Early embryology; chromosome count correction! (Introduction)

by David Turell @, Saturday, August 27, 2011, 02:37 (4624 days ago)

I'd love some Darwinist explain this phenomenon to me. How did evolution add this protective mechanism to embryoes that are in the 3 to 5 day range of development? How does natural selection operate in this situation? -http://www.sciencedaily.com/releases/2011/07/110705071546.htm

Early embryology; chromosome count correction!

by xeno6696 @, Sonoran Desert, Monday, August 29, 2011, 03:45 (4621 days ago) @ David Turell

I'd love some Darwinist explain this phenomenon to me. How did evolution add this protective mechanism to embryoes that are in the 3 to 5 day range of development? How does natural selection operate in this situation? 
> 
> http://www.sciencedaily.com/releases/2011/07/110705071546.htm-Cells have had an ability for self-repair-->Not everyone who gets sunburned develops cancer... I don't see how this challenges NS.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

Early embryology; chromosome count correction!

by David Turell @, Monday, August 29, 2011, 13:43 (4621 days ago) @ xeno6696

I'd love some Darwinist explain this phenomenon to me. How did evolution add this protective mechanism to embryoes that are in the 3 to 5 day range of development? How does natural selection operate in this situation? 
> > 
> > http://www.sciencedaily.com/releases/2011/07/110705071546.htm
> 
> Cells have had an ability for self-repair-->Not everyone who gets sunburned develops cancer... I don't see how this challenges NS.-What caused those cells to develop self-repair? These are blast cells in very early development. They are competing against their own death. I'm imagining this occuring in early evolution, as sex first appeared. This is epigenetics, not NS. Epigenetics had to be present very early as a self-defense process when organisms mated. NS is an after-thought, if you wish to use it by recognizing the organism can survive. Cells without self-defense will not.

Early embryology; clockwork construction plan

by David Turell @, Saturday, October 15, 2011, 14:59 (4574 days ago) @ David Turell

Any construction has to have a timing plan. Parts have to be set up to put in place in an orderly fashion. In a building you cannot sheetrock before wires and pipes in the wall are in place.

The same is true in the embryo, but in the beginning all one sees is a ball of blast cells. Eventual areas of the potential 'body' must be identified, placed properly and then development started. Here is the initial clockwork process:

http://www.sciencedaily.com/releases/2011/10/111013153943.htm

Early embryology; clockwork construction plan

by dhw, Sunday, October 16, 2011, 08:22 (4573 days ago) @ David Turell

DAVID: Any construction has to have a timing plan. Parts have to be set up to put in place in an orderly fashion. In a building you cannot sheetrock before wires and pipes in the wall are in place.
The same is true in the embryo, but in the beginning all one sees is a ball of blast cells. Eventual areas of the potential 'body' must be identified, placed properly and then development started. Here is the initial clockwork process:

http://www.sciencedaily.com/releases/2011/10/111013153943.htm

Another illustration of the astounding complexity of life’s mechanisms, but this one has a tremendous sting in the tail:

“The mechanism [the Hox clock] that we have discovered must be infinitely more stable and precise [than the Circadian and menstrual clocks]. Even the smallest change would end up leading to the emergence of a new species.”

I need guidance on this, but they seem to be homing in on the mechanism which actually drives evolution (as opposed to natural selection, which only ensures that innovations survive). It’s frustrating that they throw this titbit in at the last minute without further explanation, but perhaps David you could enlighten us with your own slant on that last sentence.

Early embryology; clockwork construction plan

by David Turell @, Sunday, October 16, 2011, 14:49 (4573 days ago) @ dhw


[/i]http://www.sciencedaily.com/releases/2011/10/111013153943.htm

Another illustration of the astounding complexity of life’s mechanisms, but this one has a tremendous sting in the tail:

“The mechanism [the Hox clock] that we have discovered must be infinitely more stable and precise [than the Circadian and menstrual clocks]. Even the smallest change would end up leading to the emergence of a new species.”

I need guidance on this, but they seem to be homing in on the mechanism which actually drives evolution (as opposed to natural selection, which only ensures that innovations survive). It’s frustrating that they throw this titbit in at the last minute without further explanation, but perhaps David you could enlighten us with your own slant on that last sentence.

I wouldn't over-interpret that quote. The construction mechanism of an enbryo must be just as precise as any consruction process. Imagine a Ford plant that went haywire and two wheels were on the roof and two wheels under the pan with the axles running thru the cab. It would drive at 90 degrees from normal but wouldn't survive in traffic. The quote relates to not creating monsters, which are not likely to survive, but maintain the purity of the species. You are right in the sense that a minor mistake can create variations, but those mistakes are precisely guarded against.

There is a philosophy of science KEY point here: if under Darwin theory evolution is a chance free-flowing process, advanced by variation, guarded by natural selection, why is there a mechanism in the genome to protect so assiduously the existing form of the species, seemingly not allowing the variation the Darwin theory needs?

Any answers Darwinists and natural selectionists?

Early embryology; clockwork construction plan

by dhw, Monday, October 17, 2011, 11:28 (4572 days ago) @ David Turell

Swiss scientists have discovered a mechanism (the Hox clock) which regulates the development of the embryo with such precision that “even the smallest change would end up leading to the emergence of a new species.” I asked David for his interpretation of this, as it seems to be absolutely crucial to evolutionary variety.

DAVID: The quote relates to not creating monsters, which are not likely to survive, but maintain the purity of the species. You are right in the sense that a minor mistake can create variations, but those mistakes are precisely guarded against.

One would have expected the scientists to say that even the smallest change would result in monsters which are not likely to survive, but the wording is quite specific: “the emergence of a new species”. The scientists claim that the Hox clock demonstrates the “extraordinary complexity of evolution”, but if your interpretation is correct, your next comment proves the exact opposite – namely that the Hox clock would PREVENT the emergence of new species, which is at the very heart of evolution:

DAVID: There is a philosophy of science KEY point here: if under Darwin theory evolution is a chance free-flowing process, advanced by variation, guarded by natural selection, why is there a mechanism in the genome to protect so assiduously the existing form of the species, seemingly not allowing the variation the Darwin theory needs?

You have always said you believe that evolution happened, which can only mean that new species developed from existing species by means of heritable variations caused by innovations and/or adaptations. This must be true regardless of the Chance v. ID debate, unless you now wish to argue for the separate creation of each species, which you have never done before. Epigenetics appear to provide an explanation for adaptation, but innovation remains a grey area. Have the Swiss scientists got it all wrong, or expressed themselves misleadingly, or are they really onto the source of the mutations that result in new species?

Early embryology; clockwork construction plan

by David Turell @, Monday, October 17, 2011, 15:35 (4572 days ago) @ dhw
edited by unknown, Monday, October 17, 2011, 15:46


DAVID: There is a philosophy of science KEY point here: if under Darwin theory evolution is a chance free-flowing process, advanced by variation, guarded by natural selection, why is there a mechanism in the genome to protect so assiduously the existing form of the species, seemingly not allowing the variation the Darwin theory needs?

dhw: You have always said you believe that evolution happened, which can only mean that new species developed from existing species by means of heritable variations caused by innovations and/or adaptations.

Of course evolution happened. But you are stuck with Darwin's explanation. Open your mind. Shapiro is touting epigenetics. Darwinists are horrified. Gould trumpeted punctuated equilibrium. Gould was such a powerful figure, Darwinists could only wince. Jeffrey H. Schwartz produced "Sudden Origins", but few Darwinists noticed. And then we have the Darwin-Theory-totally-unexplained Cambrian Explosion, preceded by Edicaran and Bilateran fronds and bags, seemingly organless. The 'trade secret' to resurrect Gould is fits and starts.

The point, which is in my book, is the mechanism by which evolution progressed is very much in doubt, and for those of us with doubt, the fits and starts, the huge gaps, are both fascinating and troubling. No one really knows, as yet, how evolution proceeds. My guess is that it is already coded in the genome, but not yet discovered. Epigenetics is a portion of it. But exact preservation of a species is also a part of evolution. Here is another new finding of such protection:
http://www.physorg.com/news/2011-10-reveals-role-rna-chromosomal-replication.html


Epigenetic changes don't always survive. but some do. And that is where natural selection fits in, late to the party, passive, but a necessary component.

Early embryology; clockwork construction plan

by dhw, Tuesday, October 18, 2011, 14:36 (4571 days ago) @ David Turell

dhw: You have always said you believe that evolution happened, which can only mean that new species developed from existing species by means of heritable variations caused by innovations and/or adaptations.

DAVID: Of course evolution happened. But you are stuck with Darwin's explanation. Open your mind.

Hey, hold on! Unless you disagree with the above description of the evolutionary process (if so, please tell me why), there is nothing in your post that I have opposed. I much prefer Gould’s punctuated equilibrium to Darwin’s gradualism, am open to the epigenetic explanation of adaptation, and am in agreement with you that no-one knows how evolution proceeds – by which I mean the mechanisms that have created such a vast variety of species. The problem that concerns me most is that of innovation, and it was you who drew our attention to the Hox clock. The researchers said that “even the smallest change would end up leading to the emergence of a new species”, and they described it as demonstrating the “extraordinary complexity of evolution”. I asked for your explanation, and you said they meant monsters which were unlikely to survive. That sits uneasily with the words they used, and would block, not facilitate evolution, so I asked if they’d got it wrong, expressed themselves misleadingly, or really had got to the source of the mutations that result in new species. (Mutations should not be taken as synonymous with randomness.) It’s obvious that exact preservation is essential to the survival of existing species, but I’m asking about the emergence of NEW species, and your guess is that changes have been coded into the genome. Is there no possible link here with the Hox clock? My questions are genuine, I’d never heard of the Hox clock till now, and I’m not pushing any particular theory. You should know me better!

Early embryology; clockwork construction plan

by David Turell @, Tuesday, October 18, 2011, 15:38 (4571 days ago) @ dhw

dhw: The researchers said that “even the smallest change would end up leading to the emergence of a new species”, and they described it as demonstrating the “extraordinary complexity of evolution”. I asked for your explanation, and you said they meant monsters which were unlikely to survive.......

Their meaning was my best guess. I think it was a throw away line. I apologize for misunderstanding your brief statement re the definition of evolution.

That sits uneasily with the words they used, and would block, not facilitate evolution, so I asked if they’d got it wrong, expressed themselves misleadingly, or really had got to the source of the mutations that result in new species. Is there no possible link here with the Hox clock? My questions are genuine, I’d never heard of the Hox clock till now, and I’m not pushing any particular theory. You should know me better!

Hox genes ( from the word homeobox) are the master planning genes in the genome for various parts of the musculoskeketal body and for organ systems.. They have great power, which is why they are under tight controls and they MUST act in time sequence. Thus the Hox clock, also a new term, and 'cute'.

Now you have made me wonder: could there be a major Hox controlling code that allows for the jumps that result in new species? Random mutations are too dangerous to relay on them for advancement. Not through the clock mechanism but a major coordinated set of changes in the Hox genes.

Early embryology; clockwork construction plan

by dhw, Wednesday, October 19, 2011, 12:32 (4570 days ago) @ David Turell

DAVID: Hox genes ( from the word homeobox) are the master planning genes in the genome for various parts of the musculoskeketal body and for organ systems.. They have great power, which is why they are under tight controls and they MUST act in time sequence. Thus the Hox clock, also a new term, and 'cute'.

