Uncommon Descent Serving The Intelligent Design Community

David Tyler: Demolishing Junk DNA as an icon of evolution

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For many of us, an important characteristic of science is self-correction. We are proud of the way new findings catalyse re-evaluation and, if corrections are needed, the development of new knowledge. If you are like this, be prepared to be shocked when you read Jonathan Wells’ latest book. The concept of Junk DNA was widely held by evolutionary biologists during the 1990s, but only a few were prepared to expose the hypothesis to tests of its validity. Yet this is when publications started to accumulate that reported functionality in genetic material widely regarded as “nonsense”. Instead of alerting popularisers of science to be cautious, these writers treated the new data as unrepresentative exceptions. They pressed on with their claim that the bulk of the genome is useless. The trickle of challenging research findings became a stream, but the ‘consensus’ about junk DNA was not corrected. The stream became a river, but still the much-needed correction was lacking. Here is Richard Dawkins’ comment from The Ancestor’s Tale (2004, page 22):

Rest here.

Comments
gpuccio:
For me, the real meaning of common descent is simply that the design is modular, and that existing code is reused in further projects. Object Oriented Intelligent Design, if you want.
For me the meaning of common descent is that there is no independent special creation, by which I mean new species are "poofed" into existence rather than originating from a prior species by descent with modification. For me, intelligent design is not an alternative theory to common descent. Creationism "poofing" would be an alternative theory. What ID questions is the nature of modification in "descent with modification." Yet one more piece of evidence that ID is not creationism. But I think code reuse predated OOP. I also think an interesting ID research project would be to investigate "design patterns" in nature. Certainly code reuse is one such pattern. So is encapsulation. And inheritance. Polymorphism? [I won't say that those are "design patterns" per se, but they are aspects of OOP.]Mung
July 17, 2011
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Why is it that people can understand the role of inference in assigning a common ancestor but cannot understand the role of inference in ID?Mung
July 17, 2011
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Elizabeth. The point seems lost on you. Darwinian theory is incoherent. Arguments for Darwinism are full of ad hoc assumptions. For example, the idea that there is somehow a limit on how much junk DNA darwinian processes can produce is completely ad hoc. And as you once again demonstrate, your theory requires a foil, a perfect Designer who makes no mistakes and knows everything in advance. Well, ID is not that foil. Your repeated references to "the Designer" or "an Intelligent Designer" shows how you are just not willing to honestly engage ID on the merits.Mung
July 17, 2011
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Of interest: Vitamin C (GLO) pseudogene refutation By Jonathan Wells - from appendix of 'The Myth Of Junk DNA' pages 109-114 by Jonathan Wells https://docs.google.com/document/pub?id=18LV9Xp1RJv4k2KRQDOpN3_cjSCwBC_XXb8WGVNP4L8Mbornagain77
July 17, 2011
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Liz: "That’s interesting. So how do you see this working? Do you see the design process as something continuous? That the ID modifies the system from time to time?" It's not interesting as much as it simply what we observe of designed systems. "In which case, why do you think the GULO gene was deactivated in great apes?" If ID in biological systems is true, then, like any designed system, a modification would be to further increase the functionality in some way of the system. Whereas some fragmented and obsolete "files" may remain.junkdnaforlife
July 16, 2011
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Elizabeth: There is no special reason to believe that the GULO gene was deactivated by the designer. It's possible, but there are many other possibilities, including a trivial random error in reproduction. It's only complex functional information that requires a designer. Simple destruction is in the range of natural laws.gpuccio
July 16, 2011
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Elizabeth: A short answer is due here, before gpoing to bed. First of all, I completely agree with what junkdnaforlife has just said. The designer acts in a context, He cannot do everything, he is not probably interested in doing everything. He just implements his plans accordin to a puprose, and according to the existing context. If the GULO gene breaks, there may not be any special reason for the designer to correct that. Biological reality is full of many apparent imperfections, at least as much as it is full of beauty and efficiency. The designer acts with purpose, but in a context, and we probably don't really understand the context. Many critics of ID are essentially metaphysics: they say: if I were an omnipotent God, I would do things very differently! Well, I am usually very happy that they are not omnipotent gods :) In ID, we are empirical. We don't identify the designer with God, least of all with an omnipotent God. Not because it could not be, but because we stick to facts, and facts tell us that yhere is a designer (or more designers), but at present cannot tell us exactly who the designer, or designers, is. That is the simple truth. All data about homologies, pseudogenes, viruses and similar apparently non functional structures conserved in species are, at best, support for common descent. They say nothing about the causal mechanism of variation. My only firm belief about the designer of life is that, at all points where we can demonstrate a "jump" in functional information that in no way can be explained by any existing theory, an input of active information must have taken place. That is ID, in its essence. I have some models of how that could have taken place, too (guided variation, intelligent selection, or both). Finally, when I say that I believe in common descent, that does not mean that I believe in gradualism. For strictly empirical reasons, I believe that most transitions in evolution are rather sudden. Let's say that I believe in a form of ID "a la Gould". For me, the real meaning of common descent is simply that the design is modular, and that existing code is reused in further projects. Object Oriented Intelligent Desing, if you want.gpuccio
July 16, 2011
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junkdnaforlife
Because it happens when designed systems get modified. It should not however, constitute a majority of the OS.
That's interesting. So how do you see this working? Do you see the design process as something continuous? That the ID modifies the system from time to time? In which case, why do you think the GULO gene was deactivated in great apes?Elizabeth Liddle
July 16, 2011
