also known as allosteric sites, in two of the most common human proteins, revealing they are abundant and identifiable.

***

"Proteins play a central role in all living organisms and carry out vital functions such as providing structure, speeding up reactions, acting as messengers or fighting disease. They are made of amino acids, folding into countless different shapes in three-dimensional space. The shape of a protein is crucial for its function, with just one mistake in an amino acid sequence resulting in potentially devastating consequences for human health.

"Allostery is one of the great unsolved mysteries of protein function. Allosteric effects occur when a molecule binds to the surface of a protein, which in turn causes changes at a distant site in the same protein, regulating its function by remote control. Many disease-causing mutations, including numerous cancer drivers, are pathological because of their allosteric effects.

"Despite their fundamental importance, allosteric sites are incredibly difficult to find. This is because the rules governing how proteins work at the atomic level are hidden out of sight. For example, a protein might shapeshift in the presence of an incoming molecule, revealing hidden pockets deep within its surface that are potentially allosteric but not identifiable using conventional structure determination alone."

Comment: This is a study of how protein molecules automatically react in living processes. This automaticity is required to allow the fantastic speed of the processes , a speed that is required for life to exist.

Biological complexity: bacterial stress protection

by David Turell @, Thursday, April 14, 2022, 20:33 (715 days ago) @ David Turell

They need protection from oxidation and nitrogen like all of us:

https://phys.org/news/2022-04-identification-enzyme-involved-stress-bacteria.html

"All organisms, from humans to bacteria, have to be able to respond to a wide range of stresses that result from changes in their environment.

"Common amongst these are so called oxidative and nitrosative stresses, which occur when an organism is exposed to high concentrations of reaction oxygen or reactive nitrogen species, respectively. When this happens, fragile component of the cell are damaged, leading to loss of function and, in some cases, cell death.

"Unsurprisingly, organisms have evolved a multitude of stress response systems that detect and alleviate particular stresses.

"Iron-sulfur clusters, which consist of iron and inorganic sulfur, are found in all cell types where they play essential roles in a wide range of cellular processes. Because they are so reactive, they are often the first cellular components to become damaged under stress conditions. (my bold)

"The di-iron protein YtfE, found widely in bacteria, is generally believed to function directly in the repair of iron-sulfur clusters that have been damaged under stress conditions. This activity has been variably proposed to involve donation of iron for re-building of iron-sulfur clusters, or the removal of nitric oxide (NO) from damaged clusters.

"Recently, new evidence came to light from studies of YtfE function in cells that suggested its activity is associated with an increase, and not a decrease, in the concentration of NO. This prompted researchers in the School of Chemistry to re-examine the function of YtfE.

***

"They showed that YtfE does not efficiently remove NO from damaged iron-sulfur clusters, nor is it an effective donor of iron for cluster assembly.

"The YtfE-catalyzed production of toxic NO from nitrite (NO2-) may seem odd, but YtfE is co-regulated with another enzyme, called Hcp, which functions to detoxify NO (via its reduction to nitrous oxide, N2O).

"The coupled YtfE/Hcp detoxification pathway represents an effective means by which the cell deals with toxic levels of nitrite that can occur under anaerobic conditions."

Comment: bacteria started life long before oxygen was present in any significant amount, so the first very simple bacteria did not require this protection, which was then added later. All makes sense, start with a simple design and improve later. Since this new system had a complex enzyme to do the work, only design fits.

Biological complexity: making cilia and their functions

by David Turell @, Wednesday, April 20, 2022, 15:02 (709 days ago) @ David Turell

Highly dsigned complexity:

https://phys.org/news/2022-04-insights-cilia.html

"Researchers from the group of Patrick Matthias and the FMI Structural Biology platform determined the structure, at near atomic resolution, of a protein complex that plays an essential role in the assembly of cilia—and causes ciliopathies when it is mutated.

"Cilia are hair-like structures that extend from the surface of almost all cell types of the human body. In addition to being "motors" that enable cell propulsion and fluid movement, cilia act as cellular antennae to sense environmental cues, for example during development, and are essential for passing on signals.

***

"This complex event is under strict regulation in space and time and involves dozens of proteins. Three proteins called CPLANE proteins play a particularly important role in governing ciliogenesis, but little is known about them.

"Gerasimos Langousis, postdoc in the lab of Patrick Matthias, and colleagues from the FMI Structural Biology platform used cryogenic-Electron Microscopy (cryo-EM) to study CPLANE. They showed that the three proteins assemble to form a complex they called the CPLANE complex. They determined the structure—at near-atomic resolution—of the human and the mouse complex bound to a small Rab GTPase, an enzyme that is essential for regulating cellular activity. They also studied how the complex binds to phospholipids, the key components of cell membranes (where the cilia are anchored), and what may go wrong in ciliopathies. They could demonstrate that a ciliopathy CPLANE mutant protein exhibits altered phospholipid binding. (my bold)

"These results illuminate how the CPLANE complex orchestrates lipid binding and Rab signaling. The study, published in Science Advances, provides critical structural and functional insights into the enigmatic process of ciliogenesis as well as new molecular rationales for ciliopathies."

Comment: Again, the high degree of complexity demand a designing mind at work. The bold emphasizes the importance of enzymes, giant molecules required to make living biochemistry work. Each enzyme requires design.

Biological complexity: fast healing oral mucosa

by David Turell @, Thursday, April 21, 2022, 19:16 (708 days ago) @ David Turell

With teeth biting at hundreds of pounds per square inch and a wandering tongue pushing food around, no wonder oral mucosa is designed to heal fast:

https://www.realclearscience.com/blog/2022/04/21/your_mouth_has_super-healing_abilities...

"Your mouth has remarkable regenerative powers. A wound to your oral mucosa – the lining of the inside of your mouth – heals three to four times faster than an identical cut on your skin, with less likelihood of leaving a scar.

***

"For starters, they noted that the structures of the external skin and oral mucosa are noticeably different. Chiefly, the oral mucosa is much thicker, with a slightly looser structure enabling it to bend more easily, and it has more blood vessels. Additional blood flow could certainly factor in to speedier healing.

***

"Studies show that immune cells like neutrophils, macrophages, and T-cells build up quickly in oral mucosa then leave just a fast, while their arrival and departure are comparatively delayed in skin cells. The rapid and robust arrival of blood clotting cells called platelets in the mouth seems to trigger a large and speedy release of signaling proteins called chemokines, which trigger the waterfall of immune cells.

"In the ensuing healing phase, called proliferation, endothelial cells, fibroblasts, and epithelial cells – all of which either comprise or repair skin – migrate into the wound bed to regenerate the tissue. Here, the warm, moist, saliva-filled environment of the mouth seems to speed things along. Scabs do not form in the mouth, unlike on the skin, and so protein-rich saliva and even friendly oral microbes appear to aid in the healing process.

"Finally, in the remodeling phase of healing, immune cells send out small proteins called cytokines that reduce inflammation around the wound. Again, this process of reducing inflation occurs faster in the mouth compared to the skin. Then, over days, weeks, or months, fibroblasts and myofibroblasts get to work remodeling the structure that supports surrounding cells, called the extracellular matrix. Studies suggest that when this occurs in the presence of inflammation, scars are more likely to form (which explains why picking scabs, thus inflaming the tissue, leads to increased scarring).

"'It can be concluded that faster wound closure, the presence of saliva, a more rapid immune response, and increased extracellular matrix remodeling all contribute to the superior wound healing and reduced scar formation in oral mucosa, compared to skin," the authors summarized."

Comment: A very logical design. I might add a bitten tongue heals as quickly. but a deeply bitten tongue will require stitches.

Biological complexity: importance of enzymes

by David Turell @, Sunday, May 01, 2022, 15:45 (698 days ago) @ David Turell

No biological reaction occurs without them; without them no life:

https://www.sciencealert.com/engineers-create-an-enzyme-that-breaks-down-plastic-waste-...

"A new study outlines the use of a specially created enzyme variant that vastly reduces the time it takes to break down the components of plastics.

"We could even use the enzyme variant to clean up sites contaminated by plastic pollution, say the team that developed it.

"In tests, products made from the polymer polyethylene terephthalate (PET) were broken down in a week and, in some cases, 24 hours – these are products that can take centuries to degrade properly in natural conditions.

"'The possibilities are endless across industries to leverage this leading-edge recycling process," says chemical engineer Hal Alper from the University of Texas at Austin.

"'Beyond the obvious waste management industry, this also provides corporations from every sector the opportunity to take a lead in recycling their products."

"The team has called the enzyme FAST-PETase (functional, active, stable, and tolerant PETase). They developed the enzyme from a natural PETase that allows bacteria to degrade PET plastic and modified it using machine learning to pinpoint five mutations that would enable it to degrade the plastic faster under different environmental conditions.

***

"Right now, the most common methods for disposing of plastic are to throw it in a landfill where it rots at a very slow rate, or to burn it – which costs a lot, uses up plenty of energy, and fills the atmosphere with noxious gas. It's clear that alternative strategies are desperately needed, and this could be one of them.

"'This work really demonstrates the power of bringing together different disciplines, from synthetic biology to chemical engineering to artificial intelligence," says biochemist Andrew Ellington from the University of Texas at Austin."

Comment: Without enzymes any biochemical reaction takes many, many years. Life requires constant split-second reactions. Enzymes are giant organic molecules, often with metal atoms tucked in. Essentially, specific regions trap two organic molecules and force them to react. Enzymes are organized/designed groups of thousands of amino acids in specific sequences. They work specifically based on that design. Therefore, they are irreducibly complex and cannot have evolved naturally. Enzymes had to be present when life started. One conclusion fits this. Design is required. Note humans had to start with living bacteria to reach this designed enzyme

Biological complexity: before splitting cells dump garbage

by David Turell @, Thursday, May 12, 2022, 16:20 (687 days ago) @ David Turell

Just cleaning house:

https://www.sciencedaily.com/releases/2022/05/220510122446.htm

"'Our hypothesis is that cells might be throwing out things that are building up, toxic components or just things that don't function properly that you don't want to have there. It could allow the newborn cells to be born with more functional contents," says Teemu Miettinen, an MIT research scientist and the lead author of the new study.

***

"In cells undergoing mitosis, the researchers used their new technique to study what happens to cell mass and composition during that process. In a 2019 paper, Miettinen and Manalis found that buoyant mass increases slightly as mitosis begins. However, other studies that used quantitative phase microscopy suggested that cells might retain or lose dry mass early in cell division.

"In the new study, the MIT team measured three types of cancer cells, which are easier to study because they divide more frequently than healthy cells. To their surprise, the researchers found that the dry mass of cells actually decreases when they enter the cell division cycle. This mass is regained later on, before division is complete.

"Further experiments revealed that as cells enter mitosis, they ramp up activity of a process called lysosomal exocytosis. Lysosomes are cell organelles that break down or recycle cellular waste products, and exocytosis is the process they use to jettison any molecules that aren't needed any more.

"The researchers also found that the density of the dry mass increases as the cells lose dry mass, leading them to believe that the cells are losing low-density molecules such as lipids or lipoproteins. They hypothesize that cells use this process to clear out toxic molecules before dividing. "What we are seeing is that cells might be trying to throw out damaged components before dividing," Miettinen says.

"The researchers speculate that their findings may help explain why neurons, which do not divide, are more likely to accumulate toxic proteins such as Tau or amyloid beta, which are linked to the development of Alzheimer's disease."

Comment: the result shows obvious purpose. Newly formed daughter cells have a fresh start. The comment about neurons not dividing suggests to me an unknown mechanism may clean neurons. The designing mind would not leave that as an unsolved problem

Biological complexity: exercise induced liver enzyme

by David Turell @, Friday, July 14, 2023, 15:17 (259 days ago) @ David Turell

Found in mice many benefits:

https://www.the-scientist.com/news-opinion/an-exercise-induced-liver-enzyme-boosts-meta...

"Plenty of scientific evidence indicates that exercise is good for our health. It benefits our hearts, bones, and muscles, boosts brain health, and may even fight off cancer.1,2,3 Now, a study shows that alongside the muscles and heart, the liver contributes to some of the positive effects of exercise.

"Researchers at Stanford University found that after consistent exercise, the liver produces an enzyme that boosts exercise performance, enhances weight loss, and improves glucose tolerance in mice. Published in Cell Metabolism, the study challenges the conventional muscle-centric view of exercise, revealing that tissues throughout the body respond to breaking a sweat.

***

"A particularly striking finding, said Long, was that in response to exercise, liver cells secreted a family of molecules called carboxylesterase 2 (CES2), which were previously thought to be intracellular proteins. Other studies had revealed that boosting CES2 production inside the liver can increase metabolism in mice.6 However, the team showed that CES2 is also released into the body in response to exercise, and it may influence a number of other organ systems.

"To further understand the role of CES2, the researchers genetically engineered mice to overexpress CES2 in their livers and found that the protein improved overall metabolic health. Mice lost weight and had greater endurance and better glucose tolerance than non-genetically engineered mice. The CES2-overexpressing mice could also run faster and for a longer time than their non-genetically engineered counterparts.

"The researchers next genetically engineered a type of CES2 that mice couldn’t keep inside their livers. Mice that expressed this modified CES2 on top of their regular CES2 still experienced increased benefits from exercise compared to normal mice.

"Lisa Chow, an endocrinologist at the University of Minnesota who was not involved in the study, said that the findings were exciting. “When we think about exercise, we always think about the muscle and the heart or the blood vessels. But that's not the case here,” she said.

"However, Chow said that it’s unclear whether exercise, weight loss, or body composition drove the observed changes in protein secretion. In addition, the study was primarily conducted on male mice. “We need to look at female mice and across species, including humans,” Chow said, also noting that considering how the context of exercise, such as time of day, might affect proteins."

Comment: all early hominins and homos lived hard and exercised hard. It is not difficult to imagine beneficial effects would develop.

Biological complexity: life's required specific metals

by David Turell @, Tuesday, June 07, 2022, 21:55 (661 days ago) @ David Turell

Copper required to pop open seed pods:

https://phys.org/news/2022-06-copper-seed-pod

"Their findings show that a key micronutrient—copper—is essential for laying down a precise pattern of lignin in the seed pods. Lignin is an abundant plant polymer found in lignocellulose, the main structural material in plants. It is present in plant cells walls and is responsible for making wood stiff.

***

"As Hay explains, "the mechanical design that allows these pods to explode depends on lignin being laid down in a precise pattern in this single layer of cells. We know little about what controls this pattern of lignin deposition, and so we set out to identify the genes that control this process. We found three genes that are required to lignify the cell wall in exploding seed pods. These genes code for enzymes, called laccases, that polymerize lignin. When C. hirsuta plants lack all three laccase genes, they also lack lignin in this specific cell type."

"The research team also discovered another gene, called SPL7, required for C. hirsuta seed pod lignification. This gene encodes a protein that regulates copper levels in plants. The researchers discovered SPL7 in a mutant screen. Mutant plants that lack this gene, also lack lignin in endocarpb cell walls. Without lignin, they could no longer disperse their seeds widely. These effects were reversed when the SPL7 mutant plants were grown in soil with high copper levels, but not when they were grown in soil with low copper levels. SPL7 therefore helps C. hirsuta plants to acquire enough copper to develop fully exploding seed pods, especially when copper levels are low.

"But how does copper affect the mechanical structure of these exploding seed pods?

"Interestingly, laccases are copper binding proteins that depend on copper for their function. "The link between these two findings is copper," says Hay. "Plants need SPL7 to cope when there's too little copper in the soil, and laccases need to bind copper for their enzymatic activity. Since lignin is critical for the mechanics of exploding seed pods, and copper-requiring laccases regulate this lignification, this makes seed dispersal dependent on the control of copper levels by SPL7."

"These findings provide important new insights into the genes and cellular processes that generate these extraordinary exploding structures. They also shed new light on the role of copper in this process and on the process of lignification itself, which remains little understood. One reason for this is that large families of genes are involved in lignin polymerization in plant cell walls. Working out how each gene is involved is therefore a challenge, but one that could be addressed using approaches reported in this study, such as CRISPR/Cas9 gene editing and conditional gene expression.

"Copper deficiency in soil affects plants and trees in many different ways and is tackled by using copper fertilizers. It is a particular problem for forestry, as low copper levels can cause tree weakening as a result of poor lignification. "Our work makes a molecular link between copper and lignin via SPL7 and laccases. These insights could inspire new approaches for sustainable forest management," Hay explains."

Comment: how does a blind evolutionary process reach out to choose copper specifically for the active proteins. Not hunt and peck but a designer wouild have no problem

Biological complexity: architecture of human membrane pore

by David Turell @, Friday, June 10, 2022, 20:37 (658 days ago) @ David Turell
edited by David Turell, Friday, June 10, 2022, 20:47

Took over two years to piece it out:

https://phys.org/news/2022-06-decoding-key-cell-atom.html

"Among those pieces of machinery, and one of the most complex, is something known as the nuclear pore complex (NPC). The NPC, which is made of more than 1,000 individual proteins, is an incredibly discriminating gatekeeper for the cell's nucleus, the membrane-bound region inside a cell that holds that cell's genetic material. Anything going in or out of the nucleus has to pass through the NPC on its way.

"The NPC's role as a gatekeeper of the nucleus means it is vital for the operations of the cell. Within the nucleus, DNA, the cell's permanent genetic code, is copied into RNA. That RNA is then carried out of the nucleus so it can be used to manufacture the proteins the cell needs. The NPC ensures the nucleus gets the materials it needs for synthesizing RNA, while also protecting the DNA from the harsh environment outside the nucleus and enabling the RNA to leave the nucleus after it has been made.

***

"Working their way through the proteins in this way eventually produced the final result of their paper: a 16-protein wedge that is repeated eight times, like slices of a pizza, to form the face of the NPC.

***

"In the other paper, titled "Architecture of the linker-scaffold in the nuclear pore," the research team describes how it determined the entire structure of what is known as the NPC's linker-scaffold—the collection of proteins that help hold the NPC together while also providing it with the flexibility it needs to open and close and to adjust itself to fit the molecules that pass through.

"Hoelz likens the NPC to something built out of Lego bricks that fit together without locking together and are instead lashed together by rubber bands that keep them mostly in place while still allowing them to move around a bit.

"I call these unstructured glue pieces the 'dark matter of the pore,'" Hoelz says. "This elegant arrangement of spaghetti noodles holds everything together."

***

"The assembly of the NPC's outer face also helped solve a longtime mystery about the nuclear envelope, the double membrane system that surrounds the nucleus. Like the membrane of the cell within which the nucleus resides, the nuclear membrane is not perfectly smooth. Rather, it is studded with molecules called integral membrane proteins (IMPs) that serve in a variety of roles, including acting as receptors and helping to catalyze biochemical reactions.

"Although IMPs can be found on both the inner and outer sides of the nuclear envelope, it had been unclear how they actually traveled from one side to the other. Indeed, because IMPs are stuck inside of the membrane, they cannot just glide through the central transport channel of the NPC as do free-floating molecules.

"Once Hoelz's team understood the structure of the NPC's linker-scaffold, they realized that it allows for the formation of little "gutters" around its outside edge that allow the IMPs to slip past the NPC from one side of the nuclear envelope to the other while always staying embedded in the membrane itself.

***

"Taken together, the findings of the two papers represent a leap forward in scientists' understanding of how the human NPC is built and how it works. The team's discoveries open the door for much more research. "Having determined its structure, we can now focus on working out the molecular bases for the NPC's functions, such as how mRNA gets exported and the underlying causes for the many NPC-associated diseases with the goal of developing novel therapies," Hoelz says."

Comment: Everything works together in a coordinated fashion. It must do that all at once. It cannot be constructed bit by bit by evolution, because it won't work properly until it is complete. This is the very definition of irreducible complexity which requires a designing mind. Ingress an egress must tightly controlled always. When a molecule wants to enter it emits an alerting signal to trigerv the pore, and teh same at exiting. The signals can e chemical, electrical or physical force. All have been described. This is why the cells look lintelligent: the molecules follow intellgently designed signals. This can be only fully understood when the molecular architecture is found and its actions described.

Biological complexity: cleaning up 'bad' molecules

by David Turell @, Saturday, June 11, 2022, 15:29 (657 days ago) @ David Turell

How to control molecular garbage:

https://www.sciencedaily.com/releases/2022/06/220609131839.htm

"A prime example is the RNA exosome. RNA molecules perform many roles in cells. Some of them are translated into proteins; others form a cell's protein-building machinery. The RNA exosome is a cellular machine that degrades RNA molecules that are faulty, harmful, or no longer needed. Without this microscopic Marie Kondo to prune what doesn't spark joy, our cells would become dysfunctional hoarders, unable to function.

"'RNA surveillance and degradation pathways exist in all forms of life," explains Christopher Lima, Chair of the Structural Biology Program in the Sloan Kettering Institute. "From bacteria to humans, all living things have mechanisms to monitor the quality of RNA and to purposely degrade it."

***

"...it turns out that these degradation pathways are highly regulated and control everything from embryonic development to the progression of the cell cycle.

***

"In a new paper published June 9, 2022 in Cell, Dr. Lima and M. Rhyan Puno, a postdoctoral fellow in the Lima lab, present findings that help explain how the RNA exosome locates the RNA that needs to be degraded. With the help of cryogenic-electron microscopy (cryo-EM), an advanced type of imaging technology, the scientists were able to decipher the structure of a protein assembly called Nuclear Exosome Targeting (NEXT) Complex, which is a key part of the degradation machinery.

"'We knew that NEXT targets and delivers RNA to the exosome, but biochemically and structurally, we didn't have a clue what it looks like or how it works," Dr. Puno says.

***

"From the cryo-EM pictures, the scientists were able to see that the NEXT proteins form a very flexible dimer -- meaning that two copies of NEXT proteins join together as a functional unit.

"'That was really, really puzzling," Dr. Puno says, noting that dimer formation hasn't been visualized before for these types of proteins.

"From biochemical experiments we performed, we know that dimerization is somehow important for degradation," he continues. "But it's still a mystery to us what role the dimer plays in guiding RNA to the exosome."

***

"But defects in RNA degradation pathways also play a role in several types of cancer. In fact, two of the genetic mutations that MSK's genetic testing platform, MSK-IMPACT®, tests for are found in genes related to the RNA exosome pathway, including a protein in NEXT.

"And it's not only messenger RNA that needs proper quality control, Dr. Lima explains.

"'The reality is if you have defective RNA quality-control pathways, your ribosomes don't work, your transfer RNAs don't work, your spliceosomes don't work." The list goes on and on.

