The Nature of Mutations

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crashfrog: I don't have to provide evidence for a naturalistic paradigm.

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Phsopho: Yes, you do. Especially when that naturalistic paradigm is assumed, not proven.

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You'll not be able to advance this argument any further without more clarity. Crashfrog made it pretty clear that for him the naturalistic paradigm is the default because it requires no supernatural entities. Phospho is really just saying "no" but giving no clearly argued reason for this. Simply saying to each other "prove it" and "don't need to" is pretty pointless.A more constructive approach could be taken by considering not absolute positions of what holds and does not hold, but a process-oriented view. Are we using an inductive strategy that can reliably lead to truth, and if so, is my "working hypothesis" of the moment compatible with that process?I'll put my cards on the table and say that I think the naturalistic hypothesis is entirely compatible with "inference to the best explanation." It may be that the "best explanation" turns out to be a supernatural one. But that does not mean that adopting a "supernatural" paradigm during the inductive process is compatible with a reliable inductive strategy.In other words, asking one or other to prove a paradigm as true is simply neither useful or necessary - in fact it may even be incompatible with a suitable strategy. The really interesting question is whether the inductive strategy can be improved or not.I suppose it could be said that believers in supernaturalism claim to have found - through the Bible perhaps - a more efficient strategy for reaching the truth. That may well be so. The question remains, however, as to which strategy is appropriate for science.In this context, then, crashfrog need not prove the chosen paradigm tombe true, only that choosing that paradigm is compatible with an appropriate inductive strategy.

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First there has to be agreeement on the definition of mutation. Could someone propose a definition?

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The original definition for mutation was a random change in DNA made to a gene during its replication via copying error that was not caught and corrected by correcting enzymes. This included additions (not insertions performed by specific enzymes), deletions (not extractions performed by specific enzymes), or substitution of one or more nucleotides. I concede that the accidental copying of an entire gene can be considered as a mutation.What is NOT considered a mutation (except by evolutionary theorists, and that illegitimately) are any other genetic changes, including adaptaion and variational changes, because these have proven to be not by random chance events, but mediated by specific organismic mechanisms.Greetings!

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FK: And because of the benefits of the modified protein, the low level of HDL are irrelevant. In other words, a person with this mutation is better off than without it. It is beneficial. The significance of HDL in this context is diminished. HDL prevents plaque buildup. The new protein does the job more effectively; hence the mutation is beneficial.

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You are confusing the actual nature of the mutation with its by-product effect. The mutation is a deleterious mutation because it deminishes the original purpose of the protein. Period. This causes the protein to malfunction and not produce HDL up to standard levels. It is a deleterious mutation. I did not deny that it has a beneficial side-effect. But nice try.As for the rest of your post, see the previous posts on transposons and adaptational variants. Single genetic pieces or entire sequences turning on and off gene expression. As for the "major" creationist organizations, I don't know, I haven't talked to any of them. But I bet that if we got down to the nitty-gritty, they would be agreeing with me rather than you.Again, I have not stated that there are no mutations that confer beneficial side-effects upon their bearers. What I have stated is that there are no strictly beneficial mutations that lend any aid to the evolutionary paradigm. All you quibble over is adaptational changes, but since these are not mutations, there is no such thing as micro-evolution (which is a misnomer). Therefore, there is no macro-evolution.Try again.Greetings!

Once again, you've assumed purpose in a context where "purpose" is a meaningless term. There is no purpose in biology, only function. Your dismissal "only if you're talking about art" is simply false - function can arise without design, as well as design without function.Again with the talk about the "nature" of the mutation... throughout this thread you've made the assumption that objects can have inherent purpose. I do not believe this to be so. This is an assertation you'll have to support.Why do you insist that if the protien is different than in other individuals that it is broken? By the same reasoning, if I replace my computer's hard drive with a larger one, I've broken my computer because the old hard drive no longer has purpose. The fact that I can hold a lot more mp3's is just a "beneficial side-effect". Do you see how fallacious your reasoning is? Detrimental AND beneficial can only be judged in context of function, not of purpose. Didn't you, earlier, accept duplicate genes as mutations? The mosquitos who generated additional levels of pesticide-digesting enzymes did so through gene duplications. Unless you can point out a derimental effect to these additional levels of enzyme you'll have to conclude that it was a purely beneficial mutation, by your own reasoning.[This message has been edited by crashfrog, 05-02-2003][This message has been edited by crashfrog, 05-02-2003]

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Phospho's "rebuttal" to the RNASE mutation is in error. He misunderstands "adaptive" as meaning "non-random" rather than "beneficial". As his rebuttal rests on that error, it fails and the example remains unchallenged.

