molecular genetic proof against random mutation (1)

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:

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This is not our battleground [non-random mutations] - our batleground is the origin of distinct kinds.

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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.

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Why exactly do you doubt that DNA and protein sequences can vary and be selected for? Althoug it took a breakthorgh by Darwin and then the later NDT genetics reformulation it is dead obvious that life MUST work this way. I have seen this with my own eyes in viral evoltuion in the lab. And bacteria can routinely evolve improved enzymes if stressed.

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But this is precisely anti Neo-Darwinism, provided the improved enzyme resulted from a non-random mutation! I don’t mean to speak for Peter, but I don’t believe he disputes what you observe above, in fact the above fits nicely within the creationist framework. Where the contention lies is whether or not the evolved strain is the result of random mutation, or non-random mutation. If it got there by non-random mutation, this explicitly means the information was already present in the genome and no upward evolution occurred. It also falsifies NDT.Disclaimer: I do not believe this would spell the end for the fairytale of evolution. The general theory as a whole has been set up to not be falsifiable (which makes it a bad theory, really no better than a low-grade hypothesis). My guess is that the evolutionists will simply discard NDT in its current form and re-write the theory to accommodate non-random mutations. I believe it was the famous evolutionist geneticist Lewontin who admitted that evolutionists are committed to naturalism at all costs!

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Genomes were designed by God but move to non-random nearby positions in seqeunce space via NDT. Are you saying you don't beleive this at a microevoltuionary level?

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It sounds like we are both being tripped up by the other’s view of what NDT is. I agree that random mutations occur, and that selection works as a conservation mechanism to preserve the species. But this isn’t NDT. NDT argues that random mutation/selection is the mechanism that has taken a cell to a fish to a frog to a man. NDT therefore requires the existence of beneficial mutations that add or increase the information in the genome.

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OK, so what you're saying is that there is some evidence of directed mutations or that Futuyama says there is?

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Futuyama disputes the existence of adaptive mutation. He recognizes that it would be the death-knell of NDT.Here's what he said in his college textbook "Evolutionary Biology": "The argument that adaptively directed mutations does not occur is one of the fundamental tenets of modern evolutionary theory" p 282

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I understand what you are saying but even if there is some bizaree mechanism for non-random mutaitons why would that invaldiate random mutaitons/selection as a mechanism also?

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It wouldn’t invalidate random mutation/selection, but as far as Futuyma et al are concerned, they don’t want to find any adaptive mutations. This gets to the heart of why Futuyma and his fellow evolutionists will fight directed mutations tooth and nail. Non-random mutations imply that the information was already coded in the genome some time in the past, and that the environment merely acted as a switch to enable the information. This clearly points to a programmer, something evolutionists obviously do not want to admit to! Can you imagine the evolutionist trying to explain how a code could arise by pure random processes? They are totally helpless because they cannot use their magic wand of selection. The odds such a capability arising by pure chance would be greater than the number of atoms in the universe many times over (ie impossible). That is why thy will fight, rightly so from their POV, adaptive mutations. It clearly invalidates the synthetic theory (NDT).

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OK - I see what you are getting at. The penny has dropped. OK. 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 ). 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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I personally believe adaptive mutations exist, because it makes great design sense. If you do not believe there is evidence for adaptive mutations, I can understand your objection on scientific grounds (I’ll get back to this). But what is your objection on Biblical grounds? Again, please realize that I am not saying that random mutations are not occurring. In fact I would say they are in the vast majority. All life is in decay, and the scientific evidence strongly supports this (I think we are in agreement here?).My wife called so I have to go home (I will try to follow-up on this and get to Scott's post tomorrow)

TB, let me begin by saying that my belief and search for evidence of such mutations is not because I think it's some magic bullet. It’s just one of many things I’m interested in, and I recognize it could turn out to be a wild goose chase.When I engage evolutionists on internet boards I tend to delve into corner cases and not repeat the same arguments that many of the skeptics have already heard. However, when I give presentations or witness in public, I begin with the same powerful evidence that Paul talks about in Romans 1, that God’s attributes are clearly seen, and that there is no excuse to believe in fairytales like evolution. So, coming right out of the gate there is no better argument for creation than the creation itself, hence I will stress design when first engaging people. When evolutionists meet their Creator, and they will whether they like it or not, it will be because of the patently obvious design in nature why they will have absolutely no excuse for denying his existence or his handwork. I realize I’m preaching to the choir, I just wanted to make it clear that adaptive mutation isn’t some magic bullet evidence I’m looking for. Without it the evidence is still overwhelmingly in favor of creation. I first responded to this thread to defend Peter’s claim that the existence of adaptive mutations would indeed invalidate NDT, as prominent evolutionists such as Futuyma admit. I then added that it would not kill the evolutionary theory in general, as the naturalists (evolutionists) would merely shift the paradigm and find some way out.OK, back to the topic at hand.

