Francisco Ayala Responds to “Signature of Controversy”

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May 28, 2010 Tags: Design

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

Francisco Ayala Responds to “Signature of Controversy”


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 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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Harry - #15973

June 2nd 2010

Rich, I’d recommend you take a look at Dennis Venema’s talk from the ASA last year. It is a comparison of common descent and common design as competing hypotheses;

Part 1 of 5 (each linked succesively underneath) -

Venema and Falk also did posts on this blog;
Signature in the Synteny
Signature in the Pseudogenes, Part 1
Signature in the Pseudogenes, Part 2

It is quite obvious to anyone willing to understand the data that common descent is a far superior explanation. Even YEC biologists such as Todd Wood reject common design as ad hoc and a currently inferior explanation.

Rich - #15974

June 2nd 2010


I did not speak of superior explanations versus inferior explanations.  I spoke of proofs versus inferences that were less than proofs.

I have no problem with someone who makes a vigorous argument for common descent as “the best explanation”.  I do have a problem for anyone who thinks that the sort of arguments made by Falk and Venema count as “proofs”.  Such people need to take some time off from biology and take a few courses in logic and epistemology.

By the way, intelligent design is not incompatible with common descent, as the examples of Behe, Denton and Sternberg show.  It depends on how one conceives of the mechanisms of common descent.  Intelligent design is incompatible with pure neo-Darwinism, but not with all forms of evolution.  Some good points about this are made in the debate I linked to in 15953 above.

beaglelady - #15977

June 2nd 2010


As far as I know, science doesn’t really work by proofs; it works on the basis of best explanation.

Harry - #15978

June 2nd 2010

Rich, science doesn’t deal in ‘proofs’, it deals with evidence, and the genomic evidence for human-chimp common ancestry is massive and compelling. Nobody is saying the evidence is conclusive ‘proof’ but it is convincing beyond any reasonable doubt. I find it odd how ID advocates insist that ID is “not incompatible with common descent” (this is constantly repeated) and yet when pressed they basically all deny it and resort to meaningless ‘common design’ arguments which even YECs who understand the biology don’t use. Rich, if you can’t be honest about the data where it is clear and unambiguous (human-chimp common ancestry) then you aren’t going to be taken seriously in a discussion where it is less so (origin of life, or even land mammal to whale morphological transition).

Gregory - #15984

June 2nd 2010

Not wanting to put words in Rich’s mouth, but afaik, he accepts that human beings have pre-human ‘ancestors.’ In other words, there were ‘pre-Adamites.’

It just doesn’t help Rich’s arguments much to admit this because he is busy openly doubting macro-evolution and specifically the modern evolutionary synthesis’ way of explaining and/or describing it.

If you ask him simple questions, about his personal views, this will likely save much of the controversy by this unorthodox ID advocate.

and sometimes you have to repeat simple questions, e.g.:

“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”?”

Rich - #15988

June 2nd 2010


It’s nothing to do with “honesty” about the data.  I’m as intellectually honest as any person you will ever speak to, and I daresay more intellectually honest than many people in the TE camp, if the shameless literature bluffs and willful misrepresentations of ID I’ve seen here are any indication.

The use of such words as “honesty” and “integrity” by TEs implies that people who do not come to the same conclusions as they do are twisting the facts to reach some pre-conceived conclusions.  (And of course, *no* TE would *ever* do that!)  It does not allow for the possibility that people as intelligent as oneself might interpret the data differently.  It implicitly accuses others of being either unintelligent or dishonest.  I’m neither. 

While denying the concept of “proof” to science theoretically, you are trying to slip it in practically, by using words like “compelling” and “clear” and “unambiguous”.  Sorry, but I’m not buying.  The “evidence” is only “compelling” within a framework of tacit assumptions about naturalism and about what a designer would do.  If you’d say “more persuasive”, I could tolerate that, but your vocabulary is trying to sneak “proof” in through the back door.

Rich - #15991

June 2nd 2010

Harry (continued):

But as I said, I have no difficulty with common ancestry, even up to man.  I’ve made plain to everyone here that there are two types of ID people, those who are opposed to common descent and those who aren’t, and I’m in the latter category.  But supposing common descent, then what?  What is the main driver of macroevolution?  Darwinian processes?  That’s where I’m properly skeptical, and TEs are mostly uncritical.  And plenty of bright people, who know the relevant science well, are skeptical of the power of Darwinian mechanisms, by themselves, to deliver the goods.  I’ve mentioned Behe, Denton and Sternberg, all believers in common descent. 

