AgnosticWeb.com - Front end loading and loss of information

Front end loading and loss of information (reply)

David Turell — Sun, 19 Jun 2016 18:40:12 +0000

One of the major discoveries in the study of DNA across species, as pointed out by Michael Behe is loss of information is what drives evolution. This is now being confirmed i9n recent studies. This implies that all the information for evolution was present at the beginning of life and with removal of some of it evolution advances, the exact opposite of what one would expect: - http://www.nature.com/nrg/journal/v17/n7/full/nrg.2016.39.html - Abstract: "The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine." - This is how the ID group views this: - http://www.uncommondescent.com/intelligent-design/the-war-is-over-we-won/ - "Many years ago, I predicted that modern genome sequencing would eventually prove one side of the argument to be right. This review article indicates that ID is the correct side of the argument. What they describe is essentially what ID scientist, Michael Behe, has termed the “First Principle of Adaptation.” (Which says that the organism will basicaly ‘break something' or remove something in order to adapt) This paper ought to be the death-knell of Darwinism, and, of course, “neo-Darwinism,” but, even the authors who report this new “perspective” have not changed their Darwinian perspective. Somehow, they will find a way to tell us that the Darwinian ‘narrative' always had room in it for this kind of discovery. - *** - From the paper: - "However, genomic data, which is accumulating as a result of recent technological and methodological advances, such as next-generation sequencing, is revealing a new perspective of gene loss as a pervasive source of genetic change that has great potential to cause adaptive phenotypic diversity." - Author interview: " The genome sequencing of very different organisms has shown that gene loss has been a usual phenomenon during evolution in all life cycles. In some cases, it has been proven that this loss might mean an adaptive response towards stressful situations when facing sudden environmental changes” says Professor Cristian Cañestro." - “In other cases, there are genetic losses -says Cañestro- which even though they are neutral per se, have contributed to the genetic and reproductive isolation among lineages, and thus, to speciation, or have rather participated in the sexual differentiation in contributing to the creation of a new Y chromosome. The fact that genetic loss patterns are not stochastic but rather biased in the lost genes[pav: IOW, this is where you're going to find the genomic differences between species you compare] (depending on the kind of function of the gen or its situation in the genome in different organism groups) stresses the importance of the genetic loss in the evolution of the species." - Comment: Perhaps God did start life front end loaded!

Front end loading (reply)

David Turell — Sat, 29 Aug 2009 17:31:50 +0000

http://www.wired.com/wiredscience/2009/08/reduciblecomplexity/ > It occurred to me that the concept of "neutral evolution" is very similar to "front end loading", but requiring no divine input. - Uncommen Descent has an answer for this: - Wired.com has a new article about why ID isn't science because it's been falsified. Usually the tactic against ID is that it isn't a science because it isn't falsifiable. I reckon use whatever club is closest at hand when you're interested only in beating ID instead of being consistent. The article states: - "You look at cellular machines and say, why on earth would biology do anything like this? It's too bizarre," he said. "But when you think about it in a neutral evolutionary fashion, in which these machineries emerge before there's a need for them, then it makes sense." - "In which these machineries emerge before there's a need" for the machineries. I don't see how that makes any sense. Evolution is supposed to be a stepwise mechanism of solving problems, now they get solved before there is a problem. The article basically makes the assertion that if parts of a whole mechanism are found somewhere else, operating or not operating in any other capacity whatsoever, then the whole mechanism in question is explained by virtue of finding some component parts. If I found an engine foreign to me, I would not be overjoyed to explain it, as a whole, by finding bolts and cylinders and iron lying about, and noticing that the engine uses all three. My first inclination would not be "It was simply a matter of time before they came together into a more complex entity." But that is exactly the argument being made: - But new research comparing mitochondria, which provide energy to animal cells, with their bacterial relatives, shows that the necessary pieces for one particular cellular machine â€” exactly the sort of structure that's supposed to prove intelligent design â€” were lying around long ago. It was simply a matter of time before they came together into a more complex entity. - The pieces "were involved in some other, different function. They were recruited and acquired a new function..." - It was just a matter of time before they came together into more complexity? Really? That's a belief system showing it's cards. And how this follows, without seeing the "coming together" itself, is fanciful, to use a kind word. - According to evolutionary theory, however, cellular complexity is reducible. It requires only that existing components be repurposed, with inevitable mutations providing extra ingredients as needed. - Repurposed, recruited, with a dash of mutation for the bread to rise. Did we witness this recruitment, or must it be so for an evolutionary explanation? It must be so, and it has not been witnessed. And what was the purpose before that purpose? Do you have an infinite regress of purposes and recruitments until you get to single molecules that had no purpose? It seems so: - The process by which parts accumulate until they're ready to snap together is called preadaptation. It's a form of "neutral evolution," in which the buildup of the parts provides no immediate advantage or disadvantage. Neutral evolution falls outside the descriptions of Charles Darwin. But once the pieces gather, mutation and natural selection can take care of the rest, ultimately resulting in the now-complex form of TIM23. - How does one even begin to sort through the assumptions? That peices gather together somehow, none falling off the wagon, snap together, fit, that somehow even if they did gather together it wouldn't be a total wreckage, but rather become a cohesive and intricately connected and symbiotic whole beginning to operate as a machine at 3:00 pm on a Thursday, with mutation and natural selection thrown in to supervise the whole endeavor and "take care of the rest", whatever that means. - Well, you get the idea. And it is an idea, if nothing else. Not an evidentially discerned causal explanation, only, rather, the only possible explanation that a Darwinist has. Find the parts, add natural selection and mutation, and you get the whole. What about actual observation, you ask? Apparently, not necessary, because we are, after all, only trying to satisfy a philosophical presupposition of explanation that must turn from simple to complex, and finding some scattered parts is good enough. Actually seeing the increase in the complexity is not necessary for this kind of "science."