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My difficulty is understanding why you think non-adaptive mutaions might be so pervasive as well as understanding why you as a YE-creationist are so interested in it.

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Actually, while I suspect they exist, I don’t know how pervasive they are. My interest in them stems from two things:1) As a design engineer, I look for patterns in nature that make good design sense while also thwarting explanation via natural processes. The existence of such an obviously pre-ordain mechanism cries out design. Evos are completely helpless because they cannot bring selection to their rescue.2) Next is the part Scott alluded to regarding our past exchanges on this. They may help explain the rapid diversity since the flood. It all stems from Haldane’s Dilemma that mathematically demonstrated the limit on how fast a mutation under positive selection can reach fixation in a population. The rate is primarily governed by reproductive capacity. Haldane showed that even when using assumptions favorable to the evolutionary POV, you could only get 1 substitution per 300 generations. If Haldane’s model reflects reality, it deals a serious blow to the evolutionary theory. So what does this have to do with adaptive mutations? Well, evolutionists rightly pointed out (as did creationists including Kurt Wise) that it would also pose a dilemma’ for YECers because of the diversity we see since the flood 5K years ago. I argued that one possible way out for creationists were via adaptive mutations because they incur absolutely NO cost because the information already exists in the population’s gene pool. Thus you could theoretically have a new trait go from one to many in a single generation (despite Page's claim to the contrary, I have given this rationale many times in the past).This takes me to Scott’s complaint that I haven’t produced an article I promised over a year ago on adaptive mutations. There are three reasons:1) (related to #2 above) As I have studied Haldane’s model, I’m starting to see how creationists could explain the post-flood diversity without invoking adaptive mutation as one possible solution. I can intuitively see how high mutation rates + founder effect + genetic drift can account for the diversity we see since the flood. Evolutionists can’t invoke high mutation rates + founder effect + drift because they require beneficial mutations to be part of the mix, while creationists do not have such a requirement. It is simply indisputable that high mutation rates + founder effect + drift (ie small populations) is a bad vehicle for upward evolution. Many evolutionists recognize this, and thus will argue that upward evolution occurs in large populations, while many others are in denial of the impact of small populations on upward evolution. The key is the mutation rate. There are far more deleterious ones than beneficial ones, which does not bode well for small populations from an evolutionist POV, but may account for wide-scale diversity from a YEC POV.
2) I’m watching the adaptive mutation wars to see how they play out. Just do a search on stationary-phase mutations at Yahoo, Genetics.org, etc.
3) I have had little time available for creation research since much of my personal PC time was taken up when I took over the CRS website last year (this time constraint will hopefully lessen now that I’ve finished the online store)

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My big question: are you proposing that adaptive mutations led to theistic macroevoltuion, or are you simply trying to put down finch etc microevoltuion to adaptive mutations?

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Not at all. I propose it may be one of several mechanisms that produced diversity since the flood. BTW, evolutionists have become equivocal with macroevolution in recent years by including alloptric speciation (a type of speciation creationists do not dispute), in the definition. I’ll take it you mean micro-evolution through allopatric speciation.

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Originally posted by SLPx:
Indeed, the 'discoverer' of the phenomenon [adaptive mutations], 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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Citation please.

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I see your point from the creaitonist POV - what's wrong with radiation induced mutations during the flood?

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Regardless of the amount of radiation during the flood, the starting pair would still have at most 4 alleles per locus between them (sure, the animals in sevens would have more). Any radiation event that would have any significance toward diversity would have to occur several generations after the flood.

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Is this irrelevant becasue Haldane's result show the limiting parameter is number of generations?

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The true limiting parameter is the reproductive capacity of the animal. A new allele can go from few to many only so fast, and this rate is governed by how many offspring the parents can produce in their lifetime. A certain percentage of offspring are going to suffer genetic death (via sickness, rock falling on head, being a prude, etc). The remaining offspring are available to pass on new traits.Note that Haldane’s problem pertains to the spread of beneficial mutations, something required by evolution and not by creation. So, while radiating local populations (demes) might do the trick for the creation model, it actually makes matters worse for the evolution model because the cost of harmful mutation increases.

