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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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Arthur Hunt - #15759

June 1st 2010

Oh well - this site isn’t cooperating.  Sorry about the last two posts.

Here is the web site, without the failed mark-up attempts:


Rich - #15764

June 1st 2010


Jack Szostak’s remarks, as conveyed through Darrel Falk, do not consitute a scientific book review of Meyer.  You clearly are evading the issue, as is Dr. Falk.  The issue is plain:  Based on the evidence presented by Dr. Falk and everyone else here, *no origin-of-life theorist has signed his name to a proper, formal, book review of Meyer’s book, published not on a private blog but in a proper scientific journal that reviews scientific books*.  Therefore, it is simply academically irresponsible to assume that all origin-of-life theorists reject Meyer’s book, or that none of them find any value in it whatsoever.  Dr. Falk may believe, based on what he’s heard “through the grapevine”, that OOL theorists aren’t impressed by Meyer’s book, and he may be right.  But he isn’t an origin of life scientist, he has no statistically meaningful number of opinions of the thousands of origin-of-life scientists around the world, and he has no right to pretend to be informing the world of “the official view of OOL scientists” regarding Meyer’s book.

Rich - #15767

June 1st 2010


I read your account of the Meyer debate.  It is not clear to me, from your limited remarks concerning one or two points, whether or not you read all 600 pages of *Signature in the Cell* with care, as I did.  It seems to me that, whether or not you were right on the technical points you mention, your remarks don’t come anywhere near to dealing with all the important issues that Meyer raises in his book.  In any case, what I saw was not a proper scientific book review.  I suggest you look at Gert Korthof’s site for examples of how this should be done.  Korthof carefully summarizes the books he is criticizing, usually chapter by chapter, trying to represent the book at its strongest (not merely presenting the weak aspects that are easily knocked down), and in his critical remarks he judiciously assigns both praise and blame, as warranted,  He is not at all an ID proponent, but he doesn’t see his role as to be reflexively negative about ID.  What I see on Biologos is mostly reflexive hostility towards ID, and it is this that I continue to oppose, not criticism of ID as such.

Malcolm - #15773

June 1st 2010


You said “stand aside and wait to see what the big origin-of-life researchers have to say, instead of guessing about their opinions and motivations.” The opinions of two leading origin-of-life researchers were included in that link. My point remains; scientists are not in the habit of reading and responding to every book, article, or internet post that claims to be about ‘science’. You scoff at my comparisons to bigfoot but that is how ID is viewed by the scientific community; a scientifically useless form of apologetics. If Meyer has a case it should be made at an origin of life conference, not before a crowd of conservative Christians at Biola.

Meyer insists that he has the superior explanation and that it is only “philosophical bias” that prevent scientists from acknowledging so. Yet, if this were true, and his case were so strong, it would be embraced by the vast majority of Christian scientists (at least). This however is clearly not the case. As Steve Matheson asked, why is that?

Arthur Hunt - #15779

June 1st 2010

“It is not clear to me, from your limited remarks concerning one or two points, whether or not you read all 600 pages of *Signature in the Cell* with care, as I did.  “

Honestly, Rich.  If you read Meyer’s book with the care that you did the many essays I have written that refute many of Meyer’s claims, including the central theme of his book, then I fear you haven’t read his book at all.  I have spelled out in many places how Meyer is wrong about the nature and origins of the genetic code, why I think IDists miss the boat completely when it comes to the OOL, why Meyer is totally wrong when it comes to the nature of information in proteins, and why Meyer et al. are wrong when it comes to junk DNA.

Rather than dance around the technical aspects that Meyer has botched, why not pick out one of my essays (say, perhaps, the one with the title Signature in the Cell?) and explain to me why I am wrong on the technical points.  Don’t dance around the issue, try to avoid my points, or change the subject.  Just tell me, in your own words, where the technical aspects of my essay(s) falls short.

I’ll invite pds to do the same.

Rich - #15831

June 1st 2010


How could you have read Signature in the Cell and not dealt with one of its *major* points, which is the difference between modes of argument in the historical and the experimental sciences?  I read the comments you linked me to, and they didn’t address that point *at all*.  That’s why I wonder if you’ve read the book carefully. 

