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Francisco Ayala Responds to “Signature of Controversy”

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May 28, 2010 Tags: Design
Francisco Ayala Responds to “Signature of Controversy”

Today's entry was written by Francisco Ayala. Please note the views expressed here are those of the author, not necessarily of BioLogos. You can read more about what we believe here.


Written by Darrel Falk

It has been almost one year since Signature in the Cell by Stephen Meyer was released. The book was on Amazon’s 2009 best seller list for science books and now has 245 reviews there. One year later, it still remains in the top 3,000 overall in books sold. By many accounts, this is a highly successful book.

Signature in the Cell is a book about biology. It actively engages original literature in biochemistry, molecular biology and molecular genetics. To get tens of thousands of people reading about RNA catalysis and nucleotide biochemistry, among many other arcane biological details is a noteworthy accomplishment. Dr. Meyer has done this through his engaging, detective-style writing, and his ability to continually persuade people of the topic's importance. His website, for example, puts the book into this all-important framework:

Meyer is developing a more fundamental argument for intelligent design that is based not on a single feature like the bacterial flagellum, but rather on a pervasive feature of all living systems. Alongside matter and energy, Dr. Meyer shows that there is a third fundamental entity in the universe needed for life: information.

It is difficult to imagine a topic of more fundamental significance to our understanding of the universe than showing for the first time that there is a third entity alongside matter and energy.

So Signature in the Cell is a biology book and it addresses issues of great importance. As interesting as this book is to non-biologists, given the assertions it makes, it also ought to be engaging to those who have spent their lives exploring the biochemistry and molecular biology of cells—the biologists themselves.

To my knowledge the only public appraisal of this book by a biologist who holds a faculty position at a secular research university is that of Dr. Francisco Ayala of the University of California, Irvine. It was not favorable. There were several reviews by biologists at Christian colleges (see here, here, and here), but each of these also spoke of the quality of its science in highly unfavorable terms.

Although he is not a biologist, we also refer readers to the commentary by Dr. Randy Isaac, Executive Director of the ASA, the organization of American scientists who are Christians. He concluded his detailed analysis of a key section of the book this way:

It is laudable that Meyer takes the step to explore predictions that ID would make. Predictions that are testable are a vital part of the scientific process. But just making a prediction isn’t sufficient to indicate viable science. Astrologers and tasseologists can also make predictions and sometimes they may be right. Predictions must also be based on causal factors that are understood independently to exist and whose adequacy can be independently verified. The predictions must clearly differentiate between competing hypotheses.

It is unfortunate that this set of dozen predictions is very weak on all counts. It is unlikely to make any difference in the debate.

If this book “shows that there is a third fundamental entity in the universe for life,” why does it seem that the book has been ignored by the biology community as a whole, except in a few cases where it has been reviewed unfavorably?

I have asked the following sort of question on two other occasions related to the discussion of Signature in the Cell and so far there has not been one positive response:

Are there biologists who hold a faculty position in a biology department at a secular research university anywhere in the world who would speak out in favor of the book? If you know of anyone who fits this category, please have them contact us at info@biologos.org. We commit to maintaining anonymity, if desired.

How have the group of scientists at Discovery Institute reacted to the huge popularity of the book on the one side, but the silence or disapproval of the experts who have spent their careers studying what Dr. Meyer writes about? The Discovery Institute has just published a 103 page copyrighted electronic book, Signature of Controversy which shows how disappointed they are.

The book singles out Dr. Ayala (the one person I am aware of who holds a biology faculty position at a research university) who has taken the time to read the book and to write about it. Dr. Ayala had expressed considerable concern about the scientific quality of the book. They sent a copy of their frankly worded e-book to Dr. Ayala. Below is his response.

Response to Signature of Controversy

by Francisco Ayala

Dr. Stephen Meyer writes: "eminent evolutionary biologist Francisco Ayala does not appear to have even made a search for the crib notes online. Indeed, ... it appears that he did little more than glance at the title page and table of contents" (p. 9). David Klinghoffer disagrees: "My colleague Dr. Meyer thinks Ayala did read the Table of Contents, but I must disagree" (p. 19).