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OK so Haldane required a certain anount of 'beneficial mutaions'. How did he measure/quantiate that?

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Haldane didn’t make statements that I know of pertaining to some required number of mutations under positive selection required for evolution.

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Using Haldane's formalism could be a good start. Are you doing this?

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To a certain degree. Something that falls out of Haldane’s model is the cost of harmful mutations. I wrote an article on this: http://www.evolutionfairytale.com/articles_debates/mutation_rate.htmTo 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. Evolutionists have no answer for this other than the just-so story of strong epistasis/truncation selection (I discuss these in the article). Note that my article need not rely on the validity of Haldane’s substitution cost.(another note: I wrote the article shortly before the gene count studies that reduced the estimate to ~30K; Regardless, recent studies show the problem is worse than when I first wrote of this; see addendum at bottom of article).

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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). 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.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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My main point is that random mutations definitely generate at least short term improvements in fittness in real life examples (bacteria etc). I have no doubt it works in nature too. Yes, whether it works long term (without causing extinction) is a good question.

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But even evolutionists acknowledge that in the vast majority of cases the wild-type is still more viable than the mutated strain that developed resistance through a random mutation. Evolutionists are always very hard-pressed to present compelling evidence where the mutated type is superior to the wild-type. I am aware of examples where the evolved strains develop compensatory mutations; but these mutations appear to only have positive selective value with already-debilitated drug-resistant strains. BTW, these compensatory mutations ironically provide indirect evidence for non-random mutation. For example, see: http://www.pnas.org/cgi/content/abstract/95/7/3949?ijkey=uy2u8EdSMiAIQNote the AAC-AGA mutation and it’s implications for adaptive mutation. Evidence? Yes. Proof? No.Gotta run. My time may be limited in the near future.

As far as I can tell, Cairns is still feuding with Rosenberg et all that these mutations are happening in a non-Neo Darwinian fashion. See: http://www.genetics.org/cgi/content/full/156/2/923?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=Cairns&searchid=1027378300880_2030&stored_search=&FIRSTINDEX=0&journalcode=genet icsApparently there is something about Cairns original proposal that he no longer holds to. However, Cairns doesn’t accept the idea that only a small subpopulation is being hyper-mutated, and that is how Rsoenberg et al are able to make the claim that the mutations are random as required by NDT.

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Originally posted by SLPx:

LOL!

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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...

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Scott, you are showing your insecurity yet again. Is that what, the 30th time now you've mentioned the funcional vs genic mistake I made over a year ago? Need I remind you of your numerous mistakes, including claiming that SNPs are fixed, and that a fixed mutated allele can still have the wild-type within the population? You are a PhD biologist. What is your excuse again?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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YOU SAY:
No, if there were an intergenic locus of 5kb that showed no change between species in 20 million years, I would be a bit suspicious. But nothing in 300+ bps? Chance alone can probably explain that...
I SAY:
Chance alone? Calculate a bit on it, please. Demonstrate the odds.

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SLP: Mutation rate estimates are along the lines of 1 mutation per 10^9 bps per generation. At a 20 year generation time, that amounts to 1 million mutations in 20 million years. So any given site in a 3.2 billion bp genome has about a 0.03125% chance of 'suffering' a mutation in that time frame. That works out to less than 1 in 300 bases.
Very rough estimate and calculation, but it demonstrates my point.

