refutation of Williams, part 2

This is the second part of my rebuttal of Williams' second reply.
Anything that Williams' had quoted from my last reply is in italics and blue, his replies are in blue and normal text. My new replies are in black normal text.

Page: Williams writes “entire population” for a reason – the connotation of “entire population” is that the population is extremely large, such as the human population of today. This is an unreasonable allusion.
How so? Haldane also made such an "allusion" in both his 1957 and 1960 papers on the topic. A large population is actually a favorable assumption for evolution. The smaller the population, the proportionally greater impact of genetic drift, which means proportionally greater genetic load since there are far more deleterious mutations than beneficial ones that drift can move to fixation.

I am not sure why Williams put allusion in quotes. “Allusion' and 'connotation' have meanings that apparently Williams does not understand.

Page: Williams then writes that all those lacking the mutation and all of their descendants had to be removed from the population. As worded – and probably as understood by Williams – it sounds as though all non-mutation holding organisms must be literally removed. This is incorrect.
No, it is entirely correct, unless you believe our ancestors are all still alive!

How ridiculous. I was clearly referring to a time-dependant explanation.

Page: In reality, a 'genetic death' does not require the actual death (i.e., removal) of the individual from the population. Rather, it means that the genome of the individual lacking the mutation/mutant allele is not 'passed on.'
What happens to this “genetic death”? Does this organism persist in the population, discoverer of some fountain of youth, or does he/she/it die? I repeat, ALL of those without the mutation must be removed from the population. It surprises me you question this fact.

A 'genetic death' means simply that THAT particular suite of alleles is not passed on. Simple, really, and I am not sure why Williams is belaboring this.

Regarding your claim I don't know what a genetic death is, I wrote the following on the Baptist board several days before you posted your rebuttal, a post you responded to. You didn't seem to have a problem then with my interpretation of genetic death! I really think you would be better served to not resort to such rhetoric, though it does serve as an indicator that you are arguing from a losing position.

Me on Baptist board, 2/15/02: “Once this hurdle is surpassed and the plate is reached, there still are additional payments needed for those surviving organisms that may suffer subsequent genetic death due to ugliness, prude-ness, random death, etc.”

I am surprised that Williams would mention not responding to certain points during discussion board exchanges. He has made a 'career ' out of simply ignoring points made by others that he does not have some sort of pre-fabricated ad hoc pseudoexplanation for.

Page: Since, as Haldane notes in his 1957 paper that surely Mr.Williams must have - or at least must have read - that the majority of evolutionarily important alleles are dominant or nearly so, the descendants of individuals lacking the mutant allele do in fact not have to be removed form the population.
First, Haldane assumed ALL beneficial mutations are dominant for a very good reason, because the fixation time and substitution cost of a recessive allele would obviously be vastly higher. So, this is a favorable assumption in favor of evolution. Second, Page makes no sense here. He appears to be employing a non sequitur. What does the type of mutation (dominant or recessive) have to do with whether or not someone without it need not be removed from the population?!!

This follows from your previous statements, which I was simply responding to. One of the shortcomings of the 'point-by-point' response style.

Page: Williams seems to conflate 'genetic death' with an actual death of an organism. This is a common occurrence in the so-called creation/evolution debate. The creationist, spurred on by their overconfidence – their 'knowledge' of THE TRUTH – do not or cannot see that they are making claims based on an ignorance of the very topics they present themselves as being 'expert' or at least very knowledgeable in. Williams, an electrical engineer by education and profession, has a long history of making such blunders.
As I proved above with my post to Baptist board (I can provide many other examples), I knew what a genetic death was, and Page even responded to that post so he must have read it. Regarding “blunders”, Page is notorious for dwelling on mistakes, saving them on his hardisk and bringing them up over and over again, all the while forgetting the many blunders he has made, including major gaffes in this very post I am responding to. I will sum up Page's errors at the end of this post.

