Adaptive mutations: Evidence of an ID mechanism?

Maybe "mechanism" is the wrong term. I was referring to the processes involved in DNA replication, particlarly those related to reproduction. Right. It is my expectation that these differences of chemistry can evolve.Apologies for delayed reply.

Yes, absolutely. However, I think nwr is going a step further by suggesting that the mechanism could evolve to repair or prevent detrimental mutations more often than it would neutral/beneficial mutations. In other words, something in the evolved system would allow the detrimental/neutral/beneficial nature of a given mutation to be recognized as such before organism-level selection acted upon it, and allow or disallow the mutation accordingly.This is basically what some of the adaptive mutation models are suggesting, from my scanning of the above references. (I'm just not sure how I feel about it yet...)

nwr-I don't think you are wrong, and you seem to be suggesting something similar to the adaptive mutations models. Perhaps they "chemically" evolved, and 4-base double-helix DNA itself is the optimized "chemical."Also, that sequence differences themselves result in different chemical properties, and DNA plus DNA-associated proteins result in different chemical/biochemical properties between bound/unbound regions.However, I'm still trying to wrap my own mind around the molecular mechanism that would bias/distinguish bad from neutral/good mutations specifically - one adaptive mutation "selective generation" model uses transcriptional read-through as a means to recognize beneficial mutations, but I see this as being quite specific to cells-in-crisis that need a specific frameshift mutation to survive. If my understanding of the experimental system/model used in the OP references is correct, this can not be generalized very far beyond that system.No need to respond to this post unless you have something to add, I recognize that these are half-thought-out ramblings to some extent...

Thanks for the support and encouragement. (You are correct, however, in that assessment).An additional comment. Showing some sort of bias would not help randman, in my opinion. To advance his cause, that there is evidence for a designer, I think one would need evidence that the mutations were evidence of an externally imposed plan. If biases are there only because the biases evolved, in my opinion that would not help randman at all. I am at a disadvantage of knowing little biochemistry. But here is one possibility. If we assume that some parts of the DNA strand are more stable (mutate less frequently), then a gene for which most mutations are fatal might somehow migrate to that stable area. And a gene where most mutations are near neutral might migrate to a less stable part of the DNA. I am assuming that migration is possible, as suggested by the work on transposable genes (or did I misunderstand that).

Actually, I was referring to my own half-thunk ramblings, not yours! But at least we're both on the same page there... Yes, migration appears to be very possible. I guess what you state above could be possible for some specific cases. Other aspects I'm thinking about-(I think) More transcriptionally active genes are more susceptible to some types of mutation - this would mean that commonly or continuously needed genes are more susceptible to mutation, even though by their very nature their mutation could be highly detrimental. (However, neighboring genes that aren't as transcriptionally active could potentially leave the neighborhood to reduce susceptibility by association.)Repetitive DNA sequence is hypermutable - yet some gene coding seqences still contain stretches of repetitive DNA. It appears that these genes evolve, and can drive evolution of morphology, because of this repetitive DNA. Though not all mutations are neutral/beneficial in this context. A free full-text reference examining this hypothesis.A lot of stuff is going on just with what is currently known; like I said, I'm still trying to get my mind round it all... I agree. He stated earlier (my bolds): In my mind, he uses the word "design" where he should repeat "mechanism", and maybe he didn't intentionally use "design" as in ID. But I think this is often a leap that randman and others (Faith) make - that if mutation is non-random (as in biased), then there is a pattern, then there must be a program, then there must be a programmer. It doesn't follow.Instead of his statement "There is a design...", how about "There is an evolved mechanism... within the organism that can determine the need for a certain mutation and produce that." Since the mechanism hasn't been figured out either way, I prefer to go with the mechanism source that has some evidence for its existence.Sorry - that post got lengthy...

I was thinking of a mechanism that has 'learned' certain bad mutations so that it would be able to {prevent\block\correct} them as they occur. It could be incorporated into the genome quite easily within the standard repair mechanisms.There would be no need to 'learn' to prevent neutral or beneficial ones, so those would still be allowed to occur.That's my ramblin thoughts on it.

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randman responds to me:

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Selection pressures can be so great that they force the appearance of specific mutations.

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That wholly contradicts the evo claim of random mutations.

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Incorrect. You are forgetting about selection. Selection works hand in hand with mutation.Let's take a trivial example: Mutagens. Mutagens are selective aspects because they come from the environment. For example, 5-bromouracil functions very much like thymine and is incorporated into the genes where thymine would normally reside. However, 5-bromouracil is much more likely to pair with guanine rather than adenine. Thus, 5-bromouracil is a powerful mutagen transforming A-T pairs into G-C pairs.But that will only happen at places where thymine exists in the genetic code. It doesn't force itself into just anywhere in the gene. It only does its magic where the gene will allow it to happen.Therefore, selective pressures (presence of 5-bromouracil) can be so great as to force specific mutations (A-T to G-C).Note, I said this was a trivial example. There are other ways in which selection pushes the mutation. There are environmental stressors that also result in higher incidences of mutation that don't involve the direct introduction of mutagens.

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Selection cannot dictate the mutation to occur if the mutations are random.

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Incorrect. Selection most certainly can because selection is not some passive force.

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It selects among the mutations.

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Incorrect. Selection drives evolution. You can't mutate what doesn't exist. If you have been selected against, your genetic sequences literally do not exist to be mutated for the next generation. And the environment can induce pressures so great as to drive certain mutations.

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I think you are missing the idea here.

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Strange, I was going to say the exact same thing to you. You have completely missed the point about what selection is. It is not passive. It is one of the major driving factors of evolution. It is not simply waiting around for everything else to do its job and then sweeping out the leftovers.