"The breadth of functions that RNA performs explains why defective RNA degradation pathways can have such cascading disease-causing effects.

"Making sense of these effects will require a deeper and more extensive understanding of not just the RNA exosome itself, but also the "upstream" proteins, like NEXT, that help surveil RNA and decide when an RNA is defective or no longer needed."

Comment: the biochemistry of life comes with required quality controls Ju st like feedback loops stabilize output of processes, garbage molecules must be destroyed, to avoid clogging up the cells. Another example of irrreducible complexity. A cell cannot be designed to produce a product and not have this mechanism also it place. A designer is required.

Biological complexity: utilizing highly toxic selenium

by David Turell @, Friday, June 17, 2022, 19:03 (651 days ago) @ David Turell

The very reactive antioxident is part of an essential amino acid and invovled in many biochemical processes:

https://phys.org/news/2022-06-vital-cellular-machinery-body-incorporation.html

"A Rutgers scientist is part of an international team that has determined the process for incorporating selenium—an essential trace mineral found in soil, water and some foods that increases antioxidant effects in the body—includes 25 specialized proteins, a discovery that could help develop new therapies to treat a multitude of diseases from cancer to diabetes.

***

"First, selenium is encapsulated within selenocysteine (Sec), an essential amino acid. Then, Sec is incorporated into 25 so-called selenoproteins, all of them key to a host of cellular and metabolic processes.

***

"The incorporation of selenium takes place deep within an individual cell's intricate machinery. Scientists already knew which proteins and molecules of RNA—a nucleic acid present in all cells involved in the production of proteins—enabled the process. However, they were not able to discern the critical step of how these factors worked in tandem to complete the cycle, dictating the function of the cell's ribosome—a large macromolecular machine that binds RNA to make more proteins. What they found was that the processes that occur are not like any understood to take place anywhere else in the human body.

"'This amino acid gets attached to a unique RNA molecule and that has to be carried to the ribosome via a unique protein factor," said Copeland, whose lab has spent the past 20 years working to understand how these biomolecules function on a biochemical level. "And all of this evolved in humans specifically to allow selenium to be incorporated into this handful of proteins."

"Once Sec is ensconced in the selenoproteins, the proteins perform a wide range of vital functions necessary for growth and development. They produce nucleotides, the building blocks of DNA. They break down or store fat for energy. They create cell membranes. They produce the thyroid hormone, which controls the human body's metabolism. And they respond to what is known as oxidative stress by detoxifying chemically reactive byproducts in cells.

"Diseases and disorders such as cancer, heart disease, male infertility, diabetes and hypothyroidism can arise when the production of selenoproteins is disrupted."

Comment: selenium, a trace element vital to life, is found in volcanic soils. Large amounts are highly toxic, so we humans must take in only one two micrograms a day. But high in the Andes llamas have adapted to the selenium abundance in those soils and injest at least two milligrams a day. If selenium is so hard to handle and kills, why did it appear in life? A designer can do this, but chance development is not reasonable.

Biological complexity: enzyme control of protein shapes

by David Turell @, Saturday, August 27, 2022, 19:03 (580 days ago) @ David Turell

In a plant study:

https://phys.org/news/2022-08-enzyme-proteins-ease.html

"A group of researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) studying the world's most abundant protein, an enzyme involved in photosynthesis called rubisco, showed how evolution can lead to a surprising diversity of molecular assemblies that all accomplish the same task. The findings, published today in Science Advances, reveal the possibility that many of the proteins we thought we knew actually exist in other, unknown shapes.

***

"The reconstruction suggests that the gene for form II rubisco has changed over its evolutionary history to produce proteins with a range of structures that transform into new shapes or revert back to older structures quite easily....According to the authors, it was assumed that most protein assemblies were entrenched over time by selective pressure to refine their function, like we see with form I rubisco. But this research suggests that evolution can also favor flexible proteins.

"'The big finding from this paper is that there's a lot of structural plasticity," said Shih, who is also an assistant professor at UC Berkeley. "Proteins may be much more flexible, across the field, than we've believed."

"After completing the ancestral sequence reconstruction, the team conducted mutational experiments to see how altering the rubisco assembly, in this case breaking a hexamer into a dimer, affected the enzyme's activity. Unexpectedly, this induced mutation produced a form of rubisco that is better at utilizing its target molecule, CO2. All naturally occurring rubisco frequently binds the similarly sized O2 molecule on accident, lowering the enzyme's productivity. There is a great deal of interest in genetically modifying the rubisco in agricultural plant species to increase the protein's affinity for CO2, in order to produce more productive and resource-efficient crops. However, there has been a lot of focus on the protein's active site—the region of the protein where CO2 or O2 bind."

Comment: rubisco, as an enzyme, is a giant molecule of thousands of amino acids, which must be in a special arrangement to allow rubisco to do its work. How did natual selection find it? There are enormous odds against a natural discovery. It reeks of design.

Biological complexity: how ant queens live so long

by David Turell @, Friday, September 02, 2022, 19:27 (574 days ago) @ David Turell

They block insulin metabolism:

https://www.sciencenews.org/article/insulin-longevity-aging-ant-queens

"Now, researchers have shown how one ant species pulls off this anti-aging feat. When queens and wannabe queens of the species Harpegnathos saltator gear up to reproduce, a part of what’s called the insulin signaling pathway gets blocked, slowing aging, the researchers report in the Sept. 2 Science. That molecular pathway has long been implicated in aging in mammals, including humans.

***

"In a rare behavior for ants, when a queen H. saltator dies, some female workers begin competing in duels for the chance to replace her (SN: 1/17/14). These hopeful royals develop ovaries, start laying eggs and transition into queenlike forms called gamergates. When a worker transitions to a gamergate, her life span becomes five times as long as it was. But if she doesn’t end up becoming queen and reverts back to a worker, her life span shortens again.

"The researchers exploited this behavior to investigate the molecular underpinnings of anti-aging in these ants. H. saltator gamergates, it turns out, extend their life spans by taking advantage of a split in the insulin signaling pathway, the chain of chemical reactions that drive insulin’s effects on the body. One branch of this pathway is involved with reproduction, while the other is implicated in aging.

***

"Examining patterns of gene activity, Yan and colleagues found that gamergates have more active insulin genes than regular worker ants and, as a result, have increased metabolic activity and ovary development. But the secret sauce protecting the ants from the insulin’s aging effects appears to be a molecule called Imp-L2, which blocks the branch of the insulin pathway linked to aging, experiments showed. The branch involved in reproduction, however, remains active.

“'What we don’t understand is how Imp-L2 can act on one aspect of the pathway and not on the other,” says study coauthor Claude Desplan, a developmental biologist at New York University.

"These results represent a leap forward in our understanding of extreme social insect longevity, the researchers say, while also showcasing an anti-aging evolutionary adaptation that hasn’t been seen in the wild before.

Comment: this new finding reeks of design. How did a naturally advancing evolution find just the right controlling protein to keep these queens alive for such extended periods? Not by chance!!!

Biological complexity: moving iron through the body

by David Turell @, Friday, September 02, 2022, 19:55 (574 days ago) @ David Turell

Using very complex molecules:

https://phys.org/news/2022-09-biochemists-reveal-complex-molecule-iron.html

"For years, scientists knew that mitochondria—specialized structures inside cells in the body that are essential for respiration and energy production—were involved in the assembly and movement of iron-sulfur cofactors, some of the most essential compounds in the human body. But until now, researchers didn't understand how exactly the process worked.

"New research, published in the journal Nature Communications, found that these cofactors are moved with the help of a substance called glutathione, an antioxidant that helps prevent certain types of cell damage by transporting these essential iron cofactors across a membrane barrier.

"Glutathione is especially useful as it aids in regulating metals like iron, which is used by red blood cells to make hemoglobin, a protein needed to help carry oxygen throughout the body, said James Cowan, co-author of the study and a distinguished university professor emeritus in chemistry and biochemistry at Ohio State.

"'Iron compounds are critical for the proper functioning of cellular biochemistry, and their assembly and transport is a complex process," Cowan said. "We have determined how a specific class of iron cofactors is moved from one cellular compartment to another by use of complex molecular machinery, allowing them to be used in multiple steps of cellular chemistry."

"Iron-sulfur clusters are an important class of compounds that carry out a variety of metabolic processes, like helping to transfer electrons in the production of energy and making key metabolites in the cell, as well as assisting in the replication of our genetic information.

***

"By using a combination of cryo-electron microscopy and computational modeling, the team was then able to create a series of structural models detailing the pathway that mitochondria use to export the iron cofactors to different locations inside the body. While their findings are vital to learning more about the basic building blocks of cellular biochemistry, Cowan said he's excited to see how their discovery could later advance medicine and therapeutics.

"'By understanding how these cofactors are assembled and moved in human cells, we can lay the groundwork for determining how to prevent or alleviate symptoms of certain diseases," he said. "We can also use that fundamental knowledge as the foundation for other advances in understanding cellular chemistry.'"

Comment: another example of extreme complexity of a mechanism vital to iron transport control. Not by chance!!!

Biological complexity: mitochondria controlling stem cells

by David Turell @, Friday, September 02, 2022, 20:06 (574 days ago) @ David Turell

New discovery in muscles:

https://phys.org/news/2022-09-reveals-starring-role-shape-shifting-mitochondria.html

"Mitochondria are remarkable shape-shifting organelles that have long been understood as the powerhouses inside our cells. But relatively little is known about how the constant fission and fusion of these tiny energy generators impacts stem cell function and tissue regeneration.

"Now, compelling new research from Dr. Mireille Khacho's lab at the University of Ottawa Faculty of Medicine reveals a starring role for mitochondrial dynamics within adult muscle stem cells—those unique and primitive cells that serve as the body's raw material for muscle renewal and repair.

***

"In essence, her lab suggests a wide-ranging repertoire for mitochondria. Not only do they act as internal sensors and communicators, but their fragmentation plays a big part in overall stem cell maintenance and functioning. Through a series of manipulations with a unique mouse model, the researchers showed that the essential mitochondrial shaping protein OPA1 regulates the dormant state of adult muscle stem cells. And the chronic loss of this protein and persistent fragmentation leads to severe muscle stem cell defects.

"Dr. Khacho's team says the findings show for the first time that the protein OPA1—one of the main regulators of mitochondrial fusion—is essential for muscle stem cell maintenance and function. They pieced together a connection between the depletion of stem cells and mitochondria becoming imbalanced and dysfunctional.

***

"The tiny structure's role is somewhat counterintuitive. Generally, fragmentation of mitochondria is a destructive phenomenon for cells in tissues, Dr. Khacho explains. But in their experiments with adult muscle stem cells, her team found that their fragmentation also serves as a physiological mechanism that activates signaling to the nucleus. It does this by increasing levels of an antioxidant peptide called glutathione. Even more intriguing is that they uncovered a new function for this peptide: it acts as a signaling molecule that mediates the crosstalk between mitochondria and the nucleus."

Comment: another example of extreme complexity. Counterintuitive? No, just an example of God's designs at work.

Biological complexity: mitochondria ADP structure

by David Turell @, Wednesday, September 07, 2022, 21:00 (569 days ago) @ David Turell

ATP supplies teh enefgy we need in all cells:

https://phys.org/news/2022-09-important-component-body-energy-mechanism.html

"Within the mitochondria, complex biochemical processes occur that convert the energy contained in the carbohydrates that we eat into the important energy-storage molecule ATP (adenosine triphosphate). ATP is essentially the "fuel" that powers all of the processes in living cells. If ATP production is inhibited for some reason, there can be serious consequences for the human body, including severe illness and death.

"The regions in the mitochondria where ATP synthesis takes place are known as the cristae, which are folded protrusions on the inner mitochondrial membrane. "The cristae house molecular machines that act like turbines and use the controlled flow of hydrogen ions to drive ATP synthesis," explained Martin van de Laan, Professor of Medical Biochemistry at Saarland University. "This elegant mechanism can only function if the internal fine structure of the mitochondria and the formation of the cristae are continuously maintained," added Prof. van der Laan.

"Working with his team and with colleagues from the Max Delbrück Center for Molecular Medicine in Berlin, van der Laan has been able to gain insights into the molecular structure of a large and complex scaffold-like protein assembly that plays an important role in controlling cristae architecture. Their results have now been published inScience Advances.

"This molecular device, known as the Mitochondrial Contact Site and Cristae Organizing System (MICOS), effectively functions as the entry gate to the cristae compartments. The MICOS protein subunits Mic60 and Mic19 both have membrane-shaping capabilities and together they function like a "doorman," permitting only selected molecules to enter or exit the interior of the cristae.

"The research team have now shown how the MICOS components Mic60 and Mic19 form filamentous bundles that can assemble themselves to form a vaulted molecular structure that spans the entrance to the cristae. "This dome-like assembly is elastically tethered to the mitochondrial membranes," explained Professor van der Laan. "The design and architecture of MICOS provides us with important insights into how MICOS can act as a flexible but controllable gateway into the cristae and thus regulate mitochondrial energy metabolism.'"

Comment: Think about it. If ATP is such a vital part of cellular energy supply, which came first the ATP energy supply system or the cells? But the cells cannot live without ATP. The answer is everything had to appear at once by design. dhw cannot escape this issue. I await his answer.

Biological complexity: cyanobacteria anatomy

by David Turell @, Saturday, September 10, 2022, 17:50 (566 days ago) @ David Turell

How it supports photosynthesis:

https://www.sciencedaily.com/releases/2022/09/220909160338.htm

"Published Aug. 31 in the journal Nature, the findings immediately shed new light on microbial photosynthesis -- specifically, how light energy is captured and sent to where it's needed to power the conversion of carbon dioxide into sugars

**

"The cyanobacterial antenna structures, which are called phycobilisomes, are complex collections of pigments and proteins, which assemble into relatively massive complexes.

***

"One surprise, for example, came in how a relatively small protein can act as a surge protector for the massive antenna. Before this work, researchers knew the phycobilisome could corral molecules called orange carotenoid proteins, or OCPs, when the phycobilisome had absorbed too much sunlight. The OCPs release the excess energy as heat, protecting a cyanobacterium's photosynthetic system from burning up.

"Until now, there's been debate about how many OCPs the phycobilisome could bind and where those binding sites were. The new research answers these fundamental questions and offers potentially practical insights.

"This kind of surge-protecting system -- which is called photoprotection and has analogs in the plant world -- naturally tends to be wasteful. Cyanobacteria are slow to turn their photoprotection off after it has done its job. Now, with the complete picture of how the surge protector works, researchers can design ways to engineer "smart," less wasteful photoprotection, Kerfeld said.

***

"'If you think of this like Legos, you can keep building up, right? The proteins and pigments are like blocks making the phycobilisome, but then that's part of the photosystem, which is in the cell membrane, which is part of the entire cell," Sutter said. "We're climbing up the ladder of scale in a way. We've found something new on our rung, but we can't say we've got the system settled.'"

Comment: unfortunately, I cannot look at the article itself to see the architecture. Just more indication of extreme complexity requiring design.

Biological complexity: mitochondrial transport control

by David Turell @, Thursday, September 15, 2022, 19:23 (561 days ago) @ David Turell

Across its double membrane:

https://www.sciencedaily.com/releases/2022/09/220915104719.htm

"Mitochondria, often referred to as the powerhouses of the cell, are bounded by a double membrane. The inner of the two membranes hosts a series of proteins that transfer electrons along what is called the electron transport chain. This electron transport is a crucial part of the processes that extract chemical energy from nutrients and ultimately store it in energy-rich molecules of adenosine triphosphate (ATP).

"The new insight from the Duke-NUS team reveals that small microproteins (also called peptides) play a previously unrecognised role in allowing the electron transport chain to form. Specifically, they appear to work together to assist and control the assembly of one of the central proteins of the chain, called Complex III. This role allows the microproteins to participate in regulating the levels of electron transport chain proteins, and therefore energy supply, in response to changes in energy demand.

"'Microproteins have fascinated but also mystified biologists from diverse fields for a long time," said Mr Liang Chao, co-first author of the study, who is a PhD candidate at Duke-NUS. "Our study provides an example of what they can do and how they participate in controlling energy metabolism at the deepest level of molecular detail."

"'Mitochondria are the batteries and factories of our cells, making not only energy but also many of the building blocks required for cells to multiply and stay alive," said Dr Shan Zhang, formerly a research fellow with Asst Prof Ho's Endogenous Peptides Lab, under Duke-NUS' CVMD Programme, and now an Assistant Professor at Zhejiang University, China. "We clearly see that modulating the levels of these microproteins can lead to or protect against mitochondrial dysfunction, which is a feature that underlies almost all types of common diseases.'"

Comment: What is not noted is mitochondria are controlled by their own DNA which is maternally sourced. This intricate system must have been designed.

Biological complexity: mitochondria and chloroplasts

by David Turell @, Friday, September 16, 2022, 17:45 (560 days ago) @ David Turell

Have similar patterns of control:

https://phys.org/news/2022-09-science-reveals-universal-cells-power.html

"Mitochondria are compartments—so-called "organelles"—in our cells that provide the chemical energy supply we need to move, think, and live. Chloroplasts are organelles in plants and algae that capture sunlight and perform photosynthesis. At a first glance, they might look worlds apart. But an international team of researchers, led by the University of Bergen, have used data science and computational biology to show that the same "rules" have shaped how both of these organelle types—and more—have evolved throughout life's history.

***

"For a fresh perspective on this question, the scientists took a data-driven approach. They gathered data on all the organelle DNA that has been sequenced across life. They then used modeling, biochemistry, and structural biology to represent a wide range of different hypotheses about gene retention as a set of numbers associated with each gene. Using tools from data science and statistics, they asked which ideas could best explain the patterns of retained genes in the data they had compiled—testing the results with unseen data to check their power.

"'Some clear patterns emerged from the modeling," explains Kostas Giannakis, a postdoctoral researcher at Bergen and joint first author on the paper. "Lots of these genes encode subunits of larger cellular machines, which are assembled like a jigsaw. Genes for the pieces in the middle of the jigsaw are most likely to stay in organelle DNA."

"The team believe that this is because keeping local control over the production of such central subunits help the organelle quickly respond to change—a version of the so-called "CoRR" model. They also found support for other existing, debated, and new ideas. For example, if a gene product is hydrophobic and hard to import to the organelle from outside, the data shows that it is often retained there. Genes that are themselves encoded using stronger-binding chemical groups are also more often retained, perhaps because they are more robust in the harsh environment of the organelle.

***

"To their surprise, the team also found that their models trained to describe mitochondrial genes also predicted the retention of chloroplast genes, and vice versa. They also found that the same genetic features shaping mitochondrial and chloroplast DNA also appear to play a role in the evolution of other endosymbionts—organisms which have been more recently captured by other hosts, from algae to insects.

"'That was a wow moment," says Johnston. "We and others have had this idea that similar pressures might apply to the evolution of different organelles. But to see this universal, quantitative link—data from one organelle precisely predicting patterns in another, and in more recent endosymbionts—was really striking.'"

Comment: They have found pure convergence in this comparison. I'm not surprised at it. Convergence is evidence of design. And this common pattern in two very divergent forms is very strong evidence for design.

Biological complexity: lysosome function

by David Turell @, Tuesday, September 27, 2022, 21:04 (549 days ago) @ David Turell

How molecular garbage is dumped:

https://phys.org/news/2022-09-world-lysosomes.html

"'Found in cells throughout the human body, lysosomes are tiny organelles responsible for breaking down cellular waste products and salvaging reusable molecules as building blocks for cellular components," explained Ms. Menglan He, co-first-author of the study and MD-Ph.D. candidate with the Integrated Biology and Medicine Ph.D. track at Duke-NUS. "When lysosomes malfunction due to rare genetic disorders, this creates a build-up of toxic cellular waste products and affects other organelles, causing organ and cellular pathologies such as neurodegeneration."

***


"Their findings revealed that an MFS protein called Spns1 transports the broken-down products of two phospholipids, phosphatidylcholine and phosphatidylethanolamine—which are important building blocks for the structure and function of living cells—out of lysosomes and into the cytoplasm. The two molecules then go through pathways that recycle them into their original lipid forms so they can be reincorporated into the cell.

"'Scientists know quite a lot about the molecular processes involved in breaking down and transporting some molecules out of lysosomes," added Dr. Alvin Kuk, who is also a co-first-author of the study and Postdoctoral Research Fellow with the Cardiovascular & Metabolic Disorders (CVMD) Program at Duke-NUS. "But when it comes to the two lipids, phosphatidylcholine and phosphatidylethanolamine that represent the most abundant phospholipids of cell membranes, very little is known."

"The scientists further found that Spns1 deficiency in cells and preclinical models led to the pathological accumulation of breakdown products of the two lipids inside lysosomes. This accumulation led to various disease states, including signs of increased inflammation.

""Historically, it has been difficult to identify lysosomal lipid transporters, limiting our understanding of the role of the lysosome in lipid metabolism and disease," said Professor David Silver, the lead senior co-author of the study and Deputy Director of the CVMD Program at Duke-NUS. "This study provides a framework to investigate how this new transporter works and its role in health and disease.""

Comment: a complex design that requires very specific molecules requires a designer. Not by chance.

Biological complexity: cells housekeeping under stress

by David Turell @, Wednesday, September 28, 2022, 22:44 (548 days ago) @ David Turell

A new study:

https://phys.org/news/2022-09-discoveries-mystery-cells-stress.html

"In new research recently published in the journal Cell Reports, a team of scientists from the University of Massachusetts Amherst delved into the mysteries of how cells weather stress. Using bacterial cells, the researchers discovered that a damage-repairing enzyme, called ClpX, can not only mutate to fix multiple cellular issues but can respond to changing levels of cellular energy to help keep a cell healthy.

"'What we're really interested in," says Peter Chien, professor of biochemistry and molecular biology at UMass Amherst and the paper's senior author, "is how cells respond to stress. We study a class of enzymes, called proteases, which target and destroy harmful proteins within a cell. These proteases can selectively recognize specific, individual proteins singular proteins. But how do they do this? How can they choose between healthy proteins and harmful ones?"

"To answer this question, Chien and his co-authors focused on two specific proteases, known as Lon and ClpX, each of which is exquisitely tuned to recognize a different harmful protein. It had long been thought that Lon and ClpX functioned like keys: Each could open only a specific lock and no other, and if a cell lacked either, then serious side effects would occur.

***

"But, after a series of experiments that involved deleting Lon from colonies of bacterial cells, Chien's team started noticing something odd: Some of the colonies were surviving.

