Sunday, December 28, 2008

Dr. Francisco Ayala's response and my rebuttal

I posted the following on,

In case anyone is interested in what the NAS experts may respond to my email to them, I here make public the response from NAS member Dr. Francisco Ayala who headed the NAS panel that wrote the booklet. I also post here my rebuttal. I have yet to hear from Dr. Ayala again after my rebuttal of 11/18/2008, suggesting that he is no longer willing to engage in this exchange and in persuading me to his view. All I know is that if I have the truth, I would be very generous with my time to relentlessly persuade every honest truth seeker in the world to my view, even if I have to do it individual by individual.

Since these email exchanges are purely scientific in nature, I see no reason why they cannot be made public. Dr. Ayala is a very public person anyway and has in my view taught false information, perhaps unknowingly, to my children and millions of others', and should therefore be made publicly accountable for his views. But I have deleted any personal information such as email address. If this public exposure could stimulate anyone to debate me in public with the aim of seeking truth and teaching only truth to our children, I would indeed be very pleased. The well known policy of the Darwinian mainstream to not to engage in debate with competing parties is not conductive to seeking truth and is a pure sign of weakness.

Date: Fri, 14 Nov 2008 11:15:03 -0800
To: "Labov, Jay"
From: "Francisco J. Ayala" < email address deleted >
Subject: RE: evolution teaching
Cc: Shi Huang < email address deleted >

Dear Jay:

Our statements are correct as they stand, but of course we don't explain everything that can be said about the subject, including apparent and real variations around the expected average values in molecular and other differences. Perhaps Dr. Huang might be willing to read one of my numerous papers concerning the vagaries of the molecular clock, showing that the rate of molecular evolution is not stochastically constant (as predicted by the neutral theory of molecular evolution) and that it varies from gene to gene and from group to group of organisms, which does not invalidate the statements we make in the booklet, neither in the 1999 or in the 2005 versions. Would Dr. Huang consider invalid the statement that people who have a healthy diet and exercise live longer than those who don't, just because some people who do, die younger than some people who don't?

Two papers, among many, that Dr. Huang might want to read are:

-F.J. Ayala, "On the virtues and pitfalls of the molecular evolutionary clock," The Wilhelmine E. Key Award lecture of the American Genetics Association, J. of Heredity 77:226-235, 1986.

-F.J. Ayala, "Vagaries of the molecular clock," PNAS 94:7776-7783, 1997.

Best wishes,

P.S. I find it nothing short of amusing to read Dr. Huang's statement that "The experts [who prepared the NAS booklet] simply have not understood molecular evolution well enough to teach it." As you may know, over the years I have published in top journals well over 100 papers on molecular evolution (and edited a book with that title as early as 1976).

Date: Fri, 18 Nov 2008 4:04 -0800
To: "Francisco J. Ayala" < email address deleted >
From: Shi Huang < email address deleted >
Subject: RE: evolution teaching
Cc: "Labov, Jay" < email address deleted>

Dear Dr. Ayala,

Thank you very much for the comment and the papers. I appreciate very much as it helps me see where you are coming from in believing what you do. I now see that you are an honest true believer of what you do. The only way for an honest person to believe in an incoherent theory is to rationalize the contradictions in a mistaken way, which is what has unfortunately happened to most people in the molecular evolution field. People who are honest and did not happen to make a logical lapse have only one way to go, leaving the field, which is what happened to one of my college classmates after doing her graduate work on molecular evolution in Japan. She found contradictions that she could not resolve and have since held a very low regard of the field. In the recent 25 year reunion, she advised me not to touch this field but I told her that I have sorted it all out. Just an example of the absurd state of affairs in this field, experts could not even agree on whether the molecular clock is a hypothesis or a fact. Your papers show that you consider it a hypothesis. But professor Chung-I Wu of University of Chicago insisted to me that it is a fact not a hypothesis, when I met him this summer in Beijing.