Front end loading (reply)

George Jelliss — Sat, 29 Aug 2009 16:04:24 +0000

I've just been reading this article which was cited on RD.net: - http://www.wired.com/wiredscience/2009/08/reduciblecomplexity/ - It occurred to me that the concept of "neutral evolution" is very similar to "front end loading", but requiring no divine input. - However, as I've expressed before, it seems obvious that evolution can only work with what it has, by cobbling together preexisting bits. How else could it work?

Front end loading (reply)

David Turell — Sun, 30 Nov 2008 22:54:48 +0000

A. C. Grayling has answered this better and more comprehensively than I can. < - I agree with Grayling that the conclusion about children is a stretch. In American Child Psychiatry class it is pointed out that children believe in magic, and don't have the initial experience to figure out why certain things happen as if by magic. An extreme example is young chidren can get very angry about restrictions, and wish someone injured or dead. If the injury or death then occurs in close proximity in time to the child's thought, the child thinks he really caused the event, and may need counselling to straighten out the true understanding of what happened. - On the other hand, as I have mentioned in the past, Andrew Newberg's book, "Why God Won't Go Away", tells us of his studies of how the brain responds to religious activities and may enhance them. There appears to be more going on than just chilhood belief in magic.

Front end loading (reply)

George Jelliss — Sun, 30 Nov 2008 11:49:37 +0000

A. C. Grayling has answered this better and more comprehensively than I can. - http://www.guardian.co.uk/commentisfree/2008/nov/28/religion-children-innateness-barrett - His article is also reproduced on richarddawkins.net, with many more comments. - I also heard Lewis Wolpert express similar views in a radio interview about this "research". - There was also a recent Radio 4 serialisation of a book by a missionary who spent many years with an Amazonian tribe, and lost his faith, when he found that they did not have any belief in a god. They just accepted nature as what it is, but had a concept of other layers of worlds, above and below.

Front end loading (reply)

dhw — Sun, 30 Nov 2008 08:30:57 +0000

David has referred us to a report in the Telegraph: Dr Justin Barrett, a senior researcher at Oxford University, claims that children have a predisposition to believe in a supreme being. He thinks that if young children were "raised alone on a desert island, they would come to believe in God." (Comment by Mike Goldthorpe: "Sorry, why God in particular?") Children are "more likely to believe in creationism rather than evolution" and are "prone to believe in divine creation and intelligent design. In contrast, evolution is unnatural for human minds, relatively difficult to believe." - It's great to hear that children are debating evolution, creationism and intelligent design rather than committing virtual murder on their computers, but...erm...(1) Has no-one told Dr Barrett that lots of people believe in God and in evolution? (2) Who decides what is "natural" and "unnatural" for human minds? (3) If something is difficult to believe, is it wrong? (4) I have a theory that new-born babies believe the universe is made of milk (whereas of course it's actually made of chocolate). If my theory about the babies is right, does that mean the universe is made of milk? (5) What is Dr Barrett trying to prove?