"This observation led to their first discovery: ClpX can mutate to perform a Lon-like function, though it loses some of its ClpX abilities. It's as if in order to keep your dorm-room clean, you started washing your roommate's socks, but had to sacrifice some of your own clean laundry in order to do so.

"In tracing out exactly how the ClpX mutation allowed the protease to expand its function, the team made its second discovery: Wild, non-mutant ClpX can also perform some of Lon's duties, under the right conditions.

"It turns out that ClpX is highly sensitive to ATP, an organic compound that is the energy source for all living cells. At normal levels of ATP, ClpX focuses on its own duties, but at a specific, lower threshold it suddenly starts cleaning up after Lon.

"'This is a real breakthrough in the basic understanding of how cells work," says Chien. "It changes the rules: Not only does cellular energy control how fast a cell works, but how it works, as well.'"

Comment: ClpX is an enzyme which does magical things, but the key to understanding the need for design is ClpX is a huge molecule of a specific design to work. Hundreds of amino acids in a specific required order. Not by chance.

Biological complexity: enzyme's new functions found

by David Turell @, Friday, September 30, 2022, 20:42 (546 days ago) @ David Turell

In cyanobacteria:

https://phys.org/news/2022-09-swiss-army-knife-like-functions-powerful-enzyme.html

"Blue-green algae (AKA cyanobacteria) have a superpower which likely helps them be highly successful as invaders of waterways. They have an extraordinary ability to store energy and nitrogen in their cells for times of need. But how exactly they do so remains only partly understood.

"Now researchers from McGill University and their collaborators at ETH Zurich have uncovered an intriguing hitherto unknown ability of the enzymes (known as cyanophycin synthetases) that are active in creating these food reserves. Their findings, described in a recent paper in Nature Communications, are not only scientifically surprising, but take us a step closer to being able to use these environmentally friendly polymers for everything from bandages to biodegradable antiscalants to animal food.

"Enzymes such as cyanophycin synthetases (called polymerase enzymes because they synthesize long chains of polymers) usually require primers in the form of short "starter chains" to start assembling the long chains. Polymerases act as catalysts for a wide range of biological functions, from kickstarting the process of RNA and DNA replication to converting glucose into glycogen as a way of storing energy for later use. Cyanophycin synthetases from many different cyanobacteria were thought to need primers like all the other polymerases, but then the researchers spotted something new.

"'We were working with several cyanophycin synthetases and found that one of them didn't need to be given primer," says lead author Itai Sharon, a McGill Ph.D. student in Biochemistry. "After three years of experiments, trying to figure out why not, we discovered that this cyanophycin synthetase had a hidden reaction center within it that cleaves bonds between amino acids, instead of linking amino acids, which is this polymerase's main job."

"The researchers discovered that cyanophycin synthetase could slowly make extremely small numbers of long cyanophycin polymers in absence of primer, which the newly discovered reaction center cleaves into many short chains that are then used as primers for fast polymerization.

"'We call cyanophycin synthetase a 'Swiss army knife enzyme' says Martin Schmeing, corresponding author and Director of the McGill Center de recherche en biologie structurale. "It combines three enzymatic functions—two bond-making and one bond-breaking—into one elegant, self-sufficient polymerizing machine.'"

Comment: cyanobacteria, which create oxygen, play a vital role in evolving the Earth to support life. See the study to appreciate how large this enzyme molecule is. Hundreds of amino acids in an exact order to function properly. Not by chance.

Biological complexity: ATP's importance

by David Turell @, Thursday, October 06, 2022, 19:01 (540 days ago) @ David Turell

Every life form uses it:

https://www.sciencealert.com/every-life-form-on-earth-uses-the-same-chemical-for-energy...

"ATP is an organic molecule, charged up by photosynthesis or by cellular respiration (the way organisms break down food) and used in every single cell. Every day, we recycle our own body weight in ATP.

"In both the above systems, a phosphate molecule is added to ADP (adenosine diphosphate) through a reaction called phosphorylation – resulting in ATP.

***

"How ATP ascended to metabolic dominance, in place of many possible equivalents, has been a long-standing mystery in biology and the focus of the research.

"'Our results suggest… that the emergence of ATP as the universal energy currency of the cell was not the result of a 'frozen accident'," but arose from unique interactions of phosphorylation molecules, explains evolutionary biochemist Nick Lane from University College London (UCL).

"The fact that ATP is used by all living things suggests it has been around since life's very beginning and even before, during the prebiotic conditions that preceded all us animate matter.

"But researchers are puzzled as to how this could be the case when ATP has such a complicated structure that involves six different phosphorylation reactions and a whole lot of energy to create it from scratch.

***

"Pinna and team suspect some other molecules must have been involved initially in the complicated phosphorylation process. So they took a close look at another phosphorylating molecule, AcP, that's still used by bacteria and archaea in their metabolism of chemicals, including phosphate and thioester – a chemical thought to have been abundant at the beginning of life.

"In the presence of iron ions (Fe3+), AcP can phosphorylate ADP to ATP in water. Upon testing the ability of other ions and minerals to catalyze ATP formation in water, the researchers could not replicate this with other substitute metals or phosphorylating molecules.

"'It was very surprising to discover the reaction is so selective – in the metal ion, phosphate donor, and substrate – with molecules that life still uses," says Pinna.

"'The fact that this happens best in water under mild, life-compatible conditions is really quite significant for the origin of life."

"This suggests that with AcP, these energy-storing reactions could take place in prebiotic conditions, before biological life was there to hoard and spur the now self-perpetuating cycle of ATP production.

"Furthermore, the experiments suggest that the creation of prebiotic ATP was most likely to take place in freshwater, where photochemical reactions and volcanic eruptions, for instance, could provide the right mix of ingredients, the team explains.

***

"'Our results suggest that ATP became established as the universal energy currency in a prebiotic, monomeric world, on the basis of its unusual chemistry in water," Pinna and colleagues write.

"What's more, pH gradients in hydrothermal systems could have created an uneven ratio of ATP to ADP, enabling ATP to drive work even in the prebiotic world of small molecules.

"'Over time, with the emergence of suitable catalysts, ATP could eventually displace AcP as a ubiquitous phosphate donor, and promote the polymerization of amino acids and nucleotides to form RNA, DNA, and proteins," explains Lane."

Comment: life started in water. But fresh water in this example is on land. Life did not arrive on land until millions of years after life was rampant in the oceans. Once again we see intelligent design in the lab strained to fit natural events in the wild.

Biological complexity: photosynthesis controls

by David Turell @, Friday, October 14, 2022, 17:47 (532 days ago) @ David Turell

Varied in evolution:

https://phys.org/news/2022-10-resurrecting-billion-year-old-enzymes-reveals-photosynthe...

"The central biocatalyst in photosynthesis, Rubisco, is the most abundant enzyme on earth. By reconstructing billion-year-old enzymes, a team of Max Planck Researchers has deciphered one of the key adaptations of early photosynthesis.

"Present day life fully depends on photosynthetic organisms like plants and algae that capture and convert CO2. At the heart of these processes lies an enzyme called Rubisco that captures more than 400 billion tons CO2 annually. Organisms alive today make staggering amounts of it: the mass of Rubisco on our planet outweighs that of all humans. In order to assume such a dominant role in the global carbon cycle, Rubisco had to adapt constantly to changing environmental conditions.

***

"Rubisco is ancient: it emerged approximately 4 billion years ago in primordial metabolism prior to the presence of oxygen on earth. However, with the invention of oxygen-producing photosynthesis and rise of oxygen in the atmosphere, the enzyme started catalyzing an undesired reaction, in which it mistakes O2 for CO2 and produces metabolites that are toxic to the cell. This confused substrate scope still scars Rubiscos to date and limits photosynthetic efficiency. Even though Rubiscos that evolved in oxygen-containing environments became more specific for CO2 over time, none of them could get completely rid of the oxygen capturing reaction. (my bold)

"The molecular determinants of increased CO2 specificity in Rubisco remain largely unknown. However, they are of great interest to researchers aiming to improve photosynthesis. Interestingly, those Rubiscos that show increased CO2 specificity recruited a novel protein component of unknown function. This component was suspected to be involved in increasing CO2 specificity, however, the true reason for its emergence remained difficult to determine because it already evolved billions of years ago.

"To understand this key event in the evolution of more specific Rubiscos, collaborators at the Max Planck Institute for Terrestrial Microbiology in Marburg and Nanyang Technological University in Singapore used a statistical algorithm to recreate forms of Rubiscos that existed billions of years ago, before oxygen levels began to rise. The team led by Max Planck researchers Tobias Erb and Georg Hochberg resurrected these ancient proteins in the lab to study their properties. In particular, the scientists wondered whether Rubisco's new component had anything to do with the evolution of higher specificity.

"The answer was surprising, as doctoral researcher Luca Schulz explains: "We expected the new component to somehow directly exclude oxygen from Rubisco catalytic center. That is not what happened. Instead, this new subunit seems to act as a modulator for evolution: recruitment of the subunit changed the effect that subsequent mutations had on Rubisco's catalytic subunit. Previously inconsequential mutations suddenly had a huge effect on specificity when this new component was present. It seems that having this new subunit completely changed Rubisco's evolutionary potential."

"This function as an "evolutionary modulator" also explains another mysterious aspect of the new protein component: Rubiscos that incorporated it are completely dependent on it, even though other forms of Rubisco can function perfectly well without. The same modulating effect explains why: When bound to this small protein component, Rubisco become tolerant to mutations that would otherwise be catastrophically detrimental. With the accumulation of such mutations, Rubisco effectively became addicted to its new subunit.

"Altogether the findings finally explain the reason why Rubisco kept this new protein component around ever since it encountered it. Max Planck Research Group Leader Georg Hochberg explains: "The fact that this connection was not understood until now highlights the importance of evolutionary analysis for understanding the biochemistry that drives life around us. The history of biomolecules like Rubisco can teach us so much about why they are the way they are today. And there are still so many biochemical phenomena whose evolutionary history we really have no idea about. So it's a very exciting time to be an evolutionary biochemist: almost the entire molecular history of the cell is still waiting to be discovered.'"

Comment: Rubisco was on the scene before life started!! Life was/is oxygen dependent. Sounds like a designed plan with pre-preparation.

Biological complexity: protozoal movement, no brain

by David Turell @, Saturday, October 15, 2022, 00:19 (531 days ago) @ David Turell

Pattern movement observed:

https://www.sciencealert.com/clockwork-like-computer-discovered-inside-brainless-micros...

"microscopic pond dwellers called Euplotes eurystomus have mastered a way to walk brainlessly – scurrying about like insects, with their 14 little appendages.

"They appear to move a bit like the Dutch-designed kinetic sculptures called Strandbeasts, with clockwork-like connections cycling them through a pattern of set states that can be adjusted in response to their environment.

"'There seemed to be this sequential logic happening with the movements," says biophysicist Ben Larson from the University of California, San Francisco (UCSF). "They weren't random, and we began to suspect there was some sort of information processing happening."

"These protozoans – single-celled organisms with animal-like characteristics – have 14 stingy bundles of cilia that work together as legs called cirri. They can use these cirri to swim and walk while actively hunting for prey.

***

"The cirri are made of tubulin fibers, like the rest of the cell's scaffolding structures (its cytoskeleton). These fibers also act as a support structure between the different cirri so they also function as a kind of mechanical communication.

"'Euplotes uses these connections to facilitate an elaborate walking motion, " explains UCSF biophysicist Wallace Marshall.

"Computer modeling revealed that tension and strain on the fibers dictated which set pattern of cirri positions was possible at each moment. Some cirri store stress at different stages of a gait; when that stress is released it propels the cell to move forward into the next state, causing a cyclic transition between these states."

Comment: programmed biochemical reactions can easily create this animal's movement. Other sngle-celled animals move their bodies, as amoba sith no legs.

Biological complexity: hearing mechanism

by David Turell @, Sunday, October 16, 2022, 16:12 (530 days ago) @ David Turell

How a specialized protein works:

https://www.sciencealert.com/finally-scientists-have-figured-out-a-key-molecular-mechan...

"Researchers have known for some time that the transmembrane channel-like protein 1 (TMC1) complex performs an important role in hearing, but the exact makeup has remained elusive.

"This is the last sensory system in which that fundamental molecular machinery has remained unknown," says senior author Eric Gouaux, a senior biochemist at OHSU.

"Thanks to this new research, published in Nature, we now know that this protein complex operates as a tension-sensitive ion channel that opens and closes depending upon the movement of hairs inside the inner ear.

"Using electron microscopy, the researchers discovered that the protein complex "resembles an accordion", with subunits "poised like handles" on either side.

"Sound waves traveling through the ear strike the eardrum (tympanic membrane), then to the inner ear where it jiggles the ossicles; three of the body's tiniest bones. The ossicles strike the snail-like cochlear, which in turn brushes microscopic finger-like hairs called stereocilia against membranes.

"These stereocilia are embedded in cells that have the ion channels formed by the TMC1 complex that open and close as the hairs move, sending electrical signals along the auditory nerve to the brain to be interpreted as sound."

Original paper abstract:

https://www.nature.com/articles/s41586-022-05314-8

"The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid–protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.*

Comment: so many parts working in a coordinated fashion must be considered irreducibly complex and must be created all at once by design.

Biological complexity: actin fibers discovery and unknowns

by David Turell @, Wednesday, October 26, 2022, 21:11 (520 days ago) @ David Turell

The fibers are active, support cell structure and their own structure is sstudied:

https://phys.org/news/2022-10-pocket-full-moleculeshow-actin-filaments.html

"Actin filaments are protein fibers that make up the internal skeleton of the cell. As active elements of our cells, actin filaments support the cell's fusion, movement and are involved in many other cellular processes. Importantly, they are also a major constituent of muscle cells. The structural complexity of these filaments has fascinated scientists since its discovery in the 1940s—and has opened a sea of unanswered questions behind their ability to facilitate many processes of the cell.

"For the first time, researchers at the Max Planck Institute of Molecular Physiology in Dortmund, Germany, have been successfully able to visualize hundreds of water molecules in the actin filament, representing a quantum leap in actin research.

"Using the technique of electron cryo microscopy (cryo-EM), the group of Stefan Raunser reveals in unprecedented detail how actin proteins are arranged together in a filament, how ATP—the cell's energy source—sits in the protein pocket, and where individual water molecules position themselves and react with ATP.

"'We are answering fundamental questions of life that scientists have been trying to answer for several decades," says Raunser. In eukaryotic cells, actin proteins are abundant and tend to join together (polymerize) into filaments.

***

"Researchers knew already that the filaments' dynamics is regulated by ATP hydrolysis—the reaction of ATP with water that cleaves a phosphate group and generates energy. What previously remained unanswered, however, was the exact molecular details behind this process.

***

"In their current study published in Nature, Raunser and his colleagues were able to set a new resolution record: they obtained all three actin-states with a resolution of about 0.2 nanometers, making previously invisible details visible. The three-dimensional maps not only display all amino-acid sidechains of the proteins but also reveal where hundreds of water molecules are placed.

"Through comparison between these new structures and those of isolated actin, they were able to infer how water molecules move. Upon polymerization, water molecules relocate in the ATP pocket in such a way, that only a single water molecule remains in front of ATP, ready to attack one phosphate and initiate hydrolysis.

***

"The authors also cast light on the final fate of the phosphate. Previously, scientists believed there to be a back door in the ATP pocket that remains open after ATP hydrolysis to facilitate the exit of the phosphate. However, the new cryo-EM structures show no trace of open backdoors. Hence, the release mechanism remains a mystery.

"'We believe there to be a door, but it likely opens momentarily," comments Raunser, who now wants to use mathematical simulations and time-resolved cryo-EM methods to demonstrate just how the phosphate exits. Evidently, these exciting discoveries have opened the door for scientists to dig deeper in the hopes of discovering even more details behind the processes by which actin filaments contribute to the cell's motion."

Comment: actin fibers had to be designed all at once, as they are obviously irreducibly complex. More definite evidence for design.

Biological complexity: bacterial colonies cooperation

by David Turell @, Wednesday, November 02, 2022, 15:04 (513 days ago) @ David Turell

In recent Vibrio studies:

https://www.quantamagazine.org/ocean-bacteria-reveal-an-unexpected-multicellular-form-2...

"The growth curve for her Vibrio cultures, however, didn’t show the usual smoothly rising line but rather a bumpy squiggle like the track of a roller coaster. No matter how many times she repeated the process, the bacteria didn’t produce the expected cloudiness in the broth.

"To check what was going on, Schwartzman deposited a droplet of the culture solution on a glass microscope slide and peered through the lens at 40 times magnification. What she and Ebrahimi saw were not swarms of individual Vibrio but rather beautiful, layered orbs consisting of hundreds or thousands of bacteria living together

"Further work showed that the hollow spheres were Vibrio’s solution to the complicated challenge of eating at sea. An individual bacterium can produce only so much enzyme; breaking down alginate goes much more quickly when Vibrio can cluster together. It’s a winning strategy, Schwartzman says — up to a point. If there are too many Vibrio, the number of bacteria outstrips the available alginate.

"The bacteria resolved the conundrum by developing a more complex life cycle. The bacteria live in three distinct phases. At first, an individual cell divides repeatedly and the daughter cells huddle in growing clumps. In the second phase, the clumped cells rearrange themselves into a hollow sphere. The outermost cells glue themselves together, forming something rather like a microscopic snow globe. The cells inside become more mobile, swimming about as they consume the trapped alginate. In the third phase, the brittle outer layer ruptures, releasing the well-fed inner cells to start the cycle anew.

"In effect, Vibrio become a heterogeneous mixture of cells, with the bacteria using different genes to control their behavior in each phase. As the cells interact with their neighbors in the structure, what emerges is “a surprising amount of complexity,” said Schwartzman, who is launching her own lab at the University of Southern California in January. “The bacteria are constantly taking in information from their environment, and sometimes they respond in ways that change the environment.”

"This complexity pays off for Vibrio in several ways. By altering their life cycle to include a multicellular stage, the bacteria can digest the alginate efficiently: Their numbers increase, and the hollow shell helps to concentrate the enzymes. Meanwhile, the structure of the community prevents too many cells from being born. The cells in the shell lose the opportunity to reproduce, but their DNA lives on in the next generation anyway, since all the cells in the orb are clones.

***

"James Shapiro, a retired microbiologist from the University of Chicago, has little doubt that she’ll find it.

"Beginning in the 1980s, Shapiro and other microbiology luminaries such as Bonnie Bassler at Princeton University showed that the single-celled lifestyle of well-studied bacteria was often an artifact of the artificial flask environments in which they were grown. In a 1998 article in the Annual Review of Microbiology, Shapiro argued that bacteria aren’t unicellular loners. “I came to the conclusion that basically all bacteria are multicellular organisms,” he said.

"Over his four-decade career, Shapiro saw his hypothesis transform from nearly heretical to incontrovertible. “At first, I got just bemused attention, but now it’s become conventional wisdom,” he said. “Multicellularity is an inherent property of bacteria.'”

Comment: this work shows that bacteria contain the beginnings of multicellularity. Our old friend Shapiro is supported in his work.

Biological complexity: bacterial colonies cooperation

by dhw, Thursday, November 03, 2022, 08:37 (512 days ago) @ David Turell

QUOTES: "In effect, Vibrio become a heterogeneous mixture of cells, with the bacteria using different genes to control their behavior in each phase. As the cells interact with their neighbors in the structure, what emerges is “a surprising amount of complexity,” said Schwartzman, who is launching her own lab at the University of Southern California in January. “The bacteria are constantly taking in information from their environment, and sometimes they respond in ways that change the environment.”

Shapiro argued that bacteria aren’t unicellular loners. “I came to the conclusion that basically all bacteria are multicellular organisms,” he said.

"Over his four-decade career, Shapiro saw his hypothesis transform from nearly heretical to incontrovertible. “At first, I got just bemused attention, but now it’s become conventional wisdom,” he said. “Multicellularity is an inherent property of bacteria.'”

DAVID: this work shows that bacteria contain the beginnings of multicellularity. Our old friend Shapiro is supported in his work.

Once more my thanks for your integrity in presenting material which you know I can use to support theories opposed to your own. The versatility of these bacterial communities seems to foreshadow the vast diversity of life forms as cell communities go on “taking in information from their environment” and responding, not just by changing their environment but also by changing themselves. This in a nutshell is Shapiro’s own theory of evolution, and of course he is a champion of the theory of cellular intelligence.

Biological complexity: bacterial colonies cooperation

by David Turell @, Thursday, November 03, 2022, 17:24 (512 days ago) @ dhw

QUOTES: "In effect, Vibrio become a heterogeneous mixture of cells, with the bacteria using different genes to control their behavior in each phase. As the cells interact with their neighbors in the structure, what emerges is “a surprising amount of complexity,” said Schwartzman, who is launching her own lab at the University of Southern California in January. “The bacteria are constantly taking in information from their environment, and sometimes they respond in ways that change the environment.”

Shapiro argued that bacteria aren’t unicellular loners. “I came to the conclusion that basically all bacteria are multicellular organisms,” he said.

"Over his four-decade career, Shapiro saw his hypothesis transform from nearly heretical to incontrovertible. “At first, I got just bemused attention, but now it’s become conventional wisdom,” he said. “Multicellularity is an inherent property of bacteria.'”

DAVID: this work shows that bacteria contain the beginnings of multicellularity. Our old friend Shapiro is supported in his work.

dhw: Once more my thanks for your integrity in presenting material which you know I can use to support theories opposed to your own. The versatility of these bacterial communities seems to foreshadow the vast diversity of life forms as cell communities go on “taking in information from their environment” and responding, not just by changing their environment but also by changing themselves. This in a nutshell is Shapiro’s own theory of evolution, and of course he is a champion of the theory of cellular intelligence.

Glad you enjoyed this entry. There is no question multicellularity came from bacteria. But for me God designed that step.

Biological complexity: phase separation

by David Turell @, Sunday, November 06, 2022, 16:40 (509 days ago) @ David Turell

Reaction areas without actual physical wall separation:

https://knowablemagazine.org/article/living-world/2020/what-is-liquid-liquid-phase-sepa...

"... a big question mark remains: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?

" Over the last decade, cell biologists have come to appreciate what many believe to be a whole new way that cells shape their internal landscape. Like blobs merging, then dispersing, in a lava lamp, or a salad dressing that separates into bubbles of oil and vinegar, groups of proteins can sometimes congeal into distinct droplets. One key way these droplets form is through a process called liquid-liquid phase separation.

