Darwin in the Genome

Hi paul,In response to:The INMR report cited earlier claims that "We have also studied the a-actinin-3 gene throughout evolution and have demonstrated it appears to be essential in all other species — including mice, chickens, baboons and chimpanzees."PB says:These guys -and you- may be under the impression that they have studied evolution, but they didn't. If they really had studied the ACTN genes throughout evolution it would have taken them millions of years to perform the study.
In contrast, all they show is a study on the ACTN3 genes in several distinct organisms. MPGs if you like. Nothing evolved here. That they think they are studying evolution -while all they do is checking distinct sequences in distinct organism- is tale telling for you evo guys: conclusion jumping based upon assumptions.best wishes,
Peter

I see that you still have not managed to offer an explanation of how mutatiosn are "random" according to NDT. THe best resposne you can manage is to demand that I do the work of explaining a basic point which you claim to understand - even though I have already done so more than once.I also notice that you feel the need to throw irrelevant personal attacks at Dawkins for no apparent reason. I suggest you keep your personal hatreds out of your posts.I also notice that you defend your comments by falsely claiming that they have been misrepresented. However rather than explain why your ideas were not the nonsense I suggest you instead claim that they are a strawman (since they do not represent the views of your opponents).
I also note that in a later post you drop the idea of explaining the data in an evolutionary context altogether - to answer data which points to a viable alternative (the non-redundancy of actinin-3 in other species).Your admission that you did not knwo what neutral selection was is a further evidence of your general lack of knowledge in the area of evolutionary theory.As to your final point your argument fails to deal with the fact that actinin-3 does seem to confer a benefit (that some individuals MAY gain that benefit by other means does not change the fact that the evidence shows that there is a benefit). And it seems that your argument agaisnt evolution also applies to your own GuToB - only more so. Why have non-random mutations not inactivated the ACTN-3 gene in the entire human population ?

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PB: Apparently you still don't get the example: it was on a 360 bp mtDNA region in ancient human mtDNAs (0-62 kY BP). Maybe you could provide the other references on ancient human mtDNA in several ancient human species.

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Maybe you can point out out for us where in the Adcock et al. paper it is explained that their chimp samples are also ancient.
For if they are not, your "take home message" is premised on what YOU considewred comparing 'apples and oranges'.

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Maybe I should also mention that a good theory requires to be right in extreme conditions. For instance Einsteins' gravitational theory proven over and over through extraordinary predicted observation. The mtDNA could be such extraordinary case. It turns out to falsify evolutionary assertions. To me it is clear that evolutionism is a bad theory.

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Borgerism.Police develop a 'theory' about a serial arsonist. 100 fires have been set. They catch the crook in action. He admits to setting 99 of the 100 fires, but has a rock-solid alibi for the 100th.The police scratch their heads.."I guess we should let him go" one finally utters."Yup" says another "if he didn't do all of them, I guess he must not have done any. Our theory is refuted."

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PB, after pasting part of an abstract that I had provided some days ago:
PB: The paper is on gene classification.

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Why, yes it is, in part. But how is it, Dr.Borger, that these folks went about their classification? Guesswork? mere assertion? The results of their analyses do not seem to jive with your repeated unsupported assertions, that there was no evidence of 'descent', right?

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And the explicit assumption that the one gene arose from the other.

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Why do you suppose that they use that assumption?
And if the reults had not conformed to that assumption, (if we are to accept your interpretation), what would we have expected?

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However, my comments posted to you yesterday questioned this scenario.

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Of ocurse they do. All creationists are required to question valid, evidence backed assumptions when they are contrary to the creationist line.

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It is my comments that I would like to have addressed, pubmed abstracts I can find for myself.

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Really? I find it odd then that you had not seen that one, considering the fact that some very important keywords are right in the title.

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Anyway, the final addition is interesting and in accord with Austin Hughes work: genomes can not be explained by chromosome duplications (e.g. Genome Res 2001, vol11, p771-780; J Mol Evol, vol48, p565-576).

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And th red herring swims by...

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So, the only remaining possibility for genome expansion is duplication of preexisting genes and other DNA elements. This scenario is based upon assertions that duplication and divergence of the duplicates yield new genes.

