Adaptive mutations: Evidence of an ID mechanism?

Adaptive mutations are non-random mutations that occur in response to the environment. They are thus directed mutations, but in a general sense.Are they real, and if so, evidence for an ID mechanism?Some links for reference. On the Specificity of Adaptive Mutations | Genetics | Oxford Academic http://star.tau.ac.il/~inon/wisdom1/node4.htmlhttp://www.i-sis.org.uk/TMONTM.php
http://www.actabp.pl/pdf/2_2000/451-457s.pdf

This is not new knowledge. You are forgetting that selection is not a random process. Selection pressures can be so great that they force the appearance of specific mutations.Note, however, that this does not mean that if you take two different genomes and subject them to the same intense selection pressures, you wind up with the same genetic sequence as the genome goes through mutation. Selection and mutation can only work on what you have. This is why bats and birds do not have the same genetic sequences that develop wings, and yet they both have wings and can fly.This is not "intelligent design." This is good old evolution right in front of your eyes. Look at the very last sentence in the abstract you quoted: [Emphasis added]What do you think they're talking about when they say that selection has been applied? That's evolution. Evolution is not simply mutation. It is mutation followed by a whole host of other mechanisms including SELECTION.Your second link doesn't work.Your third link is only more of the same: Evolution is producing these changes, not "intelligent design." However, their claim that the Central Dogma has fallen by the wayside leads one to conclude that they don't understand their own writings.Your fourth link is, again, more of the same: Evolution is producing the changes, not "intelligent design." Read the final section regarding the mechanism for the change: It's all about metabolic changes brought about by environmental factors. That's evolution.If you're going to prove intelligent design, you're going to have to do it in a population that is not under stress. Selection is an evolutionary process, not an "intelligent design" process. Selection is not random. Selection is not passive.

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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.

That wholly contradicts the evo claim of random mutations. Selection cannot dictate the mutation to occur if the mutations are random. It selects among the mutations.I think you are missing the idea here. 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. There is a design within the organism that can determine the need for a certain mutation and produce that. Those are somewhat meaningless statements, more like slogans that something germane here. Selection is just as much part of ID as evolution. Heck, even creationism involves selection.This message has been edited by randman, 12-16-2005 06:12 PM

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

Randman, I've said it before, and I'll say it again:Mutation is non-random.(You never respond when I make this statement, perhaps because it would ruin your ability to make your claim that it is an "evo claim".)Mutation is non-random. However, that is a far cry from being preprogrammed, which often seems to be the leap you make from non-random.There is strong mutation biases that are well known in the field of molecular genetics. However, there appears to be enough of a random component that essentially "anything can happen"; that is, there is no evidence that certain bases are immune to certain types of mutations. As long as this holds to be the case, any and all sequence variants are possible for selection to act upon, and thus the theory of evolution remains unscathed. When "evos" claim mutations are random, they are either ignorant of the molecular genetics, or they are using "random" as shorthand for "contains a random component".
______________But on to adaptive mutations - you bring up a very interesting aspect of mutation, but it is not clear how general a case can be made from the bacterial examples.Also, it is not clear that you read the entirety of the papers you reference, since they are still arguing for randomness:You argue... ...yet this contradicts your sources. From your first source, by Hall: Now, Hall is careful to specify that his experiments cannot distinguish between "selective capture" (only those with proper mutations are observed) and "selective generation" (only proper mutations occur) models, and thus the latter cannot be ruled out entirely, but he essentially states that selective capture (of "random" mutations) is the most reasonable model given our current understanding.However, it is also important to note that even the models that fall under "selective generation" involve random mutation, albeit with non-random/selective repair; from your Janion reference: Still random mutation under selection.

Could not a mutation arise in both environments, while only providing a survival advantage in one? In this situation, it will flourish in that environment but go nowhere in the other and basically disappear. Thus, appearing to be specifically adaptive to the environment.

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"Thank you Slartibartfast, that will be all."

Yes, that's what we expect from normal mutations. Adaptive mutations are something different. They refer to mutations that seem to respond to the need to mutate. They separate 2 identical groups of bacteria into 2 different environments, and the group that does not need to mutate shows no mutations of the type they are looking for. The claim is it simply does not reflect a certain mutation at all, not that it is not selected for.The other half of the group of bacteria are placed in a more hostile environment, and they do start to mutate according to the type they are looking for.The term adaptive mutations thus doesn't refer to mutations that are adapted, but mutations that appear as the need arises, as if there is a programmed response to mutate certain positive mutations in response to particular environments.