"Exactly what happens within these droplets largely remains a mystery. The blobs might act as temporary breakout spaces for specific cellular events, for example. Or their formation might result from a stage in some key cellular process. But whatever their precise functions turn out to be, some biologists think that their formation promises to fundamentally reframe our understanding of how the cell does its essential business.

***

"To understand the concept, it helps to understand the properties of the cell’s interior, or cytoplasm. Researchers call it a fluid, but it’s more oozy than watery, like cornstarch mixed with a bit of water. That’s because it’s chock-full of dissolved molecules, explains Stephanie Weber, a cell biologist at McGill University in Montreal. When clusters of those molecules begin to separate out, they create even gooier, molasses-like pockets of cytoplasm called biomolecular condensates.

"Structurally, the proteins within a condensate are a bit like a tangle of cooked spaghetti, if you can imagine spaghetti strands made of weak Velcro. They bind lightly to many parts of the other proteins in the condensate, in no particular orientation. (Contrast that with the key-in-a-lock kind of binding that occurs when an enzyme attaches to a target or a chemical sticks to a receptor.) Many of the proteins or protein regions that make these weak connections are what biochemists call disordered, meaning they don’t take on a firm three-dimensional shape like most proteins do. The sum of all those weak forces holds the droplet together.

***

"The biggest, broadest hypothesis for the function of these droplets is that they concentrate specific sets of proteins and other molecules so as to house, kick-start or speed up the reactions the proteins engage in.

***

"The phase separation may rev up a molecular process that normally ticks over barely above idle, the researchers proposed.

"And work from geneticist Richard Young’s lab at the Massachusetts Institute of Technology suggests that phase separation concentrates droplets of proteins needed to turn on the activity of genes or prod a chromosome to start copying itself at the correct places on the DNA strand. Rather than relying on chance for the right proteins to appear where they are needed, the droplets form what Young calls “a goody bag” of all the components that are necessary for these processes to occur.

***

"Until recently, Drummond worried that the idea of condensates as compartments was distracting researchers from thinking more broadly about what these structureless structures might be doing, though recently their focus has expanded. “There are many alternatives to the simplistic notion that this is all about encapsulating some biochemical reaction,” he says. For example, droplets might keep enzymes or other molecules out of the general cytoplasm so that they don’t undergo certain reactions, releasing them only when the cell needs them or when a process they might interrupt is completed.

"Much of the evidence for this and other functions of phase separation is circumstantial so far, because direct proof is tough to get. Researchers generally test how cellular processes work by perturbing them, but it’s hard to disrupt phase separation without also breaking up protein interactions that are closely associated with it, making it challenging to draw conclusions about cause and effect.

"Or, as Drummond’s own work suggests, some proteins may phase-separate in response to an environmental cue, such as temperature. In that scenario, a cell’s ability to detect the change might serve as a finely tuned sensor.

***

"Mittag and others agree that they have barely scratched the surface of how this new field might transform cell biology. “I think there’s no doubt that phase separation plays a very important role for cells,” she says. Researchers so far have identified at least 20 different types of phase-separated droplets, each consisting of different proteins and other molecules and emerging under different circumstances.

"Some condensates, like P granules, are long-standing characters in the cell, newly identified as products of phase separation. Others are just emerging. The diversity is not surprising, says Lee: Just like cell organelles that are bounded by membranes all have different functions, membraneless ones probably do too."

Comment: physical chemistry has come to biology, and it is not an easy fit.

Biological complexity: phase separation

by dhw, Monday, November 07, 2022, 12:41 (508 days ago) @ David Turell

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?

Thank you for this. It’s almost impossible for us large organisms to get our heads round the fact that this unit of life – so tiny that we can’t even see it with the naked eye - is itself an immensely complex community of interactive parts. There is no way the organization can be left to chance, and the author offers only one alternative: cells actively organizing themselves. And if they do this individually, they will also do it collectively in the cell communities that cooperate to form organs and organisms, as well as to make the changes that respond to new circumstances and result in new species. Human societies self-organize in the same way, and we would laugh at the idea that they run automatically (see “quorum sensing” below). Our communities are organized by their own intelligence, no matter what may have been the original source of that intelligence. And so if cells self-organize as we do, and their communities self-organize as our communities do, is it not logical to argue that their self-organization is run by their intelligence, just as ours is?

Quorum sensing: how it works in bacteria and viruses

DAVID: obviously both bacteria and viruses have receptors for these specific signaling molecules and built-in automatic responses to the levels involved.

As usual you shove in the word “automatic” but the process described above is the equivalent of describing all the physical processes by which we humans communicate and act once we have taken a mental decision on what to do. Yes, if I decide to talk to you, I will activate all kinds of chemicals and tissues and muscles and electrical impulses. But they are all the consequences of what is NOT automatic: namely the decision to talk to you. Bacteria and viruses must decide on the best course of action before they set in motion the physical processes that will implement their decisions.

Biological complexity: phase separation

by David Turell @, Monday, November 07, 2022, 18:05 (508 days ago) @ dhw

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?

dhw: Thank you for this. It’s almost impossible for us large organisms to get our heads round the fact that this unit of life – so tiny that we can’t even see it with the naked eye - is itself an immensely complex community of interactive parts. There is no way the organization can be left to chance, and the author offers only one alternative: cells actively organizing themselves. And if they do this individually, they will also do it collectively in the cell communities that cooperate to form organs and organisms, as well as to make the changes that respond to new circumstances and result in new species. Human societies self-organize in the same way, and we would laugh at the idea that they run automatically (see “quorum sensing” below). Our communities are organized by their own intelligence, no matter what may have been the original source of that intelligence. And so if cells self-organize as we do, and their communities self-organize as our communities do, is it not logical to argue that their self-organization is run by their intelligence, just as ours is?

It is also just as logical to see a designed arrangement running on instructions given by God is His designing efforts.


Quorum sensing: how it works in bacteria and viruses

DAVID: obviously both bacteria and viruses have receptors for these specific signaling molecules and built-in automatic responses to the levels involved.

dhw: As usual you shove in the word “automatic” but the process described above is the equivalent of describing all the physical processes by which we humans communicate and act once we have taken a mental decision on what to do. Yes, if I decide to talk to you, I will activate all kinds of chemicals and tissues and muscles and electrical impulses. But they are all the consequences of what is NOT automatic: namely the decision to talk to you. Bacteria and viruses must decide on the best course of action before they set in motion the physical processes that will implement their decisions.

As usual you elevate bacteria, viruses and single cells to the human thought level.

Biological complexity: phase separation

by dhw, Tuesday, November 08, 2022, 09:26 (507 days ago) @ David Turell

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?

dhw: Thank you for this. It’s almost impossible for us large organisms to get our heads round the fact that this unit of life – so tiny that we can’t even see it with the naked eye - is itself an immensely complex community of interactive parts. There is no way the organization can be left to chance, and the author offers only one alternative: cells actively organizing themselves. And if they do this individually, they will also do it collectively in the cell communities that cooperate to form organs and organisms, as well as to make the changes that respond to new circumstances and result in new species. Human societies self-organize in the same way, and we would laugh at the idea that they run automatically (see “quorum sensing” below). Our communities are organized by their own intelligence, no matter what may have been the original source of that intelligence. And so if cells self-organize as we do, and their communities self-organize as our communities do, is it not logical to argue that their self-organization is run by their intelligence, just as ours is?

DAVID: It is also just as logical to see a designed arrangement running on instructions given by God is His designing efforts.

On the surface, it may seem so, but the idea that 3.8 thousand million years ago your God supplied the first cells with instructions to be passed on for the creation of every new organ and organism and every decision for every new set of problems for every new combination of cells suddenly makes the theory a little less convincing for me, as does the theory that he is on hand all over the planet to provide organisms with the solutions to their problems of survival as and when the problems arise. Just imagine him spotting that poor old opossum in the depths of the forest and whispering in its ear: “Lie down and pretend you’re dead!”

Quorum sensing: how it works in bacteria and viruses

DAVID: obviously both bacteria and viruses have receptors for these specific signaling molecules and built-in automatic responses to the levels involved.

dhw: As usual you shove in the word “automatic” but the process described above is the equivalent of describing all the physical processes by which we humans communicate and act once we have taken a mental decision on what to do. Yes, if I decide to talk to you, I will activate all kinds of chemicals and tissues and muscles and electrical impulses. But they are all the consequences of what is NOT automatic: namely the decision to talk to you. Bacteria and viruses must decide on the best course of action before they set in motion the physical processes that will implement their decisions.

DAVID: As usual you elevate bacteria, viruses and single cells to the human thought level.

A silly exaggeration. Do you really think I’m arguing that bacteria, viruses and cells philosophize, design rockets to the moon, write novels and symphonies, and conduct forums discussing the existence of God and of cellular intelligence?

Biological complexity: phase separation

by David Turell @, Tuesday, November 08, 2022, 15:51 (507 days ago) @ dhw

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?

dhw: Thank you for this. It’s almost impossible for us large organisms to get our heads round the fact that this unit of life – so tiny that we can’t even see it with the naked eye - is itself an immensely complex community of interactive parts. There is no way the organization can be left to chance, and the author offers only one alternative: cells actively organizing themselves. And if they do this individually, they will also do it collectively in the cell communities that cooperate to form organs and organisms, as well as to make the changes that respond to new circumstances and result in new species. Human societies self-organize in the same way, and we would laugh at the idea that they run automatically (see “quorum sensing” below). Our communities are organized by their own intelligence, no matter what may have been the original source of that intelligence. And so if cells self-organize as we do, and their communities self-organize as our communities do, is it not logical to argue that their self-organization is run by their intelligence, just as ours is?

Of course, a science article cannot allow God to put His toe in. Those molecules somehow know exactly what to do in the soup


DAVID: It is also just as logical to see a designed arrangement running on instructions given by God is His designing efforts.

dhw: On the surface, it may seem so, but the idea that 3.8 thousand million years ago your God supplied the first cells with instructions to be passed on for the creation of every new organ and organism and every decision for every new set of problems for every new combination of cells suddenly makes the theory a little less convincing for me, as does the theory that he is on hand all over the planet to provide organisms with the solutions to their problems of survival as and when the problems arise. Just imagine him spotting that poor old opossum in the depths of the forest and whispering in its ear: “Lie down and pretend you’re dead!”

That is a brilliant opossum who was able to conceptualize the trick on his own.


Quorum sensing: how it works in bacteria and viruses

DAVID: obviously both bacteria and viruses have receptors for these specific signaling molecules and built-in automatic responses to the levels involved.

dhw: As usual you shove in the word “automatic” but the process described above is the equivalent of describing all the physical processes by which we humans communicate and act once we have taken a mental decision on what to do. Yes, if I decide to talk to you, I will activate all kinds of chemicals and tissues and muscles and electrical impulses. But they are all the consequences of what is NOT automatic: namely the decision to talk to you. Bacteria and viruses must decide on the best course of action before they set in motion the physical processes that will implement their decisions.

DAVID: As usual you elevate bacteria, viruses and single cells to the human thought level.

dhw: A silly exaggeration. Do you really think I’m arguing that bacteria, viruses and cells philosophize, design rockets to the moon, write novels and symphonies, and conduct forums discussing the existence of God and of cellular intelligence?

Thank you for finally recognizing the difference. They signal with molecules they are built to sense.

Biological complexity: phase separation

by dhw, Wednesday, November 09, 2022, 12:17 (506 days ago) @ David Turell

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?
[…]
DAVID: Of course, a science article cannot allow God to put His toe in. Those molecules somehow know exactly what to do in the soup.

Yes, they do. And I don’t know why a theist shouldn’t accept the possibility that his all-powerful God, who has endowed humans with the intelligence to organize their own forms of cooperation etc., might endow micro-organisms with the intelligence to organize THEIR forms of cooperation.

DAVID: It is also just as logical to see a designed arrangement running on instructions given by God is His designing efforts.

dhw: On the surface, it may seem so, but the idea that 3.8 thousand million years ago your God supplied the first cells with instructions to be passed on for the creation of every new organ and organism and every decision for every new set of problems for every new combination of cells suddenly makes the theory a little less convincing for me, as does the theory that he is on hand all over the planet to provide organisms with the solutions to their problems of survival as and when the problems arise. Just imagine him spotting that poor old opossum in the depths of the forest and whispering in its ear: “Lie down and pretend you’re dead!”

DAVID: That is a brilliant opossum who was able to conceptualize the trick on his own.

Two tiny tales for you:

One day, Pete Opossum spied a dead opossum in the distance. A predator approached the dead body, took one look, said “Yuk!” and walked away. The next day, Pete saw a predator before it saw him. There was no escape route. It meant certain death, unless...maybe you can guess the rest.

One day God, who has the whole world (even universe) to watch over, spotted Pete Opossum and a predator in the wilds of North America. As for some unknown reason Pete’s individual survival was crucial to God’s plan for all humans and their ecosystems, he whispered in fluent Opossumese: “Lie down, Pete, and pretend you’re dead.” And Pete did lie down, and thus he was saved.

I wonder which of these tales tickles your fancy.

Quorum sensing: how it works in bacteria and viruses

DAVID: obviously both bacteria and viruses have receptors for these specific signaling molecules and built-in automatic responses to the levels involved.

dhw: As usual you shove in the word “automatic” but the process described above is the equivalent of describing all the physical processes by which we humans communicate and act once we have taken a mental decision on what to do. Yes, if I decide to talk to you, I will activate all kinds of chemicals and tissues and muscles and electrical impulses. But they are all the consequences of what is NOT automatic: namely the decision to talk to you. Bacteria and viruses must decide on the best course of action before they set in motion the physical processes that will implement their decisions.

DAVID: As usual you elevate bacteria, viruses and single cells to the human thought level.

dhw: A silly exaggeration. Do you really think I’m arguing that bacteria, viruses and cells philosophize, design rockets to the moon, write novels and symphonies, and conduct forums discussing the existence of God and of cellular intelligence?

DAVID: Thank you for finally recognizing the difference. They signal with molecules they are built to sense.

“Finally”? When have I ever claimed that bacteria etc. were as intelligent as humans??? Back to the subject: bacteria signal, and they respond to signals, using the communication mechanisms at their disposal, just as we do. The question is how they decide on the correct interpretation of signals they receive, and how they decide on what messages to send. You only want to focus on the signalling and gloss over the whole process of decision-making.

Biological complexity: phase separation

by David Turell @, Wednesday, November 09, 2022, 21:37 (506 days ago) @ dhw

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?
[…]
DAVID: Of course, a science article cannot allow God to put His toe in. Those molecules somehow know exactly what to do in the soup.

dhw: Yes, they do. And I don’t know why a theist shouldn’t accept the possibility that his all-powerful God, who has endowed humans with the intelligence to organize their own forms of cooperation etc., might endow micro-organisms with the intelligence to organize THEIR forms of cooperation.

Evidence of intelligent actions takes us to their DNA and related factors, all of which
I think was coded by God.


dhw: Two tiny tales for you:

One day, Pete Opossum spied a dead opossum in the distance. A predator approached the dead body, took one look, said “Yuk!” and walked away. The next day, Pete saw a predator before it saw him. There was no escape route. It meant certain death, unless...maybe you can guess the rest.

One day God, who has the whole world (even universe) to watch over, spotted Pete Opossum and a predator in the wilds of North America. As for some unknown reason Pete’s individual survival was crucial to God’s plan for all humans and their ecosystems, he whispered in fluent Opossumese: “Lie down, Pete, and pretend you’re dead.” And Pete did lie down, and thus he was saved.

I wonder which of these tales tickles your fancy.

You are a great author!

Quorum sensing: how it works in bacteria and viruses

DAVID: As usual you elevate bacteria, viruses and single cells to the human thought level.

dhw: A silly exaggeration. Do you really think I’m arguing that bacteria, viruses and cells philosophize, design rockets to the moon, write novels and symphonies, and conduct forums discussing the existence of God and of cellular intelligence?

DAVID: Thank you for finally recognizing the difference. They signal with molecules they are built to sense.

dhw: “Finally”? When have I ever claimed that bacteria etc. were as intelligent as humans??? Back to the subject: bacteria signal, and they respond to signals, using the communication mechanisms at their disposal, just as we do. The question is how they decide on the correct interpretation of signals they receive, and how they decide on what messages to send. You only want to focus on the signalling and gloss over the whole process of decision-making.

All of the responses are controlled by fully coded signals.

Biological complexity: phase separation

by dhw, Thursday, November 10, 2022, 12:22 (505 days ago) @ David Turell

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?
[…]
DAVID: Of course, a science article cannot allow God to put His toe in. Those molecules somehow know exactly what to do in the soup.

dhw: Yes, they do. And I don’t know why a theist shouldn’t accept the possibility that his all-powerful God, who has endowed humans with the intelligence to organize their own forms of cooperation etc., might endow micro-organisms with the intelligence to organize THEIR forms of cooperation.

DAVID: Evidence of intelligent actions takes us to their DNA and related factors, all of which I think was coded by God.

I’m not sure whether “coded” means that 3.8 billion years ago your God gave precise instructions for every form of cooperation, or that he pops in to change the code whenever it’s necessary, or that he gave organisms the ability to design their own ways to cooperate. Perhaps you could be a little more precise?

dhw: Two tiny tales for you:
One day, Pete Opossum spied a dead opossum in the distance. A predator approached the dead body, took one look, said “Yuk!” and walked away. The next day, Pete saw a predator before it saw him. There was no escape route. It meant certain death, unless...maybe you can guess the rest.
One day God, who has the whole world (even universe) to watch over, spotted Pete Opossum and a predator in the wilds of North America. As for some unknown reason Pete’s individual survival was crucial to God’s plan for all humans and their ecosystems, he whispered in fluent Opossumese: “Lie down, Pete, and pretend you’re dead.” And Pete did lie down, and thus he was saved.
I wonder which of these tales tickles your fancy.

DAVID: You are a great author!

Thank you. Which of the two tales do you think is more likely?

Quorum sensing: how it works in bacteria and viruses

No further comment needed.

Biological complexity: phase separation

by David Turell @, Thursday, November 10, 2022, 17:25 (505 days ago) @ dhw

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?
[…]
DAVID: Of course, a science article cannot allow God to put His toe in. Those molecules somehow know exactly what to do in the soup.

dhw: Yes, they do. And I don’t know why a theist shouldn’t accept the possibility that his all-powerful God, who has endowed humans with the intelligence to organize their own forms of cooperation etc., might endow micro-organisms with the intelligence to organize THEIR forms of cooperation.

DAVID: Evidence of intelligent actions takes us to their DNA and related factors, all of which I think was coded by God.

dhw: I’m not sure whether “coded” means that 3.8 billion years ago your God gave precise instructions for every form of cooperation, or that he pops in to change the code whenever it’s necessary, or that he gave organisms the ability to design their own ways to cooperate. Perhaps you could be a little more precise?

I wish I could be precise. God doesn't tell me how to think. I believe God puts all the information into DNA and other levels of the genome when He evolved them. There had to be specific information from Dod when God started life and when He evolved new steps. I cannot know how much information started life, but it was obviously huge, with smaller amounts needed with further steps. Precise enough?


dhw: Two tiny tales for you:
One day, Pete Opossum spied a dead opossum in the distance. A predator approached the dead body, took one look, said “Yuk!” and walked away. The next day, Pete saw a predator before it saw him. There was no escape route. It meant certain death, unless...maybe you can guess the rest.
One day God, who has the whole world (even universe) to watch over, spotted Pete Opossum and a predator in the wilds of North America. As for some unknown reason Pete’s individual survival was crucial to God’s plan for all humans and their ecosystems, he whispered in fluent Opossumese: “Lie down, Pete, and pretend you’re dead.” And Pete did lie down, and thus he was saved.
I wonder which of these tales tickles your fancy.

DAVID: You are a great author!

dhw: Thank you. Which of the two tales do you think is more likely?

Second one but it wasn't whispering but information in opossum's DNA from God.

Biological complexity: phase separation

by dhw, Friday, November 11, 2022, 12:35 (504 days ago) @ David Turell

QUOTE: How do the right proteins organize themselves in a sea of fluid swarming with millions of molecules? Do they bump into each other by chance, or does the cell actively organize its fluid space to bring the correct partners together?
[…]
DAVID: Of course, a science article cannot allow God to put His toe in. Those molecules somehow know exactly what to do in the soup.

dhw: Yes, they do. And I don’t know why a theist shouldn’t accept the possibility that his all-powerful God, who has endowed humans with the intelligence to organize their own forms of cooperation etc., might endow micro-organisms with the intelligence to organize THEIR forms of cooperation.

DAVID: Evidence of intelligent actions takes us to their DNA and related factors, all of which I think was coded by God.

dhw: I’m not sure whether “coded” means that 3.8 billion years ago your God gave precise instructions for every form of cooperation, or that he pops in to change the code whenever it’s necessary, or that he gave organisms the ability to design their own ways to cooperate. Perhaps you could be a little more precise?

DAVID: I wish I could be precise. God doesn't tell me how to think. I believe God puts all the information into DNA and other levels of the genome when He evolved them. There had to be specific information from Dod when God started life and when He evolved new steps. I cannot know how much information started life, but it was obviously huge, with smaller amounts needed with further steps. Precise enough?

I think so. It would mean basic powers such as reproduction and flexibility were there from the start, but your God dabbled to create every innovation, lifestyle, strategy, natural wonder etc., including all those that had nothing to do with his one and only purpose.

dhw: Two tiny tales for you:
One day, Pete Opossum spied a dead opossum in the distance. A predator approached the dead body, took one look, said “Yuk!” and walked away. The next day, Pete saw a predator before it saw him. There was no escape route. It meant certain death, unless...maybe you can guess the rest.
One day God, who has the whole world (even universe) to watch over, spotted Pete Opossum and a predator in the wilds of North America. As for some unknown reason Pete’s individual survival was crucial to God’s plan for all humans and their ecosystems, he whispered in fluent Opossumese: “Lie down, Pete, and pretend you’re dead.” And Pete did lie down, and thus he was saved.
I wonder which of these tales tickles your fancy.

DAVID: You are a great author!

dhw: Thank you. Which of the two tales do you think is more likely?

DAVID: Second one but it wasn't whispering but information in opossum's DNA from God.