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ROTFL! Very ROUGH indeed! This is bogus beyond words. First, it’s 1 million generations, not mutations. Second, the rate you cite is way too low; your source must be either deleterious only, or rate/year, not generation. Estimates I’ve seen for *all* mutations (harmful through neutral through beneficial) runs at roughly 100 per diploid/generation, or 3 x 10^-8 bps/generation.Finally, last and certainly not least, you assume a constant population size of 1 through that entire 20 million years! I didn’t realize we were asexual, and that there really was no Eve, ever. Just Adam, Adam Jr, Adam III, etc! ROTFL!Granted this isn’t a straightforward computation. It’s an interesting problem. Here’s my rough estimate:Let’s first try to calculate the number of organisms after 20 million years who should have a mutation at a specific neutral site. Assume 3x10^-8 bps/generation, and a population size of 1M. Also assume 20 year/generation. In 20 million years this is 1M generations. So, after 20 million years we will roughly have 3x10^-8 * 10^12 = 31,250 organisms with a mutation at a specific site. This is a rough estimate and will actually be lower because 1) duplicate hits are not accounted for, 2) it assumes the mutation is always inherited. Number 1 is negligible and can be ignored, number two however impacts the number by roughly 50% (due to mendelian genetics). So, that leaves 31,250/2 = 15,625. Out of a population of 1M, after 20 million years 1.6% have the mutation at a specific site.Now we need to know what the odds are that 80 bps will avoid the mutation. This is given by:P = 1 - [(100 — f)/100]^N, where f = frequency, N is number of attempts. In our example,P = 1-[(100 — 1.6)/100]^80 = .725.
This means there is a 72.5% chance that at least one of the 80 neutral sites should have been mutated. Or, there is a 1 in 3.6 chance we would not see a mutation within the 80bp window.For 300 sites, we get P = .992, or 99.2% chance, which means the odds are 1 in 125 we do not see a mutation within a 300bp window.These odds obviously do not favor evolution, but they are also not near significant enough to declare the ZFX sequence anomaly a nail-in-the-coffin evidence against the theory. Still 1 in 125 chance IMO refutes your claim that chance alone can explain it. Maybe you got lucky, again. Evolution always gets lucky! LOL!BTW, it does get really bad if the sequence were 5Kb. Better hope we don’t find one like that. The number becomes P = 9*10^-36![criticisms welcome — I went through this pretty fast]

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Very rough - I made a simple math error.

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You made several errors, and they were huge. You still don’t recognize one of them:

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Fred: Finally, last and certainly not least, you assume a constant population size of 1 through that entire 20 million years! I didn’t realize we were asexual, and that there really was no Eve, ever. Just Adam, Adam Jr, Adam III, etc! ROTFL!
Yes, ROFTL!
Do you not assume a conststant population size when you hawk Haldane's dilemma?
Or is there some sort of double standard going on here?

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Assuming a constant population is fine, ye ole dimbulb. What isn't fine is assuming a constant population size of ONE through the generations! Adam begot Adam Jr, begot Adam III, begot Adam IV Somewhere along the line a female mutated from the male. But wait! We can’t do that, because Scott is assuming a population size of ONE throughout the generations! ROTFL indeed! Its not Adam & Eve, or Adam & Steve, its Adam and, well NOBODY!

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Williams the young earth creationist - who believes that 8000 Kinds on the ark hyperevolved to produce the extant diversity of today via magical evidence-free 'non-random mutations' - laughs at many things. I laugh at someone that actually thinks that the bible is literally true - indeed, I am still waiting for the evidence that leprosy can be ured by killing a couple of pigeons over running water and binding their wings with red thread...

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First, there could easily have been 30K kinds or more. Second, I never claimed non-random mutations were the only possible solution, and in fact have stated that I recently (within last 6 months) can see other mechanisms that can exmplain the rapid diversification in 5K years (in fact we see many examples in nature, such as Darwin’s finches). You ignore this though I’ve told it to you before. It is because you are the internet king of misrepresentation. I also never said leprosy can be cured in the manner *you* prescribed.

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It is the Ks value ("In contrast, the Ks value between human and hominoid primates for the ZFX gene was 0.008 for each comparison") - Ks being synonymous substitutions - that is the same, NOT the exact nucleotide sequence!

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That is why I gave a number for 80 bps (and later one for 300 bps). I haven’t had time to check the papers or look up the sequence of these genes. I was just doing calculations on your’s and Peter’s claims. Even for 80 bps sequence, we would have expected to see some variation, but not to an extent that offers compelling evidence against evolution, as I stated. There still could also be something wrong with my analysis, particularly since I had to make some assumptions that may be flawed.

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You remember Luke Randall, right? The creationist microbiologist/geneticist that claimed that the human genome has 3 billion codons?

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Yes, it's one of your favorite stored chestnuts you like to bring out every couple weeks or so. Hmm, I also remember a certain PhD biologist who admitted to not taking a SINGLE class in pop genetics, yet is now developing a class at his university called evolutionary biology, which according to books I have on the topic is mostly pop genetics! I hope this certain biologist now knows that SNP means single nucleotide polymorphism, and therefore cannot represent a fixed alelle (key word polymorphism). I also hope he now realizes that when a mutant allele reaches fixation in a population then it follows that the original wild-type is no longer present in the same population. I also hope this certain biologist realizes that sound math above the hasbro-level is crucial to population genetics.