You proved absolutely nothing. Your post on the 'Baptist Board' (interesting that you bring this up, as I will show below) is not what I responded to in my rebuttal, is it? I 'dwell' on your mistakes not because that is all I have, or that I don't make them, rather it is because you NEVER admit to making them! And worse - on those rare occasions that you might hint at having made a minor error, you declare that you have 'corrected' it when you had not donje so, or declare the problem to be in everyone else's interpretation of what you worte! You should recall – and I can easily document – that you for many, many months conflated the terms “genic” and “functional”, despite my repeated explanations that such a conflation in error. As for my 'many gaffes' in my rebuttal, I already responded to them at the Evolution versus Creation bulletin board, where you posted them already. Indeed, you wanted me to 'specifically address' the list you posted there. Shame you either never checked back, or ignored my reply. I will present that in rebuttal to your 'blunder list' later.

Here is another interesting post from the Baptist Board:

March 7
SCOTT PAGE

I was wondering if Williams would be so good as to explain, in detail, how this "40 offspring per breeding couple" keeps a population form deteriorating.

Specifically, I would like to see his population genetics model that describes how this works (NOTE: I am not asking about the accumulation of mutations, I am asking how - exactly - having 40 offspring overcomes this accumulation). In addition, it would do him well to present some real-life examples.

Thank you.

No reply as of yet.

Page: As Haldane explains in his 1957 paper that Williams puts much stock into and surely has read, a reasonable frequency for a mutant beneficial phenotype in a population is on the order of 0.0001. In a population of 1000, this means that 1 individual has the mutant.
A minor nit-pick. That would be a population of 10,000, not 1000.

So, I'm not a math major J. Minor nit-pick, indeed.

Page: In just 9 generations, the mutant allele reaches fixation in 100% of the population, even without any physical 'removals' of the wild type allele (Keep in mind that under Haldane's model, the population size remained constant. Since Williams puts much stock into Haldane's formulation, he should not argue this point.) And since the mutant is dominant in this scenario, the wild type allele can still remain in the population, that is, it does not even have to be 'replaced' as such. [NOTE - I did not specify here, but should have been obvious, that I was referring to an adaptive phenotype, not the mutant allele as such]
Dr Page, if a mutant allele reaches 100% fixation in a population, then THE WILD TYPE ALLELE IS GONE! I think you should spend less time talking about your education and how lowly engineers are not qualified to discuss genetics, and more time reading up on genetics! J

I never said all engineers are not qualified to discuss genetics, just those with an agenda and no relevant background education. Well, I did say that I am not a population geneticist, didn't I? Unlike the typical creationist, I do not present myself as being 'expert' in something I am not, such as claiming to be an expert in “Information Theory” by virtue of designing communications systems...
Of course, I am in error here, no doubt about that. The dominant, adaptive Phenotype, however, can become 'fixed' in a population while the wild type allele that governs the phenotype remains.

Page: Regardless, this brings up another interesting conundrum for Williams: ReMine indicates in his book that there must be at least “500,000 genetic changes” between humans and their ape-like ancestor, if evolution is correct.
This overstates Remine's claim. I've loaned out my book, so I'll have to revisit this. I recall Remine stating that 500,000 base pair differences does not intuitively seem to be enough given the 1-3% DNA differences between chimp/man, which amounts to 30-90 million bp.

Williams misrepresents me.

“Take an ape-like creature from 10 million years ago, substitute a maximum of 500,000 selectively significant nucleotides and would you have a poet philosopher? What does that sound like to you?” (p.209)

“Think about it again. Is 1,667 selectively significant nucleotides enough to make a sapien out of a simian?” (p. 217)

Nowehere does ReMine say anything about “given the 1-3% DNA differences between chimp/man, which amounts to 30-90 million bp.”. There are only so many ways to interpret ReMine's claims. The most likely is that he simply cannot believe such a thing, and so he insists that it therefore cannot be true. He is simply appealing to the lay masses – who obviously were/are the target of his pap.