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Adaptive mutations occuring in one environment but not another indicates some sort of mechanism for triggering the right mutations in order to survive, and thus the mutation is directed and not random.

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Incorrect. You are confusing the action as part of mutation. It is not. It is part of selection. Selection is not passive. It is active. At the most trivial level, that is how artificial selection works. Those that are selected against are so not because of any biological or environmental trait. They are selected against due to societal desire.

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There is a design within the organism that can determine the need for a certain mutation and produce that.

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Incorrect. The drive is not a "need." It is purely environmental. You have a very poor understanding of the biological role of selection.

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Selection is an evolutionary process, not an "intelligent design" process. Selection is not random. Selection is not passive.

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Those are somewhat meaningless statements, more like slogans that something germane here.

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Only because you don't understand what selection is. I suggest you read up on some Gould. Hen's Teeth and Horse's Toes, if I recall the title correctly (though it may have been Ever Since Darwin) goes into the topic of how selection is an active, driving process, not a passive one.

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Selection is just as much part of ID as evolution. Heck, even creationism involves selection.

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No, creationism involves the direct appearance of traits ex nihilo. There is no selection involved. Selection is an evolutionary process, not a creationist one.What is the main claim of "intelligent design"? That's right, "irreducible complexity." That there are some structures that simply cannot arise through natural, biological means. No amount of selection could possibly do it because the process cannot possibly exist in any stable form until all pieces are in place. Since those pieces cannot be in place until all the others are, they cannot be selected for. Therefore, they must have been put in place, ex nihilo.Deny selection and you deny evolution.

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Rrhain

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Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

NosyNed responds to me:

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I think, Rrhain, that the quotes say that mutation is happening at a specific site.

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Yes, I know. Reread what I said: Selection pressures can be so great as to force the appearance of specific mutations. The mutations are there and are very real. They are happening at specific sites rather than at others, though those others are equally mutable.But the reason the mutations are happening at those specific sites is because of intense selection pressure.

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What I don't see is how they are sure that they aren't only seeing what they select for but mutations are happening at both (or all) places.

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One way to do that is to look at the genomes at cellular division and see how many times a mutation occurs at a specific point compared to at another point. There is another paper (Bell? Ball? The name is escaping me for the moment) regarding this phenomenon of how selection drives mutation.

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Rrhain

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Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

O.k., biogeniuses, not to drag your debate too far off topic, but can you help me out? I`m most of the way through 'Microcosmos'--Lynn Margulis, and following her thoughts on the evidence of microbial insertions in our ancient mitochondria, chloroblasts, rods and cones of the eye (the 9+2 formation of microtubules), with her later works coming up. My question concerns whether we know of more up-to-date insertions, or are they all ancient? Are the Thalassemia and sickle-cell presences relatively recent? Is there any way of exploring whether digestive bacteria in the Homo sap gut is recent or old, and what it replaced? What`s the historical limit when tracing mitochrondrial DNA back from the present? Any help gracefully accepted.

I'm still having trouble with what all this is supposed to mean.To me selection is something which picks and choses from the existing genome. That genome may have just popped into existance because of a mutation but only then can it be selected for.Your earlier example of a mutagen is not, to me, selection. Selection isn't everything that comes from the environment it is the processes that weeds out some traits and not others. A mutagen is affecting the genome but to call that selection seems to me to be streching the definition.I need more explanation.

This would drag the debate distinctly off-topic. Perhaps you could flesh this out a bit and produce an OP for a new PNT instead.TTFN,AW

Basically, all that posting and 0 substance. Selection just selects among the mutations. It doesn't dictate what the mutations are, just the mutations that remain. You're insistence on selection as some sort of magical driving force, etc,....is short on substance, and frankly I am not even sure what you are claiming.Are you stating that natural selection causes the desired mutations or just selects among them?

NosyNed responds to me:

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I'm still having trouble with what all this is supposed to mean.

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To me selection is something which picks and choses from the existing genome.

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It isn't. This is the same misguided conceptualization of selection that randman has. Selection is not a passive process that only comes in after all the other mechanisms involved in evolution have done their work to clean up their mess.

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That genome may have just popped into existance because of a mutation but only then can it be selected for.

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But the act of selection is a process affecting the genome.

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Your earlier example of a mutagen is not, to me, selection.

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Then what is it? It is an environmental factor that externally acts upon the genome. It is not an inherent part of the chemical action of replication or the functional aspect of the genome, itself, such as recombination.

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Selection isn't everything that comes from the environment it is the processes that weeds out some traits and not others.

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It is so much more than that, though. Evolution is not just about the mutations.

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A mutagen is affecting the genome but to call that selection seems to me to be streching the definition.

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To call it anything else is to slight selection, though. Gould wrote about the power of selection and one of the articles can be found here: Darwin's Untimely Burial: Dispite reports to the contrary, the theory of natural selection remains very much alive.In order for selection to be of any use, you have to be able to determine which ones are going to be selected before the variants show up. Selection is helping to drive the system.

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Rrhain

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Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

randman responds to me:

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Are you stating that natural selection causes the desired mutations or just selects among them?

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Asked and answered. Read my posts.But just in case you're unwilling, the answer is "Both." What do you think "selection pressures can be so great as to drive certain mutations" means?

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Rrhain

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Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

OK, explain the mechanism by which natural selection tells the organism what to mutate, not merely selecting for the mutations.Also, I am well aware that environmental factors can cause mutations, though generally harmful, but those sorts of environmental factors are not natural selection, right?I will be looking for your mechanism by which the organism "knows" in advance what to mutate.