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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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Rich - #15904

June 1st 2010


I respect specialists when they limit themselves to technical details.  I don’t respect them when they go beyond the bounds of their expertise.  If a geneticist tells me that gene 13246 is responsible for the difference between the eye colors in two types of fruit fly, I’ll defer.  But if that same geneticist tells me that it’s an unshakable result of modern biology that neo-Darwinian processes produced the whale, I’ll deny the statement, and stand my ground, because I know he’s bluffing, and claiming way more than he can prove.  And I don’t care if his name is Miller or Ayala or Coyne.  A bluff is a bluff, and philosophically trained people are very good at spotting them.  And if over-claiming biologists dislike this, that’s nothing new.  Socrates was widely hated in Athens precisely because he challenged the self-appointed experts, asking them to demonstrate what they claimed to know, but were only bluffing about.  Nothing is more humiliating than for a supposed expert to have his inadequacy exposed to the public.  The way to avoid this humiliation, however, is simple:  Stop overclaiming, and stop bluffing.  Act like cautious, tentative scientists, instead of snake-oil salesmen for Darwin Inc.

Unapologetic catholic - #15925

June 1st 2010

”  I am just pointing out whale evolution as one of those places where neo-Darwinians make *huge* assumptions, while providing nothing close to the sort of detailed account we expect in physics, chemistry, engineering, etc.”

Not true.  I understand that wpoep are unwilling to actually study the literature or are unwilling to believe what they want to believe is simply not true.

unapologetic catholic - #15927

June 1st 2010

Thre are numerous methods demonstrating whale evolution from land mammals, including morphological studies, paleontological evidence and molecualr biology.  All three get to the same approximate result.

Most of the online literature is not free, but here’s one free scholarly article that carefully sets out the relationship known since 1994:

“However, a close phylogenetic relationship between cetaceans and ungulates was first suggested more than 100 yr ago and was more recently confirmed
by paleontological and molecular studies Several independent approaches support a sister-group relationship of cetaceans with artiodactyl ungulates. Accordingly, artiodactyls are more closely related to cetaceans than they are to perissodactyl ungulates.”

I’ve deleted the extensive citaitons to literature to get under the character count.  This 1994 peer reviewed artice is already out of date becausee there is even more fossil and molecular evidence, although conclusions are valid

Gregory - #15934

June 2nd 2010

“Whales may well have pre-whale ancestors.” - Rich

A striking admission, from a man who has been chanting ‘show me the pathways’ at BioLogos with a feverish pitch. Whales probably evolved too, we just don’t know exactly how!

I find it peculiar Rich is launching tirades vs. BioLogos, equating it with neo-Darwinism as he does; not connecting it with Schloss, McGrath or Alexander, but with others.

He cites Coyne time & time again. But how is Coyne someone that BioLogos is promoting?

He cites Ayala. Yet Ayala is not a ‘BioLogos’ person according to this Blog. (Then why promote him here?) Ayala is a ‘liberal Christian.’ No problem at all imo with Rich wondering aloud on-line why Ayala does exactly what Darwin did: refuse to speak about theology anymore in public.

Will BioLogos address this, since it is an overtly Christian site, or not?

The problem for Rich is that BioLogos strongly respects biology & the significant role Darwin has played there. It seeks fruitful dialogue between scientists & people of faith, especially evangelical Christians who are often YECs, which Rich is not.

Rich is thus misdirecting his attacks on a ‘BioLogos’ of his own imagination at an audience not intended for this site.

Rich - #15935

June 2nd 2010

Re U.C.‘s comment 15927:

I’m not contesting common descent, but just as a point of logic, neither molecular similarities nor fossil similarities in themselves, nor both together, logically establish descent.  I can show you 30 consecutive models of Corvette that are very close “morphologically” and “chemically” (similar metals, paints, etc.), but they did not spring genetically from each other.  What is needed to confirm descent is a plausible set of mutational recipes for turning feet into fins, for moving nostrils back on the skull, for completely changing the lactation system, etc. —all the changes itemized by Sternberg.

The article cited is just one of many which list yet more molecular similarities, without explaining anything about how new organs and body plans are formed.  Thus, the reasoning is circular:  the mere similarity of forms is improperly used as evidence for the unknown genetic mechanisms, and then the mechanisms are taken for granted, and used to explain the similarity of forms.  The only way of breaking out of the circle is to provide plausible genetic pathways for each significant morphological change.  That is not done in the cited article, and is rarely done in any article.

Gregory - #15937

June 2nd 2010

I remember listening to the Sternberg, Prothero, Shermer debate awhile back.

Could you clarify for two things:

1) Sternberg believes in/accepts a ‘young’ earth or an ‘old’ earth’?
2) Sternberg believes in/accepts the mutability of species or not, that is, he believes in/accepts that one species can mutate into another species or not?

We can leave aside common ancestry or ‘common descent’ for now, as far as I’m concerned.

