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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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…
Here is David Tyler’s Article on the paper:
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.
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’:
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;
Michael Behe talks about the preceding paper on this podcast:
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!!!
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.
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.
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!
And YEC, OEC and ID are all OK with mutations and variations.
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.
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.
They just are, apparently.
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.
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:
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.
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.
Terminus repeatus!