Is this the kind of language Meyer and Klinghoffer want to use to engage in constructive dialogue with their critics? Or does it represent a distinctive way in which members of the Discovery Institute seek to practice Christian charity?

For the record, I read Signature in the Cell.

Dr. Meyer writes: "In fact, it [Signature in the Cell] spends only 55 pages out of 613 pages explaining why origin-of-life researchers have ... come to reject the chance hypothesis" (p. 10).

The "chance hypothesis" entry in the Index of Signature in the Cell has 13 sub-entries, each citing one to several pages; the first page cited is 106, the last one is p. 359. On p. 499-503, there are at least four additional references, not cited in this entry, about the insufficiency of the chance hypothesis.

The next entry in the Index is "Chance and Necessity," which has 14 sub-entries; the first page cited is 173, the last one is p. 356.

There is also an entry for "chance association," and one for "chance elimination," which includes three sub-entries citing pages between 179 and 356.

A final sub-entry under "chance hypothesis," says "See also scientific theories."

The entry for "scientific theories" has 20 sub-entries, citing pages between 24 and 444. A final sub-entry says "See also biological science; chance hypothesis; evolutionary theory; intelligent design (ID) theory; natural selection; self-organization theories."

"Only 55 pages out of 613 pages ... to reject the chance hypothesis." Really?

An outside observer reading Dr. Meyer's statement that Signature in the Cell "spends only 55 pages out of 613 pages explaining .. the chance hypothesis" might be justified in wondering whether Dr. Meyer has read his own book. The pervasiveness of the references to chance and their spread over 397 pages out of the 508 pages of text in Signature in the Cell are fully consistent with the statement in my review of the book that the keystone argument of Signature in the Cell is that chance, by itself, cannot account for the genetic information found in organisms.

For the record, I have not read Signature of Controversy. I read a few early pages, glanced at the rest, and decided that it was not worth reading.

Francisco Ayala is a philosopher and the Donald Bren Professor of Biological Sciences at the University of California, Irvine, and a former Dominican priest. He is a popular author and lecturer on the compatibility of science and religion. He has received numerous awards and honors, including a 2001 National Medal of Science, the highest honor given by the government to scientists, and the 2010 Templeton Prize.

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Gregory - #16103

June 2nd 2010

You express a lot of off-the-cuff and overreaching too, Rich. It is no wonder that you haven’t published anything on ‘intelligent design’ in a serious journal.

Still waiting for a name or more than one from #15995: who at BioLogos said what you suggest of them?

You don’t even know if Richard Sternberg is a YEC or not! Maybe you are Rich Sternberg?

You accept that whales probably had ancestors, so blaming *any* biological or zoological or comparative anatomical theory for not ‘proving the pathways’ is disingenuous.

What’s your theory? You’ve said you don’t have one. You know that ‘intelligent design theory’ does not have an answer. So why put your focus on Darwinism when many people no longer hold to this self-label?

Have you read a BioLogos leader actually call themself a ‘Darwinist’?

Rich - #16106

June 3rd 2010


You obviously did not read my previous comment to you (15991):  I’m not going to answer your question.  It’s the wrong question.

Your complaint about my alleged lack of publications is typical of this place.  I offer arguments and criticisms.  My arguments and criticisms stand or fall on their merits.  Questions about publications, degrees, etc. are absolutely irrelevant.

I only mentioned Sternberg’s degrees because so many people here seem to worship such things.  Giberson says the non-biologists should defer to the biologists, so I turned that around on him:  the regular biologists (e.g., cell biologists, geneticists, embryologists, physiologists, etc.) should defer to those who *specialize in evolutionary biology*.  That means that Ayala, Collins, Falk, Ken Miller, etc. should defer to Sternberg.  But you and Giberson don’t like the argument from authority when it’s turned against you, do you? 