According to the Eyre-Walker and Keightly paper that Williams refers to so endearingly, if we extrapolate their numbers, some 620,000 amino-acid altering mutations have become fixed in the lineage leading to humans in 6 million years†. Clearly, not all would be beneficial (though many deleterious ones are purged by selection, as E-W and K point out), yet ReMine says that not all changes required to account for the phenotypic differences between ancestors and descendants have to be beneficial. Is not 620,000 more than ReMine's number? Inquiring minds want to hear Williams explanation…
Page is again engaging in circular reasoning.

I had already explained that this was presented by someone else. But it is again interesting to see that Williams charges 'circular reasoning' despite the fact that this is just a logical conclusion form the data supplied in a paper that HE heaps accolades on.

This is the same circular argument I refuted earlier, only Page has dressed it slightly differently. The study assumes chimp/man ancestry to arrive at the 4.2 substitution rate that yields 620,000. Page then implies that since 620,000 is more than the alleged 500,000 Remine requirement, it therefore lends credence the chimp/human shared ancestry hypothesis! This is clear circular reasoning, no way around it.

Williams is predictable and entertaining, if nothing else.
He did not refute a thing earlier, unless we are to allow Williams to apply one standard in one instance and another elsewhere. Of course, as is so often the case, Williams applies much too much significance to this. I presented this not as a 'ReMine buster', but as yet another example of how the creationist engages in the application of double standards. Williams has no problem using the Eyre-Walker paper to support his claims, yet when the same paper is used to show problems with his preferred belief, he cries 'circular reasoning.' Enough about that.

Me: It is no surprise to creationists that sexual recombination, in an environment where beneficial mutations are very rare while the vast majority are deleterious to nearly neutral, would 1) reduce the accumulation of harmful mutations when contrasted to an asexual species (clonal lineages), and 2) result in an increased accumulation of beneficial mutation when contrasted to asexual species.

Page: If it is no surprise to creationists, one should wonder why then creation scientists did not discover this benefit of sexual recombination first.
What's to "discover"? It is common sense that the spread of harmful mutation will be slower in a sexual species compared to an asexual species. This is not an earth-shattering observation.

Even less of an excuse for some 'creation scientist' to have produced evidence for this, since we are told that 'creation scientists' were the 'original' scientists and this sort of thing…

Me: Let's assume an environment where there are no deleterious mutations, just beneficial ones. Given this scenario it is quite obvious that the mutation would spread through an asexual species much more rapidly than through a sexual species, as all of the asexual species' offspring will inherit the mutation, as opposed to only half for the sexual species.

Page: This is not obvious at all. If there were no deleterious mutations, then beneficial mutations would by necessity spread throughout a sexual species as well, since those are the only mutations available.
This is population genetics 101. I challenge Dr Page to find any qualified population geneticist who supports his claim that a beneficial mutation will spread through a sexual species just as fast as an asexual species given the deleterious mutation free environment I specified. In a sexual species, only half the offspring will receive a new mutation. The offspring who received the mutation could suffer a genetic death and the story ends there. Population geneticists generally assign a 1 in 50 probability that a beneficial mutation will ever even reach fixation in a sexual species2. For those offspring who do not receive the mutation, at some time in the future their lineage will need to pick this mutation up. Such stringent barriers do not exist in an asexual species since ALL the offspring receive the mutation. In order for the mutation to exit the population, ALL the offspring who received it must suffer a genetic death.

I deal with this laughable gibberish from Williams in the post from the Evolution versus Creation board pasted below. Just a quick clarifiaction for the comprehension-challenged Williams:

I had written, in respopnse to HIS hypothetical scenario in which ONLY beneficial mutations were present:

“"If there were no deleterious mutations, then beneficial mutations would by necessity spread throughout a sexual species as well, since those are the only mutations available.”