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Please stop borgering the data. In reality, it is not ASSERTIONS that indicate this, it is DATA.
Please stop projecting your way of doing 'science' upon others.

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If genes are around that can not be explained accordingly (and they are), I see a little evolutionary paradox. [Also, preexisting sound a lot like........yep, GUToB]

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Such as?

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Page wonders: Who to believe?

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PB: That's a very good question. Although I do not object to the data, the evolutionary interpretation is questionable (at the least).

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Hardly...Now, did you or did you not read mine and Goodman's stuff?you claimed to have done so; your words indicate that you did not...

Quoting message 1 of this topic:

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In doing a search on another topic, I came across the thread on this forum regarding molecular evolution. I have just written a book on this topic, discussing the effect of natural selection on the mechanisms that generate genome variation [which is affected by a whole range og biochemical activities, from polymerases to proofreading to mismatch and other repair, to the sizes of nucleotide pools, to recombination].
I have come to the conclusion that through natural selection, many mutations move away from being completely random.
It is important to note that it was not Darwin who suggested that variation was generated by completely random changes in DNA, and, in fact, the concept that the mechanisms that generate genome variation fall under natural selection not only is consistent with the Darwinian framework, but also gives us a deeper sense of the potential power of natural selection.
For those interested in more detail, there is a links page at http://www.DarwinGenome.info that includes other writing on this subject, including the conference volume "Molecular Strategies in Biological Evolution". There also will be a review in the 2003 volume of Annual Reviews of Microbiology.

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I think this is too good of a topic to let it die, but it sure seems to me that it is getting badly wounded.Time for the participents to refresh themselve, on the content of the early part of the topic?As always, I may be wrong.Adminnemooseus------------------
{mnmoose@lakenet.com}

Hi Page,Page says:Borgerism.
Police develop a 'theory' about a serial arsonist. 100 fires have been set. They catch the crook in action. He admits to setting 99 of the 100 fires, but has a rock-solid alibi for the 100th.The police scratch their heads.."I guess we should let him go" one finally utters."Yup" says another "if he didn't do all of them, I guess he must not have done any. Our theory is refuted."PB: You do not have 99 sure cases. All you have is 99 biased interpretations. Even your best evidence of common descent is not free from NRM (as I will point out later), and thus not compelling. It should be obvious that you cannot convince me with such data. If you are going to claim common descent you have to exclude all other possibilities (that is the scientific method), since 'evolution-from-microbe-to-man' is an extraordinary claim. And as you know extraordinary claims require extraordinary evidence.best wishes,
Peter

dear Paul,PK: I see that you still have not managed to offer an explanation of how mutatiosn are "random" according to NDT. THe best resposne you can manage is to demand that I do the work of explaining a basic point which you claim to understand - even though I have already done so more than once.PB: I did that several times. As expected, you won't buy whatever I say and thus I am still waiting for your evo vision.PK: I also notice that you feel the need to throw irrelevant personal attacks at Dawkins for no apparent reason. I suggest you keep your personal hatreds out of your posts.PB: If you had read my previous mails you would have known that I have nothing personal against Dawkins. I have something against his silly outdated claims and the propgation there of. I will have to object to that from a scientific stance.PK: I also notice that you defend your comments by falsely claiming that they have been misrepresented.PB: No, you have misinterpreted the content of my mail. (as described in my previous mail).PK: However rather than explain why your ideas were not the nonsense I suggest you instead claim that they are a strawman (since they do not represent the views of your opponents).
I also note that in a later post you drop the idea of explaining the data in an evolutionary context altogether - to answer data which points to a viable alternative (the non-redundancy of actinin-3 in other species).PB: If you make links to what you claim I can respond to it. Keep it scientific please.PK: Your admission that you did not knwo what neutral selection was is a further evidence of your general lack of knowledge in the area of evolutionary theory.PB: Neutral selection is a contradictio. It is nothing.PK: As to your final point your argument fails to deal with the fact that actinin-3 does seem to confer a benefit (that some individuals MAY gain that benefit by other means does not change the fact that the evidence shows that there is a benefit).PB: As a redundancy it is going to be inactivated over time.PK: And it seems that your argument agaisnt evolution also applies to your own GuToB - only more so. Why have non-random mutations not inactivated the ACTN-3 gene in the entire human population ?PB: Usually I don't do why-questions, since it is metaphysics. But to explain the GUToB I will make an exception. The GUToB holds that there are two types of mutations, random mutations (RM) and non-random mutations (NRM). Evo's think that RM do the trick, and deny NRM (probably they start to see now that they cannot longer deny NRM). The stopcodon that inactivates the ACTN3 gene is likely introduced by RM, not NRM. So, it is a loss of functional gene (=GUToB rule 3).Best wishes,
Peter

