Following is my reply to Scott Page's response to my first rebuttal. My comments are in blue. It is a fairly long rebuttal. At the end of this rebuttal I summarize my arguments and Dr Page's errors.  

Page: Creationist Fred Williams, author of what he has referred to as a “saterical” [sic] website mocking evolution , is an electrical engineer with McData Systems.  He has no education, training, or research experience in the biological sciences.

  Dr Page spends quite a bit of energy in his reply focusing on my “lack of training” in “the biological sciences”.

I have never claimed to be an “expert” in “the biological sciences”, but I have read a wealth of material on the subject (particularly genetics) and am quite capable of identifying obvious inconsistencies with evolution.

I should note that Dr Page has admitted to me in the past that population genetics is not his area of expertise (you'll soon see this is the case, in glaring fashion), yet he insists on making a formal education on the topic an issue. He also is guilty of applying a double-standard, since in the past he has referenced evolutionist Robert Williams' page on Haldane's Dilemma. Robert Williams also does not have a degree in genetics or biology, yet this didn't stop Dr. Page from referencing his work. Finally, I should remind Page that Charles Lyell, 1800s champion of uniformitarianism, did not have formal training in geology, nor did Darwin in biology. 

  Dr Page's objection regarding my level of education and training should be a good early indication to the reader that he was unable to answer my rebuttal effectively, as we shall soon see. Otherwise there would be no need to resort to such rhetoric. Also, I did not misspell “saterical” [sic] as he implies.

  Now to Dr. Page's rebuttal:

  Page: Haldane admitted that his conclusions would probably need “drastic revision” (“The cost of natural selection”. 1957.). Indeed – Haldane's estimates were made without the benefit of actual genetic data, unlike the Genetics* paper I cite . Numerous solutions to 'Haldane's dilemma' – and we should keep in mind that that this is a mathematical model - have been proposed, despite the fact that Haldane's model had several unrealistic constraints in it, none of which have met the personal, usually arbitrary standards of the various creationists that use 'Haldane's dilemma' as the crux of their anti-evolution arguments.

This particular debate is not on the merits of Haldane's argument.

Dr Page seems to have completely missed this point. The debate is whether or not Page's citation "Positive and Negative Selection on the Human Genome"[1] is a refutation, or for that matter has anything to say, of Haldane's Dilemma.

I could concede all the points Page made above, and his original claim that the above citation rebuts Haldane's cost argument would still be wrong.

I will repeat the key point in my original rebuttal: The paper Page cited assumes that common decent between simians and humans is true, and arrives at its 10 generation fixation time based on this assumption.

This fixation rate is in stark contrast to Haldane's calculation of 300 generations, so that's why Dr. Page cites this study. But Haldane's cost argument is a mathematical model that is not based on the assumption that simian/man ancestry (or any other form of large-scale evolution) is true.

You cannot compare the conclusions of a mathematical model void of assumptions of the validity of evolution, to the conclusions of a study that derives its numbers on the assumption that evolution is true! I suspect this is why Dr. Page's attempts to get the authors to support his claim were fruitless.

1. Haldane's model was shown to be in error (or at least easily overcome) shortly after he presented it, as I will show below. Williams is unaware of this because he gets all of his information on this topic from fellow creationist engineer Walter ReMine's book "The Biotic Message", which contains misquotes and interestingly cites only a single paper that proposed a solution to Haldane's 'dilemma, and then only to deride the author.
2. Haldane's model, again, was premised explicitly on the assumption of evolution.
3. Williams again falsely claims that I tried to get the authors of the papers to "help" me, despite the fact that I presented the verbatim message that I sent to Dr.Wu in which it is obvious that all I did was inform them that they were being accused of circular reasoning and such by a creationist. The reader should wonder why Williams continues to make this false claim.

 

Page: Famous mathematician Sir Fred Hoyle, in his book “The Mathematics of Evolution”, explains that “Haldane's so-called cost principle is an illusion." (p123).