Williams, in what I hope is an elaborate joke, interprets this through the creation-colored glasses he wears then responds thusly:

“ I challenge Dr Page to find any qualified population geneticist who supports his claim that a beneficial mutation will spread through a sexual species just as fast as an asexual species given the deleterious mutation free environment I specified.”

I thoroughly rebut this below, but briefly, Williams misrepresents me in a malicious fashion here – that, or he is monumentally ignorant of common English.

“As well” means “too,” not “the same way as”….

Me: It is NOT an advantage to evolution. It is only an advantage when contrasted to asexual reproduction in a harmful mutation environment. Recombination remains an "enigma" to evolution.

Page: How in the world can a reduced accumulation of harmful mutations and an accelerated accumulation of beneficial ones NOT be an advantage to evolution? Why, because Williams says so
Page misses my entire point, again. I will repeat, but with emphasis this time. It is only an advantage when CONTRASTED to ASEXUAL reproduction in a harmful mutation environment. Consider this analogy. You have two men who want to travel across a terrain. Both are given bikes that are the same, except for the size for the tires. Bike 'A' has thin “street” tires, bike 'B' wide “off-road” tires. The optimum surface for efficiency is a flat surface. In a race on such a surface bike 'A' will be have a distinct advantage every time. But as you add bumps to the surface, bike 'A' begins to lose ground, and bike 'B' starts to gain ground. As you make the surface bumpier, at some point bike 'B' becomes the faster and thus more efficient of the two bikes. So under bad race conditions, bike 'B' (analogous to a sexual species) is the better bike, under good race conditions, bike 'A' (the asexual species) is the better bike. But even when bike 'B' is the better bike, it still cannot go as fast as it would if it were racing on a smoother surface. It is still impeded in its progress, but not as much as bike B is impeded.

What a completely irrelevant, inapplicable analogy. No contrasting is necessary. In a 'harmful mutation environment', reducing the number of them that become fixed in the population, via whatever means, is a benefit, no matter how you look at it.

Page: It is not misleading when one understands the entirety of the information presented.
No, it is very much misleading, and you are a testimony to this! Your being misled resulted in you citing the paper as evidence for evolution, when it is no such thing.

I did not present it as “evidence for evolution” – I presented it as evidence that the typical claims of harmful mutations accumulating fast enough to prevent evolution – as is often implied by Williams and his ilk – is in error. And in this it succeeds. Williams misrepresents by position and my rationale, not to mention his malicious claims about the authors of that paper.

Summary

Dr Page is incorrect to claim that the Wu paper1 refutes, or for that matter has anything to offer, the problem called Haldane's Dilemma. You cannot use a study that assumes evolution is true to rebut a mathematical model that is void of such assumptions.

This is simply outrageous. For Williams to continue to claim that Haldane's model was NOT premised on evolution simply belies his grasp of the situation. Again, if it were not, what is the rationale for the variable called “selection coefficient” being used at all? If there were no impetus for a population to replace an allele with one that allows the organism to be better adapted – that is, to evolve – why on earth would something called “selection” play a role at all?
Since evolution is a valid assumption – indeed, the only assumption that can accommodate chimp-bonobo ancestry, as I demonstrated above – the Wu paper certainly does damage the assumption that Haldane's model is all-encompassing and set in stone. Williams' refusal to see this, or more likely, his attempt to hand-wave it all away, is indicative of his dogma-driven pseudoscientific beliefs rather than his 'refutation' of anything.

Dr Page is also incorrect to imply that the Rice study3 supports the evolutionist position. The Rice study merely shows the advantage of recombination when contrasted with an asexualspecies in a harmful mutation environment. This is not evidence for evolution, though the paper gives some misleading statements to imply this.

Williams' continued attempts at disparaging Dr.Rice and colleagues is duly noted. Again, I had included the Rice paper because it provided empirical data indicating that the oft-cited 'too many harmful mutations for evolution to occur' schtick is not all it is made out to be.