The point is that arguments from authority are silly.  The moment someone argues from authority, you know he has a weak case.  The fact that Biologos so often has to argue from authority suggests that it, too, has a weak case.

Rich - #16107

June 3rd 2010


I answered your question about Sternberg and YEC in 15953 and 15951 above.  Please read all my replies to you before complaining that I haven’t answered your questions.

The rest of your questions are either insulting (“disingenuous”), demonstrably illogical (there’s no logical contradiction at all between accepting common descent while saying neo-Darwinism has a lousy explanation for it), or simply repetitious of things you’ve asked me before.  Can you not remember answers you’ve read only a few days ago, sometimes even a few hours ago?  Re-read all my previous answers.  I’ve sufficiently defined or explained microevolution, macroevolution, fact vs. mechanism, design vs. chance, different causal explanations for evolution, etc., *many times each*, either to you or to others, so that my position should be clear.  Clear, that is, to anyone who will take the time to read with patience, rather than with an argument ready on the tip of his tongue before he’s finished my first sentence.  I’m not going to do any more work for you, Gregory, until you exert a little effort and convince me that you’ve actually read and digested what I’ve written.

Gregory - #16108

June 3rd 2010

I’m still waiting for a name and a quotation to back up your haughty huffing and puffing, Rich.

When I asked the question the second time, I used your own words. Thus, it cannot be the ‘wrong’ question, since you stated it yourself and I asked it to you.

1) “Will you go on record, Rich, saying that someone at BioLogos (in the BioLogos category in the Resources link) actually *has* stated that “we know exactly how whales evolved”?”

2)  *Who* at BioLogos..has said “we know exactly how whales evolved” or “we have a *complete list* of needed morphological changes, and plausible corresponding genetic pathways, for turning a land mammal into a whale”?

Do you have no answer? Would you admit it if so? Somehow I doubt it due to integrity.

(Aside: I dislike stooping to such game-like tactics.)

Rich - #16109

June 3rd 2010


I never said that anyone at Biologos has stated “we know exactly how whales evolved”.  If anyone at Biologos were so stupid as to affirm that, I could crush him in argument with ease.

The problem is that you are not listening to my posts and arguments with nearly enough care before you raise your objections.  If you were listening, you’d know that my argument is:

*Granting for the sake of argument that the land-animal-to-whale evolutionary process did in fact occur, unless a neo-Darwinian can set forth a full list of the morphological changes that would be necessary to move from the given land ancestor to a whale, and unless that neo-Darwinian can provide *specific* neo-Darwinian mechanisms (not general ones like “mutation” or “selection”) which could (at least in principle) account for all (or at least most) of those morphological changes, the neo-Darwinian has no right to affirm that it was in fact neo-Darwinian mechanisms that effected the transformation.*  (continued)

Rich - #16110

June 3rd 2010

Gregory (continued):

If I am right in my argument, then, since no neo-Darwinian here, upon challenge, has been able to meet the stated requirements, *all* of the neo-Darwinians here should be saying, “You’re right; the capacity of neo-Darwinian mechanisms to turn a hippo-ancestor into a whale *has not been demonstrated*.”  Who here has said that, Gregory, other than you and Malcolm?  And why *hasn’t* anyone else said it?  Why does such an empirically accurate admission choke in everyone’s throat?  Since you think I’m too uncharitable, I’ll let *you* speculate about the motives in this case.

pds - #16215

June 3rd 2010

Arthur Hunt - #16082,

Meyer’s basic argument is that design is the best explanation for the origin of life.  You defeat that by showing that another theory is the better explanation.  Meyer looks at the current OOL theories and shows why they are not plausible.  It seems to me that you have to show a competing theory that is more plausible than the design explanation.  I don’t see you doing that.

“The supposedly arbitrary nature of the genetic code is a very important pillar upon which Meyer builds his argument that the genetic code is designed.”

I don’t see that as a critical pillar of Meyer’s argument.