Now you have made me wonder: could there be a major Hox controlling code that allows for the jumps that result in new species? Random mutations are too dangerous to rely on them for advancement. Not through the clock mechanism but a major coordinated set of changes in the Hox genes.

And you have made me wonder too. Thank you for this explanation, which is a real eye-opener, particularly with your use of the word “coordinated”. So many evolutionists gloss over the implications of “random mutations” as if the words themselves were an explanation, but any mutation would require coordination with the rest of the body if it were to be useful and to survive. If Hox genes control both organ systems and parts of the musculoskeletal structure, it doesn’t seem unreasonable to suppose that they would adjust themselves to accommodate any innovations. Maybe only one in a million such changes might actually work, but that would suffice over time to account for the variety of new organs and new species. It would also account for the general absence of transitional forms (because, as you say, the process would have to work by the “jumps” which Darwin categorically rejected) and even for species explosions like the Cambrian, since a change in atmosphere might make its presence felt on the whole Hox mechanism – perhaps including the clock? (That’s a question, because I’m way out of my depth here.)

It all brings me back to one of my hobbyhorses. Once we strip the word “mutations” of its association with “randomness”, isn’t this a view of evolution that might be acceptable on both sides of the fence? The theist can carry on claiming that the mutations have been coded into the Hox mechanism (or the UI has intervened), while the atheist can carry on claiming that they have come about through chance and/or environmental pressures. I certainly find this scenario immeasurably more convincing than the creationist insistence on separate creation, and Dawkins’ “smooth gradient up Mount Improbable”.

,

Early embryology; clockwork construction plan

by David Turell @, Wednesday, October 19, 2011, 16:06 (4570 days ago) @ dhw


It all brings me back to one of my hobbyhorses. Once we strip the word “mutations” of its association with “randomness”, isn’t this a view of evolution that might be acceptable on both sides of the fence? The theist can carry on claiming that the mutations have been coded into the Hox mechanism (or the UI has intervened), while the atheist can carry on claiming that they have come about through chance and/or environmental pressures. I certainly find this scenario immeasurably more convincing than the creationist insistence on separate creation, and Dawkins’ “smooth gradient up Mount Improbable”.


Your hobbyhorse creates more problems if it backs up. Where in the world would a master Hox gene come from to coordinate the formation of a single-celled organism to launch life? The genes we have now started somehow! I don't think I've seen a paper describing a Hox gene for epigenetic changes to the genome, but just what does control that area of genome activity?

Early embryology; clockwork construction plan

by dhw, Thursday, October 20, 2011, 15:53 (4569 days ago) @ David Turell

Dhw: It all brings me back to one of my hobbyhorses. Once we strip the word “mutations” of its association with “randomness”, isn’t this a view of evolution that might be acceptable on both sides of the fence? The theist can carry on claiming that the mutations have been coded into the Hox mechanism (or the UI has intervened), while the atheist can carry on claiming that they have come about through chance and/or environmental pressures.

DAVID: Your hobbyhorse creates more problems if it backs up. Where in the world would a master Hox gene come from to coordinate the formation of a single-celled organism to launch life? The genes we have now started somehow! I don't think I've seen a paper describing a Hox gene for epigenetic changes to the genome, but just what does control that area of genome activity?

All hobbyhorses create problems if they back up! But I’m only trying to follow through your own speculation that the “jumps” that lead to new species might have come about through a “major coordinated set of changes in the Hox genes.”

My (extremely amateur) speculation doesn’t concern a Hox gene for epigenetic changes, but the exact reverse. We know that epigenetic changes occur in response to changes in the environment. According to Wikipedia, dietary changes in mice have been seen to affect expression of the agouti gene (influencing fur colour and weight), and “more than 100 cases of epigenetic transgenerational inheritance phenomena have been reported in a wide range of organisms, including prokaryotes, plants and animals.” If environmental changes could affect one gene, why not others (Hox)? You say that “the genes we have now started somehow!” The same applies to all the complex organs we have now. And if the Hox genes plan organ systems and structures, they would appear to be the obvious “breeding ground” for innovative organs and, ultimately, new species. If there really was a link to epigenetic changes, wouldn’t this vastly reduce the unlikely role of chance? I’m talking only of evolution, not of the origin of life or of the mechanisms themselves, and I’m asking because I’m in no position to judge the feasibility of such speculation. So please feel free to shoot me down if it’s all nonsense.

Early embryology; clockwork construction plan

by David Turell @, Friday, October 21, 2011, 01:31 (4569 days ago) @ dhw


My (extremely amateur) speculation doesn’t concern a Hox gene for epigenetic changes, but the exact reverse............ If there really was a link to epigenetic changes, wouldn’t this vastly reduce the unlikely role of chance? I’m talking only of evolution, not of the origin of life or of the mechanisms themselves, and I’m asking because I’m in no position to judge the feasibility of such speculation. So please feel free to shoot me down if it’s all nonsense.

I don't think you have shot yourself in the foot to use a Texan term. I have stated before that I think epigenetics was there from the beginning of life. How else would organisims survived on the early Earth, just over being bombarded by asteroids, etc; going through rampant volcanism; markedly shifting temperatures, such as 'snowball Earth'; mobile continents changing climates and mountain ranges; marked sea level changes; and so on? And also what I published here about ten days ago, an early one-celled organism with an organelle:


"Wow!!! New studies suggest that an organelle was present in early life forms. But, bacteria aren't supposed to have organelles. Was early life more complex than we imagine? Was there pre-planning, i.e., intelligent design?

http://www.physorg.com/news/2011-10-universal-common-ancestor-complex-previously.html "

I'll bet there were Hox genes. A co-author of the article (James Whitfield, not the Hollywood actor (;>()) noted: "We may have underestimated how complex this common ancestor actually was." I' am willing to bet there were lots of genome parts around. In a sense there has to be planning for the future. Early amoebas didn't envision having arms and legs one day. Hox genes allow for sudden origins as I noted a few days ago. As you know I don't think chance played much of a role.

Early embryology; clockwork construction plan

by David Turell @, Tuesday, November 15, 2011, 06:05 (4543 days ago) @ David Turell

Video of fertilization until birth. And Darwinism can explain this?

http://www.youtube.com/watch?v=fKyljukBE70

Early embryology;size control

by David Turell @, Saturday, March 02, 2013, 23:19 (4070 days ago) @ David Turell

Peptide hormones related to insulin receptors are used, in the fruit fly, to control size of body parts in larval development.-http://www.the-scientist.com/?articles.view/articleNo/34435/title/Instant-Messaging/

Early embryology;sexing the brain

by David Turell @, Wednesday, April 01, 2015, 15:04 (3310 days ago) @ David Turell

It is methylation in a pre-optic area in the female, with testosterone effects:-http://www.the-scientist.com//?articles.view/articleNo/42555/title/Female-Brain-Maintained-by-Methylation/-"Differences in male and female rodent sexual behaviors are programmed during brain development, but how exactly this occurs is not clear. In the preoptic area (POA) of the brain—a region necessary for male sex behavior—the female phenotype results from repression of male-linked genes by DNA methylation, according to a study published today (March 30) in Nature Neuroscience.-"There is very little known about how the brain is masculinized—and even less about how it is feminized—even though the question has been studied for more than 50 years, said Bridget Nugent, study author and now a postdoctoral fellow at the University of Pennsylvania.-"These sex differences in the brain are programmed toward the end of fetal development, through to one week after birth in rodents. In males, testicular hormones drive masculinization of the brain; this was thought to occur by direct induction of gene expression by hormone-associated transcription factors. Because a feminized brain occurred in the absence of ovarian hormone signals, most researchers assumed that the female brain and behavior was a sort of default state, programmed during development when no male hormones are present. But the downstream mechanisms of how hormones can modify gene expression were not previously known.-"'This study reveals that DNA methylation plays an important role in regulating sexual differentiation,” said Nirao Shah, who also studies the neural basis for sex-specific behaviors at the University of California, San Francisco, but was not involved with the work."

Early embryology;merging male and female DNA

by David Turell @, Wednesday, April 01, 2015, 15:17 (3310 days ago) @ David Turell

Sperm meets egg, DNA's mix. This is how they merge:-http://phys.org/news/2015-04-heterochromatin-formation-onset-life.html-"Antoine Peters and his group at the Friedrich Miescher Institute for Biomedical Research (FMI) have elucidated the mechanisms controlling the packaging of chromatin in the early embryo. They have identified two molecular pathways that direct heterochromatin formation around centromeres in a manner dependent on the parental origin of the DNA.
********
"These findings are noteworthy as they reflect differences in the preparation of chromatin for fertilization during male and female gametogenesis. During the development of the male gamete, the DNA packaging is substantially altered so that the whole genome can fit in the tiny head of the sperm. After fertilization, the packaging of paternal DNA is reprogrammed, in a series of steps, to the canonical form present in oocytes and somatic cell types. As the embryo grows, the differences between maternal and paternal chromatin thus disappear. Peters comments: "We are intrigued by the remarkable diversity in heterochromatin formation at the onset of life. Our current research is focusing on how the mechanisms described may contribute to gene regulation during early embryogenesis.'"- Read more at: http://phys.org/news/2015-04-heterochromatin-formation-onset-life.html#jCp -I show the embryologic molecular genetic reactions to illustrate just how complex the biochemistry has to be. And tell me how this developed by chance.

Early embryology; making nerve networks

by David Turell @, Tuesday, May 19, 2015, 14:39 (3262 days ago) @ David Turell

Neurons guide each other:-http://medicalxpress.com/news/2015-05-nerve-cells.html-
"When nerve cells form in an embryo they don't start off in the right place but have to be guided to their final position by navigating a kind of molecular and cellular "map" in order to function properly. In a recent research study published in Nature Communications, neurobiologist Sara Wilson of Umeå University found that during embryonic development different parts of the nerve cell are important for guiding other nerve cells into their physical positions.
 
"'We found nerve cells do this in two ways, either acting as barriers preventing cell bodies to move further than they need to, or by acting as guides opening a corridor that the cell bodies can travel along", she says.-"The nervous system is analogous to a biological "computer" with different nerve cells forming connections that continuously send neural information around the spinal cord, brain and body and back again. Each nerve cell has a kind of "GPS coordinate" and exactly where nerve cells are physically located is very important so they can connect correctly with other nerve cells.-*****-"'This means the axons from some nerve cells are influencing the position of the cell bodies of other nerve cells meaning that the nerve cells are creating a "map" for other nerve cells to find their way" Sara Wilson says.-"'This is the first time that axons have been shown to act as barriers and it could have important implications for understanding how the nervous system forms in all animals, including humans" Sara Wilson concludes.-"Overall, this work and other work from the group focuses on understanding the mechanisms (genetic, cellular and molecular) of how the precise "anatomy" of the nervous system first forms and how that influences neuronal function and dysfunction. This basic science research has important medical implications for understanding the cause of some neurodevelopmental disorders: For example do the genes that are associated with such disorders generally control cell body guidance and is that what leads to dysfunction?"
-Raises dhw's issue of cell cooperation; under gene control or independent cell cooperation?