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Liz: "Well, why would an Intelligent Designer break a GULO gene and just leave it there?" Because it happens when designed systems get modified. It should not however, constitute a majority of the OS. "Everytime you install & uninstall software and modify system components your Windows registry is left fragmented with obsolete, corrupted and harmful files." However... "Beginning in the 1970s, there were some who thought that a majority of our genome is junk and some (I am one) still think that as much as 90% could be junk." --Larry Moranjunkdnaforlife
July 16, 2011
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Well, why would an Intelligent Designer break a GULO gene and just leave it there? But I take your point - yes, they are excellent evidence for common descent, but not specifically for Darwinian evolution. I'd have thought they were more consistent with Darwinian evolution than with Intelligent Design, though. Although I guess it depends on what specific ID theory you are talking about. What is your theory? Does the Designer constantly intervene to provide useful new genes and/or alleles as necessary? In which case, why can't broken ones be deleted? Or do you subscribe to some kind of front-loading idea? In which case what prevents stored unused sequences from being degraded by mutations?Elizabeth Liddle
July 16, 2011
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Elizabeth: And these phylogenies themselves are good evidence for Darwinian evolution, and evidence against intelligent design (the broken GULO gene being the poster child). Why? At most, they can be evodence in support of common descent. What have they to do with intelligent design?gpuccio
July 16, 2011
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Mung, I've pointed this out to you before, I think, but let me try again: Sometimes theories make very specific predictions which, if contradicted by data, would falsify the theory. They also make predictions that indicate what you might expect, and, if contradicted by the data, might entail a slightly modification to the theory. There are also predictions that can be made which are only of mild interest because many other theories predict the same thing (nested hierarchies, for instance). In the case of junk DNA, yes, it seems likely that if Darwinian evolution is true AND DNA is cheap, that there will be no great selective pressure on useless lengths of DNA to be omitted. So you'd expect DNA to be a kind of "fossil record" of old genes, old viruses and old mutations, all of which are replicated, even though they are no longer functional, because there are no,or minimal reproductive costs to the organism in doing so. And, as it turns out, this appears to be the case. But it's not a prediction on which Darwinian evolution stands of fails. Had we not, in fact, found evidence of broken genes, old viruses, large repeated sequences etc, then it would have raised an interesting question: Is making DNA expensive to the organism? However, because we have in fact found those things, we can conclude that the answer to that question is No. Which is kind of handy, because it means we have a rich source of genetic data from which to construct phylogenies. And these phylogenies themselves are good evidence for Darwinian evolution, and evidence against intelligent design (the broken GULO gene being the poster child).Elizabeth Liddle
July 16, 2011
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Larry Moran has pointed out on his blog, that junk DNA is already non-Darwinian.
And yet here at UD, Elizabeth Liddle has repeatedly asserted that junk DNA is to be predicted from Darwinism. So once again we see how the same theory results in contradictions. It's not just ID people who should find fault with Darwinism, it is any person capable of reason.Mung
July 16, 2011
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as to, 'an important characteristic of science is self-correction.' I use to believe that science was like that, but now, after encountering dogmatic neo-Darwinists, I believe Max Planck was much closer to the truth about how science advances: “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it” - Max Planck ================= Planck also stated: "As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter." Max Planck - The Father Of Quantum Mechanics - Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944)(Of Note: Max Planck Planck was a devoted Christian from early life to death, was a churchwarden from 1920 until his death, and believed in an almighty, all-knowing, beneficent God (though, paradoxically, not necessarily a personal one) http://en.wikiquote.org/wiki/Max_Planck Moreover this 'spooky' quantum world, that Planck was instrumental in elucidating the foundation of, has just recently been found in DNA on a massive scale: Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/bornagain77
July 16, 2011
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Neil: The idea that evolutionists don’t put this to the test of evidence seems mistaken. We would not be hearing of roles for junk DNA if they were not researching it. The idea that finding roles for junk DNA would demolish evolution also seems mistaken. I would just say that some hard core of darwinists seem to be specifically hostile to the idea that junk DNA may have com plex functions. That is probably simply because the more functional complexity is discovered in the genome, the more neo darwinian theory shows its faults. It's just as simple as that. The hard core of neo darwinists is not the same thing as the biological community. They are just the ideological controllers of the biological community. So, it's perfectly normal that the biological community is actively investigating non coding DNA, because it is evidently one of the most promising frontiers of biological research. And it is perfectly normal that the hard core od neodarwinism is actively doing its "best" to minimize, negate or reinterpret their findings.gpuccio
July 16, 2011
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NR: News is putting the relevant facts straight, which is its own justification. And no, immoral equivalency rhetoric does not hack it. GEM of TKIkairosfocus
July 16, 2011
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I'm not sure what is the point here. Larry Moran has pointed out on his blog, that junk DNA is already non-Darwinian. So if the point is just that the Darwinian (or neo-Darwinian) account of evolution is not quite right, then Larry Moran and quite a few other evolutionists would agree. Personally, I have long assumed that the junk DNA would probably be found to have some sort of functional role. And, from time to time, I see reports indicating discoveries related to this. It does not cause me to question the broad picture of evolution as the basis for biological diversity. Discoveries of a role for junk DNA just help to fill in the picture. The idea that evolutionists don't put this to the test of evidence seems mistaken. We would not be hearing of roles for junk DNA if they were not researching it. The idea that finding roles for junk DNA would demolish evolution also seems mistaken. If the intention is merely to point out that there has been some excessive rhetoric, then I'll grant that. I see excessive rhetoric from both supporters and opponents of evolution.Neil Rickert
July 15, 2011
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