Front end loading (reply)

David Turell — Sat, 29 Nov 2008 00:44:35 +0000

There are many examples of front end loading in evolution. > - The Telegraph article cited here raises another issue. Karen Armstrong in her book, 'The History of God', makes the point that we seem to be created to believe. The temporal lobe of the brain contains an area, called the "God Spot", which gives some people religious experiences, and can be set off by epilepsy, for example. The Telegraph article describes research which seems to show that children are programmed to believe. http://www.telegraph.co.uk/news/newstopics/religion/3512686/Children-are-born-believers...

Front end loading (reply)

David Turell — Fri, 21 Nov 2008 00:45:14 +0000

The new and amazing findings keep pouring out of the literature. Cyanobacteria are blue-green algae, and so ancient (about 3.5 bya) they appeared about the time life started on Earth. They had to come first or we would not be here. They use photosynthesis for energy (as do all plants generally), burning CO2 and making oxygen as a result. At the time they appeared the atmosphere had very little oxygen, and what became present allowed animal life to appear. - Like many organisms they have a circadian rhythm, which allows adaption to light and dark, day by day. The biochemical mechanism has now apparently been found: http://www.sciencemag.org/cgi/content/abstract/322/5902/697 The article itself describes a complex cascade of biochemical reactions, but note the sentence in the summary about the organism's chromosome changing every day and the changes drive the molecular reactions in one direction only. It looks like Paley's watch mechanism has been found! Unless driven by enzymes many organic chemical reactions can result in back and forth reactions. - The moral: Darwin's mechanisms have only a finite time to create all of this complexity, but the apparent complexity of living matter continues to increase and increase exponentially, continuing to raise the issue: was there enough time for Darwin's theory to create us?

Microcosms (reply)

David Turell — Thu, 20 Nov 2008 15:07:55 +0000

I am the sum of all my parts, but I sense that I am more than that sum, that I have a character that transcends my physical self. > but it poses the question: are we ourselves microcosms? If so, of what? - Here I am giving a link to a mind/body symposium. I have read several of the participants and they are non-materialistic scientists. Bruce Greyson is a psychiatrist who studies near to death. Newberg scans meditating brains. These folks believe the mind arises from the material brain, and feelings of self as a separate entity are real. Materialist scientists think the self is an illusion. http://www.mindbodysymposium.com/ I do not agree with the materialists. Baby brains are stimulated to grow and develop thru intellectual contact, one mind contacting another developing one. - We are a microcosm of 10 million cells many of which are doing their own thing. We have autonomic and voluntary nervous systems, for example.

Microcosms (reply)

dhw — Thu, 20 Nov 2008 09:27:39 +0000

David is keeping us up to date with the latest discoveries relating to the "complexities of life". - First of all, I'd like to thank you for this invaluable research service, and for the brief summaries with which you comment on the articles. For non-scientists like myself, all of this is extremely helpful. - I was particularly impressed with the "tunnelling nanotubes". David and George disagree on whether such extraordinary mechanisms denote the workings of design or of chance, but reading about them has set me off on another track. Our bodies are simply filled with these organisms over which we have no control, and of which we are not even conscious. It's as if we ourselves are worlds harbouring various kinds of life, which operate independently yet interdependently. The unifying force is our self. This brings us back to the question of our identity: I am the sum of all my parts, but I sense that I am more than that sum, that I have a character that transcends my physical self. - If we stretch the analogy further, we might see the universe as a body. Its parts work independently but interdependently. And just as I am the unifying force for my cells, my DNA, my "tunnelling nanotubes", perhaps there is another unifying "I" that binds together our universe. I don't want to carry the analogy any further at this stage, and am aware that there is nothing original about the idea ... it is, after all, the very basis of David's panentheism ... but it poses the question: are we ourselves microcosms? If so, of what?

Front end loading (reply)

David Turell — Tue, 18 Nov 2008 22:17:17 +0000

This is a second article I discovered today. I have always wondered how cells communicated in adult animals or plants but also in the embryonal stage when the morphology of the organism is being built. We have all seen blueprints for our homes, and there also is a building plan to order the timing of construction so as not to get one part in the way of another. Can't cover the walls until the electric lines are in place, as a simple example. This is a totally new finding in the past four years. http://www.newscientist.com/article/mg20026821.400-tunnelling-nanotubes-lifes-secret-ne...