Early embryology; making nerve networks

by Balance_Maintained @, U.S.A., Tuesday, May 19, 2015, 16:51 (3262 days ago) @ David Turell

The critical question is whether that behavior is in the DNA, or if it originates within the cell. If it is DNA, we have STRONG evidence for preplanning. If it arises automagically in the cell, then it is STRONG evidence for intelligent cells

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

Early embryology; making nerve networks

by David Turell @, Tuesday, May 19, 2015, 17:09 (3262 days ago) @ Balance_Maintained

Tony: The critical question is whether that behavior is in the DNA, or if it originates within the cell. If it is DNA, we have STRONG evidence for preplanning. If it arises automagically in the cell, then it is STRONG evidence for intelligent cells-From my viewpoint, since a given body plan is a body plan repeatedly reproduced in embryology, the creation from one cell to complete organism is thoroughly planned. In human anatomy there are variations all the time, so that the human anatomy texts are an average of cadaver findings with vessel and nerve pathways. For example Meckel's diverticulum, a remnant of the umbilical cord to the intestine is present 2% of the time. I have an artery an my left hand on top of a palmer muscles instead of under it. Right course but slightly off position. It is obvious parts develop under guidance, which has to be genetic, as different cell types take care to express different genes characteristic of the specific type.

Early embryology; making a formed body

by David Turell @, Thursday, May 21, 2015, 00:20 (3261 days ago) @ David Turell

How to form a body with head and tail and two symmetrical sides:-http://www.evolutionnews.org/2015/05/heads_or_tails096081.html-"These signaling pathways pre-date the animals that use them now. Based on genomic analyses, these signaling molecules have been around well before the first bilaterian animals ever existed. They are expressed in organisms that lack these body axes completely. Even more surprising, many of the molecules used to make complex structures such as muscles, eyes, and brains also predate their use for those purposes.-"What were these signaling molecules used for before there was a left and right, a top and bottom, a head and tail? How did they come to be at all, and why did they persist until they could be co-opted for the establishment of body axes? It has been suggested that they were used to establish body sections in the earliest multicellular animals, but that only pushes the question back a step. Where did that use come from? How did the signaling pathways start?-"With these questions, I conclude the series I began to address the white space in evolutionary thinking -- how to account for the evolution of C. elegans. First there is the problem of getting a cell, then of getting a eukaryotic cell, then of getting a multicellular animal, and now of getting one with a head and a tail and multiple cell types. Saying C. elegans didn't have to solve the problem all at once is merely to suggest that the problems are easier if taken one step at a time. They are not."

Early embryology; making a brain

by David Turell @, Saturday, November 12, 2016, 19:33 (2719 days ago) @ David Turell

How to take stem cells and create the complexity of a brain with its different types of cells is now begun to yield to research:

https://www.sciencedaily.com/releases/2016/11/161111120737.htm

"It is mind-boggling to imagine how our brain develops from just a handful of cells at the early embryo into a highly convoluted biochemical and bioelectric system comprising more than 100 billion neurons in adults. Scientists at the Institute of Molecular Biotechnology (IMBA) in Vienna have published new research in EMBO Journal, in which they reveal how cells are instructed by a small RNA molecule to shape the complex layered structures of developing mouse brains.

"When stem cells divide to form new tissues and organs, they have to position their cell division apparatus in a specific orientation to position their daughter cells at sites where they experience different fate cues defining their subsequent function. The newly formed cells may then go on to take a specialised function -- in the brain, for example, they can become various types of neurons to generate and transmit electrical impulses -- or stay stem cells that will keep dividing to generate more cells. Failure to correctly induce fate decisions leads to multiple developmental brain disorders.

***

"Fededa describes the approach: "By visualizing the spindle of the cells with a fluorescent marker in live cells, we observed that a family of six microRNAs called miR-34/449 influenced the spindle orientation during cell division. We then tested whether these micro-RNAs could also influence the orientation of mitotic spindles in developing mouse brains, using methodology established in Jürgen Knoblich's laboratory at IMBA. Indeed, we found that after deletion of miR-34/449 genes, mice developed smaller brains and these contained a larger proportion of stem cells called radial glial cells. This showed us that radial glial cells can grow relatively normally, but suggested that they are unable to further differentiate into more complex cells. We therefore concluded that miR-34/449 microRNAs must be required for normal brain development."

"The scientists at IMBA compared the gene expression patterns in cells with or without miR-34/449 and discovered a difference in the expression of a protein called JAM-A. This protein was interesting, as it was previously shown to have a role in orienting the mitotic spindle in other tissues. By engineering a JAM-A gene version that is insensitive to miR-34/449, the team at IMBA was able to pinpoint its relevance for mitotic spindle orientation. "Our findings show that in developing mouse brains, miR-34/449 regulates JAM-A to ensure the correct orientation of dividing cells and accurate formation of brain layers" concludes Daniel Gerlich. "The current research provides insights into the role of micro-RNAs in brain development, but similar mechanisms might be at place in other organs.'"

Comment: These are genomic proteins working automatically to achieve a proper organization of the brain. Imagine this throughout the embryo. Not by chance!

Early embryology; making a formed body

by David Turell @, Monday, December 05, 2016, 23:58 (2696 days ago) @ David Turell

Embryonic stem cells take both biochemical and mechanical clues to decide what to become:

http://phys.org/news/2016-12-powerful-technique-reveals-mechanical-environment.html

"Whether building organs or maintaining healthy adult tissues, cells use biochemical and mechanical cues from their environment to make important decisions, such as becoming a neuron, a skin cell or a heart cell.

***

"The growth and development of a living organism is a choreography of cellular movements and behaviors that follow internal genetic guidelines and specific biochemical and mechanical signals. All these events conspire over time to create a variety of complex forms and textures that make our tissues and organs functional.

***

"'Growing stem cells on synthetic surfaces with different levels of compliance showed that stem cells would become a different cell type depending solely on the mechanical environment they perceive. If you put embryonic stem cells on a substrate like Jell-O—mechanically similar to brain tissue—they turn into neurons. But if you put them on something harder, similar to embryonic bone, they turn into bone-like cells."

***

"The scientists applied their new technique to study how the vertebrate body axis is mechanically built. Using embryos of zebrafish, which was selected for its rapid development and optical transparency, they could show that the mechanical properties of the tissue change along the body axis, facilitating the extension of the body at its posterior end. Inserting magnetic droplets at different locations in the tissue, and generating forces by applying a magnetic field to the droplets, the researchers showed that the tissue behaves like a fluid while growing, with similar mechanical characteristics as thick honey. The data showed that the tissue is more fluid at the posterior end where it was growing, and becomes less fluid far from the growing region.

"'It is similar to glass-blowing," said Campàs. "The tissue is more fluid in growing regions and 'fixes' its shape by becoming less fluid where it does not need to expand."

"The scientists' findings have wide implications in the effort to understand how organs are sculpted into their shapes and how cells respond to their native mechanical environment both in healthy tissues and during disease. The Campàs lab is studying several of these questions, including how limbs are built and how mechanical changes in tumors affect the behavior of malignant cells and the growth of the tumor."

Comment: This is not growth or development by cell committee. Each cell has to respond exactly to the stimuli it receives chemically, mechanically and genetically to form a proper organisms from early embryo to completed form with proper functions. All automatic. Logically multicellularity develops from single cells. If those single cells were originally basically automatic in their responses to stimuli, it is easy to imagine how they agglomerated into multicellular with full cooperative behavior. If they were accustomed to act independently, necessarily they had to give up that independence to join in a multiple cell, multiple organ animal. To me it seems like multicellularity occurred more easily if the original joining cells were automatic.

Early embryology; making a formed body

by dhw, Tuesday, December 06, 2016, 10:28 (2695 days ago) @ David Turell

DAVID’S comment: Logically multicellularity develops from single cells. If those single cells were originally basically automatic in their responses to stimuli, it is easy to imagine how they agglomerated into multicellular with full cooperative behavior. If they were accustomed to act independently, necessarily they had to give up that independence to join in a multiple cell, multiple organ animal. To me it seems like multicellularity occurred more easily if the original joining cells were automatic.

I don’t know why you find it easy to imagine cells originally agglomerating and cooperating automatically. Why would they bother if they were functioning independently? Of course they had to give up their independence in what I have called the quest for improvement. That is the very essence of Margulis’s argument that cooperation is a crucial driving force in evolution – and she believed in cellular intelligence. It may seem to you that multicellularity occurred more easily if it was automatic, because you are convinced that your God organized it. But it would have occurred just as easily if your God had given cells the intelligence to work out new forms of life to cope with or exploit an ever changing environment.

Early embryology; making a formed body

by David Turell @, Tuesday, December 06, 2016, 14:32 (2695 days ago) @ dhw

DAVID’S comment: If they were accustomed to act independently, necessarily they had to give up that independence to join in a multiple cell, multiple organ animal. To me it seems like multicellularity occurred more easily if the original joining cells were automatic. [/i]

dhw: It may seem to you that multicellularity occurred more easily if it was automatic, because you are convinced that your God organized it. But it would have occurred just as easily if your God had given cells the intelligence to work out new forms of life to cope with or exploit an ever changing environment.

Your 'if God' comment wants cellular intelligence to plan new forms. Only minds can make new architectural new forms which require complex planning to succeed..

Early embryology; zygote DNA controls

by David Turell @, Tuesday, December 06, 2016, 19:05 (2695 days ago) @ David Turell

When sperm and egg meet they formed a combined DNA in a cell called a zygote. From this union any type of necessary cell is developed. A liver cell is not a kidney cell because they have turned on different codes in their DNA. Therefore a zygote's DNA is kept under control as stem cells are formed and those controls are removed on arrival at the site of the new organ formation. this research is a hint of how it all must work:

https://www.sciencedaily.com/releases/2016/12/161206094241.htm

"'We are particularly interested in the events that are required when the cells are to divide so many times and develop in so many different ways, for example cells from the skin, and the liver, and the heart," the researcher explains. In a current study, she and her team approached this problem by examining the so-called chromatin, which refers to the DNA and the proteins (histones) around it. "We looked at how certain histones are changed after fertilization, which allowed us to explain a new mechanism."

***

"The authors discovered that the molecule Suv4-20h2, a so-called histone methyltransferase, travels over the chromatin and attaches small chemical changes (dubbed methyl groups) to the histones. When the addition of these chemical changes occurs, the cell is constrained in its division and development, Torres-Padilla explains. But once fertilization occurs, the attachments disappear and the fertilised ovum can develop into a new organism.

"In order to confirm these results, the researchers used an experimental model to test the effect of keeping the Suv4-20h2 active in the fertilized ovum. "We were able to demonstrate that in this case, the methyl groups remain on the histones," explains first author Andre Eid, doctoral candidate at the IES. "This arrests the development and the cells did not progress beyond the first division."

***

"'In further experiments, the team was able to show that this mechanism is probably based on the fact that the methyl groups on the histones lead to a defect during the duplication of the genetic material, referred to as replication. This defect causes then a replication 'check point', whereby the cell cycle comes to a standstill.
"Our results have given us insight into the complex connections between the chromatin and the ability of cells to develop into other types of cells -- so-called totipotency," Torres-Padilla states as she puts the results into perspective. This is an important step both for human embryology."

Comment: The control molecule over methylation is an enzyme, which means it is a giant molecule, again raising the issue of how did evolution find it for its specific functional capacities? This shows that methylation is not just epigenetic controls but embryological controls to allow stem cells from a dividing zygote to differentiate into specific cell types, hundreds of them. Not be chance!