  This is worth noting. Hoyle indeed made this claim in his book, but he didn't rely on circular reasoning in his argument! Hoyle used mathematics to argue against Haldane's mathematical model, which is a valid approach. I haven't had an opportunity to review Hoyle's argument in detail, though it's worth noting that evolutionist Maynard Smith was not convinced by Hoyle's argument (see Walter Remine's review of the book at Amazon.com) .

  Regardless, I want to stress again that at least Hoyle went about attacking the argument in a proper fashion. Whether or not Hoyle is right doesn't matter, it does not vindicate Dr. Page's use of faulty logic. Dr Page engaged in circular reasoning, which rendered his argument completely spurious.

  The Genetics paper I refer to does, as Williams indicates, 'estimate' the number, but again, unlike Haldane's estimates, these are inferred from analyses of actual data. This important fact is ignored by Williams.

  Again, I did not ignore this “important fact”. The Genetics study conclusions are indeed inferred from analyses of actual data. But this data is derived from the initial assumption that simians and humans share a common ancestor. It is circular to use the Genetics study conclusion to argue against a mathematical model that contradicts simian/human ancestry.

 

Page: I do not take this or any one paper to 'be a refutation of Haldane's dilemma.'  

Then why did you write: “According to an extrapolation of Haldane's 1957 paper, no more than 1667 fixed, beneficial mutations could accrue in the lineage leading to humans from an ape-like ancestor. 1667 is too few to account for this (unsupported assertion), therefore, humans must not have evolved at all. According to the first paper mentioned, the number is off - way off.” [emphasis mine]

  Page: It also brings up a conundrum for Williams. In his other essays on the topic available on his web site, he uses publications that utilized evolutionary assumptions and models in their experimental methods. He usually concludes that evolution is impossible. If his conclusion is correct, then the conclusions of all such publications are moot, and Williams has no logical, scientific, or rational reason for using them – that is, if the evolution models are wrong, then so are the conclusions of the papers and they therefore cannot be used to support anything.

  I thought Dr Page understood this part of my argument, many others have (including Sumac, whom Page cited in his response). Re-read my article, particularly the conclusion. The only part of the evolutionist study I believe is flawed is the initial assumption that simians and humans share a common ancestry. The only other realistic possibilities are that their data gathering or posteriori mathematical analysis is flawed. But this is unlikely, especially since there have been several studies since then producing similar results.  

Do I accept the conclusions of the studies, that the mutation rate is >3? No. The truth is we don't know what the rate is. What we do know is that any study that compares two species supposedly related by common ancestry, and produces a rate >3 is very likely flawed somewhere. Such a rate is way too high for a mammalian species to tolerate. The logical conclusion is that the problem lies in the study's core assumption that simian and man share a common ancestry. Remove this assumption, that is, stop comparing human DNA to simian DNA in an attempt to determine the mutation rate, and the problem goes away.

Nature 1980 Jul 10;286(5769):176-8
Efficiency of the adaptive response of Escherichia coli to alkylating agents.
Cairns J.

Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-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 have surrounded 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 adaptive mutation 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.

"Researchers first noticed this happening in 1988 when John Cairns, then at Harvard University, showed that mutation rates in the bacterium Escherichia coli increased when the microbes needed to evolve new capabilities in order to survive changes in their environment. At the time, it seemed that only those genes directly involved with the adaptation changed, and this idea of adapative or directed evolution caused quite a stir.

But then last year, molecular geneticist Susan Rosenberg at Baylor College of Medicine in Houston and her colleagues showed that mutation rates increase throughout the genome, although only in a subset of the population. Another group also found that more than just the relevant genes changed."

(How the Genome Readies Itself for Evolution, Elizabeth Pennisi, Science, vol 281, Number 5380, Issue of 21 Aug 1998, p1131-1134)

  For the record, I have never claimed these studies demonstrate evolution is impossible. I merely provide them as solid evidence that simians & humans do not share common ancestry.