Front end loading (reply)

David Turell — Tue, 18 Nov 2008 22:07:59 +0000

I would like to continue to present the newly found complexities of life by exhibiting science articles written for the lay public: they are easy to follow. This article discusses what happens when DNA is unwound to do some copying, which is the way copying happens, and then DNA has to be rewound. The authors have found an enzyme that does just that. http://www.sciencedaily.com/releases/2008/10/081030144615.htm When Darwin thought his living matter was simply blobs of protoplasm, his theory was easy to concoct. We no know that cells are manufacturing factories with very complex feedback loops, hundreds of different proteins, hundreds of amino acids long, and folded properly in order to fulfill their required fuction.

Front end loading (reply)

David Turell — Sun, 16 Nov 2008 01:43:05 +0000

Yes, I found that article fascinating. But it doesn't seem to me to show the DNA/RNA system to be "complex" in the sense of being designed. It shows just how chaotically "undesigned" it is. Engineers would not design a machine in which one component "drags along unnecessary excess baggage" or which gets contaminated by the "rotting carcases" of extraneous interlopers! > Here are some quotes from the article: - George: It is a fascinating ability of yours to quote only those portions of the article that support your position. The article in totality describes an extraordinary overlay of RNA control which makes many segments of DNA able to make over 5 different proteins, thereby changing our paltry number of genes (now 21,000) into an instrument of heredity that is equal to the 100,000 genes originally predicted before DNA was analyzed into gene structure. - Yes, some junk genes are discarded, viral DNA sequestered, etc., but once again you are confusing 'optimal design' with 'perfect design'. After all what we are seeing is an optimal design if we conclude that evolution proceeded from simple to complex and handled the errors and viral invasions as well as it did. Human engineers are not faced with invaders of their machines, but we do have viruses attacking our computers, and lo-to-behold, engineers have found a way to thwart them! So did the DNA/RNA mechanism. I think it is amazingly complex, junk and all.

Front end loading (reply)

George Jelliss — Sat, 15 Nov 2008 19:37:15 +0000

Yes, I found that article fascinating. But it doesn't seem to me to show the DNA/RNA system to be "complex" in the sense of being designed. It shows just how chaotically "undesigned" it is. Engineers would not design a machine in which one component "drags along unnecessary excess baggage" or which gets contaminated by the "rotting carcases" of extraneous interlopers! - Here are some quotes from the article: - David Haussler, another Encode team member at the University of California, Santa Cruz, agrees with Dr. Birney. "The cell will make RNA and simply throw it away," he said. - Dr. Haussler bases his argument on evolution. If a segment of DNA encodes some essential molecule, mutations will tend to produce catastrophic damage. Natural selection will weed out most mutants. If a segment of DNA does not do much, however, it can mutate without causing any harm. Over millions of years, an essential piece of DNA will gather few mutations compared with less important ones. - Only about 4 percent of the noncoding DNA in the human genome shows signs of having experienced strong natural selection. Some of those segments may encode RNA molecules that have an important job in the cell. Some of them may contain stretches of DNA that control neighboring genes. Dr. Haussler suspects that most of the rest serve no function. - "Most of it is baggage being dragged along," he said. - --- - "Our genome is littered with the rotting carcasses of these little viruses that have made their home in our genome for millions of years," Dr. Haussler said. - --- - These new concepts are moving the gene away from a physical snippet of DNA and back to a more abstract definition. "It's almost a recapture of what the term was originally meant to convey," Dr. Gingeras said. - This is another good example of the way scientific research moves on. Older over-simplified ideas get discarded in light of new information.

Front end loading (reply)

David Turell — Sat, 15 Nov 2008 16:42:06 +0000

George, we shall wait for you to return from your house move, but in the meantime please read this article from the N.Y. Times showing how complex the DNA/RNA system is, how far beyond Watson-Crick: http://www.nytimes.com/2008/11/11/science/11gene.html?pagewanted=1&_r=1 I get dizzy thinking about how many complex moves those little molecules have to do, with RNA leading exons around like we take a dog for a walk!