Early embryology; using giant 3-5 part enzymes

by David Turell @, Friday, January 27, 2017, 05:02 (2643 days ago) @ David Turell

The question is how did evolution every invent the complexity seen in enzymes used early in development of the embryo. The giant molecules had to all be put together at once to be effective in helpin the embryo:

http://www.agnosticweb.com/index.php?mode=posting&id=23654&back=entry

"Very early embryos (at the two- or four-cell stage in mouse or human respectively) undergo a critical transition: they have to go from relying on RNAs and proteins loaded into the egg before fertilization by the mother, to making their own RNA and protein.

"The phenomenon is called embryonic genome activation. In order to activate their genomes, embryos have to remove maternal and paternal epigenetic modifications and create new ones appropriate to the embryonic genome.

"such major reprogramming of the genome requires metabolites such as α-ketoglutarate, essential for protein and DNA demethylation, acetyl-CoA required for protein acetylation, [and] ATP for phosphorylation of substrates.

"Normally these metabolites are made by specialized enzymes that are part of the tri-carboxylic acid (TCA) cycle. The TCA cycle takes place in the mitochondria, specialized organelles that produce energy for the cell. The mitochondria take up a compound called pyruvate, which is then converted to acetyl-CoA by the enzyme pyruvate dehydrogenase (PDH), and the resulting acetyl-CoA enters the TCA cycle, to produce the other metabolites and ATP.

***

"Pyruvate is absolutely required for development to proceed. It can come from the fluid in the oviduct -- it can be imported by the embryo. PDH is also absolutely required for development. But where is PDH enzyme activity if not in the mitochondria? And what about the TCA cycle enzymes?

***

"I looked up pyruvate dehydrogenase and found to my astonishment that it is not one enzyme but an enormous complex of three different enzymatic activities clustered together on a cube-shaped core of 24 units, or alternatively a dodecahedral core of 60 units. The enzymes work together to turn pyruvate into acetyl CoA in a three-step process, handing off to each other as the reaction proceeds.

"Let me emphasize: this is a core enzymatic activity. The TCA cycle is important to the process by which cells make ATP, the energy currency of the cell. PDH is the link that connects glycolysis, the breakdown of sugars, to the TCA cycle. Without it cells would obtain much less energy from the breakdown of sugars. But it is also essential for embryonic development past the two- to four-cell stage (in mice and humans, and presumably other mammals).

"It's also essential for bacteria like E. coli, where it has a similar structure and three-step reaction. This is an ancient enzyme complex, yet of great sophistication.

"How could early cells have assembled such a structure, bringing together separate enzyme activities to work cooperatively? Getting enzymes to assemble into multi-subunit structures is non-trivial, requiring multiple side-chain interactions and three-dimensional fit. Even further, the genes encoding these enzymatic activities of the PDH complex are clustered together into a single operon in E. coli. They are neighbors, side-by-side in E. coli's genome, and co-expressed. Of course, that's how an intelligent designer would do it. What's the use of part of a complex? Make the enzymes together and assemble them into a factory to turn pyruvate into acetyl CoA -- it's much more efficient.

***

"Update: Since I wrote this piece I discovered that according to Voet and Voet's biochemistry textbook, PDH complex carries out five enzymatic activities to produce acetyl-CoA, not three, and they state that the PDH complex is the largest eukaryotic enzyme complex known."

Comment: the usual chicken and egg problem in the chemistry of evolution. How was this complex developed to support fetus development. It had to be all at once, not step by step, which would not produce embryos. Design agency is an obvious answer to the problem, not natural chance.

Early embryology; not wholly guided by DNA

by David Turell @, Saturday, February 11, 2017, 23:32 (2628 days ago) @ David Turell

Membranes form axes and contain formation information. DNA does not contain this information:

http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2

"Abstract: Embryo development (ontogeny) depends on developmental gene regulatory networks (dGRNs), but dGRNs depend on preexisting spatial anisotropies that are defined by early embryonic axes, and those axes are established long before the embryo’s dGRNs are put in place. For example, the anterior-posterior axis in Drosophila and the animal-vegetal axis in Xenopus and echinoderms are initially derived from the architecture of the ovary through processes mediated by cytoskeletal and membrane patterns rather than dGRNs. This review focuses on plasma membrane patterns, which serve essential ontogenetic functions by providing targets and sources for intracellular signaling and transport, by regulating cell-cell interactions, and by generating endogenous electric fields that provide three-dimensional coordinate systems for embryo development. Membrane patterns are not specified by DNA sequences. Because of processes such as RNA splicing, RNA editing, protein splicing, alternative protein folding, and glycosylation, DNA sequences do not specify the final functional forms of most membrane components. Still less does DNA specify the spatial arrangements of those components. Yet their spatial arrangements carry essential ontogenetic information. The fact that membrane patterns carry ontogenetic information that is not specified by DNA poses a problem for any theory of evolution (such as Neo-Darwinism) that attributes the origin of evolutionary novelties to changes in a genetic program—whether at the level of DNA sequences or dGRNs. This review concludes by suggesting that relational biology and category theory might be a promising new approach to understanding how the ontogenetic information in membrane patterns could be specified and undergo the orchestrated changes needed for embryo development.

***

"biological membranes are patterned in complex ways. Those patterns serve important functions in cells, tissues and embryos. The following sections summarize the roles of plasma membrane patterns in (a) providing targets and sources for intracellular transport and signaling, (b) regulating cell-cell interactions by means of a “sugar code,” and (c) generating endogenous electric fields that provide three-dimensional coordinate systems for ontogeny.

***

"So membrane patterns—the three-dimensional arrangements of membrane-associated proteins, lipids and carbohydrates, as they change over time—carry essential ontogenetic information. Yet (as I demonstrate below) the information carried by membrane patterns cannot be reduced to sequence information in DNA, for at least two reasons. First, the vast majority of proteins in eukaryotes are not completely specified by DNA sequences. Second, even if DNA sequences completely specified all proteins, DNA would not specify their spatiotemporal arrangements in membranes.

***

"Thus, according to Cavalier-Smith, the idea that the genome contains all the information needed to make an organism “is simply false. Membrane heredity, by providing chemically specific two-dimensional surfaces with mutually conserved topological relationships in the three spatial dimensions, plays a key role in the mechanisms that convert the linear information of DNA into the three-dimensional shapes of single cells and multicellular organisms. Animal development creates a complex three-dimensional multicellular organism not by starting from the linear information in DNA... but always starting from an already highly complex three-dimensional unicellular organism, the fertilized egg, which membrane and DNA heredity together have perpetuated”.

***

"In embryo development, however, membrane heredity cannot be the whole story. During ontogeny many new membrane patterns arise that cannot be traced back to patterns in pre-existing membranes. The new patterns do not arise haphazardly; they are highly specified. Yet there is no evidence that they—any more than the patterns that precede them—are determined by a program in the organism’s DNA. Whether membrane patterns are templated or form de novo, they carry ontogenetic information that is specified independently of DNA sequences. This fact has serious implications both for evolutionary theory and for our understanding of ontogeny.

***

" In the 1950s, mathematical biologists Nicholas Rashevsky and Robert Rosen introduced a new approach they called “relational biology” [432−434]. Unlike Newtonian biology, which gives ontological priority to matter (i.e., molecules), relational biology (as the name implies) gives ontological priority to the relations that constitute an organized system. Although molecular biology has been successful at a certain level, its methods involve discarding the organization of a cell while keeping the matter. Yet the former, once discarded, cannot be recovered from the latter—and living things are fundamentally characterized by their organization."

Comment: This paper says DNA does not wholly control the embryo formation, but that membranes, like the walls of a house, organizes areas and rooms in a coordinated whole. DNA makes proteins, not spatial relations

Early embryology; process of egg to embyo

by David Turell @, Saturday, June 17, 2017, 00:35 (2503 days ago) @ David Turell

A fascinating dance of enzymes:

https://www.sciencedaily.com/releases/2017/06/170614210915.htm

"The transition from an egg to a developing embryo is one of life's most remarkable transformations. Yet little is known about it. Now Whitehead Institute researchers have deciphered how one aspect -- control of the all-important translation of messenger RNAs (mRNAs) into proteins -- switches as the egg becomes an embryo. That shift is controlled by a beautiful mechanism, which is triggered at a precise moment in development and automatically shuts itself off after a narrow window of 20 to 90 minutes.

"As an egg develops, it stockpiles mRNAs from the mother because it will not have time to create new mRNAs during the rapid development of a very early embryo. When fertilized the egg becomes an embryo, the stashed maternal mRNAs are pressed into service for a brief window before the embryo starts transcribing its own mRNAs. This change occurs very early; in humans, only two to four cell divisions occur before this transition is executed. Whitehead Member Terry Orr-Weaver studies the control of translation of maternal mRNAs in the model organism Drosophila, or the fruit fly.

"In the current research, Orr-Weaver and her lab determined that key to the transition are the three molecules that form the enzyme PNG kinase: PNG, PLU, and GNU. Orr-Weaver describes PNG and PLU as "tight buddies" that are always locked together, including in the mature egg. At that point in development, GNU has phosphate molecules tacked to it, which impede its binding to PNG-PLU.

"When an egg is activated, levels of another enzyme that adds phosphates to GNU in the egg precipitously drop, allowing GNU to lose its phosphates and bind to PNG-PLU. Once together, the trio comprises the PNG kinase that triggers the translational control of the maternal mRNAs. Because PNG kinase also triggers the break down of GNU, the kinase self-destructs, which quickly and irreversibly squelches the translation of maternal mRNAs. This elegant feedback loop and the switch it controls are described in an article in eLife. (my bold)

"The design of this transition could tell scientists more about how human cells work and embryos develop. For example, the switch could be a model for how cells massively and globally change mRNA translation. Also, similar kinase activity during early development has been noted in worms, which may mean that a comparable approach is used in other organisms, including humans."

Comment: Note the feedback loop using giant enzyme molecules. All parts of the loop must be put together at once. There is no way it can be constructed stepwise. Evolving one step or one enzyme provides no advantages and by itself is useless, and there would be reason for natural selection to retain it. God at work. Sexual reproduction is not explained by Darwin.

Early embryology; glial cell guidance

by David Turell @, Friday, September 01, 2017, 17:20 (2426 days ago) @ David Turell

In fruit flies glial cells guide connecting neural connections to the brain:

https://cosmosmagazine.com/biology/how-glial-cells-wire-up-a-fly-s-eye

"Glials cells, or glia, are cells that were long thought to be nothing more than the glue or connective tissue that holds the hard-working neurons together. They are now understood to also provide nutrition and oxygen to the neurons, and also remove pathogens and detritus from the brain.

"Now Vilaiwan Fernandes and colleagues have found new role for them: wiring up the fly eye during development, to create the neural circuits that map visual space.

"The fly’s visual system is made up of modular circuits that process visual inputs: each of the 800 parts of the fly’s compound eye sends information to a corresponding group of neurons in the optic lobe of the brain. Connecting the photoreceptors with the optic lobe neurons requires precise coordination during development. (my bold)

"The researchers found that cells called wrapping glia, which grow in a sheath around photoreceptor axons that project into the optic lobe, act as relay stations in this coordinated growth.