If you DID offer such an explanation then please link to the posts where you did. However, I am certain that you have not offered such an explanation. If you do not provide links then I will regard it as an admission that your claim to have provided such an explanation is a lie.Having read your posts you certainly DO seem to hav something personally against Dawkins, given by your need to inject attacks on him into the conversation for no apparent reason at all.I have already provided links - and you apparently feel that it cannot be discussed.The term neutral selection may be misleading but so far as I can tell it is called that simply because it occupies the ground between purifying and positive selection.And no, "why" questiosn of this sort are NOT in the slightest metaphysical - unless you are claiming that the mechanisms of your non-randmom mutatiosn are metaphysical.

I think the thread is still on topic. Dr. Caporale's book deals with NRM, and NRM is the primary justification Peter Borger cites in support of his GUToB theory.But you're right about the topic being badly wounded. Some participants seem more interested in posturing than discussion.--Percy

So many fallacies packed into so little space. No one is claiming that common descent is free of NRM. You're issuing a valid defense, but it's of a challenge that wasn't made. It is your claim that the presence of NRM invalidates the ToE that is being challenged, and which you seem unable to defend. Hence you defend that which was not challenged and ignore that that was. It does not matter whether we can convince you or not. What is important is that the ToE is the accepted theory of the vast majority of scientists working in evolutionary biology, while your views seem to be confined to you alone. In other words, the explanatory power of the ToE has convinced many, while your view has convinced only you. By this measure your proposals fall far short of the ToE. Science is tentative. There is no way to permanently exclude all but one possibility. You are incorrect to state that the scientific method includes such a requirement. The extraordinary claim is that which is out of the ordinary. Since the ToE is the ordinary everyday theory accepted by most scientists and described in all textbooks and supported by mountains of evidence gathered over a couple centuries, it is therefore your claims that are the extraordinary ones and require extraordinary evidence.--Percy

It's hard to escape the feeling that you're being purposefully evasive. No one here, except you, is proposing anything other than the standard ToE, which you can find in any textbook on evolutionary biology. There is no need for you to wait for PaulK's personal "evo vision," because there is no such thing. We're all waiting for some convincing evidence or argument supporting your views, but about the best you can muster is bald assertions with no supporting evidence or argument, such as this: And evasive non-sequiturs like this: Why can't Peter Borger muster any defense of his views? Must be metaphysics.--Percy

Hi Percy,You say:--------------------------------------------------------------------------------
Peter Borger in reply to PaulK writes:
I did that several times. As expected, you won't buy whatever I say and thus I am still waiting for your evo vision.Percy: It's hard to escape the feeling that you're being purposefully evasive.PB: I am not the evasive one. Evo's have to present compelling scientific evidence for their extraordinary claim of microbe-to-man-evlution, but I haven't seen anything that cannot be distincly interpreted. The NRM has been denied for 6 months or so, untill I got backed up by Dr Caporale. So, I can imagine that it is a bit of a nuiance. It demonstrated that my vision is tre right one.Percy: No one here, except you, is proposing anything other than the standard ToE, which you can find in any textbook on evolutionary biology.PB: They all talk about random mutation and selection.Percy: There is no need for you to wait for PaulK's personal "evo vision," because there is no such thing.PB: That there is no such thing I could have expected. Evolutionism is 'ad hoc-ism'. There is no standard evolutionary theory, I guess, otherwise my question was not so hard to address. Even the Futuyma argument mark24 provided last year falls.Percy: We're all waiting for some convincing evidence or argument supporting your views, but about the best you can muster is bald assertions with no supporting evidence or argument, such as this:Neutral selection is a contradictio. It is nothing.PB: This is a very typical remark for evo's. I have presented several lines of evidence and now you ask me to provide evidence. It is impossible to discuss with people who deny scientific data. It demonstrates that you don't care about science. All you care about is to keep up your worldview.
And about neutral selection, it is nothing. In our first encounter you even admitted that (in the case of the 1g5 gene).Percy: And evasive non-sequiturs like this:Usually I don't do why-questions, since it is metaphysics.PB: You forget to metion that next I discussed the inactivation of the ACTN3 gene in a GUToB way. It elegantly explained.Percy: Why can't Peter Borger muster any defense of his views? Must be metaphysics.PB: Why can't evo's give simple answers to even simpler questions? Since evolutionism = metaphysics, I guess.Best wishes,
Peter[This message has been edited by peter borger, 03-03-2003]