You accept that whales could have evolved from non-whales, Rich. That admission is enough to make much of your demonstrating about Darwinism beside the key points for me.

Gregory - #15938

June 2nd 2010

better to say ‘away from’ than ‘beside’ in #15937.

In other words, Rich called the Darwin conferences of 2009 ‘pagan festivals.’

I don’t find this kind of language helpful in science, philosophy and religion dialogue that seeks a spirit of cooperation and mutual respect.

Rich - #15939

June 2nd 2010


My position has not changed at all.  When I say, “show me the pathways”, I’m addressing that to those who are convinced that random-mutation-plus-natural-selection can get us from hippo ancestor to whale.  I never denied that there might have been such a transition; I’m skeptical that neo-Darwinism can explain the transition.  And my query (which I came up with independently, years ago) is Sternberg’s as well, which puts me in good company, and tells you that non-biologists can have sound biological instincts.  I suspected that no one could explain these embarrassing details, and Sternberg confirms that, as of 2009, no one yet had.  And I see no shame involved in admitting we don’t know how whales evolved.  I think it’s shameful to bluff, not to confess ignorance of mechanisms.

I can’t think of very many Biologos people whose notion of evolution is not *primarily* neo-Darwinist, except possibly Lamoureux and Conway Morris.  Everyone else speaks the lingo of neo-Darwinism, which is why I line them all up with Coyne, Dawkins, Ayala, etc.  (BTW, I read Alexander’s book, and he appears solidly neo-Darwinian, too.)

Rich - #15940

June 2nd 2010


I have no idea what Sternberg believes about the age of the earth, though I would infer from other things he says that he thinks it’s 4.5 billion years, like just about everyone else.  He certainly grants, at least for the sake of argument, the possibility of macroevolution and of wholly natural mechanisms for it, which doesn’t sound like a YEC to me.  But I have not watched the entire debate yet, and therefore will withhold further comment.

It should not surprise you that I grant the possibility of common descent.  I’ve indicated sympathy with Behe, Denton and Sternberg, all of whom, as far as I can tell, believe in it.  I’ve also on this site vigorously attacked the literalism of YEC people, showing that I find no Biblical barrier to common descent.  The threat of classic Darwinism to Christianity does not lie in affirming evolution as God’s means of creation; it lies in the particular form of evolution that Darwinians hold.  As I’ve said many times, “theistic evolution” is not a scientific or theological problem for me, but neo-Darwinism and modern TE are problems for me, the former scientific, the latter theological.

Gregory - #15942

June 2nd 2010

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*?

You don’t know what Sternberg believes about the age of the earth?! Don’t you think its important to know since you are championing him in the face of BioLogos? That is, a vast majority of BioLogos people, if not *every* BioLogos person believes in/accepts an ‘old’ earth. If Sternberg does too, then, thank God, Rich, you have found some common ground to speak of.

“The threat of classic Darwinism to Christianity does not lie in affirming evolution as God’s means of creation; it lies in the particular form of evolution that Darwinians hold.” - Rich

Yes, I take this as an important point. It is perhaps due time for someone at or affiliated with BioLogos to write an article about Darwinism and neo-Darwinism on the Blog to be discussed, rather than just posted in the Questions section.

Rich - #15943

June 2nd 2010


You have to allow a sense of humor in these debates.  “Pagan festivals” was of course a playful jab, not meant quite literally, but still, not entirely without a point to it.

Gregory - #15944

June 2nd 2010


It may turn out that many more evangelical Christians would be able to live with evolutionary biology if they knew that they didn’t have to swallow the agnosticism of Charles Darwin’s & Thomas H. Huxley’s evolutionary scheme and many other ‘Darwinists’ along with it. I am not holding my breath that this will be placed on the agenda soon, however, given that the first problem for evangelicals is not biology, but cosmology, age of earth.

Indeed, the prospect that evangelical Christians would *ever* wish to call themselves ‘Darwinist BioLogosists’ is so far-fetched that I doubt anyone on the BioLogos management team would ever entertain it.

There is good reason to distance one-self as a Christian from the Darwinian notion of evolution that involves NO CREATOR AT ALL.

The Vatican has taken its stand on this, while respecting science in its limited realm. Perhaps BioLogos will adopt such a position openly on its website as well.

(Spent far too much time writing here tonight…)

unapologetic catholic - #15946

June 2nd 2010

“It should not surprise you that I grant the possibility of common descent.  I’ve indicated sympathy with Behe, Denton and Sternberg, all of whom, as far as I can tell, believe in it.”

Well,  no concesssion on your part to gtan the obvious.

Behe, Denton and Sternberg, of course, don’t grant common descent.  They are creationists.

Gregory - #15948

June 2nd 2010

unapologetic catholic,

not sure how to address you, given your curious pseudonym. you are not apologizing for being a catholic christian or you are not apologizing for anything you say on this list that is false?

Behe and Denton are *not* creationists. At least, neither believes in/accepts a ‘young’ earth. I’m not sure about Sternberg, but I highly doubt he is a ‘young’ earther.