"Stimulation by a photoreceptor growth factor triggers the glia to produce insulin-like peptides, and these peptides guide optic lobe neurons to develop into connecting terminals for photoreceptors.

"In the image above, development of the retina (top) is coordinated with development of the optic lobe region of the brain (sphere below). All neurons are marked by yellow and their axon projections in cyan; magenta in the optic lobe marks the specific region of the brain where the neuronal differentiation is regulated by glia."

Comment: Note my bold. Embryology must follow a plan. How did evolution develop those plans for reproduction? This is a major question current theory does not answer, because there is so much biochemical signaling that is used to guide the production and migration of newly minted cells. Embryology requires design, and is the best argument for God I can find.

Early embryology; glial cell guidance

by dhw, Saturday, September 02, 2017, 12:58 (2425 days ago) @ David Turell

DAVID: In fruit flies glial cells guide connecting neural connections to the brain:
https://cosmosmagazine.com/biology/how-glial-cells-wire-up-a-fly-s-eye

DAVID’S comment: Embryology must follow a plan. How did evolution develop those plans for reproduction? This is a major question current theory does not answer, because there is so much biochemical signaling that is used to guide the production and migration of newly minted cells. Embryology requires design, and is the best argument for God I can find.

Thank you for yet another eye-opening article. I agree that such complexities are the best arguments for your God. If he does exist, the question whether he preprogrammed them all 3.8 billion years ago, personally dabbled them, or created a mechanism enabling organisms to work out their own developments remains wide open.

Early embryology; glial cell guidance

by David Turell @, Saturday, September 02, 2017, 14:59 (2425 days ago) @ dhw

DAVID: In fruit flies glial cells guide connecting neural connections to the brain:
https://cosmosmagazine.com/biology/how-glial-cells-wire-up-a-fly-s-eye

DAVID’S comment: Embryology must follow a plan. How did evolution develop those plans for reproduction? This is a major question current theory does not answer, because there is so much biochemical signaling that is used to guide the production and migration of newly minted cells. Embryology requires design, and is the best argument for God I can find.

dhw: Thank you for yet another eye-opening article. I agree that such complexities are the best arguments for your God. If he does exist, the question whether he preprogrammed them all 3.8 billion years ago, personally dabbled them, or created a mechanism enabling organisms to work out their own developments remains wide open.

'Wide open" only for you. Giving organisms mechanisms for their own development present the same problems of complexity that have you recognize the 'best arguments' for God. Why have Him give a 'mechanism' which is second-hand design? If He could do that why not directly do it firsthand? Makes a lot more sense.

But besides God's abilities, there is no other obvious way to explain embryologic development. Chance? Never. Your suggestion?

Early embryology; glial cell guidance

by dhw, Sunday, September 03, 2017, 14:01 (2424 days ago) @ David Turell

dhw: […] I agree that such complexities are the best arguments for your God. If he does exist, the question whether he preprogrammed them all 3.8 billion years ago, personally dabbled them, or created a mechanism enabling organisms to work out their own developments remains wide open.

DAVID: 'Wide open" only for you. Giving organisms mechanisms for their own development present the same problems of complexity that have you recognize the 'best arguments' for God. Why have Him give a 'mechanism' which is second-hand design? If He could do that why not directly do it firsthand? Makes a lot more sense.

Why second-hand? Do you regard the human design of computers, spaceships, literature, music etc. as second-hand? According to you, your God created the human brain which is autonomously capable of complex design. But you insist that he could not possibly have created a mechanism enabling other organisms to make innovative changes to their own bodies (although they ARE capable of autonomously making minor adaptations). Why does your God’s personal design of every single innovation, lifestyle and natural wonder that ever existed make more sense than him designing a mechanism enabling them to do their own designing?

DAVID: But besides God's abilities, there is no other obvious way to explain embryologic development. Chance? Never. Your suggestion?

I keep telling you my suggestion! And it is not chance.

Early embryology; glial cell guidance

by David Turell @, Sunday, September 03, 2017, 15:41 (2424 days ago) @ dhw

dhw: […] I agree that such complexities are the best arguments for your God. If he does exist, the question whether he preprogrammed them all 3.8 billion years ago, personally dabbled them, or created a mechanism enabling organisms to work out their own developments remains wide open.

DAVID: 'Wide open" only for you. Giving organisms mechanisms for their own development present the same problems of complexity that have you recognize the 'best arguments' for God. Why have Him give a 'mechanism' which is second-hand design? If He could do that why not directly do it firsthand? Makes a lot more sense.

dhw: Why second-hand? Do you regard the human design of computers, spaceships, literature, music etc. as second-hand? According to you, your God created the human brain which is autonomously capable of complex design. But you insist that he could not possibly have created a mechanism enabling other organisms to make innovative changes to their own bodies (although they ARE capable of autonomously making minor adaptations). Why does your God’s personal design of every single innovation, lifestyle and natural wonder that ever existed make more sense than him designing a mechanism enabling them to do their own designing?

DAVID: But besides God's abilities, there is no other obvious way to explain embryologic development. Chance? Never. Your suggestion?

dhw: I keep telling you my suggestion! And it is not chance.

Your inventive mechanism proposal would need a human-brain-like ability as you describe above. That implies all the complexity of our brain, not found in current studies of the genome. Why do you constantly slough aside the point that development of complex changes, as seen in the gaps in evolution, require foresight of the future needs in order to start designing the plans for those changes? God gave us the brain to do that so the designs are not His second-hand. I'm convinced your nebulous hypothesis is just that in our theistic-mode discussion. How do you explain evolution without God present?

Early embryology; branching patterns

by David Turell @, Thursday, September 21, 2017, 19:34 (2406 days ago) @ David Turell

As organs develop their ducts follow simple branching patterns:

https://phys.org/news/2017-09-scientists-reveal-beautiful-simplicity-underlying.html

"Branching patterns occur throughout nature - in trees, ferns and coral, for example - but also at a much finer scale, where they are essential to ensuring that organisms can exchange gases and fluids with the environment efficiently by the maximising the surface area available.

"For example, in the small intestine, epithelial tissue is arranged in an array of finger-like protrusions. In other organs, such as kidney, lung, mammary glands, pancreas and prostate, exchange surfaces are packed efficiently around intricate branched epithelial structures.

"'On the surface, the question of how these structures grow - structures that may contain as many as 30 or 40 generations of branching - seems incredibly complex," says Professor Ben Simons, who led the study.

***

"While there's a collective decision-making process going on involving multiple different stem cell types, our discovery that growth occurs almost at the flip of a coin suggested that there may be a very simple rule underpinning it," says Professor Simons.

***

"there was very little crossover of the branches - ducts seemed to expand to fill the space, but not overlap. This led them to conjecture that the ducts were growing and dividing, but as soon as a tip touched another branch, it would stop.

"'In this way, you generate a perfectly space-filling network, with precisely the observed statistical organisation, via the simplest local instruction: you branch and you stop when you meet a maturing duct," says Dr Hannezo, a Sir Henry Wellcome Postdoctoral Fellow based at the Gurdon Institute. "This has enormous implications for the basic biology. It tells you that complex branched epithelial structures develop as a self-organised process, reliant upon a strikingly simple, but generic, rule, without recourse to a rigid, pre-determined sequence of genetically programmed events." (my bold)

"Although these observations were based on the mammary gland epithelium, by using primary data from Dr Rosemary Sampogna at Columbia University, Professor Anna Philpott in Cambridge and Dr Rakesh Heer at Newcastle University, the researchers were able to show that the same rules governed the embryonic development of the mouse kidney, pancreas and human prostate.

"'In the mammary gland, you have a hundred or more fate-restricted stem-like cells participating in this bifurcation-growth-bifurcation process, whereas in the pancreas it's just a handful; but the basic dynamics are the same," says Professor Simons. "The model is aesthetically beautiful, because the rules are so simple and yet they are able to predict the complex branching patterns of these structures."

***

"A century after the publication of On Growth and Form, it's exciting to see how the concepts of self-organisation and emergence continue to offer fresh perspectives on the development of biological systems, framing new questions about the regulatory mechanisms operating at the cellular and molecular scale," Professor Simons adds.

"While it may be too early to tell whether similar rules apply to other branched tissues and organisms, there are interesting parallels: branching in trees appears to follow a similar pattern, for example, with side branches growing and bifurcating until they are shaded or until they are screened by another branch, at which point they stop."

Comment: Many of these branching patterns follow fractal formulas. I have always had the opinion that God set up patterns to be followed in early evolution. This study certainly shows that much of it can be automatically controlled without much genetic input.

Early embryology; brain development controls

by David Turell @, Thursday, September 28, 2017, 17:37 (2399 days ago) @ David Turell

During early brain development modified mRNA's control development by their ability to produce a variety of proteins:

https://medicalxpress.com/news/2017-09-brain-birth-tightly-rna-modification.html

"A chemical tag added to RNA during embryonic development regulates how the early brain grows, according to research from the Perelman School of Medicine at the University of Pennsylvania.

***

"In the last few years, scientists have discovered chemical modifications to messenger RNA (mRNA) across the genome at certain sites and found that these changes are dynamic, meaning that a specific chemical group is added and taken off by enzymes in a regular, patterned way. The chemical group studied in the Cell paper, m6A, is the most prevalent modification to mRNA in human cells.

***

"The current thinking is that a tightly controlled molecular process guides the complicated development of the brain before birth—and that the process relies on a precise sequence of genes being turned on and off. However, even subtle mistakes in this process can become amplified later. Song likens this process to a train moving onto the wrong track and ending up miles and miles from its intended destination.

"The classic view of this control is that DNA codes for RNA, guiding which proteins will be made by cells. However, mRNA can be modified along the way so that it can produce proteins with many variations. A new field called epitranscriptomics was born out of this knowledge.
The Cell paper is the first study of epitranscriptomics in the embryonic mammalian brain, and the key is m6A, a marker for molecules bound for disposal within the cell. Normally, m6A-tagged mRNAs are related to such processes as cell replication and neuron differentiation, and m6A-tagging promotes their decay after they are no longer needed.

"If m6A is not added on the correct time schedule to a garbage-bound molecule, the developmental train goes down the wrong tracks. Ming and Song surmise that this is because developing brain cells get stuck at an earlier stage because the m6A cues for taking out the cellular trash are misread or not read at all.

"The researchers found that in a mouse model with depleted m6A, cell replication is prolonged, so that stem-cell differentiation, which normally reels out daughter cells in an orderly fashion, gets stuck. The knockout mouse develops less brain cells such as neurons and glia cells, and therefore has abnormal circuitry and a non-functioning brain.

"'We used an organoid, a mini-brain, made from human induced pluripotent stem cells to relate the mouse knockout findings to humans," Ming said. "m6A signaling also regulates neuron development in human forebrain organoids."

"Neuron development in the mini-brains that Ming has developed is similar to what happens in people, modeling fetal brain development up to the second trimester.

"'We were surprised when we found that human stem cells had a greater number of m6A tags compared to mouse cells," Ming said. "Comparing the m6A-mRNA landscapes between mouse and human embryonic brain development showed us that human-specific m6A-tagging might be related to brain-disorder risk genes.'"

Comment: Once again it is shown that planning and timing are very important in fetal development. I'm sure it is present in all organs, not just the brain, and strongly supports the obvious need for a designing mind setting up the whole process of embryology. The 'classic view' of DNA is out the window as this article points out. There are many layers of genomic control only some of which are known so far.