So in keeping with your comment above, 3.8 billion years ago your God planted information in the DNA of the very first cells, not only for the design of the opossum, but also for its play-dead strategy. Alternatively, when he dabbled to design our friend Pete, he included an automatic play-dead programme to switch itself on when needed. Or he spotted Pete in trouble, and popped in to plant the play-dead “information” in his DNA. (A whisper would surely have been quicker and simpler than that! :-) ) . Nah, come on. What’s so unbelievable about the first tale?

Biological complexity: phase separation

by David Turell @, Friday, November 11, 2022, 16:33 (504 days ago) @ dhw

dhw: I’m not sure whether “coded” means that 3.8 billion years ago your God gave precise instructions for every form of cooperation, or that he pops in to change the code whenever it’s necessary, or that he gave organisms the ability to design their own ways to cooperate. Perhaps you could be a little more precise?

DAVID: I wish I could be precise. God doesn't tell me how to think. I believe God puts all the information into DNA and other levels of the genome when He evolved them. There had to be specific information from Dod when God started life and when He evolved new steps. I cannot know how much information started life, but it was obviously huge, with smaller amounts needed with further steps. Precise enough?

dhw: I think so. It would mean basic powers such as reproduction and flexibility were there from the start, but your God dabbled to create every innovation, lifestyle, strategy, natural wonder etc., including all those that had nothing to do with his one and only purpose.

We can just continue to guess about how God did it.


dhw: Two tiny tales for you:
One day, Pete Opossum spied a dead opossum in the distance. A predator approached the dead body, took one look, said “Yuk!” and walked away. The next day, Pete saw a predator before it saw him. There was no escape route. It meant certain death, unless...maybe you can guess the rest.
One day God, who has the whole world (even universe) to watch over, spotted Pete Opossum and a predator in the wilds of North America. As for some unknown reason Pete’s individual survival was crucial to God’s plan for all humans and their ecosystems, he whispered in fluent Opossumese: “Lie down, Pete, and pretend you’re dead.” And Pete did lie down, and thus he was saved.
I wonder which of these tales tickles your fancy.

DAVID: You are a great author!

dhw: Thank you. Which of the two tales do you think is more likely?

DAVID: Second one but it wasn't whispering but information in opossum's DNA from God.

dhw: So in keeping with your comment above, 3.8 billion years ago your God planted information in the DNA of the very first cells, not only for the design of the opossum, but also for its play-dead strategy. Alternatively, when he dabbled to design our friend Pete, he included an automatic play-dead programme to switch itself on when needed. Or he spotted Pete in trouble, and popped in to plant the play-dead “information” in his DNA. (A whisper would surely have been quicker and simpler than that! :-) ) . Nah, come on. What’s so unbelievable about the first tale?

The conceptualization in the first tale assumes Pete's brain can work at that advanced level.
No way.

Biological complexity: horseshoe crab eye lens

by David Turell @, Monday, November 21, 2022, 17:47 (494 days ago) @ David Turell

Carefully analyzed:

https://phys.org/news/2022-11-scales-scientists-horseshoe-crab-cuticle.html

"The primitive compound eyes of a horseshoe crab are one the largest to be found in nature. In contrast to many insects and spiders that build their eyes from glassy proteins, the horseshoe crab uses cuticle, the same material that builds its skin and legs.

***

"The compound eyes of the horseshoe crab are primitive in comparison to other arthropods, like dragonflies or shrimp. Instead of using the typical glassy proteins to build the lens, the horseshoe crab repurposes the material that builds its exoskeleton—the cuticle. "The arthropod cuticle is a composite material consisting of proteins and a crystalline polymer known as chitin. It is the characteristic component of insects, spiders, and other arthropods who use it to build their skin and legs, the so-called exoskeleton," says Prof. Politi.

***

"The researchers looked both at the global organization of the cuticle layers, as well as the ratio of the individual components, the water content, and the elemental composition of the material. As a result, they found a variety of adaptations that together allow the cuticle to become an excellent optical element.

***

"Taken together, the team found not one but a host of adaptations at all levels that allow the horseshoe crab to use cuticle for optical elements. "Everything from the local composition of the cuticle, in particular the addition of Bromine, to multiple changes in the architecture of the composite, i.e., the ratio between its components, organization of the proteins, the varying water content, and the overall shape of the lens… It all contributes to making cuticle into a material with excellent optical properties," says Prof. Politi. (my bold)

"'What surprised us, in the end, the most was that the cuticle lenses seem to work so well that the animal needed to introduce pigments to actually reduce the amount of light that is collected by the lens," adds Prof. Politi."

Comment: the bolded statement demonstrates this is an irreducibly complex development that requires design.

Biological complexity: cells move by electric charges

by David Turell @, Thursday, December 08, 2022, 20:28 (477 days ago) @ David Turell

Studying the cell's insides:

https://phys.org/news/2022-12-cell-electrical-side-membrane-scientists.html

"Scientists at Johns Hopkins Medicine say that a key to cellular movement is to regulate the electrical charge on the interior side of the cell membrane, potentially paving the way for understanding cancer, immune cell and other types of cell motion.

"Their experiments in immune cells and amoeba show that an abundance of negative charges lining the interior surface of the membrane can activate pathways of lipids, enzymes and other proteins responsible for nudging a cell in a certain direction.

***


'Banerjee had a hunch that a general biophysical property, such as electrical charge, rather than a specific molecule, could be stimulating and organizing the activities of enzymes and other proteins related to cell movement.

***

"'Our cells are moving within our body more than we imagine," says Peter Devreotes, Ph.D., the Isaac Morris and Lucille Elizabeth Hay Professor and Distinguished Service Professor in the Department of Cell Biology at the Johns Hopkins University School of Medicine. "Cells move to perform many functions, including when they engulf nutrients or when they divide."

"Many of the molecules involved in cell movement become activated in the leading edge of the cell, or where it forms a kind of foot, or protrusion, that orients the cell in a particular direction.

***

"They found that when and where the cells formed protrusions, there was a corresponding reduction of negative electrical charge along the inner membrane. Alternatively, along the cells' resting membrane surface, the electrical charge increased, which contributes in recruiting more positively charged proteins.

***

"'The negative surface charge seems to be sufficient and necessary to activate a cascade of biomolecular reactions that have been linked to cell movement," says Banerjee.

***

"Next, the scientists are planning to study precisely how and when the electrical charges are reduced along the inner membrane in response to external cues and how, exactly, the negative charges connect with the complicated protein and lipid signaling networks that prompt cell movement and other associated physiological processes."

Comment: it appears that these are automatic processes to more toward a stimulus.

Biological complexity: actin fibers discovery and unknowns

by David Turell @, Saturday, June 10, 2023, 17:22 (293 days ago) @ David Turell

New discoveries of design for specific functions:

https://www.sciencedaily.com/releases/2023/06/230608120933.htm

"Now, researchers from the Perelman School of Medicine at the University of Pennsylvania have revealed key atomic structures of the ends of the actin filament through the use of a technique called cryo-electron microscopy (cryo-EM).

***

"Actin is the most abundant protein inside the cells of higher organisms, such as animals. It serves as the building-block for long, thin structures called filaments, which provide key structural support as part of the cell "cytoskeleton," the system that gives cells their shape and polarity. Rapid changes in actin filaments underlie key cellular events such as movement along surfaces, cell-to-cell contact, and cell division. Actin filaments also are major elements in muscle fibers.

"'The results of our study provide a mechanistic understanding of a process we have known about for more than 40 years, referred to as filament treadmilling, and impacts how we view the cellular roles of actin in health and disease," said the study senior author Roberto Dominguez, PhD, the William Maul Measey Presidential Professor of Physiology at Penn.

"The dynamics of actin filaments are governed largely by the "treadmilling" process, through which individual actin proteins are shed from one filament end, known as the pointed end, and added at the other, barbed end. Actin filaments can be stabilized by distinct so-called "capping" proteins that bind to the filament ends to stop further addition or loss of individual actin proteins. Many other proteins also bind to the barbed and pointed ends of the actin filament. But the structural details determining the specificity of these interactions -- the details that explain why these two ends function so differently -- have been murky.

***

"With artificial intelligence (AI) assistance, the researchers were able to focus on the ends of the filaments instead of their middle, as had previously been the norm in similar research. By doing so, they identified hundreds of thousands of filament end views, allowing them to obtain near-atomic scale reconstructions. These revealed a "flat" actin shape, or conformation, at the uncapped barbed end, versus a "twisted" conformation at the uncapped pointed end.

"The data also detailed the structural changes induced by two actin filament-capping proteins, CapZ at the barbed end and tropomodulin at the pointed end. These are the two proteins found at the ends of the filament in skeletal and cardiac muscles, playing an essential role in the stabilization of actin filaments in muscle fibers, and, without these proteins, our muscles would fall apart."

Comment: more irreducible complexity requiring design.

Biological complexity: photosynthesis controls

by David Turell @, Wednesday, December 21, 2022, 21:45 (464 days ago) @ David Turell

More parts unearthed:

https://phys.org/news/2022-12-decoding-secret-language-photosynthesis.html

"For half a century botanists have known that the command center of a plant cell, the nucleus, sends instructions to other parts of the cell, compelling them to move forward with photosynthesis. These instructions come in the form of proteins, and without them, plants won't turn green or grow.

"'Our challenge was that the nucleus encodes hundreds of proteins containing building blocks for the smaller organelles. Determining which ones are the signal to them to trigger photosynthesis was like finding needles in a haystack," said UCR botany professor Meng Chen.

***


"'The conductors of the symphony are proteins in the nucleus called photoreceptors that respond to light. We showed in this paper that both red and blue light-sensitive photoreceptors initiate the symphony. They activate genes that encode the building blocks of photosynthesis."

"The unique situation, in this case, is that the symphony is performed in two "rooms" in the cell, by both local (nucleus) and remote musicians. As such, the conductors (photoreceptors), who are present only in the nucleus, must send the remotely located musicians some messages over distance. This last step is controlled by the four newly discovered proteins that travel from the nucleus to the chloroplasts.

***

"Currently, a lot of research describes communication from organelles back to the nucleus. If something is wrong with the organelles, they'll send signals to the nucleus "headquarters." Much less is known about the activity-regulating signals sent from the nucleus to the organelles.

"'The nucleus may control the expression of mitochondrial and chloroplast genes in a similar fashion," said Chen. "So, the principles we learn from the nucleus-to-chloroplast communication pathway might further our understanding of how the nucleus regulates mitochondrial genes, and their dysfunction in cancer," Chen said."

Comment: this is another example of a system that must appear all at once to function. It is irreducible complex and must be designed in toto.

Biological complexity: control of aging

by David Turell @, Wednesday, December 28, 2022, 18:03 (457 days ago) @ David Turell

Complex molecular mechanisms with controlled autophagy:

https://phys.org/news/2022-12-scientists-uncover-cellular-mechanism-aging.html

"Research at the Institute of Molecular Biology and Biotechnology (IMBB) of the Foundation for Research and Technology-Hellas (FORTH), published today in the journal Nature Aging, reveals a fundamental quality control mechanism that operates in cells to safeguard the integrity and function of the nucleus. By maintaining nuclear homeostasis, this molecular mechanism contributes critically to promote longevity and fertility.

"IMBB researchers ... discovered that recycling of nuclear and nucleolar components via autophagy delays aging of somatic cells, and sustains the immortality of germ cells, which are required for reproduction.

***

"'We decided to focus on nuclear morphology in somatic cells, which deteriorates during aging. By contrast, the overall architecture of the nucleus is preserved in the germline. Our hypothesis was that a homeostatic mechanism effectively maintains the structure of germ cell nuclei, whereas it fails during aging, in the soma. We were surprised to find that autophagic recycling of nuclear material is an important factor, that preserves nuclear architecture and restricts nucleolar size. Interestingly, nucleophagy interfaces with nodal, pro-longevity signal transduction pathways, highlighting the complex crosstalk of the molecular mechanisms that influence aging,"

"The new study uncovers nucleophagy as a molecular mechanism by which diverse physiological signals are integrated to impact nuclear architecture and homeostasis. Furthermore, it identifies nucleophagy as a downstream effector of low insulin/IGF1 signaling and dietary restriction on somatic aging. Nesprin family members serve as key regulators of nucleophagy. Impairment of nuclear material recycling via nucleophagy diminishes stress resistance, undermines animal longevity and triggers progressive germline mortality.

"Therefore, nucleophagy is an essential soma longevity and germline immortality mechanism that promotes youthfulness and delays aging under conditions of stress, by preserving nuclear architecture and preventing nucleolar expansion. The tight evolutionary conservation and ubiquitous expression of the regulatory factors involved, indicate that similar pathways may govern aging in humans."

Comment: we see various aging patterns in animals from a few weeks in butterflies to 100 years in giant tortoises. Since all living forms eventually die, this is the complex control mechanism. Aging had to be designed from the beginning/origin of each form. How do you evolve an average time of death?

Biological complexity: cellular cleanup

by David Turell @, Wednesday, February 08, 2023, 19:29 (415 days ago) @ David Turell

Regular garbage disposal:

https://phys.org/news/2023-02-cells-routinely-self-cannibalize-trash-aiding.html

"Since routine cellular activity generates toxic byproducts that can damage the cell, a disposal system is needed to degrade and recycle these molecules within cells. One of these processes is autophagy, a form of self-consumption cells use to eliminate and recycle abnormal or excess components, including proteins and organelles. Derived from Greek, the term literally translates to "self-eating." In 2016, cell biologist Yoshinori Ohsumi won the Nobel Prize in Physiology or Medicine for his work on autophagy. Autophagy is essential for cellular health and longevity. When this process is not working well, it's linked to several human diseases, including neurodegenerative and cardiovascular diseases and cancer.

***

"...autophagy appears to play a paradoxical role in cancer. On one hand, some studies have shown that because this process suppresses tumors by eliminating potentially harmful material, reduced or impaired autophagy can turn a cell cancerous. On the other hand, activating autophagy after a tumor has formed can promote cancer by helping it adapt and survive, potentially leading to treatment resistance.

***

"Dysfunctional autophagy also plays an important role in most neurodegenerative diseases. The aggregation of abnormal proteins in brain cells are common features in Alzheimer's disease, Parkinson's disease, Huntington's disease and ALS. Some scientists believe that the accumulation of these proteins is due at least in part to a decline in their degradation through autophagy.

"Autophagy is also important for heart health. Researchers have found that autophagy in the heart declines with age and contributes to cardiovascular disease. Decreased autophagy in cardiac muscle cells results in accumulating cellular garbage that can affect their ability to contract and even cause their death. With fewer cells and less contraction, the buildup of toxic material in cardiac muscle cells can ultimately lead to heart failure.

"For autophagy to be efficient, it needs to specifically get rid of only damaged proteins or organelles within the cell. Uncontrolled degradation would deprive a cell of its basic needs.

"This is particularly true for mitochondria, as cells rely on them for much of their energy production. Our team has been very interested in how cells ensure that autophagy of mitochondria, also known as mitophagy, eliminates only dysfunctional mitochondria while sparing the healthy parts of the cell. Dysfunctional mitophagy has been linked to cancer, neurodegeneration and cardiovascular disease, among other diseases.

"The process of autophagy starts when the cell begins to form a membrane near damaged proteins or organelles. This membrane will expand into a vesicle, or sac, known as an autophagosome, that engulfs the damaged material. It will then fuse with another internal cell structure full of acid called a lysosome that helps degrade its cargo.

"Beclin1 is a protein known to promote the formation of autophagosomes in cells. However, its role in mitophagy is controversial, in part because very little is known about its close relative Beclin2. We wanted to disentangle the functions of these two proteins and determine their role in mitophagy. To do this, we used mouse and human cell models to examine how the presence or absence of these two proteins affected autophagy.

"We discovered that activating a region unique to Beclin1 enables it to promote autophagosome formation next to dysfunctional mitochondria, facilitating their degradation in human cells. Because a similar region isn't found in Beclin2, this meant that only Beclin1 may be essential for mitophagy.

"Interestingly, we also observed Beclin1 at discrete points of contact between mitochondria and endoplasmic reticulum during mitophagy. This supports emerging research suggesting that physical interactions between these organelles facilitate the transfer of certain molecules needed to make autophagosomes. Our work indicates that only Beclin1 promotes engulfment of damaged mitochondria at these sites. Beclin2 may perform a different role in autophagy in other conditions."

Comment: another mechanism that had to be designed in toto when first cells appeared. If the cells couldn't clean up hey would not have survived. Irreducible complexity.
=

Biological complexity: programmed cell death

by David Turell @, Thursday, February 16, 2023, 21:13 (407 days ago) @ David Turell

Several kinds:

https://www.the-scientist.com/sponsored-article/programmed-cell-death-mechanisms-for-ce...

"Over the years, researchers have described many forms of PCD. This summary provides a brief overview of three types—apoptosis, pyroptosis, and necroptosis–and their importance in health and disease.

"In general, PCD can be either lytic or non-lytic. During lytic cell death, the contents of a dying cell are released into the surrounding space as the cell’s membrane becomes damaged. In contrast, non-lytic cell death secludes the cellular remains in multiple apoptotic bodies before they are discarded.

"Apoptosis is a form of non-lytic PCD that involves condensation of the nucleus and cytoplasm, chromosomal cleavage, and plasma membrane blebbing.

***

"Intrinsic apoptosis occurs when a cell is damaged on the inside or is facing a stressful internal condition, such as DNA damage or nutrient deprivation. These conditions cause the mitochondrial outer membrane to permeabilize and release cytochrome C.1 Cytochrome C helps apoptotic protease-activating factor 1 (APAF-1) proteins assemble into a larger unit in the cytoplasm. APAF-1 is key during apoptosis because it contains a caspase recruitment domain (CARD), which activates protease enzymes called caspases that cleave proteins.

"Unlike intrinsic apoptosis, extrinsic apoptosis is triggered by a signal outside of the cell and requires membrane-spanning proteins called death receptors. The external signal, or death ligand, can come from another cell or environmental response. Activation of death receptors by death ligands such as Fas, tumor necrosis factor (TNF), or TNF-related apoptosis-inducing ligand (TRAIL), recruits two proteins to form a death-inducing signaling complex (DISC), which activates a different set of caspases from intrinsic apoptosis.

*** several rare mechanisms skipped for brevity

"Autophagy is often used by cells as a survival mechanism to protect itself from nutrient deprivation, oxidative stress, endoplasmic reticulum stress, etc.11 Here, the cytoplasm is sequestered and packaged for degradation by the lysosome, rather than being release into the extracellular space. In many cases, the material that is degraded by the lysosome can be recycled and used again as starting materials, such as amino acids for protein synthesis or carbohydrates for energy production."

Comment: obviously cells constantly develop damage or garbage. The body is in constant cleanup mode. These different mechanisms are highly complex and must have been present as cells appeared. That puts it in the realm of irradicably complex requiring design.

Biological complexity: the extracellular matrix

by David Turell @, Friday, February 17, 2023, 20:10 (406 days ago) @ David Turell

It has complex functions has direct connection with the immune system cellular activities:

https://www.sciencemagazinedigital.org/sciencemagazine/library/item/17_february_2023/40...

'The extracellular matrix (ECM) forms a dynamic structure around cells that is essential for the supply of environmental factors, mechanical support, and protection of tissues. It includes components such as fibrillar proteins, glycosaminoglycans (GAGs), proteoglycans, and mucus. The molecular, physical, and mechanical properties of the ECM regulate immune cell mobility, survival, and function. In turn, the immune system maintains and regulates healthy matrix and restores matrix integrity after injury.

***

"One function of the ECMis to guide immune cell movement and positioning. T cells, for example, move through sites containing thin ECM fibers in preference to more densely cross-linked collagen matrices, whereas heparan sulfate proteoglycans within the vasculature and tissue parenchyma bind and present chemokines to form gradients that direct cell movement. During inflammation, injury, infection, or even aging, ECM components can be released to act as “danger signals.” Conversely, the breakdown of the ECM by matrix-degrading enzymes can generate immunoregulatory fragments. Critically, because cytokines are often bound to GAGs, ECM changes can regulate cytokine availability or activity.

***

"There is increasing evidence that immune cell function is regulated by mechano-sensing receptors such as Piezo1, and these ECM changes have major impacts on immune function. Furthermore, a decline in the activity of the mechanosensing transcriptional activators YAP and TAZ during physiological aging results in failure to down-regulate inflammation. Thus, ECM composition actively regulates immune processes, but immune signals will themselves regulate ECM composition, reflecting an essential bidirectional dialog.

***

"One prominent way that the immune system regulates the ECM is through transforming growth factor–b (TGF-b), which promotes myofibroblast differentiation and collagen production and inhibits matrix-degrading metalloproteinases. Furthermore, type 2 cytokines, particularly interleukin-13 (IL-13), have emerged as modulators of ECM quantity and quality, which includes regulating the mucosal barrier. Moreover, direct biophysical interaction with chemokines or cytokines can alter ECM structure and/or function. For instance, CXCL4 (PF4) functions by binding to GAGs rather than by directly binding to chemokine receptors. This can lead to remodeling of the cell surface ECM and signaling through proteoglycans.

"Immune cells control ECM not only through the production of cytokines and chemokines but also by direct synthesis of ECM components and the enzymes that break them down. Enzymatic remodeling of the rigid basement membrane by tissue-infiltrating myeloid cells, for example, can provide routes for lymphocytes to follow. Macrophages, which are pivotal in ECM turnover through receptor-mediated uptake of and degradation of collagen, also produce collagens that may provide templates for tissue remodeling. Neutrophils can pull and carry preexisting matrix from nearby sites to wound beds early in the tissue repair process to reestablish new ECM scaffolds."

Comment: the interlocking activities of cells and the immune system through the extracellular matri x beyond mind boggling. The regulatory complexity will be picked apart bit by bit, but it serves to show us that chance can't create the interlocking system of controls. Such a system must be designed all at once to end up properly coordinated in all its various functions. Irreducible complexity once again.

Biological complexity: ATP molecular machines seen clearly

by David Turell @, Friday, March 10, 2023, 20:58 (385 days ago) @ David Turell

The molecules act in more precise and amazing ways than previously imagined:

https://www.sciencedaily.com/releases/2023/03/230309101344.htm

"F-Type ATP synthase, a catalytic complex of proteins, synthesizes adenosine triphosphate (ATP), the energy currency of living cells. A lot of ambiguity exists over the rotational mechanism of this spinning enzyme. Now, researchers from Japan have demonstrated how each chemical event of ATP metabolism is linked to the 'stepwise' rotational movement of the F1 component of ATPase. Especially, they clarified the angle of shaft rotation before ATP-cleavage, a long-standing enigma, to be 200°.