You betray the ‘truth’ of your religion, either by intentionally lying or by simply not opening up books or reading what these people have to say in ‘first person’ to know their positions.

Which is it?

Please try to be more considerate and practice CARITAS (cf. BenXVI), in the future.


Rich - #15951

June 2nd 2010

U.C.‘s comment #15946:

“Behe, Denton and Sternberg, of course, don’t grant common descent.  They are creationists.”

I just listened to the Meyer-Sternberg-Prothero-Shermer debate in full.  In it, Sternberg said directly that he was neither a young earth nor an old earth creationist, and that he accepted naturally caused macroevolution.  Behe and Denton are on record in infinite places as affirming common descent, and not even the most vigorously anti-ID Biologos supporter has ever denied this of them.

U.C. has just proved beyond a doubt that he has not done a shred of research into what Behe, Denton and Sternberg have written or said, before characterizing their position.  How anyone has the nerve to stand up and just “wing it” in these debates, inventing facts at will, is beyond my comprehension.  I won’t even try to suggest a motive for such bizarre behavior, but it certainly disqualifies U.C. from the status of informed participant in evolution-design discussions.

Rich - #15953

June 2nd 2010


See my post above for an answer to your earlier question about Sternberg.

And by the way, I recommend the aforementioned debate to all:


It’s polite and civilized.  It’s not only great on whale evolution, but on several other questions.  Near the end, in answer to a good question from the moderator, Meyer defines three different forms of “evolution”, and explains, in a very clear way, how two of them are not incompatible with intelligent design.

There’s a great moment where Shermer (typical of anti-ID debaters) completely misrepresents Sternberg’s argument, and Sternberg has to correct him, and another great moment later, when Shermer, realizing what Sternberg is actually arguing, starts to think that maybe Sternberg’s position is not so far from his after all; unfortunately, the discussion then shifts, so the element of agreement doesn’t crystallize into anything definite.  That’s always the problem with debates between more than two participants; the moderator wishes to make sure everyone gets a say, and often trains of thought get broken up or lost.

Enezio E. de Almeida Filho - #15963

June 2nd 2010

Darrel Falk’s question is very naive one. There is no chance that 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. Reason? There is no academic freedom to dissent from Darwin within the scientific community.

Falk’s naive question could be posited way back in the 1930s in Germany:

“Are there scientists who hold a faculty position in any scientific department at a secular research university anywhere in Germany who would speak out against Mein Kampf? If you know of anyone who fits this category, please have them contact us at .(JavaScript must be enabled to view this email address). We commit to maintaining anonymity, if desired.”

The ones who dared to speak against the Führer’s Mein Kampf wouldn’t be able to contact .(JavaScript must be enabled to view this email address) and remain alive, even s/he maintained anonimity: Gestapo would find them through your e-mail service.

No one is so naive to respond to Falk’s naive question.

Rich - #15968

June 2nd 2010

Gregory (15934):

I think you are right that Biologos’s “natural” conversation partner is conservative Christians from the YEC community who are hesitant about evolution.  Hence, all the articles here explaining the basics of evolution, and trying to do it in a Christian-friendly way.

I wouldn’t object to this at all, except that for some reason several Biologos columnists and several commenters seem determined to take side-swipes at ID, or even make frontal attacks on ID, in the process of their conversation with the YECs.  If they would simply address the YEC people about the age of the earth, alternate ways of reading the Bible, the circumstantial evidence from genomics and fossils, the consistency of evolution with the power and wisdom of God, etc., we ID people would be happy to stay out of it and let the YEC and Biologos people work out their own accommodation.  But when false charges are made here about ID, and when apparently condescending remarks are made about the scientific ability of ID proponents, it is only natural for ID people to defend themselves.

Harry - #15970

June 2nd 2010

Rich, how can you possibly call genomics evidence “circumstantial?” If you have already explained this forgive me but what exactly is your position with regard to common descent between humans and other apes, specifically chimps? I hardly see how anyone who dares to compare the two genomes can honestly say the evidence provided for common descent is “circumstantial.”

Rich - #15971

June 2nd 2010


Philosophers have more rigorous standards of demonstration than evolutionary biologists.  In strict logic, the mere closeness of genetic makeup between two creatures no more proves historical connection than does the closeness of their external morphology.  In order to argue, “Because these two creatures have genomes that are very similar to one another; therefore they are historically related”, you have to slip in an unproved premise about causality, i.e., that the only possible cause of such similarities is a non-intentional natural process which slowly alters one form into another.  In other words, the “proof” of common descent from common features rests on tacitly excluding the alternate explanation of common design. 

Thus, while it is logically sound to regard common features (external or genetic) as circumstantial evidence for common descent (i.e., as facts common descent would nicely explain), it is fallacious to treat these features as a proof of common descent.  I don’t reject common descent, but I avoid all over-claiming, and therefore state things more cautiously, less dogmatically, than you will generally hear them stated in these here parts.

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