Early embryology; stem cell DNA controls

by David Turell @, Thursday, October 12, 2017, 20:56 (2385 days ago) @ David Turell

Gene expression or suppression controls how a stem cell turns out:

https://phys.org/news/2017-10-d-packaging-dna-cell-identity.html

"The fundamental mechanisms governing how cells form an identity such as becoming a muscle cell or a nerve cell are not fully understood. Multiple diseases, including cancer, have been linked to cells going down the wrong developmental path during maturation. A new study from the Perelman School of Medicine at the University of Pennsylvania suggests that the ability of a stem cell to differentiate into cardiac muscle (and by extension other cell types) depends on what portions of the genome are available for activation, which is controlled by the location of DNA in a cell's nucleus.

***

"The study also suggests that knowing how to control how quickly a cell differentiates as it matures has important implications for regenerative medicine.Some regions of the genome are unavailable to be expressed because they are packaged tightly against the inner membrane of the cell nucleus (the lamina). These sequestered and silenced regions of DNA are called Lamin Associated Domains, or LADs. The Cell study suggests that the specific regions of silenced DNA at the periphery help define a cell's identity. For example, if nerve cell genes are held silent as LADs they cannot be expressed, so the cell does not become a neuron. However, if heart cell genes are released and available to be expressed, as happens during heart development, then those cells become cardiac muscle. Cell biologists have known for many years that some DNA is found near the inner nuclear membrane, but the function of this localization has been unclear. "Our work suggests that a cell defines its identity by storing away in an inaccessible closet the critical genes and programs necessary for it to mature into another cell type," Jain said. "In other words, a cell is 'who' it is because it has silenced 'who' it isn't." The Penn team found that an epigenetic enzyme called histone deacetylase (Hdac3) tethers DNA to the nuclear periphery. "We asked: Does this choreographed control of DNA availability contribute to a cell becoming a certain type?" Jain said. When they removed Hdac3 in stem cells during heart cell differentiation, they untethered regions of DNA containing heart-specific genes, allowing those genes to be activated, which led to precocious, too-fast differentiation."

Comment: Control of DNA expression is under the control of enzymes, but also the 3-D location of genes. This is a highly complex finely-tuned mechanism, which must b e exact in its actions as an embryo is developed into all its parts. Not by chance. Must be designed.

Early embryology; requires brain input:

by David Turell @, Friday, March 16, 2018, 19:23 (2230 days ago) @ David Turell

Shown in tadpole research:

https://www.quantamagazine.org/brainless-embryos-suggest-bioelectricity-guides-growth-2...

"In recent years, by working on tadpoles and other simple creatures, Levin’s laboratory has amassed evidence that the embryo is molded by bioelectrical signals, particularly ones that emanate from the young brain long before it is even a functional organ. Those results, if replicated in other organisms, may change our understanding of the roles of electrical phenomena and the nervous system in development, and perhaps more widely in biology.

“'Levin’s findings will shake some rigid orthodoxy in the field,” said Sui Huang, a molecular biologist at the Institute for Systems Biology. If Levin’s work holds up, Huang continued, “I think many developmental biologists will be stunned to see that the construction of the body plan is not due to local regulation of cells … but is centrally orchestrated by the brain.”

***

“'It’s too simplistic to consider the genome as the only source of biological information,” she said. Researchers continue to study morphogens as a source of developmental information in the nervous system, for example. Last November, Levin and Chris Fields, an independent scientist who works in the area where biology, physics and computing overlap, published a paper arguing that cells’ cytoplasm, cytoskeleton and both internal and external membranes also encode important patterning data — and serve as systems of inheritance alongside DNA.

***

"Then Levin and his colleagues decided to flip the experiment. Might the brain hold, if not an entire blueprint, then at least some patterning information for the rest of the body, Levin asked — and if so, might the nervous system disseminate this information bioelectrically during the earliest stages of a body’s development? He invited Herrera-Rincon to get her scalpel ready.

"Herrera-Rincon’s brainless Xenopus laevis tadpoles grew, but within just a few days they all developed highly characteristic defects — and not just near the brain, but as far away as the very end of their tails. Their muscle fibers were also shorter and their nervous systems, especially the peripheral nerves, were growing chaotically.

***

"Levin’s research demonstrates that the nervous system plays a much more important role in how organisms build themselves than previously thought, said Min Zhao, a biologist at the University of California, Davis, and an expert on the biomedical application and molecular biophysics of electric-field effects in living tissues. Despite earlier experimental and clinical evidence, “this paper is the first one to demonstrate convincingly that this also happens in [the] developing embryo.”

“'The results of Mike’s lab abolish the frontier, by demonstrating that electrical signaling from the central nervous system shapes early development,” said Olivier Soriani of the Institut de Biologie de Valrose CNRS. “The bioelectrical activity can now be considered as a new type of input encoding organ patterning, allowing large range control from the central nervous system.'”

Comment: Embryology has always been an issue for Darwin evolution theory. It is such a complex process, making a new individual in exactly correct form cannot be a process developed by chance.

Early embryology; requires brain input:

by David Turell @, Monday, March 19, 2018, 17:20 (2227 days ago) @ David Turell

Shown in tadpole research:

https://www.quantamagazine.org/brainless-embryos-suggest-bioelectricity-guides-growth-2...

"In recent years, by working on tadpoles and other simple creatures, Levin’s laboratory has amassed evidence that the embryo is molded by bioelectrical signals, particularly ones that emanate from the young brain long before it is even a functional organ. Those results, if replicated in other organisms, may change our understanding of the roles of electrical phenomena and the nervous system in development, and perhaps more widely in biology.

“'Levin’s findings will shake some rigid orthodoxy in the field,” said Sui Huang, a molecular biologist at the Institute for Systems Biology. If Levin’s work holds up, Huang continued, “I think many developmental biologists will be stunned to see that the construction of the body plan is not due to local regulation of cells … but is centrally orchestrated by the brain.”

***

“'It’s too simplistic to consider the genome as the only source of biological information,” she said. Researchers continue to study morphogens as a source of developmental information in the nervous system, for example. Last November, Levin and Chris Fields, an independent scientist who works in the area where biology, physics and computing overlap, published a paper arguing that cells’ cytoplasm, cytoskeleton and both internal and external membranes also encode important patterning data — and serve as systems of inheritance alongside DNA.

***

"Then Levin and his colleagues decided to flip the experiment. Might the brain hold, if not an entire blueprint, then at least some patterning information for the rest of the body, Levin asked — and if so, might the nervous system disseminate this information bioelectrically during the earliest stages of a body’s development? He invited Herrera-Rincon to get her scalpel ready.

"Herrera-Rincon’s brainless Xenopus laevis tadpoles grew, but within just a few days they all developed highly characteristic defects — and not just near the brain, but as far away as the very end of their tails. Their muscle fibers were also shorter and their nervous systems, especially the peripheral nerves, were growing chaotically.

***

"Levin’s research demonstrates that the nervous system plays a much more important role in how organisms build themselves than previously thought, said Min Zhao, a biologist at the University of California, Davis, and an expert on the biomedical application and molecular biophysics of electric-field effects in living tissues. Despite earlier experimental and clinical evidence, “this paper is the first one to demonstrate convincingly that this also happens in [the] developing embryo.”

“'The results of Mike’s lab abolish the frontier, by demonstrating that electrical signaling from the central nervous system shapes early development,” said Olivier Soriani of the Institut de Biologie de Valrose CNRS. “The bioelectrical activity can now be considered as a new type of input encoding organ patterning, allowing large range control from the central nervous system.'”

Comment: Embryology has always been an issue for Darwin evolution theory. It is such a complex process, making a new individual in exactly correct form cannot be a process developed by chance.

Further comment: If the brain controls embryological formation it must also control how the brain itself is formed and the regions connected, resulting in how the s/s/c has to be individually interfaced.

Early embryology; organizer cells found

by David Turell @, Thursday, May 24, 2018, 17:40 (2161 days ago) @ David Turell

It was assumed that organizer cells existed. They have been shown on chicken embryos:

https://www.the-scientist.com/?articles.view/articleNo/54640/title/Animals--Embryonic-O...


"The organizer, a group of cells in the embryo that directs the developmental fates and morphogenesis of other embryonic cells, has been identified in human tissue for the first time, according to a study published today (May 23) in Nature. The discovery demonstrates that the organizer is evolutionarily conserved from amphibians to humans.

***

"Rockefeller University embryologist Ali Brivanlou and colleagues report that when they grafted human stem cells that they’d treated with Wnt and Activin, two signaling proteins previously shown to be involved in organizer gene expression in other animals, into chick embryos, the grafted cells set off the developmental progress of the cells around them. The experiment establishes for the first time that the organizer exists in humans and that Wnt and Activin work in concert to make it possible for cells to direct embryonic development.

***

"In this latest experiment, when they grafted human embryonic stem cells that they treated with Wnt and Activin into chick embryos, the stem cells caused the cells around them to begin forming a second neural axis as a line of cells running along one side of the embryo. This effectively demonstrated that Wnt and Activin signaling trigger some of the cells in early human embryos to become the organizer.

“'The beautiful thing about this is that [Brivanlou] . . . has really used cutting-edge approaches to demonstrate that this idea of the organizer, and specifically the genetic and molecular mechanisms that have been described across animal systems, can be employed in the human system,” says Daniel Kessler, a developmental biologist at the University of Pennsylvania who was not involved in the study. “This is as close as we’ll get to a definitive demonstration that these principles and mechanisms apply in the human embryo.”

***

"But the discovery also has deeper meaning to him. “Human beings have always been interested in their own origins,” he says. “The amazing ability that we now have to look at our earliest moments of development and genesis is something that, to me, is as attractive—if not more—as looking at the pictures from the Hubble telescope.'”

Comment: For me the process of embryology science shows how complex it is to make an individual from a single egg. Only a desinger could create this process.

Early embryology; requires brain input:

by David Turell @, Friday, May 03, 2019, 20:28 (1817 days ago) @ David Turell

In rat embryology the thalamus guides nerve pathways to the body surface from the forming sensory cortex . It is assumed the same occurs in humans:

https://www.sciencedaily.com/releases/2019/05/190503100758.htm

"All the surface of the human body is represented in the cerebral cortex in a transversal band localized at the external part of the cerebral hemispheres: the somatosensory cortex. Each body region occupies in that band a distinct extension depending on its use and sensitivity. For instance, the hands and the lips, on which humans rely most, occupy the largest area. Thus, the 3D representation of that map forms the known sensory homunculus.

"Similar to a cartographic map, each represented region of the body in the somatosensory cortex is connected to its corresponding body surface thanks to the neuronal pathways that keep a strict topographical relationship along the nervous system. In this pathway, the thalamus, a deep structure of the brain that lies beneath the cortices, plays a key role by relaying the peripheral information to the cortex without losing the point-to-point correspondence. Using this extraordinary precision, we can discriminate which point of our body is receiving an external stimulus and have a well-defined map of the periphery. Such accurate topography constitutes the basis of the sense of touch and is essential for survival of the species.