If you are not demonstrating a plausible non-design pathway to the origin of life, you are not really touching Meyer’s argument significantly.  As with many others, you seem to be offering up vague criticisms, but nothing that goes to the core of Meyer’s main arguments.

R Hampton - #16217

June 3rd 2010

Sternberg’s argument is that “‘excess’ DNA is junk in the sense that it is largely devoid of phenotype-specifying information” is wrong, and therefore the SINE can’t be 1) junk information that 2) is caused by genetic drift. Of course this claim is refuted on scientific grounds. Even so, Sternberg does not claim that a non-natural cause and/or or evolution is disproved.

As best as I can determine, Sternberg believes there is additional order in the DNA that arises from natural laws (mathematics). I was hoping he made a more direct challenge of Evolution in his presentation of “The Generation of Essential RNA Messages from Pseudogene Transcripts by Exemplar Causation” (Baylor 2009), but the audio link is broken. I hope you have something better of his that makes your case.

Dennis Venema - #16227

June 3rd 2010

The audio link isn’t broken - it never existed. I requested a copy at the meeting, but was told that the media folks had been instructed not to record his talk. Same for Axe’s presentation.

Dennis Venema - #16230

June 3rd 2010

Actually, a correction to the above (my memory was fuzzy, but I’ve found the relevant email exchange now).

I inquired after the meeting as to when Axe and Sternberg’s talks would be posted. It was then I was informed that they had requested their talks not be recorded.

Rich - #16232

June 3rd 2010

R Hampton:

Do you even *read* my posts before you send off further objections?

Sternberg does not challenge “Evolution”.  How many times do I have to say that?  How many times does Sternberg have to say that?  Did you bother to listen to the debate I linked to?  Did you bother to watch the earlier Sternberg whale video that I linked to? 

In your first paragraph, the syntax of your first sentence is so dreadful that I can’t be sure what it means, so I’ll pass on that one.  However, adjusting the flawed syntax of your second sentence sentence so that the sentence makes sense, it appears that your meaning is that I attributed to Sternberg a belief in non-natural causes.  I never did.

What “makes my case” is the fact that neither you nor anyone here has offered a single informed answer to any of Sternberg’s arguments against the ***NEO-DARWINIAN*** (is that loud enough?) evolution of the whale.

R Hampton - #16238

June 3rd 2010

In the modern sciences, there is no practical distinction between Evolution and “Neo-Darwinism.”  The random changes of histones, as described by Epigenetics, are conserved or lost based on selective pressures (“Darwinian” mechanisms).

So I am not disputing the absence of Epigenetics when George Romanes coined the term Neo-Darwinism. But it does seem that you dispute that, today, Epigenetics is an accepted part of “Neo-Darwinian” Evolutionary theory contrary to Romanes original definition.

Rich - #16248

June 3rd 2010

R Hampton (16238):

Sternberg knows “the modern sciences”, and in particular the modern science of evolutionary biology, extremely well.  He does not need your help to determine what positions are out there, and which ones need to be criticized.  I would suggest that you listen to his thoughts on evolution with the attitude of a pupil rather than the attitude of a peer; but I infer, from your refusal to ever say “I stand corrected” despite the numerous errors I’ve demonstrated in your comments over the past month, that the attitude of a pupil is one that you find hard to adopt.

R Hampton - #16258

June 3rd 2010

My challenge is YOUR distinction between “Neo-Darwinism” and Evolution (what you consider to be natural but non-Darwin evolutionary mechanisms and/or selective methods).

I would suggest that you listen to his thoughts on evolution with the attitude of a pupil rather than the attitude of a peer

I suppose my attitude can be described thusly; “the capacity of Sterberg’s proposed mechanisms (whatever that may be) to turn a hippo-ancestor into a whale *has not been demonstrated.” Does that satisfy you?

