#9 of 2011 for ID community: DNA Repair Mechanisms Reveal a Contradiction in Evolutionary Theory.

_{Denyse O'Leary

January 6, 2012

Darwinism, News}

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Every year, Access Research Network publishes a list of the 10 most significant science news stories for the year, for the intelligent design community – in consultation with theorists and writers. For 2001, here’s #9:

New research reveals that DNA repair mechanisms limit the capability for evolution by unbounded random change. Both digital codes in computers and nucleotide codes in cells are protected against mutations by complex error correction mechanisms. In the February 2011 issue of Open Evolution Journal William DeJong and Hans Degens explore how mutation protection affects the random change and selection of digital and nucleotide codes. They illustrate their findings with a computer simulation of the evolution of a population of self-replicating digital amoebae. The authors show that evolutionary programming of digital codes is a valid model for the evolution of nucleotide codes by random change within the boundaries of mutation protection, not for evolution by unbounded random change. The findings are of considerable interest. They show that any evolutionary theory which ignores mutation protection is missing out a factor of great importance. The consequence of protection is that limitations of the evolutionary dynamics of digital and nucleotide codes are highly probable. Contradiction in evolutionary theory is a short YouTube presentation that summarizes the authors’ findings.

See also:

#1 of 2011 for ID community: 50th Peer-Reviewed Pro-ID Scientific Paper Published.

#2 of 2011 for ID community: The Design of the Butterfly Continues to Inspire and Amaze.

#3 of 2011 for ID community: Woodpecker Drumming Inspires Shock-Absorbing System.

#4 of 2011 for ID community: “Stylus” Computer Program Aims to Bridge Gap Between Real World and Artificial Evolutionary Simulation.

#5 of 2011 for ID community: Explosive Radiation of Flowering Plants Confirmed

#6 of 2011 for ID community: Golden Orb-Weaver Fossil Spider Provides New Evidence for Stasis.

#7 of 2011 for ID community: Complexity in the Universe Appears Earlier Than Thought.

#8 of 2011 for ID community: An Identity Crisis for Human Ancestors.

#10 of 2011 for ID community: Limits to self-organization of life identified

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Comments

Terminus repeatus!bornagain77_{January 8, 2012
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I really can’t see how the contradiction outlined in the article, between mutation robustness and evolvability “was cleared up early in the last century”. Please, explain.
The paradox as stated (in the video) is this: "The necessity of disabling mutation protection for evolution, and its necessity for survival". It's pretty clear the authors aren't biologists. The "Modern Synthesis" of the 1940's incorporated the mutations of the geneticists as the raw material of evolution, and the NS of Darwin as the means by which such mutations spread around the population. Add to that the drift of Kimura from the 1960's, and you have the basics of current evolutionary theory: Mutations occur, caused by imperfections in the replication process, and mechanical, chemical and radiation damage. They cover the spectrum from seriously detrimental to beneficial. The detrimental ones are eliminated by negative selection. Near-neutral ones drift within the population, mostly due to chance, while more strongly beneficial ones are assisted by positive selection. Now, this scenario does not require mutations to be 'turned on' in order to allow evolution. There is no absolute necessity for evolution to occur at all - certainly not to keep evolutionary theorists happy! All that evolution theory is saying is that IF changes happen, THEN populations will evolve, and these are the causal factors involved. Now, although no-one explicitly stated and then cleared up the "paradox" last century, if they had, the Modern Synthesis would have been perfectly up to the job of explaining why it is not a paradox at all. From the paper:
Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, codeexpanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction.
Well, it definitely does not require it to be turned off. But yes, it would have to be "dysfunctional" in order for evolution to happen. And it is, so no problem there then.
Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce.
Yeah, it's a pisser and no mistake! (Note: cancer is a disease of somatic cells, not the germ line, so it is irrelevant). Either way, you simply cannot stop cosmic rays and viruses and chemical mutagens from getting in. You cannot stop DNA polymerase from making a base-recognition mistake every n bases, or proofreading failures every y bases, or occasional slippage during homologous recombination. To perfect things, you would have to slow it down, like a computer copy process. Copy-and-verify takes a lot longer than copy alone. Slowing it down too much has undesirable consequences of its own. So there is no paradox. Nothing NEEDS mutation to happen, or not-to-happen, but it does anyway. The fact that it does is kind of handy. Without it, populations would inexorably lose variation, and become effective clones, which appears to be evolutionary suicide, for multicelluar organisms at least. Detrimental mutations for individuals are the downside of mutation; population survival the upside. Mutation-free individuals in an extinct population would be a paradox! There is a more recent vogue to talk of 'evolvability'. It is arguable that the optimum mutation rate really is zero - no cancer, better offspring, all that jazz. We then look for explanations as to why it isn't. The 'evolvability' argument is that it is beneficial to keep mutation because it keeps a drip-feed of variation going into the population, allowing it to adapt to short-term changes. That explanation can work. But the speed-accuracy trade-off argument is also valid. It is conceivable (though unlikely) that lineages develop perfect mutation protection from time to time. Because they suffocate from loss of variation, they go extinct. We are left with the organisms that did not go extinct - a survival bias in favour of those with imperfect mutation protection. But no paradox.Chas D_{January 8, 2012
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And YEC, OEC and ID are all OK with mutations and variations.
Did I say they weren't? The article is insisting that mutations require 'dysfunctioning' of mutation protection. I was arguing that this is not the case.Chas D_{January 8, 2012
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I do appreciate you revealing just how shallow the responses of Darwinist can be!
An honest attempt to address the issues raised by your cutting out of a few vaguely on-topic articles from your cut 'n' paste collection. Sorry you didn't understand it.
the vast majority of changes in the genome are now shown to be ‘non-random'