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Negative, the misunderstanding falls into your court...ACE!!!Adaptation is NOT random, this has been demonstrated since 1986. Since your rebuttal rests on the ill fated ideal that they are random, it fails, and the challenge on my end remains unmet.Greetings!

But the source of adaptation (at least, the heritable kind - which is the only kind that matters to populations) IS random. That is, whether or not a species will adapt to its environment is inherently random.Unless you can predict precisely when and how adaptations will occur? And explain why some species fail to adapt to their environment?Your specific use of a date suggests you're referring to some study or something. Could you supply it? I'd like to read it. I don't have a very deep biology background.

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technically there are two ways variation appears in an organism/population: 1) mutation and 2) recombination during meiosis. They really are two distinct mechanisms. Recombination is NOT a mutation - it's simply the randomization of existing DNA when the chromosomes split and shuffle during normal sexual reproduction (gametogenesis).

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First, where is there any evidence that mutation gives rise to variation? There is none. Provide that which you call evidence, and I will demonstrate that it is only transposon-activated genes that before hand were dormant and non-expressed.Second, chromosomal rearangements have also been demonstrated not to be random actions, but they, too, are broken and spliced together by specific enzymes.But we do agree that they are not mutations.Greetings!

Perhaps you need to say what you mean by "variation". Most people assume that to mean "differences". Biologically it tends to refer to the phenomenon where individuals in a population tend not to be genetic clones of each other.In either case, it's clear that mutations represent novel genetic sequences in organisms not decended from it's parents - making that individual different - varied - from its peers and parents.How is that not variation through mutation?

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Phospho's assertion that all mutations are lethal is just plain wrong..

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To clear up a misunderstanding...again...I never stated that all mutations are lethal, I said that of the two catagories of mutations (neutral and deleterious, of which only the deleterious affect the phenotype), those which affect the phenotype damage whatever physiological character that incurs that mutation.They will always carry a deleterious affect, whether it is lethal or not depends upon your definition. To me, when you say lethal, you are talking about the mutation killing the organism which it occurs in. Sickle Cell demonstrates that this is incorrect.Greetings!

Adaption is used quire widely. In the case of the article at U-M Web Hosting
it is clearly used to express the idea that this mutation is beneficial and no more:"Our results suggest that this is an adaptation to the more acidic environment of the small intestine in colobine monkeys," says Zhang.THe ball is right back in your court.And am I right in thinking that you are a supporter of the ideas of Lee Spetner ? His followers tend to make the same errors as you in firstly misunderstanding the idea of "random mutations" (which means only that mutations are not directed in a way that automatically produces bebnfifical changes) and in assuming that if any mechanism is involved at all the mutations must be seen as non-random. Perhaps you woud like to explain why using a more error-prone replicase is better seen as producing non-random mutatiosn rather than a greater number of random mutations - in any sense.[Added by Edit] I have created a reply to show evidence that your understanding of "adaption" is in error.[This message has been edited by PaulK, 05-06-2003]

You still haven't addressed what deleterious effect a gene duplication could have (particularly if its a duplication of a beneficial gene), given that they are, by your own admission, mutations...

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It should be - they've just changed their policy to giving free access for everything from 1996 (I think...) to one year before the current issue. Science | AAAS - registration is free.

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I tried to access it, but unless I really messed it up, I couldn't get past the registration page.Thanks!

Science articles are public access only from September '96 - that article was previous to that.

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The one problem with the definition is the vagueness regarding "changes in gene expression"...it covers epigenetic modification but does not account for variation induced by environment which is not really a mutation. I am thinking of variation in coat color in cloned cows or variation in paternal or maternal X chromosome inactivaition in female embryos which are driven by purely stochastic events....but I guess that is covered since the definition says heritable change.

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OK, so can you codify this definition again in one, easy-to-read post so that I can get a grasp of what we are agreeing too? For a minute there, it almost sounds something like what I was trying to get across, unless I just worded it wrong.This is my last post for the day, I have to go. I promise that I will try to not make it so long in between my postings. I am subject to call-in and hold-over at work, it makes it rough sometimes when the work piles up.Thanks for the discussion...and for discussing it in a cordial manner. If I have said anything to anyone that seemed out of line or uncordial, please forgive and excuse, I did not mean it to be as such.Greetings!

Articles in Proceedings of the National Academy of Science are available from 1990 to six months before the ever-advancing present. PNAS