Are James Watson and Edward O. Wilson ignorant of molecular genetics? Personally, I think you are misunderstanding the claims of evos. These guys specifically mentioned that mutations are random, not just that they have a random component.I think maybe you don't realize what evos mean by random. What they mean is that they are not directed or influenced by a Designer, and that is an unproven assumption, but as it is, evos tend to throw out a lot of terms loosely and poorly defined so that sometimes they don't even seem to know what they are talking about.

Let's see if we can clarify this.Technically, "random" is a mathematical term, not a physical term. There isn't any fact of the matter is to whether particular real events are random. It is a question of whether modelling them as random events makes for a useful mathematical model.Suppose I have a biased coin, that shows heads every time I toss it. Then, mathematically, this is still a random event. It is just that the probability distribution for that event is very different than the probability distribution that you get with tossing an unbiased coin.You can have a radioactive material, periodically emitting an particle. That's like the biased coin. Every time there is an event, it comes out alpha particle. It is still random. It is considered random, because when it emits that particle is modelled mathematically by an exponential distribution.Natural selection can certainly bias the biochemistry against certain kinds of mutations, such as those that are almost invariably fatal. And it can bias toward other mutations, those that are typically near neutral. But the timing of when mutations occur can still be random, and probably fits an exponential distribution.Even the assumption of exponential distribution for the timing is known not to be correct. In some species, mutation rates increase when the species is under stress (high selection pressure). However, this is still considered random.

Just to clarify: Mutation biases are pre-selection, though.Certain sequences/regions of DNA are more likely to mutate than others; also, certain sequences are more likely to mutate in certain ways. This is a result of biochemistry, not selection after-the-fact. The timing of mutations is also biased to certain stages of the life cycle and environmental conditions - again, pre-selection.I'm not sure how either of these biases affects the overall fit of "mutation" to a "random" mathematical model. Any thoughts?

Maybe. Is there any reason to believe that Watson and Wilson are complete experts on all facets of molecular genetics? I don't have a clue regarding their current understanding of mutational biases, and I don't know the specific language they used in their interview or the context - one reason I never make arguments from authority or defend authority, though it seems to be one of your favorite tactics.Truthfully, I find it amusing that in every single case that I've agreed with you, you still argue back vehemently as though I've said the opposite. Must you be so adversarial?I would still like a response to the bulk of my previous post, which was discussion of adaptive mutations and your references, and which you entirely ignored.

I admit that I am not a biochemist. But it seems to me that natural selection should be able to affect the mechanism, and those effects in the mechanism could bias future mutations. I'm not sure what you are saying here with your emphasis on pre-selection. The only mutations that are completely preselection are those in the original proto-life form. Once there has ever been selection, further mutations are post-selection (because they occur in organisms that derive from selection), and they are pre-selection because they set what future selection can act on. It requires that the model involve a more complex stochastic process. But it does not rule out using a mathematical model.

I guess I have always had a overly simplistic picture of what "random" means in this context.I once had a picture of it meaning that any change could happen to any place in the genome with an equal probability.I suppose there is a background of that in that a mistake or radioactive accident could happen anywhere. However, that is before the correction mechanisms come in.If we measure after those there may well be some bias in that some parts are chemically easier to catch and fix than others.Then I hadn't considered the detailed chemistry. Some parts of the DNA may be "weaker" (more easily changed by whatever). Thus the chances that a particular pieces mutates isn't even across the whole thing.It appears the next difficulty is actually measureing mutations before any selection has had a chance to happen. If changes are "selected" out by some cell chemistry very, very early it might be hard to see.There are, it seems, lots of layers to look at and lots of different ways to measure what we are attempting to talk about.It seems that underlying all this at least some of what is going on is random in the most simplistic use of the word. However, there are a lot of mechanisms through which mutation can happen so that simplistic use may not be right.

What mechanism are you referring to? (Just a hypothetical one?)As Nosy points out nicely above, there exist a variety of reasons for mutational biases. Many of them are simply differences in the chemistry of different sequences of DNA.I think I misunderstood the point of your previous post, hence my ramblings about pre-selection. You wrote: Intuitively this seems to be asking selection to work on mutations before the phenotype is produced... though now I understand that you mean a mechanism built up as a result of a history of selection. I'll have to think about this a bit.

any repair mechanism that repaired fatal (replication) mutations would be positively selected for wouldn't it?albeit the mutation would still have occurred, it would have been selected out of the mix by the repair mechanism.

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