molecular genetic proof against random mutation (1)

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Originally posted by peter borger:
Dear John,
That may be so, but as convincingly demonstrated in this reference it violates randomness and thus falsifies NDT.
Soon I will send in falsifiactions of natural selction acting on the genome. I know that the NDT has fallen.
Any questions? Do not hesitate to ask.
Peter

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Here is a question - have you ever heard the term "selection"?

I wonder, Peter - does Spetner supply any evidence supportive of his claims regarding 'directed' or 'non-random' mutation occurring in multicellular eukaryotes?

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Originally posted by peter borger:
Dear John,

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Thanks for you response, but you are wrong.
According to the authors: Almost none of the amino acid positions may be under strong selective constraint, because the fraction of polymorphic sites in the intron is comparable to the fraction of polymorphic sites in the coding region. In addition, they say that a comparison between fixed and polymorphic sites between the two species shows also no significant deviation from the assumption of a neutral evolution in this region.

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Thus, this gene is not under selective constraint and has not been selected for during millions of years. Unless you would like to assume neutral selection. I have posted a couple of e-mails to evolutionary theorist to figure out what they exacly mean by neutral selection. None of them responded, demonstrating the current problem in NDT.

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If you have a solution, please let me know.
Peter

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I believe you have make an entirely unwarranted and somewhat bizarre extrapolation."a comparison between fixed and polymorphic sites between the two species shows also no significant deviation from the assumption of a neutral evolution in this region.Apparently, you have never heard of the Neutral Theory?On another board, a chap went on a tirade against me for pointing out that a prominant creationist was commenting on areas outside of his area of expertise. Nevermind that it has been shown that this creationist, when doing so, is totally in error.
I submit that a shallow understanding of what evolution entails is responsible for these undue extrapolations.

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Originally posted by peter borger:
Dear Percy,
Thanks for you response, but I am not impressed by your rebuttal. I mailed this posting because it is a falsification of random mutation.
You did not respond to that.

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There is nothing to respond to because you falsified nothing. Again, I suggest that you become more familiar with the topics you discuss.

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Originally posted by Tranquility Base:

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This is not our battleground - our batleground is the origin of distinct kinds.

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Can you name a few distinct Kinds for us, and maybe provide some of the criteria used in establishing their Kindness?

[QUOTE]Originally posted by Fred Williams:
[B]Hi Tranquility Base. I have very much enjoyed reading your posts and contributions to this forum. But it’s no fun to agree on everything , so I’ll have to challenge you on something you said:"This is not our battleground [non-random mutations] - our batleground is the origin of distinct kinds."This is very much an important battleground! Informed evolutionists fight against environmentally directed mutations tooth and nail (case in point, resident PhD evo biologist Scott Page), because it does falsify Neo-Darwinism, as Peter stated. Evolutionist Dr Futuyama correctly noted in his 1998 college book Evolutionary Biology that its is a fundamental tenet of NDT that non-random mutations do not occur! (citation available on request)According to this leading evolutionist (and there are many others), non-random, environmentally directed mutations (technically called stationary-phase mutation) would invalidate NDT.[/QUOTE]Hi Fred. As I have written several times, I am still waiting - for over a year now - for the article you said you were working on which you claimed would provide the evidence that non-random mutation occurs as the YEC needs it to and how this can account for such things as the Haldane-busting number of mutations separating chimps and bonobos.At the OCW board, for over a year, you were asked to support your repeated mantras on this issue, and you never provided a single shred of evidence. On the other hand, I and others provided literally DOZENS of citations demonstrating that what the creationist hawks as 'directed mutation' (ala Spetner) are in fact genome-wide hypermutations resulting from oxidative stress. They were not 'directed' at any specific sites. Indeed, the 'discoverer' of the phenomenon, Cairns, after whom the phenomenon was sometimes called, retracted his original conclusions after seeing additional data.
The creationist, however, refuses to do so.

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Originally posted by Tranquility Base:
Fred
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So you are arguing for a determinstic evolution. Is that what you beleive in? Everything I know about molecular biology argues against this and if you beleive this then you need to show otherwise (I feel like I've heard this from someone before ).

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I very nmuch disagree with this viewpoint on both scientific and Biblical grounds. But I now understand where you are coming from.

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OK, now please tell me why you believe this - tell me what this evidence is for non-random mutaitons. I can think of some - I know about low mutation rates of cystines in disulfide bonded cone-shells for example.