***

"Previous investigations of the F1 subunits of Bacillus PS3 have established that ATP cleavage involves chemomechanical coupling, i.e., each rotational stepping motion is linked to a chemical reaction step. The angle of rotation between ATP binding and its cleavage at the same catalytic site has been previously estimated to be 200°. However, experimental evidence to substantiate this has so far been lacking. To address this, the researchers studied the rotation by creating a hybrid F1 using one mutant β and two wild type βs. Since the rate of both ATP cleavage and ATP binding was extremely slow in the mutant, the researchers could observe the pauses or dwells between rotational steps easily.

***

"With this study, the authors have resolved a long-term debate over the ATP-cleavage shaft angle and established the chemomechanical correlation of ATPase function. Talking about the future impacts of their novel study, Associate Prof. Masaike elaborates, "Since F1-ATPase is the world's smallest biological rotational motor protein, it can be used as a reference to understand the mechanism of energy transduction in living organisms. This knowledge can be revolutionary in developing efficient nanomachines. Moreover, ATP synthase from Mycobacterium tuberculosis has recently been identified as a potential target for drug discovery. Therefore, to stop its rotation using inhibitors, understanding the mechanism of rotation is quite important."

Comment: this is irreducibly complex and had to be developed intact all at once. Chance is an impossible event.

Biological complexity: an enzyme controls cellular stress

by David Turell @, Saturday, March 11, 2023, 20:33 (384 days ago) @ David Turell

Latest research:

https://phys.org/news/2023-03-enzyme-ate1-plays-role-cellular.html

"...Aaron T. Smith and colleagues discovered that this enzyme plays an important role in the cellular stress response.

"The enzyme is named ATE1, and it belongs to a family of enzymes called arginyl-tRNA transferases. These enzymes add arginine (an amino acid) to proteins, which often flags the proteins for destruction in the cell. Destroying proteins that are misfolded, often as a result of cellular stress, is important to prevent those proteins from wreaking havoc with cellular function. An accumulation of malfunctioning proteins can cause serious problems in the body, leading to diseases like Alzheimer's or cancer, so being able to get rid of these proteins efficiently is key to long-term health.

"The new paper demonstrates that ATE1 binds to clusters of iron and sulfur ions, and that the enzyme's activity increases two- to three-fold when it is bound to one of these iron-sulfur clusters. What's more, when the researchers blocked cells' ability to produce the clusters, ATE1 activity decreased dramatically. They also found that ATE1 is highly sensitive to oxygen, which they believe relates to its role in moderating the cell's stress response through a process known as oxidative stress.

***

"Around the same time, another group also published a slightly different ATE1 structure. The other group's structure had a zinc ion (another metal) bound in place of the iron-sulfur cluster. With the zinc in place, one key amino acid is rotated about 60 degrees. It might seem inconsequential, but Smith believes that rotation, which he presumes is similar with the cluster, is the key to the cluster's role in ATE1's function.

"The rotated amino acid is directly adjacent to where a protein would interact with ATE1 to be modified, ultimately flagging it for degradation. Changing the angle of that amino acid changes the shape of the location the protein would bind "very subtly," but changes its activity "more than subtly," Smith says."

Comment: another example of a complex enzyme doing its job. At issue is the usual question. How did this happen? Enzymes like this are giant molecules with very specific structure made from many thousands of amino acids. Not by chance. Must be designed for its job.

Biological complexity: how bacterial flagella operate

by David Turell @, Sunday, March 12, 2023, 17:29 (383 days ago) @ David Turell

At the molecular level:

https://inference-review.com/article/bacterial-swimming

"Negative-stain electron microscopy studies of the flagellar motor revealed that the machine is made up of a long filament, connected through a flexible hook to a basal body embedded in the bacterial cell envelope and comprising several rings. The cell envelope in Escherichia coli (E. coli) consists of an inner membrane and an outer membrane separated by a peptidoglycan layer. The energy for the rotation of the flagellum comes from dispersion of a proton motive force.

"E. coli has several flagella on its cell body. When these spin counterclockwise, they come together to form a bundle; the cell moves forward powered by the bundle’s in-unison rotation. If the cell encounters an unfavorable environment, chemical signals cause some of the flagella to rotate in the opposite direction. The bundle falls apart; the cell moves erratically or tumbles. Once the flagella recover and resume counterclockwise motion, the bundle forms again and the cell once more swims straight, but this time, on average, in a different direction. As tumbling is more likely under unfavorable conditions, E. coli can swim away from molecules it dislikes and toward those it likes.

"the power to drive the rotation of the flagellum is derived from the motility proteins, MotA and MotB. Further studies indicated that MotA and MotB form a stator unit with proton channel activity. It is the passage of protons down an electrochemical proton gradient and through the MotAB complex that acts as an energy source. Freeze-fracture electron microscopy studies showed that stator units surround the basal bodies in the inner membrane.5 A model emerged in which stator units, which remain anchored to the rigid peptidoglycan wall of the cell, engage with the cytoplasmic portion of the basal body, or rotor, to power the rotation of the flagellum.

***

" the C-ring, named for its position in the cytoplasmic portion of the basal body, can change its conformation upon binding the phosphorylated chemotaxis-signaling molecule CheY. One of the components of the C-ring, FliG, was shown to have two conformations involving an approximately 180° flip of a torque helix, which, in turn, was thought to interact with the MotAB complex.

***

"...the stator unit is a complex with a stoichiometry of 5:2 MotA:MotB, and not 4:2 as previously believed.16 This ratio introduces an asymmetry, as 4:2 stoichiometry would most likely have been symmetric. MotA has four helices spanning the inner membrane and a cytoplasmic domain. The part of this domain most distal from the membrane is well conserved and binds the rotor. The five MotA molecules make a nearly symmetric, ringlike structure surrounding the N-terminal helices of two MotB molecules, which contain a universally conserved aspartate residue. Each of the MotB N-terminal helices is followed by a plug helix that lies between two MotA molecules. The two plugs cross over and are thought, based on prior experiments, to block activity of the stator unit. As expected, the channel appears in closed conformation.

***

"This puzzling result can be explained if it is the rotation of MotA around MotB that drives the rotation of the motor. We proposed that one of the two MotB aspartates—call it MotB1—is protonated and anchored to MotA. This is a high-energy state for MotB1, which would drive MotA rotation were it not for the aspartate of MotB2. This aspartate is both negatively charged and unprotonated: the neutral surface of MotA cannot rotate across it. But when MotB2 accepts a proton from the periplasm, it is neutralized, and rotation of the hydrophobic MotA surface across the neutralized MotB2 aspartate can now occur. After rotation, MotB2 grabs on to MotA in this new position, and MotB1 releases its proton. MotB1 then waits at the cytoplasmic side to pick up a new proton. After these steps, a 36º rotation of the MotA ring around the MotB dimer has occurred.

***

"How does this miniature MotAB rotary motor power the rotation of a large flagellum? Upon incorporation in the motor, the C-terminal domains of MotB dimerize and bind to the peptidoglycan layer that forms part of the cell envelope. Peptidoglycan binding is accompanied by the unplugging of the MotAB ion channel, which allows ions to flow from the periplasm to the cytoplasm. Upon ion flow, MotA rotates clockwise around MotB. Given normal swimming conditions, the rotor is engaged at the proximal side of the MotA ring, and the clockwise rotation of MotA rotates the rotor counterclockwise. When all flagella spin counterclockwise, they form a bundle and swim in a straight line.

"Upon chemotactic signaling, a whole signaling cascade takes place and results in the phosphorylation of CheY. Phosphorylated CheY binds to the rotor and switches its conformation. The rotor now interacts with the distal side of the MotA ring. The same clockwise rotation of MotA around MotB induces a clockwise rotation in the motor.

***

"...bacteria swim using long filaments powered by a bidirectional, rotary proteinaceous motor. They know the molecular makeup of the rotary motor, and that this bidirectional motor is itself driven by unidirectional miniature rotary motors.

Comment: irreducibly complex. Must be designed in one step. Recognize a designer God who works intimately at this biochemical level to produce an automatically operating molecular machine.

Biological complexity: repairing lysosomes

by David Turell @, Monday, March 20, 2023, 14:12 (375 days ago) @ David Turell

Essentially garbage collectors cleaning up cells:

https://www.the-scientist.com/news-opinion/scientists-uncover-major-pathway-cells-use-t...

"Lysosomes are tiny sacs of digestive enzymes that declutter cells by breaking down waste. But they can also be troublesome: When their outer surface is damaged, their destructive proteins begin to spill into the cytoplasm and harm the cell. Indeed, the frequency of this leakiness increases as a person ages and likely plays a role in aging-associated diseases such as neurodegenerative conditions.

***

"Further experiments revealed that when the lysosome membrane is compromised, an enzyme called phosphatidylinositol-4-kinase type 2a, or PI4K2A, is recruited to the organelle’s surface, possibly in response to calcium ions leaking out of the lysosome, says Toren Finkel, a study coauthor and a professor of medicine at the University of Pittsburgh. PI4K2A generates a lipid called phosphatidylinositol-4-phosphate (PI4P), which acts as a danger signal and recruits several proteins known as ORPs (for oxysterol-binding protein-related proteins), which tether the endoplasmic reticulum to the lysosome.

"These ORPs then swap PI4P with lipids from the endoplasmic reticulum, including phosphatidylserine, which recruits the lipid transporter ATG2—the final component of the pathway. “ATG2 is like a firehose” for lipids, says Finkel, pumping molecules into the membrane to plug the hole.

***

"As an ode to the University of Pittsburgh, the two scientists christened the pathway phosphoinositide-initiated membrane tethering and lipid transport, or PITT for short.

"Tan believes that the two mechanisms have evolved to repair different types of damage, with the ESCRT complex mending small pores while the PITT pathway repairs larger holes.

"The new pathway may be performing most of the cell’s handywork. The researchers found that cells usually take around an hour to repair damaged lysosomes, but this healing requires up to 11 hours in cells lacking PI42KA. “It looks like quite a significant pathway, perhaps more so than the ESCRT pathway,” says Antony Galione, a pharmacologist at the University of Oxford in the UK who was not involved in the study."

Comment: It is my view the first bacteria appeared all at once, fully designed. In that view, lysosomes were present from the beginning, fully functional. I f not the first cells would have died of their own byproducts. Irreducible complexity, as implied, the cell was designed with all its parts fully functioning.

Biological complexity: blood stem cell self protect

by David Turell @, Tuesday, March 21, 2023, 17:33 (374 days ago) @ David Turell

They have two systems of garbage disposal:

https://phys.org/news/2023-03-ward-aging-stem-cells-trash.html

"In a study published March 21, 2023 in Cell Stem Cell, researchers at University of California San Diego School of Medicine found that blood stem cells use an unexpected method to get rid of their misfolded proteins, and that this pathway's activity degrades with age. The authors say boosting this specialized garbage disposal system could help protect against age-related diseases.

"The study focused on hematopoietic stem cells (HSCs), the cells in our bone marrow that produce new blood and immune cells throughout our lives. When their function is weakened or lost, this can lead to blood and immune disorders, such as anemia, blood clotting and cancer.

"'Stem cells are in it for the long haul," said senior study author Robert Signer, Ph.D., associate professor at UC San Diego School of Medicine. "Their need for longevity requires them to be wired differently than all the short-lived cells in the body."

***

"In most cells, damaged or misfolded proteins get individually tagged for disposal. A mobile protein destroyer called the proteasome then finds the labeled proteins and breaks them down into their original amino acid components. But in the new study, the researchers found proteasome activity was especially low in HSCs. This left the team puzzled: if getting rid of damaged proteins is so important to stem cells, why is the proteasome less active?

***

"In most cells, damaged or misfolded proteins get individually tagged for disposal. A mobile protein destroyer called the proteasome then finds the labeled proteins and breaks them down into their original amino acid components. But in the new study, the researchers found proteasome activity was especially low in HSCs. This left the team puzzled: if getting rid of damaged proteins is so important to stem cells, why is the proteasome less active?

"Through a series of subsequent experiments, the team discovered that HSCs use a different system entirely. Here, damaged and misfolded proteins are collected and trafficked into clusters called aggresomes. Once corralled into a single location, they can be collectively destroyed by the lysosome (a cell organelle containing digestive enzymes) in a process called aggrephagy.

"'What's very unusual here is this pathway was thought to only be triggered as an extreme stress response, but it's actually the normal physiological pathway that's used by stem cells," said Signer. "This emphasizes how critical it is for stem cells to prevent stress so they can preserve their health and longevity."

"So why this different system? A main advantage of the proteasome method is that it breaks proteins down immediately, producing amino acids that the cell can reuse to build new proteins. But stem cells are less interested in building new proteins. Thus the authors suggest that by storing a collection of damaged proteins in one place, stem cells may be creating their own cache of resources that can be used at a later time when they are actually needed, such as after an injury or when it is time to regenerate.

"'The body really can't risk losing its stem cells, so having this stockpile of raw materials makes them more protected against rainy days," said Signer. "Stem cells are marathon runners, but they also need to be world-class sprinters when the circumstances call for it."

"When the researchers genetically disabled the aggrephagy pathway, the stem cells started to accumulate aggregated protein, which impaired their fitness, longevity and regenerative activity.

"The team then discovered that while almost all young stem cells had aggresomes, at a certain point in aging, they were almost completely gone. The authors suggest that stem cells' inability to efficiently destroy misfolded proteins during aging is likely a key contributing factor to their declining function and the resulting age-related disorders.

***

"The authors suspect that other types of stem cells and long-lived cells like neurons have a similar requirement for strict regulation of protein homeostasis, suggesting therapeutics to boost this pathway may be beneficial across multiple organs and pathologies.

Comment: it seems the researchers have shown why HSC's have two systems. The key is in the last paragraph. Some vital cells must last a lifetime as replacement is not an option. This means these cells were designed this way from their origin, or the y would not have lasted a lifetime.

Biological complexity: intracellular protein movements

by David Turell @, Monday, April 03, 2023, 14:59 (361 days ago) @ David Turell

How Kinesin moves along microtubules:

https://www.the-scientist.com/news-opinion/high-resolution-microscope-watches-proteins-...

"Kinesin is a vital player in transporting cargo, like neurotransmitter-filled vesicles, along the microtubule rails that span our cells. Fueled by the splitting of ATP, kinesin moves by “stepping” with its two footlike head groups, which alternate their position along the microtubule.

"The researchers noticed that kinesin walks unevenly along the microtubule, in an alternating pattern of long and short strides, caused by rotation of the protein’s stalk. They also revealed that ATP binds to the protein when just one of its two head groups is planted on the microtubule. Researchers had previously been divided over whether ATP binds in the two-head state—with both head groups firmly planted—or in the one-head state, with one head lifted off the microtubule. But the new work “settles the issue,” says biophysicist Devarajan Thirumalai at the University of Texas at Austin who was not involved in the study.

***

"Martin Aepfelbacher, a microbiologist at the University Medical Centre Hamburg-Eppendorf in Germany, has already harnessed the previous iteration of MINFLUX to visualize molecular machines in bacteria. But the new technique could allow his group “to observe the movements of individual proteins in action,” he says, vastly improving the level of detail that can be observed when it comes to biological activity at the nanoscale.

"The illustration explained: KINESIN CATWALK: Researchers tweaked a type of fluorescence microscope capable of detecting individual proteins, known as MINFLUX, to enhance its spatiotemporal resolution. Researchers attached a fluorescence molecule to the motor protein kinesin and tracked it with lasers to observe it walking along a microtubule. The protein was found to meander in alternating long and short steps as its stalk rotated and attached to ATP when just a single head group was bound to the microtubule."

Comment: look at the illustration for full understanding. Kinesin's step-by-step 'walk' is explained. Certainly designed as irreducibly complex in working parts.

Biological complexity: removing cellular garbage

by David Turell @, Tuesday, May 23, 2023, 18:07 (311 days ago) @ David Turell

Another study:

https://phys.org/news/2023-05-reveal-nanomachine-cell.html

"Have you ever put off cleaning the house or decluttering the overflowing basement? Living cells cannot afford this procrastination when it comes to clearing the decks. Tiny garbage chutes are constantly active there to capture worn-out proteins, faulty cell components, or defective organelles. These garbage chutes, called autophagosomes, pick out the discarded components before they accumulate in the cell and cause damage. The cellular waste is then passed on to the cell's own recycling machinery, the lysosome, where it is digested and recycled.

"Thus, building blocks for new cellular components are quickly available again. The autophagy process, literally self-eating, thus also helps cells to survive stress or periods of starvation.

"Autophagy also serves another important purpose. It renders harmless viruses and bacteria that successfully bypass the immune system's defenses and reach the cell plasma. The consequences are correspondingly fatal if the autophagy process is faulty, too slow, or too fast.

***

"'Autophagy is a highly complex process involving many different proteins and protein complexes. We know many of them, but there are still fundamental gaps in our knowledge," reports Alex Faesen, research group leader at the Max Planck Institute for Multidisciplinary Sciences in Göttingen. "How do the protein components work together? How is the process of autophagy started and stopped? When and where is the autophagosome assembled? That is what we want to find out."

***

"...the team brought the individual protein complexes together. "The complexes self-assembled into a protein supercomplex, the autophagy initiation complex. In fact, autophagy involves a sophisticated cellular nanomachine—and it works quite differently than previously thought," the group leader says.

"To make autophagosomes, the autophagy initiation complex first creates a junction between a particular structure of the cell, the endoplasmic reticulum, and the autophagosome that forms. Under stress or in times of starvation, such as during endurance sports, this occurs within just a few minutes. "From this point on, there is no turning back: The waste disposal is assembled and collects the cellular waste," explains Anh Nguyen, one of the two first authors of the study.

"Co-first author Fancesca Lugarini adds, "Via the contact site, fat-like molecules called lipids are transported to a precursor stage of autophagosomes, where they are incorporated." These grow and, in the process, enclose the cell material to be disposed of—the finished mini-organelle is formed. Within barely 20 minutes of its formation, the autophagosome is already delivering its waste to the lysosome by fusing with it.

"But what starts the assembly of the autophagy machine, what starts it and what stops it? The researchers did not find a molecular "on" and "off" switch as in other molecular machines. Instead, the switch uses a highly unusual behavior of proteins: metamorphosis. Certain molecules, called ATG13 and ATG101, have the ability to fold in different 3D structures, thereby changing its ability to bind to proteins in the machine. "This protein metamorphosis also gives the go-ahead for the assembly of the autophagy initiation complex at the right time and in the right place," says Faesen, describing the special features of the nanomachine. Without metamorphosis, the initiation machine does not assemble."

Comment: Amazing. These changeable chameleon molecules must carefully select only what is garbage in their disposal process to keep the living cell functional. This process as so many pars it is irreducibly complex and must have been designed.

Biological complexity: how proteins fit together

by David Turell @, Thursday, April 06, 2023, 18:23 (358 days ago) @ David Turell

Parts interlock into each other:

https://phys.org/news/2023-04-role-dating-bacteria-evolution.html

"Proteins are the key players for virtually all molecular processes within the cell. To fulfill their diverse functions, they have to interact with other proteins. Such protein-protein interactions are mediated by highly complementary surfaces, which typically involve many amino acids that are positioned precisely to produce a tight, specific fit between two proteins. However, comparatively little is known about how such interactions are created during evolution.

"Classical evolutionary theory suggests that any new biological feature involving many components (like the amino acids that enable an interaction between proteins) evolves in a stepwise manner. According to this concept, each tiny functional improvement is driven by the power of natural selection because there is some benefit associated with the feature. However, whether protein-protein interactions also always follow this trajectory was not entirely known.

"Using a highly interdisciplinary approach, an international team led by Max Planck researcher Georg Hochberg from the Terrestrial Microbiology in Marburg have now shed new light on this question. Their study provides definitive evidence that highly complementary and biologically relevant protein-protein interactions can evolve entirely by chance.

***

"The Berlin team then tested whether ancient molecules could form an interaction. This way the scientists could retrace how both protein partners got to know each other. "Surprisingly, the FRP from the proteobacteria already matched the ancestral OCP of the cyanobacteria, before gene transfer had even taken place. The mutual compatibility of FRP and OCP has thus evolved completely independently of each other in different species," says Thomas Friedrich.

"This allowed the team to prove that their ability to interact must have been a happy accident: selection could not plausibly have shaped the two proteins' surfaces to enable an interaction if they had never met each other. This finally proved that such interactions can evolve entirely without direct selective pressure.

***

"'This may seem like an extraordinary coincidence," Niklas Steube says. "Imagine an alien spaceship landed on earth and we found that it contained plug-shaped objects that perfectly fit into human-made sockets. But despite the perceived improbability, such coincidences could be relatively common. But in fact, proteins often encounter a large number of new potential interaction partners when localisation or expression patterns change within the cell, or when new proteins enter the cell through horizontal gene transfer."

"Georg Hochberg adds, "Even if only a small fraction of such encounters ends up being productive, fortuitous compatibility may be the basis of a significant fraction of all interactions we see inside cells today. Thus, as in human partnerships, a good evolutionary match could be the result of a chance meeting of two already compatible partners."

Comment: so these folks prove chance interactions can occur in the lab by human interactions. Not by natural selection. Pure Darwinist pipedream. What are the real 'natural chances'? It is trying to save Darwinism from design theory attacks.

Biological complexity: new organelle found

by David Turell @, Friday, May 05, 2023, 21:14 (329 days ago) @ David Turell

More intracellular complexity:

https://mail.google.com/mail/u/0/#inbox/FMfcgzGsmWptXVfPSFMDFMVjKFmMMTFC

Biology textbooks look set for an update: researchers have just discovered a new kind of organelle, a tiny organ-like structure inside cells. Researchers made the discovery while investigating the role of phosphate in cell renewal in the guts of fruit flies (Drosophila melanogaster). The new organelle acts as a reservoir for phosphate, a nutrient that is essential for life. The discovery highlights how much there is to learn about cell physiology, says geneticist and study co-author Chiwei (Charles) Xu. “The beauty is there, it's just waiting for us to discover it.”

Darwin developed his simplistic theory of evolution knowing nothing of the underlying complexity of cellular design.
.

Biological complexity: the mechanics of phase separation

by David Turell @, Tuesday, May 09, 2023, 23:34 (325 days ago) @ David Turell

Cells conduct reactions separate from the rest of the cell by phase separation, not mechan8scaml walls:

https://www.cell.com/cell-reports-physical-science/fulltext/S2666-3864(23)00189-3?dgcid...