"How are the neurons of the somatosensory cortex organized during development to perform these functions? Neurons of this brain region, as in the rest of the cerebral cortex, are assembled into columns that are placed next to each other like building bricks. It remains unknown, however, how these columnar structures become functional correspondents of the distant regions of the periphery.

***

" Far from being a mere relay station, the thalamus guides the formation of the functional cortical columns and the concomitant somatotopic map in the still immature cortex, before external sensory experience is an effective source of information. In particular, the thalamus does so by generating and transmitting patterns of spontaneous activity (called waves) to the developing cortex. The discovery was made in rodents, in a particular and extensive region of their somatosensory cortex: the barrel cortex. This area contains the representation of the whiskers of the snout that are, for rodents, sensorially equivalent to our hands.

***

"'It is very probable that this mechanism involved in the formation of the sensory maps that we have discovered in rodents can be extrapolated to humans, because the organization of the cortex is evolutionarily conserved between species," explains López-Bendito.

"'The spontaneous activity of the thalamus is not something circumstantial, but contains important information for the construction of the brain during embryonic development. It was previously thought that neuronal circuits were built on a genetic imprint and that the postnatal sensory experience ends up defining the maps. This work questions this vision because it demonstrates the existence of these maps before birth,"; says Lopez-Bendito. "Our results indicate that the spontaneous thalamic activity during the embryonic phase is essential for the normal development of the brain, defining what in neurobiology is called a critical period, i.e. a period of time in which plastic changes are possible but after which alterations would be irreparable"; she adds." (my bold)

Comment: Arranging for maps of the body surface in the brain's cortex through information in the genome requires coordinated planning and requires complex design to develop. The thought that cellular intelligence is capable of doing this is unreasonable. Cellular intelligence can reasonably make minor adaptations within species, no more.

Early embryology; requires brain input:

by David Turell @, Friday, May 03, 2019, 20:36 (1817 days ago) @ David Turell
edited by David Turell, Friday, May 03, 2019, 21:01

In rat embryology the thalamus guides nerve pathways to the body surface from the forming sensory cortex . It is assumed the same occurs in humans:

https://www.sciencedaily.com/releases/2019/05/190503100758.htm


"All the surface of the human body is represented in the cerebral cortex in a transversal band localized at the external part of the cerebral hemispheres: the somatosensory cortex. Each body region occupies in that band a distinct extension depending on its use and sensitivity. For instance, the hands and the lips, on which humans rely most, occupy the largest area. Thus, the 3D representation of that map forms the known sensory homunculus.

"Similar to a cartographic map, each represented region of the body in the somatosensory cortex is connected to its corresponding body surface thanks to the neuronal pathways that keep a strict topographical relationship along the nervous system. In this pathway, the thalamus, a deep structure of the brain that lies beneath the cortices, plays a key role by relaying the peripheral information to the cortex without losing the point-to-point correspondence. Using this extraordinary precision, we can discriminate which point of our body is receiving an external stimulus and have a well-defined map of the periphery. Such accurate topography constitutes the basis of the sense of touch and is essential for survival of the species.

"How are the neurons of the somatosensory cortex organized during development to perform these functions? Neurons of this brain region, as in the rest of the cerebral cortex, are assembled into columns that are placed next to each other like building bricks. It remains unknown, however, how these columnar structures become functional correspondents of the distant regions of the periphery.

***

" Far from being a mere relay station, the thalamus guides the formation of the functional cortical columns and the concomitant somatotopic map in the still immature cortex, before external sensory experience is an effective source of information. In particular, the thalamus does so by generating and transmitting patterns of spontaneous activity (called waves) to the developing cortex. The discovery was made in rodents, in a particular and extensive region of their somatosensory cortex: the barrel cortex. This area contains the representation of the whiskers of the snout that are, for rodents, sensorially equivalent to our hands.

***

"'It is very probable that this mechanism involved in the formation of the sensory maps that we have discovered in rodents can be extrapolated to humans, because the organization of the cortex is evolutionarily conserved between species," explains López-Bendito.

"'The spontaneous activity of the thalamus is not something circumstantial, but contains important information for the construction of the brain during embryonic development. It was previously thought that neuronal circuits were built on a genetic imprint and that the postnatal sensory experience ends up defining the maps. This work questions this vision because it demonstrates the existence of these maps before birth,"; says Lopez-Bendito. "Our results indicate that the spontaneous thalamic activity during the embryonic phase is essential for the normal development of the brain, defining what in neurobiology is called a critical period, i.e. a period of time in which plastic changes are possible but after which alterations would be irreparable"; she adds." (my bold)

Comment: Arranging for maps of the body surface in the brain's cortex through information in the genome requires coordinated planning and requires complex design to develop. The thought that cellular intelligence is capable of doing this is unreasonable. Cellular intelligence can reasonably make minor adaptations within species, no more.

In human babies the touch map exists but works only with learned experience. What is called point discrimination appears as the infant develops experience. This has been shown by pinprick testing in very young children. Pinpricks several inches apart are not distinguished, but eventually as they mature they can appreciate pinpricks one inch apart or less.

Early embryology; connecting neurons

by David Turell @, Friday, May 03, 2019, 21:08 (1817 days ago) @ David Turell

The chemical controls are found:

https://medicalxpress.com/news/2019-05-neurons-brain.html

"About 100 billion neurons form a complex and interconnected network in the brain, allowing people to generate complex thought patterns and actions. Neurons come in all sizes and shapes, but they mostly have long protrusions that connect to neighboring cells through specialized information-transmission structures called synapses.

"How this intricate network takes shape during early development captivates many neuroscientists, including Prof. Dietmar Schmucker (VIB-KU Leuven) who has built a career studying neuronal wiring. "Proper brain functioning relies on very controlled branching of neuronal cell-extensions called axons and dendrites, and the correct formation of synapses at precise locations along these branches," he says. "Specifying synapse formation determines where and how many potential connections a neuronal cell is allowed to form. Therefore, controlling synapse numbers at each neuronal branch is essential for the correct formation of complex brain circuits."

***

"'We found differences in neuronal branching and in synapse numbers at individual protrusions of neurons of the same type," explains Olivier Urwyler, a postdoc in the lab who developed this new experimental system. Urwyler, now a group leader at University Zurich, found that a phosphatase called Prl-1 was decisive for specifying where to form the highest density of synaptic connections on a given neuron.

"In fruit flies, loss of Prl-1 led to defects in the formation of neuronal connections in several different circuits, suggesting that this protein phosphatase is of general importance in circuit formation. The team also identified through which signaling pathway Prl-1 exerts its function.

"'Surprisingly, it turns out to be one of the most ubiquitously acting signaling pathways, the Insulin receptor/Akt/mTor pathway, required in many physiological responses, cellular growth and cancer, says Urwyler. "Restricting the subcellular protein distribution of Prl-1 to a small compartment results in this potent signaling cascade to locally boost synapse formation."

"Flies that lack Prl-1 show severe locomotor problems. Interestingly, if Prl-1 is erroneously overexpressed and out of control, it can drive metastatic behavior of cancer cells.
As Prl-1 phosphatases are conserved from invertebrates to mammals, what could this imply for humans? According to Schmucker, their presence in different regions of the human brain means that Prl-1 phosphatases are poised to function in a similar way during vertebrate brain development:

"'The compartmentalized restriction of Prl-1 could serve as a specificity factor to control the precise tuning of synaptic connections in human neurons as well, similar to the effects we have shown for the assembly of neuronal circuits and synapses in fruit flies.'"

Comment: The development of the embryonal brain requires following an exact plan. It could not develop stepwise and must have been designed.

Early embryology; requires brain input:

by dhw, Saturday, May 04, 2019, 14:01 (1816 days ago) @ David Turell

QUOTE:'The spontaneous activity of the thalamus is not something circumstantial, but contains important information for the construction of the brain during embryonic development. It was previously thought that neuronal circuits were built on a genetic imprint and that the postnatal sensory experience ends up defining the maps. This work questions this vision because it demonstrates the existence of these maps before birth,"; says Lopez-Bendito. "Our results indicate that the spontaneous thalamic activity during the embryonic phase is essential for the normal development of the brain, defining what in neurobiology is called a critical period, i.e. a period of time in which plastic changes are possible but after which alterations would be irreparable"; she adds." (David's bold)

DAVID: Arranging for maps of the body surface in the brain's cortex through information in the genome requires coordinated planning and requires complex design to develop. The thought that cellular intelligence is capable of doing this is unreasonable. Cellular intelligence can reasonably make minor adaptations within species, no more.

Your usual assumption that you know what is reasonable, and anyone who disagrees with you is unreasonable. All of these processes must have had a beginning, and once a process is successful, then it will be passed on and must automatically follow the same course if it is to survive. It is the origin of each complexity that calls for intelligence, though intelligence may also be called on when environmental conditions require or allow change. The more complex the organ, the more complex the combination or map of information will have to be, both before and after birth. How does this make cellular intelligence as the origin of each complexity less reasonable than your God's 3.8-billion-year-old programme for every single one?

Early embryology; requires brain input:

by David Turell @, Saturday, May 04, 2019, 18:50 (1816 days ago) @ dhw

QUOTE:'The spontaneous activity of the thalamus is not something circumstantial, but contains important information for the construction of the brain during embryonic development. It was previously thought that neuronal circuits were built on a genetic imprint and that the postnatal sensory experience ends up defining the maps. This work questions this vision because it demonstrates the existence of these maps before birth,"; says Lopez-Bendito. "Our results indicate that the spontaneous thalamic activity during the embryonic phase is essential for the normal development of the brain, defining what in neurobiology is called a critical period, i.e. a period of time in which plastic changes are possible but after which alterations would be irreparable"; she adds." (David's bold)

DAVID: Arranging for maps of the body surface in the brain's cortex through information in the genome requires coordinated planning and requires complex design to develop. The thought that cellular intelligence is capable of doing this is unreasonable. Cellular intelligence can reasonably make minor adaptations within species, no more.

dhw: Your usual assumption that you know what is reasonable, and anyone who disagrees with you is unreasonable. All of these processes must have had a beginning, and once a process is successful, then it will be passed on and must automatically follow the same course if it is to survive. It is the origin of each complexity that calls for intelligence, though intelligence may also be called on when environmental conditions require or allow change. The more complex the organ, the more complex the combination or map of information will have to be, both before and after birth. How does this make cellular intelligence as the origin of each complexity less reasonable than your God's 3.8-billion-year-old programme for every single one?

What we are debating is the necessity of a planning mind to arrange for the complex designs we see as evolution advances for simple to very complex. You have extrapolated simple cellular responses, which have the appearance of intellectual guidance because they are purposeful in their results, to the suggestion they can actually plan for the future complexities. I find that idea as totally fanciful. I see the mind of God as necessary. We will never be able to reach an agreement on the point of how speciation works.

Early embryology; brain development chemical controls

by David Turell @, Sunday, January 26, 2020, 21:07 (1549 days ago) @ David Turell

Specialized proteins shepherd synapse connections between groups of neurons:

https://phys.org/news/2020-01-social-networks-neurons.html

"The three proteins teneurin, latrophilin and FLRT hold together and bring neighboring neurons into close contact, enabling the formation of synapses and the exchange of information between the cells. In the early phase of brain development, however, the interaction of the same proteins leads to the repulsion of migrating nerve cells, as researchers from the Max Planck Institute of Neurobiology and the University of Oxford have now shown.