What I do posit is impossible is for new information (particularly a “code”) to arise naturalistically. There are no known examples in man's history of this occurring. To originate information in a materialistic medium is as impossible as it is to create energy from scratch.

 

Page: There is no assumption – implicit or explicit – in the paper regarding the lineage leading to Homo splitting from the lineage leading to Pan. This is a complete fabrication. Indeed, the paper clearly states: “The divergence data are from 182 orthologous human and old world monkey genes (_183 kb). “

  It is beyond me why Page provided this sentence to defend his claim that no assumption on ancestry has been made to arrive at a substitution rate of 200 years per beneficial mutation. Dr Page is absolutely mistaken here. If I am wrong, then it seems it would be easy for Dr Page, who has corresponded with Dr Wu regarding our discussion, to get Dr Wu to back up Page's claim. I eagerly await his reply. This is at the very crux of our dispute.

  Let's look at an important passage from the study, emphasis mine. Particularly note the word “divergence”, which refers to the monkey/man split, and “positive selection” which is derived from the “divergence” data:   A common test for positive selection is a comparison of the A/S ratio of polymorphism and divergence (MCDONALD and KREITMAN 1991 ; SAWYER and HARTL 1992 ; TEMPLETON 1996 ). Since mutations under positive selection spread through a population quickly, they are not well represented in polymorphism but should have a cumulative effect on divergence. The A/S ratio from divergence is estimated from 182 orthologous human and old world monkey genes (Table 1). To avoid the confounding effects of deleterious mutations, which do not contribute to divergence but do make a significant contribution to polymorphism, the A/S ratio from divergence is compared to that of common SNPs (Table 1). The difference in the A/S ratio of common SNPs combined from both surveys compared to divergence is significant (2 = 8.14, P < 0.01) and can be explained by positive selection, assuming the average constraint on the divergence and polymorphism genes is the same.

  The large number of amino acid substitutions suggests a high rate of adaptive evolution in primates. The expected number of amino acid substitutions is 2382 (4151 x 70/122) based on the A/S ratio of common polymorphism and the excess is 1278. Therefore, a large proportion, 35%, of amino acid substitutions between humans and old world monkeys are estimated to have been driven by positive selection. Extrapolating this proportion to the total amount of coding DNA in the genome (5 x 107 bp) yields an estimate of up to 1 advantageous substitution every 200 years since humans separated from old world monkeys 30 million years ago (LI 1997 ).

  Page: Furthermore, I am at a complete loss as to why someone claiming to be knowledgeable in the sciences, as Williams does, would discard current data-based conclusions in favor of a nearly 50 year old estimate, premised on unrealistic assumptions (such a s a constant population size), made using observations of phenotypic variation in Peppered moths. The answer should be fairy obvious.

  The reason you are at a complete loss is because you have not understood my argument. I am discarding the current data-based conclusions of your first citation because using them to rebut Haldane's Dilemma is circular.  

Regarding Haldane's observation of peppered moths, he postulated that such intense selection likely was not common during the course of evolution (Haldane 1957, p 521). What you failed to realize is that this intense selection makes the cost problem FAR worse! Haldane estimated that n=43 for peppered moths, which yields a fitness of e-.7.  By using n=300, the fitness improves to e-.1. So if anything Haldane was ignoring his observation of phenotypic variation in Peppered moths because it made the cost problem worse! He punctuates the fact that a lower n reduces fitness by closing the pertinent paragraph with this example: "Whereas, for example, n=7.5 would reduce the fitness to e-4, or 0.02, which would hardly be compatible with survival." (Haldane 1957, p521).  

1. I don't think Williams understands proper scientific quotation. Nearly every time he mentions Haldane's 1957 paper, he writes: Haldane 1957, p521 Granted, what is mentioned above is on p.521, but Williams has cited this page on an internet discussion board and what he was mentioning is not in any way mentioned on p.521. My intuition tells me that Williams is just putting a page number up to impress the reader.
2. I have mentioned elsewhere that I committed an error of omission by not mentioning the other factors took into consideration when formulating his EVOLUTION PREMISED model.