It’s not up to me to disprove your biological charges against Meyer.  That’s for you specialists to thrash out.  As I’ve *repeatedly* said, *I am not arguing that Meyer is right*.  My argument has been that the argument advanced by Dr. Falk, *in his article above, as written*, is logically invalid.  *Nothing* can be logically inferred from the fact that no reviews of Meyer’s book have yet appeared in peer-reviewed scientific journals.  If you and Falk want to argue that Meyer is wrong; do so.  But *don’t* argue, “Meyer must be wrong because, even though no reviews have yet appeared in in peer-reviewed scientific journals, I personally have a strong hunch that the reason for that is that all the experts think Meyer’s arguments are garbage”.  Hunches are not arguments.  I’m making a logical-epistemological point here, not a biological point.

Rich - #15835

June 1st 2010


Give me citations for full, proper reviews of *Signature in the Cell*, written by *origin of life specialists* and published in either *peer-reviewed scientific journals* or *major mainstream media*, such as newspapers with prestigious book review sections, or major magazines known for high-level intellectual content (e.g., Commentary, First Things).  Otherwise, I won’t reply further.

By the way, Darwin’s *Origin* was not published at a scholarly conference.  It was published in a trade press, just like Meyer’s book.  In fact, if we apply the “expert” criterion applied in columns here by Falk and Giberson, Darwin was not qualified to talk about evolution.  His B.A. was in Classics; he had no degree in any life science at all.  But everyone here would agree that the man’s arguments, not his qualifications, are what count.  To try to shut out criticism by non-specialists is to argue against the spirit of open criticism and inquiry which allowed Darwin into the game.  The double-standard here is painfully obvious:  “If you agree with us, even though you’re not an expert; we welcome you with open arms; if you disagree, we’ll pull rank with our specialist degrees.”

Malcolm - #15841

June 1st 2010


Origin of life researchers have ignored Meyer’s book, they simply aren’t interested, but this does not vindicate his claims. Those who have commented have disagreed with Meyer’s conclusions even though they have not published full scientific responses. Scientists also ignore the endless attempts from YECs to find models to explain away the geological and astronomical evidence for an ancient earth and universe.

Comparisons with Darwin are rather pointless. Darwin and Wallace did however have a paper presented before the Linnean Society in 1858, the year before the publication of the book. This was a time when scientific understanding of biology was rather basic and so it was not difficult for Darwin to remain abreast of, and up to date with, the most recent findings without actual scientific qualifications. He performed research throughout his life and published his work before his peers (even up to and including the year of his death) . There is no doubt that he was as much an authority on the subject as anyone else who lived then.

Malcolm - #15843

June 1st 2010


We are now 150 years on and the rate of scientific discoveries and research grows daily. In order to keep up a person requires not only a high level of scientific training but also constant interaction with the appropriate literature. That is why your comparison is bogus.

Rich - #15858

June 1st 2010


Everything you say about Darwin is correct, but I am trying to point out a general attitude on Biologos—a worshipful attitude towards the specialists that leads intellectually to sterility and politically to the control of whole disciplines by weak theories and vested interests.  There must be the possibility of challenges from intelligent outsiders, to keep specialists honest.

But it wouldn’t matter, because Biologos doesn’t even accept challenges from intelligent *insiders*, i.e., very qualified biologists and biochemists.  Denton (Ph.D. plus M.D. plus track record in genetics research) Sternberg (2 Biology Ph.D.s plus ongoing advanced theoretical research), Lecomte du Nouy (biologist and mathematician) and many other science-trained intellectual giants, over several decades, have questioned neo-Darwinism, but Biologos willfully shuts its eyes.  Its goal is clearly not the wide-open theoretical exploration of biological origins, but the harmonization of neo-Darwinism with a particular modern form of Christian belief.