Percy,--------------------------------------------------------------------------------Re: borgerisms
--------------------------------------------------------------------------------PB: I notice that I almost made it into the dictionary Percy: So many fallacies packed into so little space.Peter Borger writes:
Even your best evidence of common descent is not free from NRM (as I will point out later), and thus not compelling.Percy: No one is claiming that common descent is free of NRM.PB: And since you cannot exclude the alignment being caused by NRM the evolutionary conclusions are invalid. Conlusion jumping.Percy; You're issuing a valid defense, but it's of a challenge that wasn't made. It is your claim that the presence of NRM invalidates the ToE that is being challenged, and which you seem unable to defend.PB: No, here I am challenging evidence of common descent based upon alignments of shared mutations. As long as you don't exclude NRM, the conslusions are invalid. As you should know by now, I demonstrate over and over that evo claims are founded on outdated scientific views.Percy: Hence you defend that which was not challenged and ignore that that was.PB: No, I was challenging common descent. That is evolutionary theory isn't it?PB: It should be obvious that you cannot convince me with such data.Percy: It does not matter whether we can convince you or not. What is important is that the ToE is the accepted theory of the vast majority of scientists working in evolutionary biology, while your views seem to be confined to you alone.PB: So what. Even if the pope accepted evolutionism, or the dalai lama or president Bush, Dr Watson and Dr Crick, I really don't mind. As long as it can be demonstrated to be wrong I do not see the point propagating it as fact. It is not much more than a 19th/20th century hypothesis most likely to be wrong.Percy: In other words, the explanatory power of the ToE has convinced many, while your view has convinced only you. By this measure your proposals fall far short of the ToE.PB: Where has it explanatory power? I am not aware of it. It doesn't explain the fossil record, it doesn't explain molecular biology. It doesn't even explain Page's best example of common descent (soon to be discussed here). So, please expand.
If I were you I wouldn't bet on your claim that I convinced only myself. I'd rather bet I already convinced more than 1.PB (quote): If you are going to claim common descent you have to exclude all other possibilities (that is the scientific method),...Percy: Science is tentative. There is no way to permanently exclude all but one possibility. You are incorrect to state that the scientific method includes such a requirement.PB: No, one has to exclude other possibilities. Therefor, I recommed that unbiased agnostic scientists have to reanalyse all biological data available. And find the most likely explanation for the data: evolutionism or GUToB. As an unbiased sciecntist I did that, and the data superfacially can stand the evolutionary vision. A carefull scrutiny, however, reveals unexpected things and can often not be explained by the standard ToE (as discussed on this board). I've set up the GUToB to explain all biological phenomena. That is what we should be interested in with respect to a scientific theory: its explanatory power.PB (quote): ...since 'evolution-from-microbe-to-man' is an extraordinary claim. And as you know extraordinary claims require extraordinary evidence.Percy: The extraordinary claim is that which is out of the ordinary. Since the ToE is the ordinary everyday theory accepted by most scientists and described in all textbooks and supported by mountains of evidence gathered over a couple centuries, it is therefore your claims that are the extraordinary ones and require extraordinary evidence.PB: This is simply untrue. Evolutionism (=evolution-from-microbe-to-man) is a non sequitur from the variation observed within the MPG.
What kind of evidence do you refer to? Shared mutations and alignments? Most likely caused by NRM. Molecular biology? Not to be explained by ToE. And the fossil record is simply not in accord with evolutionism, unless you accept Gould's view. But, his ideas are merely a claim not backed up by contemporary knowledge on biology.What is your best evidence of evolutionism? I am very curious what convinced you.Best wishes,
Peter