Gregory:  you’re mis-framing the relevant question.  The relevant question is:  “Is anyone here willing to concede that neo-Darwinism has so far failed to provide a complete list of needed morphological changes, and plausible corresponding genetic pathways, for turning a land mammal into a whale?”  So far, only you and Malcolm have answered “Yes”.  Everyone else has fumed, rebuked me with indignation for daring to challenge orthodoxy, or remained silent.  Why is it so hard for Darwinians to accept a reduced degree of certainty for their theory?

Gregory - #15995

June 2nd 2010

What will you concede on this matter, Rich?

You huff and puff at BioLogos, while mainly your target is TE (while you claim to the much more humble and less committal ‘te’ position of old). But *who* at BioLogos, not the respected Blog participants, rather, BioLogos’ listed figures Leading Figures, 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”?

Who has said this, Rich? You are making it look like some BioLogos person has said this. Is this true or not?

Harry - #16000

June 2nd 2010

Rich, it’s got nothing to do with “assumptions about naturalism and about what a designer would do” and everything to do with what we know common descent predicts (that modern genomes are descended from a single ancestral) genome and what they should look like. Everything common descent predicts is exactly what we see in genomes. In this case humans and chimps have essentially all the same genes, with small changes, consistent with inheritance, and then subsequent divergence, from a common ancestor. The amino acids are coded for DNA codons which are highly similar, and in many cases virtually identical. Again highly consistent with inheritance, and then subsequent divergence, from a common ancestor. The genes are arranged in conserved blocks on the chromsomes. Where there are differences they are quite easy to account for by shuffling and recombination.

Harry - #16001

June 2nd 2010

We see genes that were clearly formerly protein-coding but which have accumulated mutations preventing that now. One such example would be olfactory receptor genes, of which we have about 800 although around half are inactivated. In many cases we see that the there are identical inactivating mutations in different species (here humans and chimps) . The precise pattern predicted by common descent is matched by the inactivating mutations; those shared by humans and gorillas are also shared by chimps etc. Furthermore, evolution predicts placental mammals are descended from egg-laying organisms and when we look we see the remains of the genes in our genomes that are used by other organisms today that still lay eggs. It is not just a simple case of “molecular similarities.” If you are as honest as you claim to be, explain why this isn’t compelling evidence.

Rich - #16011

June 2nd 2010


It’s really hard for me to respond, because I’ve seen the arguments you are making about 500 times, and you’re acting as if you’re just informing me of all this for the first time.  I’ve been reading about evolution since I was, oh, maybe five years old, and I was a rabid Darwinist for all my early life. 

By “compelling”, do you mean, “very persuasive, very commonsensical, very likely”?  Then I don’t disagree.  But if by “compelling” you mean:  “Only an idiot or an ignoramus wouldn’t admit it”, then no, I don’t agree.  Paul Nelson is neither an idiot nor an ignoramus, and he doesn’t admit it.  Remember, “Harry and Dennis Venema can’t think of any logical reason why the genome would show these features other than common descent” isn’t the final word of “science” on anything.  The logic of individuals isn’t so perfect that they may not have missed something.  I like to express myself more cautiously, even though I’m inclined to agree with you.  (continued)

Rich - #16013

June 2nd 2010

Harry (concluding):

Anyhow, common descent is not the issue between ID and neo-Darwinism.  The issue is design versus chance.  Behe doesn’t disagree with Dawkins over what happened, but over why it happened.  Sternberg doesn’t disagree with Prothero over the fact of whale evolution; he disagrees over the the mechanisms.

I strongly urge you to listen to the entire audio of the debate that I linked.  It will clarify my view, but more important, will expose you to the thought of Sternberg, whose sheer command of the material is very impressive.  People like Sternberg are the future of evolutionary theory.  Orthodox Darwinists like Dawkins, Ken Miller, and Eugenie Scott are already old hat, and soon to become positively archaic.  And remember, you heard it from me first.

Harry - #16016

June 2nd 2010

Paul Nelson is a YEC, and most YECs won’t accept any evidence for evolution no matter what it was. I heard him on a radio show with I think Karl Giberson and when Giberson started talking about the genome data he just shut up. When the discussion was about the fossil record he appeared to want to talk about the Cambrian explosion, but on genome comparisons he had virtually nothing to say. When for example GULO pseudogene was mentioned he mumbled something about guinea pigs and that was it. So Paul Nelson obviously rejects the evidence not because it is deficient, or because he can find flaws in it, but because of his theology.

Harry - #16017

June 2nd 2010

Your arguments, despite your insistance to the contrary, are the height intellectual dishonesty. You simply refuse to engage the data and so resort to all sorts of red herrings and attempts to shift the burden of proof. There is a YEC in another thread making essentially all the same attempts to explain away the evidence for the age of the earth by simply saying “it’s all assumptions,” but little else.

The issue most definitely is common descent and the only reason ID advocates insist it isn’t is because they know they can’t defend their position scientifically. They want to be able to reject it without having to deal with the data. I can think of nothing more intellectually dishonest.