" We have systematically shown the effect of length on condensation of positively charged peptides and negatively charged RNA. We observed condensation for combinations of relatively short peptides and RNA, but experiments and simulations show that there does exist a lower limit in terms of RNA or peptide lengths for the systems studied here. The essential driving force for condensation is electrostatic attraction between RNA and arginine residues, counteracted by the entropic cost of condensation. The key reason for the observed length dependence is that the enthalpy of condensation scales with the number of charged units, whereas entropy scales with the number of polymers. We expect that, with peptides with lower charge density (e.g., arginine residues spaced more widely), longer peptides and/or longer RNA would be required for phase separation to be observed. On the other hand, systems with higher charge density have been proven to enable phase separation even with single nucleotides, such as UDP (−3 charge) or UTP (−4 charge), and polyR10, as observed in other work. Our study furthermore demonstrates that still shorter polymers may participate in condensates as clients or as partial drivers of condensation together with longer polymers.

" The remarkable agreement between experiment and CG simulations suggests that the computational approach could be extended to other sequences and systems as well as other dimensions in phase space, such as concentration or peptide content. The parameterization of the CG model20 explored a wide range of sequences and concentrations and accounts; for example, for the higher condensation propensity of arginine with nucleotides than lysine, as observed by Fisher and Elbaum-Garfinkle.18 However, the relative simplicity of the CG model neglects counterion effects that are known to be important factors during condensation34,35 and does not consider partial secondary structures that are present in many intrinsically disordered proteins (IDPs). Extending the model to explore the importance of these factors will be the subject of future studies.

" LLPS has practical applications for inducing high-concentration phases of certain biomolecules. The work here illustrates a quantitative framework for predicting the system components necessary for LLPS. On the other hand, this work demonstrates that a wide range of peptides and RNA can lead to LLPS. In the biological context, this means that many biomolecules may drive and/or participate in condensate formation in a dynamic manner as cellular concentrations of peptides and RNA fluctuate."

Comment: Simply charged polymers set up virtual walls around isolated reactions. This is the degree of design complexity which negates the Darwinian option of chance evolution.

Biological complexity: zinc actions in the cell

by David Turell @, Tuesday, May 30, 2023, 00:50 (304 days ago) @ David Turell

A very important trace metal in our cells:

https://phys.org/news/2023-05-zinc-homeostasis-cells.html

"A research group has unearthed how zinc transporter complexes regulate zinc ion (Zn2+) concentrations in different areas of the Golgi apparatus and revealed that this mechanism finely tunes the chaperone protein ERp44.

"The findings reveal the crucial chemical and cellular biological mechanism at play behind zinc homeostasis, something necessary for avoiding fatal diseases such as diabetes, cancers, growth failures, and immunodeficiency.

"As a trace element, zinc is essential for our health. Zn2+ are vital for enzyme catalysis, protein folding, DNA binding, and regulating gene expression, with nearly 10% of human proteome binding Zn2+ for their structural maturation and function.

"Secretory proteins like hormones, immunoglobulins, and blood clotting factors are synthesized and folded in the endoplasmic reticulum (ER), a complex membrane network of tubules. Subsequently, they are transported to and matured in the Golgi apparatus, the organelle composed of multiple flattened sacs called cisternae, which sorts and processes proteins before directing them to a specific destination. Chaperone proteins are vital for maintaining protein homeostasis and preventing the formation of misfolded or aggregated proteins in these organelles.

"The group's previous research demonstrated that Zn2+ in the Golgi apparatus plays an essential part in protein quality control in the early secretory pathway comprising the ER and Golgi. This system is mediated by the ER-Golgi cycling chaperone protein ERp44.

"In the Golgi apparatus, there exists three ZnT complexes: ZnT4, Znt5/6, and ZnT7. Yet, until now, mechanisms of how Zn2+ homeostasis is maintained in the Golgi apparatus has remained unclear.

***

"ERp44 captures immature secretory proteins at the Golgi apparatus to prevent their abnormal secretion. Previous studies have shown that mice with the expression of ERp44 suppressed suffer from heart failure and hypotension.

"Additionally, many secretory zinc enzymes are related to various diseases, including metastasis of cancer cells and hypophosphatasia. These enzymes depend on the Golgi-resident ZnT complexes to acquire Zn2+ for enzymatic activity. Male mice with ZnT5 suppressed have experienced death caused by arrhythmias, so there is possible relevance of Zn2+ homeostasis to cardiovascular disease.

"'Our findings will help us understand the mechanism by which disruptions of Zn2+ homeostasis in the early secretory pathway leads to the development of pathological conditions," adds Inaba.

Comment: many different metals play important roles in intracellular biochemistry as part of small molecules and in giant enzymes. This tight regulation is the way the cell automatically controls its environment.

Biological complexity: kidney cells self-renew

by David Turell @, Saturday, July 15, 2023, 13:29 (258 days ago) @ David Turell

Pinch it off to throw it out:

https://www.sciencedaily.com/releases/2023/07/230713192852.htm

"Scientists have discovered a previously unknown 'housekeeping' process in kidney cells that ejects unwanted content, resulting in cells that rejuvenate themselves and remain functioning and healthy. The self-renewal process, which is fundamentally different from how other bodily tissues are thought to regenerate, helps explain how, barring injury or disease, the kidneys can remain healthy for a lifetime.

***

"Unlike the liver and skin, where cells divide to create new daughter cells and regenerate the organ, cells in the proximal tubules of the kidney are mitotically quiescent -- they do not divide to create new cells. In cases of mild injury or disease, kidney cells do have limited repair capabilities, and stem cells in the kidney can form new kidney cells, but only up to a point, said Dr. Jie Zheng, professor of chemistry and biochemistry in the School of Natural Sciences and Mathematics

***

"Research has shown that gold nanoparticles generally pass unscathed through a structure in the kidney called the glomerulus and then travel into proximal tubules, which make up over 50% of the kidney. Proximal tubular epithelial cells have been shown to internalize the nanoparticles, which eventually escape those cells to be excreted in urine. But just how they escape the cells has been unclear.

***

"'Using the EM, we saw gold nanoparticles encapsulated in lysosomes inside of large vesicles in the lumen, which is the space outside the epithelial cells," Yu said.

"Vesicles are small fluid-filled sacks found both inside and outside of cells that transport various substances.

"'But we also observed the formation of these vesicles containing both nanoparticles and organelles outside of cells, and it was not something we had seen before," Yu said.

"The researchers found proximal tubular cells that had formed outwardly facing bulges in their luminal membranes that contained not only gold nanoparticles but also lysosomes, mitochondria, endoplasmic reticulum and other organelles typically confined to a cell's interior. The extruded contents were then pinched off into a vesicle that floated off into the extracellular space.

"'At that moment, we knew this was an unusual phenomenon," Yu said. "This is a new method for cells to remove cellular contents."

"The extrusion-mediated self-renewal mechanism is fundamentally different from other known regenerative processes -- such as cell division -- and housecleaning tasks like exocytosis. In exocytosis, foreign substances such as nanoparticles are encapsulated in a vesicle inside the cell. Then, the vesicle membrane fuses with the inside of the cell's membrane, which opens to release the contents to the outside.

"'What we discovered is totally different from the previous understanding of how cells eliminate particles. There is no membrane fusion in the extrusion process, which eliminates old content from normal cells and allows the cells to update themselves with fresh contents," Huang said. "It happens whether foreign nanoparticles are present or not. It's an intrinsic, proactive process these cells use to survive longer and function properly.'"

Comment: a new method for automatic cellular garbage disposal to preserve kidney function for life.

Biological complexity: immortal jellyfish

by David Turell @, Sunday, July 23, 2023, 17:52 (250 days ago) @ David Turell

This species may live forever:

https://www.sciencealert.com/the-immortal-jellyfish-can-age-in-reverse-and-possibly-liv...

"The 'immortal jellyfish' is so named because it can, theoretically, live forever. For all we know, some of these tiny, translucent blobs have been drifting along since well before the demise of the dinosaurs, around 66 million years ago.


"That might sound fictitious, but the potential to live for millions of years lies well within the realms of biology – at least for this one curious species.

"When an immortal jellyfish (Turritopsis dohrnii) grows old or damaged, the species can evade death by reverting to a baby polyp stage. It does so by reabsorbing its tentacles and coming to rest as a blob of undifferentiated cells somewhere on the seafloor.

"From here, the young polyp can then bud and produce new adult forms, each smaller than the nail on your pinky when fully grown.

"More importantly, these mature buds are genetically identical to the polyp.

***

"The creature was first described by scientists in 1883, but it wasn't until a century later that experts accidentally discovered its eternal life cycle while keeping it in captivity.

"In the years since, studies have shown that colonies of immortal jellyfish kept in the lab can regress into a polyp stage and begin life again up to 10 times in two years.

"The immortal jelly is the only known species that can rejuvenate itself after sexual reproduction, making it 'biologically immortal'.

"While the species is thought to have originated in the Mediterranean, it is now abundant in every ocean in the world.

"Despite its ubiquity, experts still don't quite understand how the jelly lives for so long. In 2022, genomic research on the genus identified no less than a thousand genes related to aging and DNA repair.

"If scientists can figure out which genes are present or missing in the immortal jellyfish, compared to its relatives, it could reveal the cellular mechanisms behind its everlasting life.

"In 2019, scientists first compared the genetic expression of cells from an immortal jellyfish polyp to a newborn adult 'medusa' with tentacles and a bell.

"They found differences in how some cells functioned, which suggests that specialized cells are somehow being reprogrammed, like resetting a clock back in time.

"This doesn't mean that immortal jellyfish can never die; they can still pass away from injury or starvation. But the possibility of life persists for these creatures like no other."

Comment: In the diversity of life anything is possible.

Biological complexity: mitochondrial repair

by David Turell @, Friday, July 28, 2023, 17:41 (245 days ago) @ David Turell

For any sort of damage or stress:

https://phys.org/news/2023-07-mitochondria-stress.html

"...This is referred to as the endosymbiotic theory, according to which that one single-celled organism was the primordial mother of all higher cells, out of which all animals, fungi and plants developed. Over the course of billions of years, the encapsulated bacterium became the cell's powerhouse, the mitochondrion, which supplies it with the cellular energy currency ATP.

"It lost a large part of its genetic material—its DNA—and exchanged smaller DNA segments with the mother cell. However, now as in the past, mitochondria divide independently of the cell and possess some genes of their own.

***

"A certain type of mitochondrial stress is caused by misfolded proteins that are not quickly degraded and accumulate in the mitochondrion. The consequences for both the mitochondrion and the cell are dramatic: Misfolded proteins can, for example, disrupt energy production or lead to the formation of larger amounts of reactive oxygen compounds, which attack the mitochondrial DNA and generate further misfolded proteins. In addition, misfolded proteins can destabilize the mitochondrial membranes, releasing signal substances from the mitochondrion that activate apoptosis, the cell's self-destruction program.

"The mitochondrion responds to the stress by producing more chaperones (folding assistants) to fold the proteins in order to reduce the misfolding, as well as protein shredding units that degrade the misfolded proteins. Until now, how cells trigger this protective mechanism was unknown.

***

"The result is that the mitochondria send two chemical signals to the cell when protein misfolding stress occurs: They release reactive oxygen compounds and block the import of protein precursors, which are produced in the cell and are only folded into their functional shape inside the mitochondrion, causing these precursors to accumulate in the cell. Among other things, the reactive oxygen compounds lead to chemical changes in a protein called DNAJA1. Normally, DNAJA1 supports a specific chaperone (folding assistant) in the cell, which molds the cell's newly formed proteins into the correct shape.

"As a consequence of the chemical change, DNAJA1 now increasingly forces itself on the folding assistant HSP70 as its helper. HSP70 then takes special care of the misfolded protein precursors that accumulate around the mitochondrion because of the blocked protein import. By doing so, HSP70 reduces its interaction with its regular partner HSF1. HSF1 is now released and can migrate into the cell nucleus, where it can trigger the anti-stress mechanism for the mitochondrion.

"As Münch explains, "It was very exciting to discover how the two mitochondrial stress signals are combined into one signal in the cell, which then triggers the cell's response to mitochondrial stress. Moreover, in this complex process, which is essentially driven by tiny local changes in concentration, the stress signaling pathways of the cell and the mitochondrion dovetail very elegantly with each other—like the cogs in a clockwork.'"

Comment: this is more easily explained by God, the designer, solving problems than chance mutations doing it.

Biological complexity: total cells in a human

by David Turell @, Thursday, September 21, 2023, 17:28 (190 days ago) @ David Turell

How fast do they reproduce:

"'Most of the skin and gut are replaced very fast, most likely within months," Olaf Bergmann, a principal researcher in the Department of Cell and Molecular Biology at the Karolinska Institute in Stockholm, Sweden, told Live Science in an email. Cells in the liver regenerate at a somewhat slower pace, Bergmann and his colleagues reported June 15 in the journal Cell Systems. For the study, the authors analyzed liver tissue using radiocarbon dating and found that most liver cells are replaced within three years.

"However, cells in other organs and systems are even slower to replicate and lag behind the seven-year cut-off.

"For example, "the human heart renews at a rather low rate, with only 40% of all cardiomyocytes [the cells responsible for the contracting force in the heart] exchanged throughout life," Bergmann said. Skeletal cells, meanwhile, need around 10 years to replicate a skeleton in its entirety, according to the New York Times.

"In the brain, cell renewal can be even more leisurely. Scientists have uncovered evidence showing that some neurons in the hippocampus are renewed, but only at a rate of 1.75% annually, according to a 2013 study in Cell. And some types of neurons within the striatum also regenerate, according to a 2014 study in Cell. But other types of neurons stay with a person for their entire lifetime, Bergmann said. And even the distinct cell populations that can rejuvenate are not replaced entirely, but only partly over a lifetime, he said."

How many cells:

https://www.livescience.com/health/anatomy/how-many-cells-are-in-the-human-body-new-stu...

"According to a new analysis of more than 1,500 papers, the average adult male human has around 36 trillion cells — that's 36 followed by 12 zeros — while adult females have 28 trillion and 10-year-old children have about 17 trillion. To arrive at these estimates, the authors of the new study, which was published Monday (Sept. 18) in the journal PNAS, considered the size and number of 400 types of cells in the body across 60 tissues, including muscle, nerve and immune cells.

***

"'Possibly most critical is our estimate of the total number of human lymphocytes, which are vital for our immune function," he said. "We estimate 2 trillion lymphocytes in the human body which is four times higher than prior estimates and could prove important in lymphocyte-related health and disease, such as HIV or leukemia.'"

Comment: Several trillion cells reproduce every day or so. New mutations, mainly as mistakes occur infrequently. Much rarer mistakes result in cancer. The editing systems keep these mistakes at a very low ratio compared to the rate of cell splitting on a daily basis. This is the answer theodicy articles give to complaints about God's works: it is the only system that works. To enjoy this life we must accept it .

Biological complexity: actions of lysosomes

by David Turell @, Wednesday, October 25, 2023, 22:26 (156 days ago) @ David Turell

Newly developed methods of study:

https://phys.org/news/2023-10-lysosomes-quick-

"The researchers were able to show for the first time that lysosomes undergo a massive transformation. A signaling lipid acts as a switch between the two states.

***

"Nutrient availability in the body is constantly changing. For example, after a full meal, cells have many more nutrients available than at the end of a long night without any food intake. "It is important for all cells and tissues to be able to respond to the current food intake in such a way that certain basic building blocks are always present inside the cell," explained Professor Volker Haucke,

"These basic building blocks are obtained through catabolism, the process by which ingested nutrients are broken down into small components that the cell uses to make the molecules it needs.

"One of the components responsible for this is the lysosome, a membrane-enclosed sac. At the same time, lysosomes are the central monitoring point that determines whether the food supply in the cell is good or bad. When there is a good supply of nutrients, the mTOR signaling pathway on lysosomes is activated, inducing cell division and growth. When nutrients are scarce, the mTOR complex is switched off to stimulate catabolic programs. As a result, lysosomes combine two opposing tasks: degradation and assembly.

***

"In a complex cascade, this process is controlled by signaling lipid molecules that induce either a starved or a fed state. Using correlative light and electron microscopy, the researchers observed that there are two pools of lysosomes in the cell: Small motile ones, located more at the periphery, act as monitoring stations.

"Meanwhile, larger, more static lysosomes, located closer to the nucleus, are responsible for degradation. What changes is the ratio: In a well-fed state, the small motile lysosomes carrying the active mTOR complex predominate, and there are relatively few static lysosomes. When the cell starves, the small motile lysosomes lose the signaling lipid marker for mTOR and acquire a new signaling lipid, activating the digestive enzymes in the lysosome.

"This response is acute, meaning that the cells are transformed immediately, and initial changes can be observed within minutes. The process from destructive to constructive metabolism is completed in one to two hours," reported Michael Ebner.

"The signaling lipids act as a switch that activates or switches off the mTOR complex, depending on nutrient availability. "Lysosome properties change completely, depending on the signaling lipid," emphasized Volker Haucke. This makes the new findings interesting for therapeutic purposes. After all, during active degradation, lysosomes also remove damaged proteins. And if you can flip the signaling lipid switch artificially, you can also influence the metabolic events in the cell."

Comment: Another example of an irreducibly complex set of on/off controls which can only be developed by design.

Biological complexity: sperm defy Newton's 3rd law

by David Turell @, Friday, October 27, 2023, 00:18 (154 days ago) @ David Turell

The action reaction law tha makes rockets fly:

https://www.newscientist.com/article/2397442-sperm-caught-breaking-newtons-third-law-of...

"To work out how the cells manage to move despite this apparent obstacle, the researchers analysed the motion of sperm and algal cells’ flagella as they swam. They found that these flagella have an unusual property, dubbed “odd” elasticity, which allows them to wave without losing much energy to the surrounding fluid.

"The researchers quantified the cells’ odd elasticity and arrived at a number called the “odd elastic modulus”. The higher this number, the more a flagellum can wave without the surrounding liquid suppressing its motion. This allows the cell to move forward non-reciprocally.

"Clément Moreau at Kyoto University, who also worked on the study, says calculating the odd elastic modulus for many different micro-swimmers could help scientists classify them and work out whether there are additional features that help them disobey Newton’s third law.

"At present, we don’t know of all the microscopic process that help tiny swimmers defy this law of motion, says Piotr Surówka at the Wrocław University of Science and Technology in Poland. He says being able to calculate the odd elastic modulus and similar numbers could help create a “dictionary” of organisms that are capable of non-reciprocal movement."

Comment: sperm have just so much energy stored. They must reach the egg quickly. The mechanics of how their flagella work, but I'll bet it mimics the bacterial method of sliding straight parts. This is a very purposeful design that cannot be developed by chance steps. Beating Newton's Third law is no mean feat.

Biological complexity: osmotic presdsure controls

by David Turell @, Friday, November 03, 2023, 21:04 (147 days ago) @ David Turell

A new way to measure in cells:

https://phys.org/news/2023-11-visualize-osmotic-pressure-tissue.html

"In order to survive, organisms must control the pressure inside them, from the single-cell level to tissues and organs. Measuring these pressures in living cells and tissues in physiological conditions is a challenge.

***

"When molecules dissolved in water are separated into different compartments, water has the tendency to flow from one compartment to another to equilibrate their concentrations, a process known as osmosis. If some molecules cannot cross the membrane that separates them, a pressure imbalance—osmotic pressure—builds up between compartments.

***

"Our cells are constantly moving molecules in and out to prevent the pressure build-up from crushing them. To do so, they use molecular pumps that allow them to keep the pressure in check. This osmotic pressure affects many aspects of cells' lives and even sets their size.

"When cells team up to build our tissues and organs, they, too, face a pressure problem: Our vascular system, or organs such as the pancreas or liver, contain fluid-filled cavities known as lumens that are essential for their function. If cells fail to control osmotic pressure, these lumens may collapse or explode, with potentially catastrophic consequences for the organ.

***

"For this pressure sensor, they introduced a water droplet into an oil droplet that permits water to flow through. When these "double-droplets" were exposed to salt solutions of different concentrations, water flowed in and out of the internal water droplet, changing its volume, until pressures were equilibrated. The researchers showed that the osmotic pressure can be measured by simply checking the droplet size. They then introduced these double-droplets into living cells and tissues using glass microcapillaries to reveal their osmotic pressure.

"'It turns out that cells in animal tissues have the same osmotic pressure as plant cells but, unlike plants, they must balance it constantly with their environment to avoid exploding, since they do not have rigid cell walls," Campàs said.

"With this simple concept, this ingenious method now allows scientists to "see" osmotic pressure in a wide range of settings. "We know that several physical processes affect the working of our bodies," Campàs said. "In particular, osmotic pressure is known to play a fundamental role in the building of organs during embryogenesis, and also in the maintenance of healthy adult organs. With this new technique, we now can study how osmotic pressure impacts all these processes directly in living tissues.'"

Comment: the first cells that existed must have had osmotic pressure controls. Only by d eseign.

Biological complexity: immune system inluences aging

by David Turell @, Tuesday, November 07, 2023, 00:03 (143 days ago) @ David Turell

A new molecular discovery:

https://medicalxpress.com/news/2023-11-immune-molecule-aging-lifespan.html

"Aging is a natural process that affects all living organisms, prompting gradual changes in their behavior and abilities. Past studies have highlighted several physiological factors that can contribute to aging, including the body's immune responses, an imbalance between the production of reactive oxygen (i.e., free radicals) and antioxidants, and sleep disturbances.

***

"Researchers at Washington University in St. Louis recently identified an immune molecule that could play a key role in modulating the process of aging and the duration living organism's lifespan.

***

"Our previous research identified a gene called Slpi as the top-upregulated gene in the meninges of old mice. Slpi is evolutionarily conserved and has an ortholog named IM33 in Drosophila, prompting us to turn to flies to study its role in aging, leveraging their powerful genetics and short lifespan," Wangchao Xu, one of the researchers who carried out the study, told Medical Xpress.

"'Concurrently, inspired by our lab's other findings suggesting that cytokines can shape animal behaviors, I used flies to screen for all immune effectors that can modulate fly behaviors and found that IM33 was a modulator of sleep."

***

"When the team knocked down this gene in the immune cells of fruit flies, they found that this increased the level of reactive oxygen species and altered the composition of microbiota in their gut. This resulted in oxidative stress and in an imbalance in bacterial composition (i.e., dysbiosis), which in turn reduced their lifespan. The researchers found that knocking down this gene also caused sleep disturbances, which have also been associated with aging and a shorter lifespan.