Front end loading (reply)

George Jelliss — Sat, 15 Nov 2008 08:57:29 +0000

DT: "All I have said is that it can be mathematically demonstrated that chance DOES NOT have a chance. Darwin thought the universe was eternal, which allowed him time for his step-by-step method. It takes a certain type of planet with a certain type of sun that ages long enough for life to appear, if we can use Earth as the proper example. There is a finite time to allow this to happen. George appears to think the step-by-step method has infinity to work, which is not the case. George is exhibiting faith in Darwin's method. Reason is not involved." - Obviously I dispute your figures. Infinity would be a slight overestimate! I don't have time at present to look more deeply into your mathematics, since I'm in the middle of moving house, but will do so in due course.

Front end loading (reply)

David Turell — Fri, 14 Nov 2008 17:22:37 +0000

George: "We know Chance exists, God is a wee bit more doubtful." > A great response, George, but not to my initial question, which was: "Shouldn't scientists remain objective and tell us what may have happened without insisting that they also know the force that made it happen?" But when a popular newspaper publishes a scientific article quoting a team of authoritative-sounding scientists, it's not so clear where science ends and faith begins. - Exactly. All I have said is that it can be mathematically demonstrated that chance DOES NOT have a chance. Darwin thought the universe was eternal, which allowed him time for his step-by-step method. It takes a certain type of planet with a certain type of sun that ages long enough for life to appear, if we can use Earth as the proper example. There is a finite time to allow this to happen.George appears to think the step-by-step method has infinity to work, which is not the case. George is exhibiting faith in Darwin's method. Reason is not involved.

Front end loading (reply)

dhw — Fri, 14 Nov 2008 15:04:07 +0000

George: "We know Chance exists, God is a wee bit more doubtful." - A great response, George, but not to my initial question, which was: "Shouldn't scientists remain objective and tell us what may have happened without insisting that they also know the force that made it happen?" What I object to is the use of expressions like "chance encounter" and "a series of unique chance events". It's a subversive way of using the supposed objectivity of science to push through a theory that has no scientific basis, i.e. that life originated by chance. I have no problem with someone's belief that this was so, but it should not be stated as if it were a fact, and that is what is implied by these subtle insertions. Imagine the howls of rage if a scientist said, "God made the amoeba engulf the bacterium", or "God used this method to create all plants, and 75m years later created the primitive land animals that followed." That, however, is just the religious equivalent of "chance" encounters, events etc. You and David are both scientists looking at the same sets of facts, and you draw different conclusions, as is clear to anyone following our discussions. But when a popular newspaper publishes a scientific article quoting a team of authoritative-sounding scientists, it's not so clear where science ends and faith begins.

Front end loading (reply)

David Turell — Fri, 14 Nov 2008 14:40:32 +0000

DT: "I think it really is an equal flip of the coin, because of the prodigious odds against chance having done the creation of what does exist." - > Given enough time and enough variation in the situations an accident of the right creative type is inevitable. - George: This is where we part ways. There are only 10^18th power seconds in the life of the universe. Calculations of information theory, using statistical Shannon information theory, indicate that there hasn't been enough time available for your 'accident of chance', particularly since life appeared about 3.6 bya leaving only 10 bya for the accident. Saying chance exists is a truism which ignores the proper definition of chance within a scientific framework of study: the scientific study of statistical probabilities and a probability bound of chance. The age of the universe is finite. The chance of your evolution accident approaches infinity. This puts the odds of an intellectual force planning evolution in my favor.

Front end loading (reply)

George Jelliss — Fri, 14 Nov 2008 10:30:19 +0000

DT: "George you are quite right." - I'm always immediately suspicious when David says he agrees with me! - DT: "I think it really is an equal flip of the coin, because of the prodigious odds against chance having done the creation of what does exist." - The odds against the existence of Chance and the existence of God are not a 50-50 flip of the coin. Chance we know exists. It obeys the laws of ststistics. God I'm pretty certain doesn't exist, but that is the whole subject of this forum. - I can only repeat what I've said many times before. Evolution depends on an initial chance event, but that is only the trigger for an inevitable sequence of events that follow, due to the action of laws of nature, such as gravity or chemical reactivity. It is not chance alone that does the creation. You may recall the golfing tragedy I used as an illustration. The overall event dhw insisted on calling an "accident" even though most of it was inevitable. Given enough time and enough variation in the situations an accident of the right creative type is inevitable.