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TB, you cannot know how pleased I am to finally see a knowledgible creationist challenge Williams on his 'matter of fact' calims.However, when it comes to getting him to support his claims, well, take a number...

One example:EMBO J 1997 Jun 2;16(11):3303-11
Genome-wide hypermutation in a subpopulation of stationary-phase cells underliesrecombination-dependent adaptive mutation.
Torkelson J, Harris RS, Lombardo MJ, Nagendran J, Thulin C, Rosenberg SM
Department of Biochemistry, University of Alberta, Edmonton, Canada.Stationary-phase mutation in microbes can produce selected ('adaptive') mutants preferentially. In one system, this occurs via a distinct, recombination-dependent mechanism. Two points of controversy havesurrounded these adaptive reversions of an Escherichia coli lac mutation. First, are the mutations directed preferentially to the selected gene in a Lamarckian manner? Second, is the adaptive mutation mechanism specific to the F plasmid replicon carrying lac? We report that lac adaptive mutations are associated with hypermutation in unselected genes, in all replicons in the cell. The associated mutations have a similar sequence spectrum to the adaptive reversions. Thus, the adaptive mutagenesis mechanism is not directed to the lac genes, in a Lamarckian manner, nor to the F' replicon carrying lac. Hypermutation was not found in non-revertants exposed to selection. Therefore, the genome-wide hypermutation underlying adaptivemutation occurs in a differentiated subpopulation. The existence of mutable subpopulations in non-growing cells is important in bacterial evolution and could be relevant to the somatic mutations that give rise to cancers in multicellular organisms.

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Originally posted by Fedmahn Kassad:
Wow! Fred has endorsed Scott as an "informed evolutionist"! Scott, you have arrived! The next time Fred says "informed evolutionist say...", you can contradict him, since you are now part of the club.

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FK

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LOL!I missed that gem! WOW! Lets just hope that Fred doesn't claim that I am one of those "informed evolutionists" that "knows" functional means the same thing as genis, as Fred once wrote, or the "informed evos" that know how to remove SNPs from a single taxon's DNA sequence, as Fred insisted for some time...

TB,Fred has claimed in the past that 'adpative mutations' - for which he claims there is a 'large and growing cache of evidence' for (yet for some reason refuses to provide a single example of) - can 'explain' the large number mutational difference between creatures that are assuredly from the same 'kind' , and that this also rescues creationist genetics (if there is such a thing) from the cost issue. The example I used to show that creationist genetics is already a farce is the common chimp -bonobo issue (see http://geocities.com/huxter4441/williams2.html, about halfway down). I have used a similar example in the past, and Williams waved it off by claiming that 'adaptive mutations' can explain it all. He never provided any actual documentation to support his claim, or even a rationale, for that matter.When I have asked other creationists for examples of this occurring in multicellular eukaryotes, I am usually presented with some phenotypic variation studies presented in Spetner's book, even when I ask for genetic analyses.

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Originally posted by Fred Williams:
Citation please.

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Sure - when you provide citations for your claims.

Oh, what the heck:Cairns Excerpt[Fixed and shortened broken link. --Admin]"The flurry of studies ultimately revealed that Cairns's original proposal was untenable, and the community, including Cairns, now at the Radcliffe Infirmary in Oxford, United Kingdom, discarded it."There was another article in which Cairns was interviewed and admitted that his original conslusions were unwarranted, but I have been unable to find it. Nevertheless, as indicated in the above quote, he has 'discarded' his original proposal.

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[This message has been edited by Admin, 07-20-2002]

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Originally posted by Fred Williams:
Oh, and your memory is horrible as usual, since I never once claimed that evos know how to remove SNPs from a single taxon's DNA. It would be greatly appreciated if you would cool it with the blatant misrepresentation. Since you invariably will respond, I suggest you move your comments to the flames section, if there is one here. No need poluting this thread further.

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In reference to molecular phylogenetics methods:Fred:... When informed evolutionists speak of the difference between chimp and man, they are referring to fixed differences.
===R: "So, here is my question: How do you discern a difference due to fixed mutations from a difference due to accumulating SNP's in 2 respective populations?"Fred: Via molecular analysis. Again, it makes no sense to compare noise (most of which likely represents deterioration) of one species to the noise (deterioration) of another to determine how much they differ. Note that the roughly 2.1 mil SNPs represents only about .07% of the genome.
========================================================Seeing as how such analyses typically deal only with single specimens, as was made perfectly clear to you prior to your making the above statements, it follows that you believe(d) that "genetic analyses" can identify polymorphic sites in a single sequence. If not, then you either: 1. Are ignorant of how phylogenetic analyses are performed (this should not be true as I already indicated, it had been explained to you by more than one person) or 2. Simply refusing to correct your own erroneous information.The only misresentation and pollution appears to be coming from you.