Indeed, the early death of a specific individual who eat healthy diet and exercise in no way contradicts the statement that people who have a healthy diet and exercise live longer than those who don't. The reason is obvious to everyone with a common sense. The statement is of course a statistical average of a population and has no predictive value when applied to any specific individual. Now, if the statement "If two species have a relatively recent common ancestor, their DNA sequences will be more similar than the DNA sequences for two species that share a distant common ancestor" is a statistical average of many splits, then it would have no predictive value to any specific splitting event. If on average, two species have 5% difference in DNA sequence after 25 million years of divergence, it could mean that some species may differ from another by 10% and some by 1%. Therefore when we see a chimp differing from human by 1%, we cannot conclude a split time of 5 million years. And yet that is precisely what has been done by the field. So, Dr. Ayala, if you want your statement to represent a statistical average that would perhaps accommodate the contradictions in your way, you have invalidated the whole molecular evolution field and most of your own work in this area. If even leaders like you would have to make this kind of logical lapses in order to justify a belief in the present theory, could anyone have any confidence in the theory?

I dont know how you got yourself into believing this but I bet it is a personal belief not widely shared by your colleagues. For the statement to be applicable in specific cases, it simply cannot be a statistical average. As far as I know no one else would consider that statement to mean what you have meant. For example, the 1969 PNAS paper by Wilson and Sarich used monkey-human divergence as calibration to date the human-chimp divergence time. Here, the monkey human data is definitely not an average.

Furthermore, there is nothing in the context of the booklet that would inform the readers that the statement means "on average". If it is about the average, then it has no use as a tool of molecular phylogeny and adds nothing useful to evolution studies or in terms of providing evidence to evolution. The fact that it is used by the field for molecular phylogeny studies of specific splitting event shows that it is not about average. If it is not about average, then it is contradicted by about half of all data. In either case, the statement as it stands is misleading and needs to be deleted from the booklet.

Another common way of making peace with a flawed theory is to overlook the contradicting facts as if they never existed. The most earth-shaking and conspicuous fact of molecular evolution that should be taught to everyone and should be the highlight of your booklet is the genetic equidistance result first reported by Margoliash in 1963. This result shows all descendants of yeast are approximately equidistant to yeasts, or more generally, sister species are approximately equidistant to a simpler outgroup. This is the most direct evidence for a constant clock and directly triggered the clock hypothesis. This result is extremely robust and universal. And yet greater than 99% of biologist dont know about it and I rediscovered it independently a few years ago. I was shocked by it, which was in part how I end up doing so much research in the molecular evolution area. The constant mutation rate interpretation of this result makes no sense to me and I want to find my own interpretation and I have now succeeded. This paper ( discusses the fallacy of the clock interpretation of the equidistance result. The paper here ( provides the real interpretation.

In your paper of 1986 that you sent me, you showed nicely that SOD does not have a constant clock and is therefore unlike CytC. But did you realize that the same data set reported in your paper can also lead me or anyone else to conclude that SOD has a perfectly constant clock, thus in direct contradiction to your conclusion. Data in table 4 shows that yeast is approximately equidistant (69-63 changes) to human, rat, horse, cow, fish, and fly. But you made no mention of this fact that shows that human, rat, horse, cow, fish, and fly all have similar mutation rate. I dont know why the field would let this kinds of contradiction go unnoticed for years. Your paper is not the only one of this kind. The Fitch and Margoliash 1967 Science paper is another that concludes non-equidistance of cytC while never mentioning the other side of their data that shows equidistance.

To falsify the constant mutation rate interpretation of the genetic equidistance result, you can ask your students to do this exercise. Use a complex organism such as human as the outgroup to compare with sister species from a simpler clade such as mollusks or the reptile/birds clade. You will find that octopus is closer to human than cockle is, or birds are closer to human than snakes are. But the constant mutation rate hypothesis would predict equidistance, regardless whether the outgroup is more or less complex. If you read my paper, you will find why the complexity of the outgroup makes a huge difference on the equidistance result.

If you read these papers of mine, you will find a completely different interpretation of all the major facts of molecular evolution. It is coherent and has no contradictions. I have no doubt that it is the correct and true story of nature. This is why I said that the experts have not really understood molecular evolution. I do not mean to be disrespectful and I value greatly the primary data generated by these experts. It is the interpretation that is in question. I realize that pointing out contradictions is no way of changing minds. The only way is offer your own theory as a target of attack by your opponents or competing parties. So please feel free to attack it anyway you wish. Real gold is not afraid of burning by fire (Chinese proverb).

I wish I have expressed my ideas clearly so that you have no need to spend time in getting back to me with questions. But I am always at your service if you would find it helpful. If my ideas are sound to you, I wish you would consider revising the booklet. If you can find flaws in my ideas, please offer your rebuttal.

Best regards,