Williams posted some 'questions' for me based on my last response on the Evolution versus Creation forum linked below. All of these 'questions' were from Williams' “Summary”. He never replied to my response. As his 'questions' for me were identical to his 'summary' , I have deleted Williams' summary and have pasted the verbatim exchange from the below link. Williams' statements are blockquoted only and preceded by "Williams".

http://www.evcforum.net/ubb/Forum1/HTML/000119-2.html [note the date – 2/27/02]

Williams: Scott, I would specifically like to see you address the errors I listed in the summary that I've pasted below. Comments from others also welcome.

· Mistakenly claiming that Haldane based his substitution estimate on the observation of peppered moths (Haldane did the opposite, see Haldane 1957, p521)

You sure like p.521. In my copy of Haldane's 1957 paper, on p.521. there is nothing at all about what he based his estimate on. You should notice that on the first page, p. 511, Haldane expends some time explaining the observations seen in peppered moths, and how he will attempt to estimate "the effect of natural selection in depressing the fitness of a species." I committed an error of omission, and should have included the fact that he considered some Drosophila experiments and such as well. However, your claim that he "did the opposite" seems to have no basis in reality.

· Williams: Implying that a large population is a bad assumption for evolution (Haldane did the opposite; see Haldane 1960, p351)

You are recklessly misrepresenting me. I claimed no such thing. Quoting from my solid refutation of your original bombast, the times I mentioned population size or Haldane's use of it:

"…premised on unrealistic assumptions (such a s a constant population size), made using observations of phenotypic variation in Peppered moths."

"Williams writes "entire population" for a reason - the connotation of "entire population" is that the population is extremely large, such as the human population of today. This is an unreasonable allusion."

I did, however, say that a constant population size is an unrealistic assumption. But 'constant' does not mean 'large.'

Misrepresentation.

Williams: · Claiming that a wild-type allele can still persist in a population even after its mutant allele reaches 100% fixation in the same population!

I see you don't understand what fixation means, or perhaps are unaware of what a dominant allele is. If 100% of a population has a DOMINANT allele, they can still be heterozygous - the individuals can still have a recessive allele for the same locus, and yet they all would exhibit the dominant phenotype.
Oh - let me rewrite that in creationese:
If 100% of a population has a DOMINANT allele, the individuals can still have a recessive allele for the same locus, and yet they all would exhibit the dominant phenotype!

[NOTE added here: I did not explain here that I had erred in my analysis as written. I further expand on this above.]

Williams: · Because of his previous error, reaches the erroneous conclusion that a dominate[sic] allele does not need to be replaced, which implies it has no reproductive cost.

More misrepresentation. If the members of a population are homozygous for the wild type, then the replacement of one allele with a dominant mutant will incur your beloved cost. However, the impact of the cost - under realistic assumptions - is not what you continue to claim it is.

Williams: · Claiming that a beneficial mutation will spread through a population in a sexual species "as well" as it would in an asexual species, even given an environment free of deleterious mutations. I wonder if there is even one population geneticist in the world who would agree with him.

I really wish that you would put a lid on your shameless attempts at revisionism. That or learn some common colloquial english:

http://www.m-w.com/cgi-bin/dictionary

"as well 1 : in addition : ALSO"

I wrote:

"If there were no deleterious mutations, then beneficial mutations would by necessity spread throughout a sexual species as well, since those are the only mutations available."

IN RESPONSE TO YOUR HYPOTHETICAL SCENARIO:

"Let's assume an environment where there are no deleterious mutations, just beneficial ones."

I am unsure whether you are purposely trying to be annoying, if you are so self-deluded that you simply ignore the context, or that your english really is that poor. Either way, all you are doing is pointing out your incompetence.

Williams: · Claims that Wu's study dos *not* assume human/simian ancestry in its determination of the substitution rate.