the vast majority of ‘random’ mutations ... are now shown to be detrimental
They just are, apparently.Chas D_{January 8, 2012
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ChasD: One of the main points of the article os that all "simulations" in GAs (including AVIDA) are simulations within the boundaries of digital mutation protection, and therefore cannot simulate biological mutation out of the boundaries of biological mutation proteiction. That is an important point. Moreover, I really can't see how the contradiction outlined in the article, between mutation robustness and evolvability "was cleared up early in the last century". Please, explain.gpuccio_{January 7, 2012
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And YEC, OEC and ID are all OK with mutations and variations.Joe_{January 7, 2012
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Well Chas, I'm not going to chase your tail in a circle of unfounded fluff, you are doing quite a fine job of doing that yourself. But I do appreciate you revealing just how shallow the responses of Darwinist can be!bornagain77_{January 7, 2012
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HMM, your rationalization would have merit save for the fact that, number 1, the vast majority of changes in the genome are now shown to be ‘non-random’:
Well, I must respectfully disagree with Dr Shapiro. "The vast majority"? "Almost always naturally engineered"? I would like to see a bit more meat on that; it sounds like hyperbole to me.
and number 2, that the vast majority of ‘random’ mutations, which do ‘leak through’ the dike (your analogy not mine :) ), are now shown to be detrimental:
Provided a proportion of mutations is not detrimental, however minor, the raw material of evolutionary variation can continue to be supplied. The vast majority of raindrops don't fall on my head, but I still get wet. Mutation in a lab environment has to be artificially accelerated - no-one is going to sit there playing cards waiting for it to happen - and this hits the boundary of mutational meltdown. A natural population has a far greater capacity to generate mutations and sift them, due to size and time. By analogy, trying to accelerate the flow of pitch can cause it to shatter. Patience. In a natural population, mutation occurs at a low level, and all the detrimental ones get snuffed out almost immediately, as if they had never happened. The rest are grist to the evolutionary mill. All polymorphisms are (so far as can be determined) the result of historic mutations. Each individual human is estimated to contain about 130 mutations. So ... non-lethal mutations demonstrably happen. Must the protection apparatus have been "dysfunctioned" in order for that to be the case? It is already dysfunctional - ie not 100% accurate.Chas D_{January 7, 2012
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HMM, your rationalization would have merit save for the fact that, number 1, the vast majority of changes in the genome are now shown to be 'non-random':
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
and number 2, that the vast majority of 'random' mutations, which do 'leak through' the dike (your analogy not mine :) ), are now shown to be detrimental: The following study surveys four decades of experimental work, and solidly supports the conclusion that the 'random' mutation rate is overwhelmingly detrimental;
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Michael Behe talks about the preceding paper on this podcast:
Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00 Where's the substantiating evidence for neo-Darwinism? https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit Mutation Studies, Videos, And Quotes http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjZjZnM5M21mZg ...Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19
so despite your claim (shallow rationalization) that the contradiction was 'cleared up' early last century, the fact is that the contradiction was never honestly dealt with and has only greatly intensified by what has been recently discovered!!!bornagain77_{January 7, 2012
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It is not a question of 'dysfunctioning' mutation protection, but that mutation is unavoidable. Nucleotide bases and the enzymes that recognise and copy or repair them are are near the quantum scale - their distinctive atoms and charges have an element of uncertainty - and DNA polymerase has an error rate as a consequence. It is not perfect. Then again, mechanical damage unavoidably occurs, and the cell can have a go at repairing it. eg a double-strand break can be repaired with a patch from a homologue in a diploid or dividing cell (or during meiosis), which is not guaranteed to produce perfect results every time, though the results may well be functional. There are many opportunities for slippage which causes both lengthening and shortening, and the same imperfect base-recognition issue is again involved. In the absence of a homologue, the only option for repair is end-joining, which again is likely to be mutational. So all in all, there is no necessity to 'enable' mutation in any way, or 'dysfunction' its protection. It is simply the case that, with all an organism's many fingers in the dyke, some still get through. Yes, mutation can be one cause of cancer. It is generally undesirable from the organism and population point of view. But there is a silver lining: it is the source of variation. This contradiction in evolutionary theory was cleared up early in the last century.Chas D_{January 7, 2012
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Here is David Tyler's Article on the paper:
The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - David Tyler - February 2011 Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation." http://www.arn.org/blogs/index.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic
bornagain77_{January 6, 2012
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Nope, you are mistaken as there aren't any contradictions in evolutionary theory. And if you think there are just close your eyes, click your heels together three times and say "There are no contradictions to evolutionary theory" over and over again. And if that doesn't work call the NCSE...Joe_{January 6, 2012
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