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Originally posted by mark24:
Peter,

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The statistical definition of "random", as it pertains to nucleotide sequences, is specifically that each site has an equal chance of mutation. Since there are hot spots where the chance of mutation is higher, mutations are therefore non-random where hot-spots exist. However, every site does have a chance of mutation, & you cannot predict where the next mutation will occur, so it is random in that sense.

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You seem to be claiming that mutations are non-random in the statistical sense, then dropping the statistical definition for a more colloquial one, meaning non-random is deliberate, rather than just not-of-an-equal-chance.

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You cannot conflate the two definitions to suit yourself.

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There isn't a random chance that a car of a particular colour will be next to drive down my road, does that therefore infer that a creator is "deciding" what colour car will be next down my street?

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Mark

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I concur.

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Originally posted by Fred Williams:
To summarize, using the most recent data we find that each breeding couple since the simian/man split would have had to produce an average of 60 offspring just to maintain genetic equilibrium in the population! This is hard evidence against chimp/man shared ancestry.

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I see that WIlliams is still refusing to explain what that measure actually means. Clearly, it sounds like an insurmountable problem - numbers are often employed that way. Is this also 'hard evidence' against within-kind variation that exhibits similar numbers, or just the human-ape question?

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It seems to me that you might have overly frustrated SLPx (is that Scott is it?) by overly stresssing adaptive mutations?
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I never "overly stressed" adaptive mutations. Scott has made it appear to be a BIG issue to me, when in fact it never has been. When we first debated Haldane’s Dilemma, I freely acknowledged it could be a problem for YEC, and suggested that one possible solution (among others) was adaptive mutations because they represent such a clean, one-generation fix. I did not hang my hat on adaptive mutation, though I did feel (and still do) that there is mounting evidence for it. Where clear misrepresentation crops in is when he claims I said 'large and growing cache of evidence'. This is embellishment, I never thought there was large evidence. I do NOT believe the evidence is overwhelming, not even close, and I expressed this then (which Scott apparently forgot).

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While I have no intention of rehashing old times, or of engaging Fred the way in which I have in the past, I do feel compelled to respond to his latest charges.
Williams claims that he has never claimed that there is a large and growing cache of evidence supportive of so-called directed mutations. Fred is correct. He never wrote (at least that I can find) that there is a large and growing cache of such information. However, such a denial is a mere nitpick, for he has written that there is a growing cache of such information. If this cache has been growing for so loong, surely, by now it must be large. Observe, emphases mine:"But there is a very good explanation, and it is backed by a growing cache of evidence. I've been a proselytizer of it here many times. John Paul has raised this too. Its called NON-RANDOM mutations; that is, environmentally cued, adaptive mutations! Such mutations incur essentially NO reproductive cost."Oh, and this too:Fred:
"Creationists have a plausible explanation for rapid diversity in a short period of time that easily handles Haldane Dilemma. Much of the diversity is likely due to 1) bottlenecks and subsequent drift (but certainly nowhere near 24 million fixed mutations, as the substitutional rate argument above shows is not plausible), and 2) many mutations may be due to environmentally cued mutations (thus addressing the rate problem)."Such a terrible, terrible misrepresentation!

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I admit I can understand how someone might misconstrue mounting evidence with large evidence, but there is a difference. Anyway, for the last few months Scott has been chasing me around with this pseudo-strawman of his, trying to get me to debate him on it.

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Talk about misrepresentation! Asking you to provide a single citation from this 'cache' of evidence - and waiting for over a year for this amazing article you said you were writing on the subject - is hardly trying to get you to debate! What an inflated ego some creationists develop...

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As a reminder, when I first popped in to this thread my purpose was not defend the Peter’s evidence for adaptive mutation. My initial intent was merely to defend Peter’s claim that their existence indeed invalidates NDT, and I cited a leading evolutionist to show this.

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Shame that you could provide no actual evidence...

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[This message has been edited by SLPx, 07-23-2002]