That is a fact. I already provided the source for their comparison's - OLD WORLD monkey. You previously stated:

"The authors of the genetics study are arriving at their estimate of 10 generations by first assuming that man and ape share a common ancestor."

Old world monkeys are not apes. Please retract your erroneous claims and your attempt to rewrite your original error.
[NOTE ADDED HERE: Observe that Williams then changed his phrasing to “simian and human” ancestry, which is correct, then made a stink about how I was 'misrepresenting' him!]
That or provide the exact quotations from their paper pointing out their assumption of human-ape ancestry - as per your ORIGINAL claim - and how it was pivotal in their mutation rate analyses.
Wu's group assumes evolution, of course. There is good reason to.

· Re-visits circular reasoning by asking why 620,000 substitutions from the Keightley study is not sufficient to account for simian/human shared ancestry, given the 500,000 he believes Remine set as a minimum.

ReMine did imply that 500,000 is a minimum. Surely, you are familiar with his clumsy prose about making a 'sapien out of a simian'?
Of course, here again we have your conundrum - you endearlingly refer the the E-W and K paper, which assumes not just evolution, but human-ape ancestry, and yet you call it 'circular reasoning' to invite you to discuss additional implications of their study! If you think it circular to look at one aspect, you should similarly dismiss the others. That is, if you are to retain credibility.

The problem is, the Keightley study also arrives at its numbers by first assuming simian/human shared ancestry. Thus, it is circular to use their numbers when contrasting against any arbitrary guestimate of mutations that would separate simian/man.

Well, lets hope that you stop referring to their flawed circular reasoning in your repeated allusions to their deleterious mutation rate.

Addendum

In reply to Page's addendum, I will only note that I did not accuse the authors of the Genetics paper of circular reasoning. In fact I specifically said: "I doubt if the authors of the study would agree with Page that their estimate invalidates "Haldane's Dilemma. If they did, it would be a classic case of circular reasoning...".
And yet, their results do run counter to Haldane's model. I do not think – nor did I ever think this – that Wu and colleagues set out to refute Haldane – they are not like creationists whose stated goals are to 'refute' evolutionists.

Here is what Williams wrote:
Circular Reasoning The authors of the genetics study arrive at their divergence estimate by comparing intra-species DNA sequences of humans (to determine SNP frequencies), to analogous DNA sequences of old world monkeys…
So what is the problem here? The authors of the genetics study are arriving at their estimate of 10 generations by first assuming that man and ape share a common ancestor. …
Their DNA sequence comparison work is based on this belief
It is all well and good to now claim that he was accusing me, not the authors of circular reasoning, but his own words imply something else.

My Summary

Electrical engineer Fred Williams makes numerous erroneous and often inflammatory claims in this and his previous contributions.
He has engaged in underhanded tactics – such as attempting to change his own claims so as to avoid having to admit error – and as such has revealed his true intentions and motivations.
He either has problems understanding simple english, is purposely deceptive, or is so deluded that he cannot see or simply does not care that he is misrepresenting my words.
In the end, even if we grant his beloved 'Haldane's dilemma' “inerrant and always applicable” status, he is still in trouble, as neither he nor his mentor, ReMine, have produced a single shred of evidence that human evolution could not have occurred, and his preferred “explanation” for observed genetic changes between related creatures is so unsubstantiated and contrary to observed genetic mechanisms as to be the stuff only of bizarre, dogma-driven fantasy.

Fred Williams makes up for his lack of scientific acumen with an overabundance of confidence. This confidence is based on his biblical literalist, absolutist beliefs. He knows that creationism is true. Therefore, he knows that evolution cannot be true. This absolute knowledge translates as confidence, and it can work wonders on the layfolk that know even less than he does about evolution.

And THAT is the real problem…

As I have recently acquired additional duties, I doubt that I will have the time - or the desire, for that matter - to make any substantive replies beyond this one. If Williams responds. I might, at some point, refute his claims, but not in a timely fashion.
I will, from time to time, update/'clean up' this response.