Following is my first rebuttal to Dr. Scott Page. I will show that both papers Page cited do not support his argument. In fact, the first paper he cited actually strengthens the creationist argument against human/ape shared ancestry! I will address this paper first.

"Positive and Negative Selection on the Human Genome"1

In the late 50s the famous evolutionist JBS Haldane addressed the cost of substitution for mammalian species, a problem that is referred to as Haldane’s Dilemma. Haldane estimated that at most, one beneficial mutation on average could become fixed in a population every 300 generations (which means that no more than 1667 beneficial mutations could have accrued in the evolution of man from an ape/man ancestor 10 million years ago)2. The genetics paper offered by Page estimates that a mere 10 generations per beneficial substitution on average is what occurred since an alleged split from old-world monkeys 30 million years ago.3

Page takes this as a refutation of Haldane’s estimate. There are several reasons why Page is mistaken:

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. They assume that "positive selection is expected to increase the number of high frequency compared to common SNPs. This effect should be stronger for A than for S". What they are essentially saying is that some proportional increase in high-frequency amino-acid-altering differences ‘A’ in relation to the number of synonymous differences ‘S’ would be evidence of positive selection at work. Synonymous differences ‘S’ would be expected to be neutral with no selection working on them. Deleterious mutations would be expected to persist at low frequency due to negative selection. Thus, high frequency SNPs would represent an indication that positive selection is at work, as represented by a larger A/S ratio.

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. If this assumption is not true, then their calculation is worthless. Haldane’s estimate of 300 generations per substitution is based on a mathematical model that need not rely on such assumptions of the validity of evolution.

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: first assume man/ape shared ancestry is true, then arrive at an estimate that is based on this assumption, then conclude it refutes a mathematical model that contradicts the initial assumption of man/ape shared ancestry.

Though Dr. Page’s claim has now been refuted (circular reasoning), let’s take a closer look at this paper. The results of the genetics author’s study forced them to assert that beneficial mutations became fixed every 10 generations on average (I think it was really no more than an observation on their part that they did not seek to emphasize, as it did not appear in their conclusions). The problem is, this number flies in the face of sound reasoning. What the reader must realize is that the authors are saying that beneficial mutations that reached fixation worked their way throughout an entire population in just 10 generations on average. In this period of time, all those without the mutation, plus all their descendants who did not receive the mutation, had to be removed from the population. The replenishment of these "genetic deaths" would be governed by reproductive capacity and reproductive cycle time of primates/humans (plus the effects of recombination). Remember that for some initial number of generations half of all offspring will not even receive the mutation (unless incest takes place, which would make matters worse due to increased genetic load, more genetic deaths, etc). Of those who do receive the mutation, they must survive to pass it on to their offspring. We also know that gestation cycles are long in comparison to most other species, and reproductive capacity is smaller than most species. Considering all these roadblocks, ten generations is an awfully short amount of time for a mutation to go from few to many. This study suggests that this phenomenal rate of fixation was maintained for 30 million years! Haldane’s mathematical model shows that this is unreasonable.

The Other Side of the Coin

Most importantly, Scott Page failed to recognize that the paper actually makes matters far worse for evolution:

The genomic deleterious mutation rate in humans was previously estimated to be at least 1.6 on the basis of an estimate that 38% of amino acid mutations are deleterious. The genomic deleterious mutation rate is likely much larger given our estimate that 80% of amino acid mutations are deleterious and given that it does not include deleterious mutations in noncoding regions, which may be quite common. [emphasis mine].

If we use a straight extrapolation we reach a new mutation rate estimate of U=3.4. This means that 60 offspring would be required per breeding couple just to maintain genetic fitness equilibrium in the population!4. To make matters even worse, this number does not include the impact of "deleterious mutations in noncoding regions, which may be quite common."! If we add James Crow’s adjustment of 1.44, the required offspring count just to maintain equilibrium goes to 243 offspring per breeding couple!!!

This article is a clear backfire on Dr Page. I must thank him for pointing it out to me. I will reference it in the future as further support for my article that provides powerful evidence against man/ape shared ancestry.

"Sexual Recombination and the Power of Natural Selection"5

Now to Dr Page’s 2nd citation. He cites this from the paper’s concluding paragraph:

"Our results experimentally verify a counteracting advantage of recombining compared to clonal lineages: reduced accumulation of harmful mutations and increased accumulation of beneficial mutations. The magnitude of this benefit will accrue over geological timeand promote the superior persistence of recombining lineages at both the level of species within communities (clonal versus sexual species) and genes within chromosomes (nonrecombining Y-linked versus recombining X-linked genes)."

At first glance, it would seem that this paper is saying that recombination promotes faster accumulation of beneficial mutations over clonal lineages (asexual species). I will show why Page, as well as the authors of the paper he cited, are misleading the reader with this conclusion. The refutation is simple.

The study is contrasting the impact of recombination against asexual, non-recombination species. The authors offer these hypotheses:

"Nonrecombining populations experience (i) faster accumulation of small-effect deleterious mutations [e.g., Muller’s ratchet], (ii) slower accumulation of beneficial mutations…, and (iii) an increased deterministic mutational load."

These hypotheses make perfect sense and are not disputed by creationists. To understand why the authors’ conclusion is misleading, we need particular emphasis on (i) and (iii). Since accumulation of deleterious mutation is much more rapid in an asexual species, it makes perfect sense that there is a threshold where asexual species will begin to incur slower accumulation of beneficial mutations when contrasted to a sexual species! The authors note that in an asexual species, nearly all mutations will become trapped in the "living dead", as they call it. Only beneficial mutations with the highest fitness can move to fixation:

In nonrecombining genomes mutations move unidirectionally from better to worse genetic backgrounds (genetic polarization) because most are trapped in low fitness genomes that are not self-sustaining and experience a net accumulation of deleterious mutations.

It is no surprise to creationists that sexual recombination, in an environment heavy in deleterious to nearly neutral mutations, and extremely light in beneficial mutations, 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.

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. But as you raise the level of harmful mutations, there is a threshold where the sexual species eventually becomes the faster environment for the fixation of a beneficial mutation, since recombination slows the spread of harmful mutation.

The author’s conclusion essentially is that beneficial mutations have a better chance of fixation in a sexual species over an asexual species, because the high level of harmful mutations in an asexual species wreak greater havoc than they do in a sexual species. If there were not such a powerful current of harmful to slightly harmful mutations at work, then beneficial mutations would clearly proliferate more easily in an asexual species. But the authors fail to emphasize this fact, so the reader can easily be left with the impression that recombination is an advantage to evolution (as happened to Dr Page). It is NOT per se 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.

In the end, this paper offers nothing more than corroborating evidence of several hypotheses, all that fit quite nicely within the creation model. The paper’s misleading conclusions only serve to confuse, and actually have little bearing on the creation/evolution debate, other than to illustrate the huge problem high mutation rates pose for evolutionary theory.

Dr. Page's reply

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1. Justin C. Fay,* Gerald J. Wyckoff* ,1 and Chung-I Wu*. Genetics 158, 1227-1234. 2001.

2. A generation period of 20 years is assumed to arrive at 1667

3. The authors estimate "up to 1 advantageous substitution every 200 years since humans separated from old world monkeys 30 million years ago". I arrive at 10 generations by using the same generation time (20 years) used to produce the 1667 figure.

4. For specifics, see my article on the mutation rate problem

5. William R. Rice* and Adam K. Chippindale 2001 Science 294:555-559

 

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