Rich - #15863

June 1st 2010


While the *details* of Darwinian arguments require a high level of scientific training, the *structure* of Darwinian theory does not.  Its main outlines can be grasped by an intelligent lay person who has carefully read Darwin and pro-Darwinian expositors like Dawkins and Ken Miller.  The kind of claims it makes, and *the sort of evidence* it would have to produce to make those claims plausible, are accessible to the intelligent lay person who knows the basic facts of biology and mathematics.  Thus, while I do not at present know what Gene X13147 does in the ichneumon fly, I *can* know for sure that if someone asserts *as fact* the claim that a land mammal turned into a whale by neo-Darwinian processes, that person *must* be able to list the morphological features which would have to change, and *must* be able to provide plausible genetic mechanisms—specific ones, not general ones like “random mutation”—which could at least in principle effect each of those listed morphological changes.  Inabilty to even specify the needed morphological changes, let alone the genetic mechanisms required to effect them, would indicate a very weak hypothesis.  (continued)

Rich - #15864

June 1st 2010

Malcolm (continued):

Thus, when Eugenie Scott was confronted with this point by David Berlinski, she raged and sputtered, but had no answer—not even a rough answer—how many morphological changes would be required, and angrily claimed that the question was unfair.  She was *wrong* in saying so, as any good experimental physicist or chemist would confirm.  Scientists have the *obligation* to propose *detailed mechanisms* and *means of testing for their existence*.  If Eugenie Scott doesn’t know that, she is a poor scientist.  And I can dare to say that, not being a scientist myself, for the same reason that I can say that a plumber whose taps always leak is a poor plumber, though I don’t know the first thing about plumbing myself.  I know what a good work of science looks like, and I know that it doesn’t contain the evasions, vaguenesses, literature bluffs, exaggerations, and ad hominem fury against criticism that characterizes the defensive writings of neo-Darwinists.  Good science claims to have proved only what it can prove, and honestly admits what it can’t.  And we *don’t* know, at present, that neo-Darwinian processes can turn a land mammal into a whale, but apparently no one here is honest enough to admit that.

Gregory - #15875

June 1st 2010


you appear to be going off the deep end again with your comments.

*I am trying to point out a general attitude on Biologos—a worshipful attitude towards the specialists* - Rich

Again, there is *NO* ´worship´ towards specialists going on at BioLogos. That is your delusion, nothing more. 1. You uncharitably misread Giberson´s article, 2. In #15831 you said: *That’s for you specialists to thrash out.*

Can´t have your cake & eat it too, Rich. You are clearly biased towards ´intelligent design´ & its ´specialists´, even if most specialists in the same fields as your heroes reject ´intelligent design´ *as a non-scientic theory*. Mike Gene says it´s not scientific.

*we *don’t* know, at present, that neo-Darwinian processes can turn a land mammal into a whale* - Rich

I agree. So what? So whales have *no* natural history, no ancestors?

Just curious, Rich, how many *origin of life specialists* do you think there are, say, in North America? In my view OoL is a *highly* speculative field, ´science+philosophy+[a]theology´.

That said, *liberal Christian* [Resources] F. Ayala´s *Response to Signature of Controversy* is embarassing to BioLogos.

Malcolm - #15881

June 1st 2010


I’m not sure if Denton still refers to himself as an ID proponent, but then you would apparently be more familiar with his views than I am. I think I have made my feelings about Sternberg known before. As for Lecomte du Nouy, somebody who died 6 years before the discovery of the DNA double helix is at best a dubious person to defer to in a modern scientific discussion.

I do rather wish that some Biologos biologists would weigh in here, as the technical details of whale evolution are way above my pay grade. My basic thoughts would be that I consider the basic evidence for whale common descent with other mammals to be very strong, but I am simply not capable of explaining the required morphological changes involved in turning a “land mammal into a whale.”

Malcolm - #15882

June 1st 2010


I’m wondering if the whale genome has been sequenced as that might help the discussion. My suspicion would be that the whale genome would be shown to be very similar to that of other mammals, with the obvious exceptions of the aquatic adaptations. As I look at it a “land mammal” (in this case the proposed ancestor of modern whales) is ultimately just the genetic code arranged in a certain way, and what we call a “whale” is just the genetic code arranged differently. I see nothing, given necessary selective pressures, to prevent the one arrangement becoming the other over time.  I accept this is not going to convince you as it is far from the “detailed mechanisms” you asked for, but it is my response as non-specialist.