Rich - #16080

June 2nd 2010


You’re not arguing in good faith.  I’ve told you my motives and my reasons, and you’re accusing me of dishonesty.  This is common among TEs, to assert that their opponents are either intellectually dishonest or scientifically incompetent.  Judgmental and condescending.  Are these the attitudes of the Christian scientist?

As for Giberson versus Nelson, given Giberson’s message a month ago about how scientists should stay within their specialties and defer to other experts, what’s a *physicist* doing running around lecturing Paul Nelson on pseudogenes?  Shouldn’t he have left such a subject to Collins?  By the way, Nelson is a philosopher, but specifically a philosopher *of biology*, and has done a great deal of study in biological matters.  I don’t agree with Nelson’s YEC, but I wouldn’t speak dismissively of him, as you have.  And there are certainly TEs who would not accept “any evidence for *design* no matter what it was”, so the YECs are not the only ones with a systemic bias.

If you’d read as much of the theoretical ID writing as I had—thousands of pages—you’d know that the issue is not common descent, but design versus chance.  Which ID books have you read—not skimmed—all the way through?

Arthur Hunt - #16082

June 2nd 2010

Hi psd,

in 15891, you said:

“You state in one post:

“In other words, Meyer is claiming that the genetic code is arbitrary, that there are no chemical or physical underpinnings to the codon-amino acid correspondence that we see in life.”

I don’t see that as critical to Meyer’s overall argument.  Could explain what OOL theory Meyer is missing?”

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.  That’s the whole point of his numerous references to Polyani.  It’s too bad the Biola event on the 14th left me so little time to ask questions - this was one of the issues I had hoped to build up to.

I don’t understand your question - I thought my essay was obvious in that it showed that Meyer had completely ducked the body of work that suggests that the genetic code has its roots in the rules of chemistry and physics.  Surely you got this much?  if not, please let me know how I can clarify this point.

R Hampton - #16094

June 2nd 2010


Richard Sternberg, labels himself a “Structuralist,”  but that doesn’t imply what you seem to think it does; “Since the structuralist perspective runs somewhat perpendicular to the origins debate, creationists and evolutionists tend to see it as inimical to their positions. The truth is structuralism has little at stake in the origins issue.”

Having said that, perhaps you can better understand that the point he makes here is essentially the same as TE:

R Hampton - #16095

June 2nd 2010

It is true that organisms display many machine-like features. But the machine metaphor is less than fully satisfying in biology. One difference between organisms and machines is that biological entities can be self-asssembling whereas machines need to be assembled by another agent, even if that agent is a another machines. We see this when proteins, added to a test tube, spontaneously arrange themselves into filaments, lattice-like patterns of organization, quasi-crystals, and so forth. Some cite these operations of self-organiation in the biological world, and they certainly are. But the very fact that these “smart proteins” have the instructions and specifications for limited self-assembly built into them also provides evidence for their detailed design.

R Hampton - #16096

June 2nd 2010

From Sternberg’s site:

The approach I am taking to this problem is a variant of structural realism, by which I mean that biological phenomena are manifestations of logico-mathematical structures. This perspective is orthogonal to the origins debate, if you will, because all historical actualities are understood to be space-time instances of pre-existing non-temporal possibilities. Within this context one can accept all that is empirically valid in evolutionary biology, while not axiomatically dismissing the position that structures as well as their “real” instantiations have an intelligent cause. My position asserts that the cosmos is fundamentally intelligible in such a way that it can be logically, mathematically, and scientifically recognized to be such; and moreover—following Proclus—that the universe emanates from Nous (mind). In this sense my thinking is compatible with intelligent design broadly defined.

Rich - #16097

June 2nd 2010

R Hampton:

I read all the material on Sternberg’s web site some time ago. 

Based on your previous misreadings of ID writers, I am not surprised that you have misunderstood Sternberg.  You still don’t grasp the bearing of the distinction between generic “evolution” and specific “Darwinian evolution”.  Nowhere in the passage cited does he endorse “Darwinian evolution”.  And in the debate I linked (which you evidently haven’t yet listened to) his attack on Darwinian evolution is crystal-clear. 

You are also wrong about Sternberg and TE.  Sternberg makes very pointed attacks upon the kind of TE that is usually upheld here on Biologos.  Read his recent multi-part article about SINEs on the Discovery web site.

Generally speaking, I do not set forth the views of a writer until I have studied that writer.  And “study” does *not* mean quickly looking up a passage on a web site, seizing upon some promising-looking key words, bolding them, and using them as proof-texts for one’s own view.  “Study” means poring over the words of the writer for hours or days or weeks, as needed, until the writer’s thought is understood.  What I present here is scholarly reflection, not off-the-cuff opinion.

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