"Well anchored, the proteins teneurin and FLRT are located on the surface of nerve cells. They are on the lookout for their partner protein, latrophilin, on other neurons. When the three proteins come into contact, they interconnect and hold the membranes together. They then trigger still largely unknown signaling cascades and thus promote the formation of a synapse at this site.

"teneurin and its partner proteins are known to establish these important cell contacts in the brain. Teneurin is also an evolutionary very old protein, with related proteins found in diverse organisms ranging from bacteria to worms, fruit flies and vertebrates. However, the role of these proteins during brain development, when neurons are not yet forming synapses, remained unknown. (my bold)

***

"During brain development, embryonic neurons migrate to "their" brain area. As the investigations have now shown, the three proteins help to guide the cells to their destination. "Surprisingly, this happens not by attraction, as in synapse formation, but by repulsion of the cells," explains Rüdiger Klein from the Max Planck Institute of Neurobiology. "This function was completely new and unexpected," adds Elena Seiradake from Oxford University. The ancient role of teneurin is not surprising, as

"Embryonic neurons often have only a cell body and short protrusions, called neurites. When teneurin and FLRT on these structures bind to latrophilin, the cells repel each other. As a result, the migrating cells partially lose their hold and progress more slowly. Thus guided, the cells reach their target brain area at the right time, where they mature and form a long axon.

"However, when on the surface of such an axon, teneurin and FLRT no longer trigger a repulsive reaction upon the encounter with latrophilin. Here and now, the proteins pull the cells together, induce the formation of synapses and ultimately lead to the assembly of networks of communicating neurons. "The same proteins thus lead to completely different reactions—depending on their location on the cell,"summarizes Elena Seiradake the results."(my bold)

comment: Note my bold. The proteins have different reactions depending upon their positions. That reeks of a special design function for these protein molecules. Not by chance but certainly by God's design. The ancient role of teneurin is not surprising, as the process of evolution, as designed, builds upon the past developments.

Early embryology; how the sperm unloads its genome

by David Turell @, Saturday, March 14, 2020, 01:12 (1502 days ago) @ David Turell

It requires a certain enzyme:

https://phys.org/news/2020-03-sperm-dad-genome-merge-mom.html

"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.

***

"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.

***

"... back in 1999, shortly after Fu published a paper that first described the enzyme's role in RNA splicing, a research group in Greece noted similarities in the sequence of amino acid building blocks that make up SPRK1 substrates (the proteins upon which the enzyme acts) and protamine.

***

"'And, surprisingly, everything we tried supported our hypothesis—SRPK1 leads a double life, swapping protamines for histones once sperm meets egg."

***

"Fu, Gou and team next want to determine the signals that instruct sperm to synchronize with the maternal genome."

Comment: Only partial knowledge of this precise series of steps is known. It has to have been designed. Chance hunt and peck could not work as a design method to produce proper coordinated fertilization.

Early embryology; controls over stem cells

by David Turell @, Thursday, July 23, 2020, 19:56 (1370 days ago) @ David Turell

Complex controlling molecules and genes are described:

https://phys.org/news/2020-07-self-eating-stem-cells-key-regenerative.html

"The new preclinical study, for the first time, shows how the stem cells keeps CMA at low levels to promote that self-renewal, and when the stem cell is ready, it switches that suppression off to enhance CMA, among other activities, and differentiate into specialized cells.

***

"Autophagy is a cell-eating mechanism necessary for survival and function of most living organisms. When cells self-eat, the intracellular materials are delivered to lysosomes, which are organelles that help break down these materials. There are a few forms of autophagy. However, unlike the other forms, which are present in all eukaryotic cells, CMA is unique to mammals. To date, the physiological role of CMA remains unclear.

"Using metabolomic and genetic laboratory techniques on the embryonic stem cells of mice, the researchers sought to better understand significant changes that took place during their pluripotent state and subsequent differentiation.

"They found that CMA activity is kept at a minimum due to two cellular factors critical for pluripotency—Oct4 and Sox2—that suppresses a gene known as LAMP2A, which provides instructions for making a protein called lysosomal associated membrane protein-2 necessary in CMA. The minimal CMA activity allows stem cells to maintain high levels of alpha-ketoglutarate, a metabolite that is crucial to reinforce a cell's pluripotent state, the researchers found.

"When it's time for differentiation, the cells begin to upregulate CMA due to the reduction in Oct4 and Sox2. Augmented CMA activity leads to the degradation of key enzymes responsible for the production of alpha-ketoglutarate. This leads to a reduction in alpha-ketoglutarate levels as well as an increases in other cellular activities to promote differentiation. These findings reveal that CMA and alpha-ketoglutarate dictate the fate of embryonic stem cells.

"Embryonic stem cells are often called pluripotent due to their remarkable ability to give rise to every cell type in the body, except the placenta and umbilical cord. Embryonic stem cells not only provide a superb system to study early mammalian development, but also hold great promise for regenerative therapies to treat various human disorders."

Comment: as usual a complex, highly controlled system, obviously designed. The better we understand it, the better we can correct errors.

Early embryology; controls over development patterns

by David Turell @, Thursday, July 23, 2020, 20:39 (1370 days ago) @ David Turell

Certain proteins from the mother control patterns of development in teh egg:

https://phys.org/news/2020-07-complex-developmental-patterns-surprisingly-simple.html

"Proper embryonic development of the fruit fly Drosophila melanogaster is governed by patterns of protein activity bequeathed to the fertilized egg by its mother. While the embryo is still a single cell, the maternal cells surrounding it deposit certain proteins inside it at specific locations. This establishes protein gradients that direct the development of embryonic features along its anterior-posterior and ventral-dorsal axes. Later, the embryo receives another round of maternal information, called terminal patterning, that guides the development of its head and tail.

"Terminal patterning is driven by a protein called Torso that is made by the mother and deposited throughout the embryo. Torso is stimulated by binding to other proteins that are also produced by the mother, but present only at the embryo's anterior and posterior ends. Torso stimulation kicks off several signaling cascades, including one called the Ras/ERK pathway, whose activation directs the expression of genes crucial to embryonic development. Mothers lacking Torso or the proteins to which it binds are sterile because their embryos fail to develop head and tail.

***

"Much of terminal patterning is driven by two genes whose expression is controlled by the Ras/Erk pathway in response to Torso signaling. In normal embryos, the expression of these two genes occurs in different cells at different times. In light-stimulated OptoSOS embryos lacking Torso signaling, however, expression of the two genes overlapped more in both space and time, suggesting their precise expression patterns are not required for development.

"The authors next investigated whether different aspects of the developmental program are triggered at the same or different stimulus thresholds. To do this, they monitored embryonic development after varying the intensity and duration of light stimulus in OptoSOS embryos lacking Torso signaling.

"'We found that the terminal pattern appears to work as a series of switches, where successively longer light pulses trigger a predictable sequence of body parts being 'rescued' one by one," explains Toettcher.

"Together, these data suggest that for terminal signaling, what appears to be a very complex developmental program is actually under the control of a relatively simple system that depends on different thresholds of Ras/Erk signaling."

Comment: Bit by bit we are learning how embryological systems work, by design.

Early embryology; cell migration controls

by David Turell @, Tuesday, September 28, 2021, 18:28 (938 days ago) @ David Turell

The first studies:

https://phys.org/news/2021-09-advanced-microscopy-reveals-molecular-tight.html

"Cell migration is fundamental for the existence of multicellular animals, including humans, as certain cells migrate throughout the embryo to form specific tissues. It is also crucial for human health throughout life—for example during acute wound healing. Its deregulation allows cancer cells to leave the primary tumor and colonize distant sites (cancer metastasis).

"Even though cell migration has been studied for a long time, how it is tightly controlled is not well understood. The polymerisation of a protein (actin) network behind the plasma membrane provides the pushing force for membrane protrusion and, consequently, cell migration.

"The research by the Krause, Stramer and Ameer-Beg Labs shows that this tight control of cell migration is mediated by the Nance-Horan Syndrome-like 1 (NHSL1) protein which inhibits the initiation of actin polymerisation at the leading edge of migrating cells. NHSL1 belongs to the poorly investigated Nance-Horan Syndrome protein family along with Nance-Horan Syndrome (NHS) and NHSL2 proteins. Mutations in the NHS gene cause Nance-Horan syndrome, which is characterized by dental abnormalities, developmental delay, and congenital cataracts.

"The scientists are now turning to NHS to study whether deregulated cell migration may play a role in the pathogenesis of Nance-Horan Syndrome. In addition, they are investigating whether the Nance-Horan Syndrome protein family act as tumor suppressors because deregulation of cell migration is a hallmark of cancer metastasis, and NHSL1 is required for tight control of cell migration."

Comment: all systems have go no-go controls or feedback loops. It is easy to predict that new research will discover them as designed. Just shows how a field of work starts.

Early embryology; the earliest blastocyst runs the show

by David Turell @, Thursday, July 07, 2022, 16:57 (656 days ago) @ David Turell

Tells the uterus what to do:

https://phys.org/news/2022-07-life-early-embryo-driver-seat.html

"One often thinks that the early embryo is fragile and needs support. However, at the earliest stages of development, it has the power to feed the future placenta and instructs the uterus so that it can nest. Using blastoids, in vitro embryo models formed with stem cells, the lab of Nicolas Rivron at IMBA showed that the earliest molecular signals that induce placental development and prepare the uterus come from the embryo itself.

"Who takes care of whom at the onset of life? The placenta and the uterus nurture and shelter the fetus. But the situation at the very early stage of development, when the blastocyst still floats in the uterus, was unclear so far. Now, the research group of Nicolas Rivron at IMBA (Institute of Molecular Biotechnology of the Austrian Academy of Sciences) uncovered basic principles of early development using blastoids.

"Blastoids were first developed by the Rivron lab from mouse stem cells (Nature, 2018) and then from human stem cells (Nature, 2021). Blastoids provide an ethical alternative to the use of embryos for research and, importantly, enable multiple discoveries.

"Now, blastoids have settled a "chicken or egg" dilemma. Using mouse blastoids, the researchers found that the early embryonic part (~10 cells) instructs the future placental part (~100 cells) to form, and the uterine tissues to change. "By doing this, the embryo invests in its own future: it promotes the formation of the tissues that will soon take care of its development. The embryo is in control, instructing the creation of a supporting surrounding," says Nicolas Rivron.

"Indeed, the team discovered several molecules secreted by the few cells from which the fetus develops, the epiblasts. They observed that these molecules tell other cells, the trophoblasts that later form the placenta, to self-renew and proliferate, two stem cell properties that are essential for the placenta to grow.

"The team also found that these molecules induce the trophoblasts to secrete two other molecules, WNT6 and WNT7B. WNT6 and WNT7B tell the uterus to wrap around the blastocyst. "Other researchers had previously seen that WNT molecules are involved in the uterine reaction. Now we show that these signals are WNT6/7B and that they are produced by the blastocyst trophoblasts to notify the uterus to react. The relevance could be high because we have verified that these two molecules are also expressed by the trophoblasts of the human blastocyst," states Nicolas Rivron."

Comment: this shows how one new organism tells another what to do. Molecular reactions control the process automatically. The two work together despite being different genetically, a major problem in transplantation of organs. This is an irreducibly complex arrangement and must be designed. Chance mutations to create this mechanism are not possible.

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