Rich - #16271

June 3rd 2010

R Hampton:

In the *original discussion* we were having about Sternberg, the *only* point I was raised was *his critique of neo-Darwinian mechanisms as the cause of whale evolution*.  Whether Sternberg’s *own* conception of how evolution works is satisfactory *was never a point raised by me*, or by anyone else here.  Your answer is therefore off-topic and evasive. 

The parenthetical part of your first sentence shows that you don’t understand at all what I have meant by “evolution” as a generic concept.  Why do you have trouble grasping that “evolution” is the name of a *process* and that “neo-Darwinism” is a theoretical *explanation* for that process?  And why do you have trouble grasping that what I (and Sternberg and Behe and countless other very intelligent people) find inadequate is the neo-Darwinian *explanation* for evolution, not “evolution” as such?  How many times, and in how many different ways, do I have to make the same distinction, before you catch on?  And if you can’t catch on to a distinction as elementary as this, what makes you think you are at the scientific level necessary to talk about Sternberg as if you were his equal?

Rich - #16272

June 3rd 2010

Correction to first sentence above:  “I was raised” should be “I was raising”.

R Hampton - #16285

June 3rd 2010

For all practical purposes, there is no other natural explanation (Orthogenesis and Lamarckism are dead). So when additional factors be discovered, like Epigenetics, they are incorporated into current Evolutionary theory—and that would presumably apply to Sternberg’s hypothetical mechanism. So in modern parlance, “Neo-Darwinism” is a meaningless term, much like macro-evolution.

Rich - #16290

June 3rd 2010

R Hampton:

Give it up with these petty objections.  Sternberg understands both the terminology and the theory far better than you do.  When you’ve improved your reading comprehension to the point that you can read his writings and listen to his lectures without distorting his meaning, then you can think about instructing him.

You don’t know how the land animal evolved into the whale; you don’t have the slighest clue how it was done.  You have no proof that *any* set of evolutionary mechanisms so far proposed can do the job.  Why don’t you have the intellectual honesty to admit that?

R Hampton - #16296

June 3rd 2010

“You don’t know how the land animal evolved into the whale; you don’t have the slighest clue how it was done”

Sure we have clues, lots of them with which you are familiar. When confronted with the evidence, you counter that they do not account for everything:

I’ll give you the dog’s tail, but that means that instead of, say, 3,000 morphological changes, you need only 2,999. The question is:  where in the neo-Darwinian literature do you find these 2,999 changes explained?

From what I have read of Sternberg he concedes that “Neo-Darwinian” causes are empirically proven but that there is at least one other undescribed natural factor. So it would seem he would be comfortable saying something like;

“We do have a broad outline for how the land animal evolved into the whale, with certain portions of the evolutionary history having more detailed explanations then others. Neo-Darwinism (Evolution) is a significant factor, but I believe that there is another natural factor at work.”

And as I said before, if Sternberg can provide such a mechanism, it too would be included in modern Evolutionary theory. Why don’t you have the intellectual honesty to admit that?

Rich - #16302

June 3rd 2010

R Hampton:

It would be intellectually *dis*honest for me to admit anything connected with your “paraphrase” of Sternberg, because it is not something Sternberg said or ever would say, but an invention of your wishful thinking.  Are you so desperate that you would put words in the man’s mouth, merely to justify yourself?  Do you really *not understand* that he is mounting a slashing attack on neo-Darwinism and on Biologos-TE, or are you misrepresenting his argument willingly?

I did not argue that neo-Darwinism cannot account for *everything*; I argued that it can hardly account for *anything*.  Last I heard, 2,999 was a larger number than 1.  Should I chalk up this further gross misreading of my argument to willful manipulation, to astoundingly careless reading, or to something else?

Tell me how the whales achieved marine lactation—specific genetic mechanisms and viable intermediate stages, please.  Tell me how they achieved each of the other alterations discussed by Sternberg.  Or admit that you don’t know how any of the changes were achieved, and that no living biologist knows, either.  Intellectual honesty requires one answer or the other.  Evade this choice, I and I go silent, winner by default.

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