Sure you're the evasive one. The theory of evolution is clearly stated in literally thousands of books and has been reiterated here many times, yet you have yet to clearly state your own theory. All we get is weird statements like, "which = GUToB rule 3". No one but you has any idea what that means. It seems that your goal is to avoid discussing your ideas by forcing discussion into attempts to get you to discuss. The reality is that Dr. Caporale contradicted you. She clearly stated that NRM fits within a Darwinian framework, which is the opposite of what you believe. This has been pointed out to you many times, yet you keep repeating this statement that clearly isn't true. If you could make a convincing case that Dr. Caporale somehow inadvertently supported your view you would have made it by now. And NRM. Its an area of ongoing research that grew out of the discovery some time ago that there are genetic "hot spots" in the genome where mutations are more likely, and that environmental stress tends to increase the mutation rate in certain genes. Your opinion that NRM represents a challenge to modern evolutionary theory reflects an ignorance of both history and the current state of research. You've misunderstood. There is no such thing as "PaulK's personal 'evo vision'" because he has doesn't have a "personal 'evo vision'". He accepts the same theory of evolution that the rest of the evolutionists here accept. Unlike you, we haven't all gone off and formed personal theories. On the contrary, you avoid discussion as much as possible and just make substanceless assertions. For instance, you replied to the citations PaulK included in his Message 133 with this in your Message 151: The above is nothing but the long way of saying, "Aw, those guys don't know what they're talking about," but nowhere do you provide any evidence or argument or even say anything that hints that you might know what *you're* talking about. This isn't discussion, it's argument by aspersion and the fallacy of ad hominem. No I didn't forget. It contained a repeat of your misstatement about evolutionary theory and didn't seem worth addressing. Specifically, you said: As I've already pointed out, NRM is already part of evolutionary theory. You can find it in evolutionary textbooks. Just look in the index of a book on evolution under "hot spots". It might be a sub-heading under "mutation".A further note on the same subject. I don't understand why you keep repeating a statement so obviously false. You yourself can look in a book on evolution and find discussions of NRMs, yet you insist here that they are not part of evolution. I've just pulled out one of my own books on evolution, Evolution by Monroe W. Strickberger, and on page 215 it says, "Also, in some instances specific nucleotide sequences cause increased mutations among adjacent nucleotides. Such 'hot spots of mutation' may act by coiling the DNA molecule in ways that influence DNA polymerase enzymes to produce replication errors. The replication accuracies of polymerase enzymes also differ; some strains carry enzymes that are apparently more prone to produce mutational errors than others."In other words, you are clearly wrong to state that NRM is not part of evolutionary theory.--Percy

We've been over this before. In cases where common descent was established through only a single gene then NRM might be a significant factor, but as you increase the number of tracking genes NRM rapidly decreases in relevance as a possible factor.The power of your ideas lies in their ability to persuade others. So far you're not persuading anybody of anything except that you like to make unusual claims, like that even though the author of Darwin in the Genome is on record as saying NRM fits within a Darwinian framework that she somehow supports the opposite. Or that NRM isn't part of evolutionary theory. Or that "evolutionism is a non sequitur." (whatever "evolutionism" is)Evolution is the better theory because of its power to persuade, which it does through it's ability to successfully explain evidence gathered over the past couple hundred years and to make successful predictions.Your theory isn't really a theory at all, but merely the idea that NRM has been a much more significant contributor to evolution than currently thought. Plus it adds more questions than it answers. For example: What is a "morphogenetic field"? What is a "creaton"? The stuff on the Internet about morphogenetic fields is New Age nonsense, for example: "Empower and heal the body, heart, spirit using sacred geometry and the Language of GeoTran." And the only place that Google finds "creaton waves" on the entire Internet is here at EvC Forum in messages posted by you.What can you tell us about "morphogenetic fields" and "creatons"?--Percy(Edit explanation: In quoting Peter I erroneously corrected what I thought was a spelling error, changing "creaton" to "creation". I changed it back to "creaton", and added a comment about it in the text)[This message has been edited by Percipient, 03-04-2003]