There appears to be a fundamental disagreement between us. I think the evidence for whale evolution (their common ancestry with other mammals and descent from a land-based creature) can be established convincingly independent of the precise step-by-step changes involved along the way, and you clearly disagree.

Rich - #15886

June 1st 2010


*we *don’t* know, at present, that neo-Darwinian processes can turn a land mammal into a whale* - Rich

I agree. So what?—Gregory

The “so what” is, why can I get *you* to agree, but not Drs. Falk or Giberson or any of the other columnists here, nor any of the commenters who have opposed my very minimal request for intellectual caution.  The reason that no one here will agree is evident.  Since it is a dogma around here that neo-Darwinian processes can do *every* macroevolutionary task, no one feels the slightest obligation to prove that it can do any macroevolutionary task in particular. 

So whales have *no* natural history, no ancestors?—Gregory

I never said that.  I never implied that.  ID does not imply it.  Whales may well have pre-whale ancestors.  I said only that the purely Darwinian explanation for the transition is nowhere near proved.  Yet even that modest criticism raises the tribal pride around here to fever pitch, as you can see from the way my healthy Socratic skepticism is greeted.  This place is like Pharyngula or Panda’s Thumb, only without the vulgar language.

Rich - #15889

June 1st 2010


Thank your for admitting the following:

I am simply not capable of explaining the required morphological changes involved in turning a “land mammal into a whale.”

This is the true intellectual humility I have been requesting from beaglelady and others here. 

I am not asking for any larger admission than this.  I am not claiming Sternberg has proved neo-Darwinism false (though I think it very likely that it is largely false).  I am not claiming that it will never be possible to explain whale evolution naturalistically.  I am not claiming that Sternberg has proved ID true.  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.  I’m saying their tone should not be that of a religious authority, but that of an inquiring Socratic investigator.  And like true scientists, they shouldn’t be brittle and defensive when criticized, as so many people here have been in response to my comments.

pds - #15891

June 1st 2010


Thanks for the reply.  I don’t see in that link anything that defeats Meyer’s arguments.  Could you explain how you think it does? 

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?

Rich - #15894

June 1st 2010


I’m aware that Lecomte du Nouy’s science is outdated now.  But when he was writing, no living “expert” biologist could answer his arguments out of the “certainties” of biology as it then existed.  And when the physicists and engineers at the Wistar Conference in 1966 (post-DNA) made analogous criticisms, the “experts” of the day couldn’t adequately answer them then, either.  And now, with biological science far beyond the 1966 level, the “experts” of the day can’t answer Sternberg.  Do you see the pattern?  I’m saying that overconfidence in the expert consensus, cocksureness, brushing off of criticism, does evolutionary science no good.  It merely makes evolutionary biologists look arrogant.  And this is why the public increasingly sides with ID.  Even the *secular* public which has *no interest in YEC or miracles*.  The public perceives the Darwinists as stubborn and dogmatic.  And they know that often, behind claims of specialist immunity, there is vested interest.  If Biologos doesn’t grasp this, if instead it tightens up in its defense of specialists and consensus (as Falk and Giberson seem to be doing), *it will lose the public relations war to ID*.  A word to the wise.

Rich - #15900

June 1st 2010


Denton does not consider himself “ID” in the sense of being a member of a certain party in the culture wars, but he certainly is “id” (lower case) in inferring design from the facts of nature.  He uses the word “design” frequently in his second book, and pointedly in his conclusion.

The key point about Denton is that he is *both* evolutionary *and* anti-Darwinian.  He thinks that the Darwinian conception of evolution is fundamentally wrong.  Not that he doesn’t grant some local power to Darwinian explanation; but for him, it is nowhere near capable of being the main driver of evolution.  It exists, but takes a back-seat role in a scheme which is overall much more deterministic.  He certainly would not see the evolution of land mammal into the whale as simply a bunch of lucky mutations that happened to fall into the right sequence to allow for marine lactation, etc.  But that’s exactly how Dawkins sees it, and, apparently, judging by all these recent columns paying homage to “randomness”, how Biologos sees it.

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