"'This is a proof-of-concept study demonstrating that an evolutionarily conserved immune molecule can serve as a messenger, conveying information between the brain and gut to regulate different levels of aging and control lifespan," Xu said. "This function goes beyond its immune role and further strengthens the contribution of neuroimmune interaction to aging.

***

""\'We suggest that peptidoglycan signaling, a conserved immune pathway, in the neuron could be a potentially novel target to slow down aging," Xu added.

"'The mechanisms through which the brain secreted IM33 shapes the gut immune environment remain mysterious and warrant further investigation. Moreover, testing the role of meningeal Slpi in mice will help determine whether this is a shared mechanism throughout evolution and provide additional supportive evidence for future translational studies.'"

Comment: it is not surprising that inflammation, oxidative stress and change in gut biome induces aging. The good our inhabitant microbiome does for us can have a bad side effect.

Biological complexity: how cells read-write their DNA

by David Turell @, Tuesday, November 07, 2023, 20:20 (143 days ago) @ David Turell

Finally unraveled:

https://phys.org/news/2023-11-cell-readwrite-mechanism-uncover-gene.html

"'Whether histone modifications are the epigenetic cause for gene expression has remained a hypothesis because no one had ever seen whether histone modifications self-replicate," explains Takashi Umehara of the RIKEN Center for Biosystems Dynamics Research.

"To explore this question, Umehara and his team focused on a protein known as p300/CBP—an enzyme that can both introduce and bind to acetyl-group modifications (acetylations) on histone proteins. Specifically, the researchers were interested in specific acetylations on the histone H3–H4 complex to which p300/CBP binds. These acetylations are known to activate gene expression in nearby DNA sequences.

"But H3–H4 is just one component of a larger "nucleosome" assembly, which also includes the histone H2B–H2A complex. All of these various histones can carry distinct acetylation patterns, and the causal relationships between their acetylations have not been well understood.

***

"The team found that p300/CBP recognizes and binds to specific acetylation marks on the H3–H4 complex. The enzyme then replicates acetylation marks to unacetylated sites of H3–H4, while also transcribing them from H3–H4 to H2B–H2A within the same nucleosome. Since this newly acetylated H2B–H2A complex is more likely to be stripped from the nucleosome, a model emerges in which it finally instructs which genes to be transcribed by the cellular transcription machinery.

"These results provide an unprecedented glimpse into how p300/CBP inherits acetylation marks to newly divided cells and utilizes those marks epigenetically for gene expression. "I could never have imagined such an elegant yin–yang mechanism for the inheritance and expression of epigenetic information," says Umehara."

Comment: another example of design in evolution. Each step must be coordinated between the necessary molecules. Irreducible complexity again.

Biological complexity: lung-gut connections in illness

by David Turell @, Wednesday, November 08, 2023, 17:59 (142 days ago) @ David Turell

An intimate relationship:

https://www.the-scientist.com/ts-digest/issue/bacterial-time-capsules-21-5?utm_campaign...

"Diet-derived molecules spur a biological mechanism in the lung barriers of mice that prevents viral lung injury.

"Andreas Wack’s research at the Francis Crick Institute focuses on understanding what influences the severity of viral infections in the lungs. An immunologist by training, Wack studied immune and lung epithelial cells for years before realizing that the lung endothelial cells, which are part of the lung barrier, could be key to an organism’s response to a viral infection.

"Evidence suggested that the aryl hydrocarbon receptor (AHR) is essential for airway epithelia and gut barrier immunity. So, Wack led a team of scientists to investigate the function of AHR in the lung endothelium. In the journal Nature, he and his collaborators described how AHR signaling prevents endothelium damage after an infection and pinpointed the contribution of dietary AHR ligands to this end.

“'Looking at the endothelium in terms of barrier function is not entirely new,” said Wolfgang Kuebler, a lung and cardiovascular physiologist at the Charité University Berlin who was not involved in the research. “But looking at how the endothelium regulates the epithelium and thereby improves barrier function, that is what matters because both cells compose the barrier and work together.”

"Wack’s team used mice that either lacked AHR or did not metabolize its ligands, leading them to build up. After a viral infection, mice lacking the receptor showed signs of lung injury that were prevented in animals with excess AHR ligands.

"By assessing gene expression changes in endothelial cells, the team found that AHR-deficient mice showed disruption of the apelin signaling pathway, which is involved in vessel function regulation. Treating mice with apelin reduced lung damage after infection in wild type but not in AHR-deficient mice, suggesting a role for AHR-apelin signaling in lung protection.

"AHR ligands come from the diet (mainly from cruciferous vegetables) or from the metabolism of gut bacteria, so the team next tested whether adding an AHR ligand to the mouse food would affect AHR activity and disease progression. The enriched diet led to fewer signs of lung damage, which according to Wack, provides an example of how gut-derived molecules can affect barrier integrity in other parts of the body.

“'A lesson for all immunologists is that you want to embed your lung immune response research into a bigger context,” said Wack. “The lung is clearly communicating with other barrier sites and organs, and we need to think about this.'”

Comment: amazing, what you eat affects your lungs' health. Your gut biome plays a role, showing the importance of friendly bacteria. Cruciferous vegetables are: "vegetables of the family Brassicaceae (also called Cruciferae) with many genera, species, and cultivars being raised for food production such as cauliflower, cabbage, kale, garden cress, bok choy, broccoli, Brussels sprouts, mustard plant and similar green leaf vegetables." https://en.wikipedia.org/wiki/Cruciferous_vegetables

Biological complexity: gating calcium signals

by David Turell @, Wednesday, November 15, 2023, 18:49 (135 days ago) @ David Turell

A double lock mechanism:

https://www.the-scientist.com/news/a-double-lock-gates-calcium-signaling-71485

Now, an international collaboration led to two papers published in Science Signaling on the mechanisms that open calcium floodgates, revealing a potential route to novel therapies while settling a debate along the way.

Ion channels expressed on organelles act like gatekeepers, controlling the passage of calcium from internal stores into the cytosol. Nicotinic acid adenine dinucleotide phosphate (NAADP) is one of many keys that unlock the gate. First discovered in the late 1980s in sea urchin eggs and later found in mammalian cells, NAADP triggers calcium release from lysosomal stores via ion channel activation, specifically a two-pore channel (TPC).


“NAADP is a very curious second messenger,” said Jonathan Marchant, a cell biologist at Medical College of Wisconsin and coauthor on the papers. Although a potent trigger for calcium release, researchers never discovered a direct binding site, or keyhole, for NAADP on TPC. Then, two papers published in 2021, including one from Marchant’s team, provided a missing link.7,8 The studies revealed the molecular identity of a protein, Jupiter microtubule-associated homolog 2 (JPT2), that facilitates NAADP binding to TPC. If NAADP is the handle of the key, then JPT2 is like the blade that slots into the TPC to open its floodgates.

Adding to the excitement in the field, another paper published later that year identified another blade—the protein like-Sm protein 12 (LSM12)—that linked NAADP to the TPC.

***

“The remarkable thing about this latest paper by Marchant's group is they seem to suggest that you need both JTP2 and LSM12 to bind NAADP and interact with the channel to open it,” said Antony Galione, a pharmacologist at the University of Oxford who was not involved in the study. “One binding protein loaded up with NAADP is not enough, which is quite controlled regulation, really.” Thus, TPC have a double lock system in place to gate NAADP-dependent activities.

Comment: again, an example of IC. All parts must work together from the beginning to create the function.

Biological complexity: does life exist on the edge of chaos?

by David Turell @, Saturday, December 16, 2023, 16:14 (104 days ago) @ David Turell

An attempted answer:

https://www.newscientist.com/article/2408679-life-may-be-less-chaotic-than-we-thought-s...

"Life may not exist at the “edge of chaos” after all. The long-standing belief has been challenged by computer simulations of dozens of processes within cells.

"A hallmark of chaotic systems is that a small disturbance can lead to an outsized effect. The famous butterfly effect offers a classic example, where a flap of an insect’s wings is proposed to cause a storm many kilometres away. Since the late 1980s, researchers have believed that life has evolved to exist right at the edge of this kind of chaos in its search for the middle ground between being adaptable to the environment and remaining stable enough to survive.

“'The idea of the edge of chaos is that cells want to have as much sensitivity as they possibly can, without going into this chaotic regime where the tiniest breeze makes the cell fall apart,” says Jordan Rozum at Binghamton University in New York. “For a long time, people have thought that this edge of chaos phenomenon happens not only at the level of whole cells or organisms, but also if you look at the specific jobs that the cell has to do.”

***

"Rozum and his colleagues set out to test the edge of chaos idea using dozens of models that are rigorously rooted in biological studies.

"They chose 72 experiment-based models representing processes ranging from cell death to gene regulation in the bacterium Escherichia coli. The models came from the Cell Collective database, which collects the work of many independent researchers.

***

"Across the models, their conclusion was the same: life is remarkably good at recovering from perturbations, which wouldn’t be the case if it existed at the edge of chaos.

"Christof Teuscher at Portland State University in Oregon says the new computational method is an exciting tool and the conclusions it led to complicate the discussion of what exactly the edge of chaos is.

"Though models rigorously rooted in laboratory studies haven’t been so extensively studied before, the new study may still include too few of them for generalising its conclusions to all life, he says. There is no question that living organisms exist at “sweet spots” somewhere between order and chaos, but it remains an open question how similar those spots are across all life forms and all of life’s processes, says Teuscher.

"For Rozum, the new study is not the nail in the coffin for the edge of chaos hypothesis, but an incentive to characterise it better. While he and his colleagues showed that many cellular processes themselves are far from the edge of chaos, it could still be true that when they all combine the cell as a whole moves closer to chaos, he says. The researchers plan on studying that idea next, using even more complex computer simulations."

Comment: 'at the edge of chaos' implies the cell might degenerate in functions if a mistake happens. That does not appear to be the case. Cells continue to function with a mistake.

Biological complexity: the source of intracellular motion

by David Turell @, Friday, February 02, 2024, 22:20 (56 days ago) @ David Turell

What is delivered on the microtubules:

https://www.newscientist.com/article/2415409-some-animal-cells-contain-tiny-tornadoes-t...


"The cells that make up all living things contain a fluid called the cytoplasm, which moves around in a process called cytoplasmic streaming. Although this internal movement was first observed more than a century ago, the full pattern and purpose of such fluid flows remain only partially understood.

***

"The team used simulations to calculate the effect these microtubules and motor proteins might have on the cell’s fluid and vice versa, finding that they could closely reproduce the patterns they found when observing the cells using microscopes.

“'The motor is working on the microtubule: it’s carrying cargo and, as a consequence, it’s stirring the fluid,” says Shvartsman. “Now the fluid can influence the buckling of the microtubules, and all of these together can lead to self-organisation of a flow that spans the cell. This is absolutely remarkable.”

"To properly grow and divide, oocytes need to have a stage where they distribute and mix different cellular ingredients together before fixing certain elements in place. These twisters seem to be an essential part of this early mixing stage, says Shvartsman, and they could occur in other animal egg cells that are sufficiently large.

"Human egg cells are about a fifth as large as fruit fly egg cells and are probably too small for this effect to take place, but many insects, fish and amphibians have larger egg cells where these flows may be important, he says.

“'It’s super interesting from the perspective of how life works,” says Robert Cross at the University of Warwick, UK. “The interesting thing is how little, nanoscale autonomous walking machines which are doing this [cargo] transport generate these very large-scale, organised structures inside the cell. That’s the mind-boggling thing.” However, it’s important to note that the rotations are happening much more slowly than a real tornado, he says."

Comment: the cute talk about tornados is beside the point. All animals are mostly water. That means each person is 90% water.

Biological complexity: metabolic plant controls

by David Turell @, Wednesday, April 04, 2018, 18:24 (2186 days ago) @ David Turell

In drought plants have chemical reactions that help retain water:

https://phys.org/news/2018-04-newly-hormone-dehydrating.html

" Researchers at the RIKEN Center for Sustainable Resource Science (CSRS) in Japan have discovered a small hormone that helps plants retain water when none is available in the soil. Published in the journal Nature on April 4, the study shows how the peptide CLE25 moves from the roots to the leaves when water is scarce and helps prevent water loss by closing pores in the leaf surface.

***

"The team began by looking at CLE peptides that are synthesized in the roots and at ABA— a hormone that is known to accumulate in leaves and help close pores in response to drought stress. Applying many CLE peptides to plant roots showed that only CLE25 led to increased ABA in the leaves and pore closure. The team determined that the link between these two events was the increase in an enzyme necessary for making ABA. In addition to this artificial situation, they showed that CLE25 levels increase in the roots of plants that are subjected to dehydration stress, leading to the same results. The next question was whether CLE25 moves through the plant circulatory system.

***

"Detecting functional peptide hormones is very difficult in living cells because the amounts are so small. "We resolved this problem," says Takahashi, "by using a high sensitive mass spectrometry system, and developing a screening system that can identify the mobile peptides moving from root to shoot." With this technology, the researchers were able to tag CLE25 molecules and visualize their movement from the roots to the leaves, indicating that it was indeed a mobile hormone and that it likely interacted with other molecules in leaves to produce ABA.

"Before investigating how CLE25 induces ABA synthesis once it arrives at the leaf, the team created mutant plants that lacked CLE25 or ABA and performed several control experiments that confirmed their findings. In particular, after only three hours of dehydration, plants without CLE25 already showed 7 times less leaf ABA and had lost more water than control plants. Finally, the team examined several mutants and discovered that BAM1/BAM3 receptors in the leaf were the link between CLE25 and ABA production."

Comment: Since droughts occur without warning, this process had to be present from the beginning in plants to maintain plant survival. Only design fits this knowledge.

Biological complexity: walking along filament

by David Turell @, Wednesday, January 04, 2017, 14:54 (2641 days ago) @ David Turell

It is found that a walking protein can be bi-directional"

http://phys.org/news/2017-01-scientists-molecular-motor-gear.html

"The research revealed a totally unexpected behavior about a "motor" protein that functions as chromosomes are segregated during cell division.

"Motor proteins are tiny molecular machines that convert chemical energy into mechanical work. They are the miniature "vehicles" of a cell, and move on a network of tracks commonly referred to as the cytoskeleton. They shuttle cellular cargos between locations and generate forces to position chromosomes. But in spite of intensive research efforts over many years, mechanisms underlying the actions of many motor proteins are still unclear.

"In this study, researchers focused on a particular motor protein, called KlpA, and used a high-sensitivity light microscopy method to directly follow the movement of individual KlpA molecules on the cytoskeleton track. They discovered that KlpA is able to move in opposite directions - an unusual finding. KlpA-like motor proteins are thought to be exclusively one-way vehicles.

"The researchers also discovered that KlpA contains a gear-like component that enables it to switch direction of movement. This allows it to localize to different regions inside the cell so it can help ensure that chromosomes are properly divided for normal cell division.

"'In the past, KlpA-like motor proteins were thought to be largely redundant, and as a result they haven't been studied very much," Qiu said.

"Qiu and colleagues say they are excited about their future research, which may uncover the design principle at the atomic level that allows KlpA to move in opposite directions. And there may be other applications.

"'KlpA is a fascinating motor protein because it is the first of its kind to demonstrate bidirectional movement," Qiu said. "It provides a golden opportunity for us to learn from Mother Nature the rules that we can use to design motor protein-based transport devices. Hopefully in the near future, we could engineer motor protein-based robotics for drug delivery in a more precise and controllable manner.'"

Comment: Cell division requires precise engineering so that each copy is made correctly without error. Such engineering requires a superb engineer, not chance construction. How much cell complexity discovery does it take before one recognizes that natural evolutionary process cannot create this degree of cellular complexity?

Biological complexity: cell filaments come and go

by David Turell @, Monday, March 12, 2018, 22:51 (2209 days ago) @ David Turell

If transport filaments (microtubules) in cells are not needed they disappear:

https://phys.org/news/2018-03-railwayin-cell-body.html

"New work from the University of Warwick shows how a microscopic 'railway' system in our cells can optimise its structure to better suit bodies' needs.

***

"Almost every cell in our bodies contains a 'railway' network, a system of tiny tracks called microtubules that link important destinations inside the cell. Professor Cross' team found the system of microtubule rails inside cells can adjust its own stability depending on whether it is being used or not.

"Prof Cross said: "The microtubule tracks of the cellular railway are almost unimaginably small - just 25 nanometres across (a nanometre being a millionth of a millimetre).The railway is just as crucial to a well-run cell as a full-size railway is to a well-run country. For cells and for countries the problem is very much the same - how to run a better railway?"

***

"Imagine if the tracks of a real railway were able to ask themselves, 'am I useful?' To find out, they would check how often a railway engine passed along them.

"'It turns out that the microtubule railway tracks inside cells can do exactly that - they check whether or not they are in contact with tiny railway engines (called kinesins). If they are, then they remain stably in place. If they are not, they disassemble themselves. We think this allows the sections of microtubule rail to be recycled to build new and more useful rails elsewhere in the cell."

"The paper, 'Kinesin expands and stabilizes the GDP-microtubule lattice' published (12 March 2018) in Nature Nanotechnology, shows that when the kinesin railway engines contact their microtubule rails, they subtly change their structure, producing a very slight lengthening that stabilises the rail.

"Using a custom built microscope, the Warwick Open Source Microscope, the researchers who are also based at Warwick Systems Biology Centre and Mathematics Institute, University of Warwick, detected a 1.6% increase in the length of microtubules attached to kinesins, with a 200 times increase in their lifetime."

Comment: This is vivid that a designer is required

Biological complexity: cell filaments controls

by David Turell @, Thursday, March 15, 2018, 13:57 (2206 days ago) @ David Turell

Another molecule has been found that controls filament formation in cells:

https://www.technologynetworks.com/analysis/news/biochemists-zero-in-on-key-molecules-t...

"The researchers examined a fibrous rope-like protein in cells called actin, which grows and branches the way limbs on trees do. When actin branches grow, they push on the cell membrane and create arm-like protrusions. These arms can pull an immune cell forward, allowing it to chase foreign invaders and wrap around and swallow them.

"Nolen and colleagues looked at the actin-related complex, Arp2/3, a large assembly of proteins that is required for actin to branch. When Arp2/3 sits down on actin it promotes a new branch to form at that site.

"This Arp2/3 complex is critical to cell motility -- the ability to move and perform myriad duties -- and for initializing the construction of a network of filaments known as the actin cytoskeleton that provides structural support for cells.

"The researchers identified two locations on Arp2/3 where an activator protein touches it. This activator protein resides in the membrane and can sense when the cell needs to crawl or engulf a foreign agent. It then triggers the branching response inside of the cell by touching Arp2/3.

"To find the precise locations where the activator protein meets Arp2/3, the research team extracted Arp2/3 and the activator protein from cells, mixed them together, and used a special method that chemically marks the two proteins at the sites where they touched. In collaboration with researchers at the University of Washington, the team zeroed in on the location of those marks using a technique called mass spectrometry.

"'What we discovered was exciting because knowing precisely how the activator protein binds to Arp2/3 complex is the first step in understanding how it turns on its branching activity," Nolen said.

"Understanding how this branching activity is turned on in malignant cells could be applicable in the development of new drugs to target cancer, the researchers said. In some disease states, including viral infections such as HIV and cancer, cells can lose control of their actin cytoskeleton.

"For example, Nolen said, a drug that blocks the site on Arp2/3 where the activator protein touches would prevent actin branching. That could stop tumor cells from crawling, or metastasizing.

"Pharmaceutical companies used similar approaches to develop paclitaxel, a cancer drug that targets another filament-forming protein called tubulin. Nolen and his colleagues said that their findings could eventually lead to new opportunities to improve human health by expanding the arsenal of disease-fighting drugs."

Comment: this biochemical mechanism is irreducibly complex. Development by chance is impossible. Design is required.

Biological complexity

by George Jelliss ⌂ @, Crewe, Saturday, July 25, 2015, 23:09 (3170 days ago) @ George Jelliss

Here&apos;s a review of two recent books:-http://www.theguardian.com/science/occams-corner/2015/jul/25/vital-question-lifes-greatest-secret-reviewed?CMP=share_btn_tw-The Vital Question by Nick Lane on origin of life.-Life&apos;s Greatest secret by Matthew Cobb on the history of DNA research.-Only wish I had the time to read them!

--
GPJ

Biological complexity

by David Turell @, Sunday, July 26, 2015, 01:34 (3169 days ago) @ George Jelliss

George: Here&apos;s a review of two recent books:&#13;&#10;> &#13;&#10;> http://www.theguardian.com/science/occams-corner/2015/jul/25/vital-question-lifes-great... &#13;&#10;> The Vital Question by Nick Lane on origin of life.&#13;&#10;> &#13;&#10;> Life&apos;s Greatest secret by Matthew Cobb on the history of DNA research.&#13;&#10;> &#13;&#10;> Only wish I had the time to read them!-Great reviews, and time is an issue, especially with all the new DNA research going on. Lane&apos;s ocean vent theory more than likely gives us the right place. Still no answer, how?

Biological complexity

by dhw, Sunday, July 26, 2015, 12:02 (3169 days ago) @ David Turell

GEORGE: Here&apos;s a review of two recent books:-http://www.theguardian.com/science/occams-corner/2015/jul/25/vital-question-lifes-great...-The Vital Question by Nick Lane on origin of life.&#13;&#10;Life&apos;s Greatest Secret by Matthew Cobb on the history of DNA research.&#13;&#10;Only wish I had the time to read them!-DAVID: Great reviews, and time is an issue, especially with all the new DNA research going on. Lane&apos;s ocean vent theory more than likely gives us the right place. Still no answer, how?-Thank you, George, and for a change I agree with you, David!-QUOTE: &#147;Cellular life in the form of bacteria (prokaryotes and archea) emerged - somehow - once these mineral cells on the ocean floor had acquired the protein machinery to generate their own proton gradients, and lipid membranes that allowed them to peel away from their rocky home and become free living.&#148;-It&apos;s the &#147;somehow&#148; that&apos;s the problem. And not just the ability to live, but also to reproduce, adapt and evolve. Yeah, otherwise he might possibly have cracked the vital secret!-Re time: &#13;&#10;&#147;Come, fill the cup, and in the Fire of Spring &#13;&#10;The Winter Garment of Repentance fling.&#13;&#10;The Bird of Time has but a little way&#13;&#10;To fly - and Lo! The Bird is on the Wing.&#148;-(Edward Fitzgerald, The Rubaiyat of Omar Khayyam)

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