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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 - #16376

June 4th 2010

1250 characters, Rich. Ever used SMS or Twitter? Please don’t feint to try regulating me in our electric-information age with anti-U demonstrations. It just shows your paleolithic age and lack of relevance. ‘Adult, educated Engish’? You don’t represent this anymore golden gramps. - Gr.

Rich - #16396

June 4th 2010


I’m not trying to regulate you, just informing you that I won’t respond to ugly forms of shorthand.  You can of course use them if you wish; it’s a free country (except of course in the universities, where speaking your mind freely can get you fired, as Guillermo Gonzalez discovered). 

Don’t get me wrong; I have nothing against Justin Bieber and Miley Cyrus fans texting each other and talking about the profound things that people of their generation talk about.  And I’m sure the reduced vocabulary they employ in their messages is entirely adequate to what they have to say.  But given the fact that most of the leading Biologos posters are older than I am, not a few having reached the six-decade mark, you might want to employ language that they recognize.  If they are so mentally inflexible that they cannot endure intellectual challenges to the neo-Darwinism they learned 35 years ago, think of how hard it must be for them give up the notions of effective English they learned 50 years ago.  Be kind to the gray-haired, Gregory; you will be one yourself some day.

pds - #16404

June 4th 2010


You should blog.  If you ever want to guest post on my blog, or start a community of ID-friendly Christian bloggers, leave me a comment. 

By the way, you have more patience and endurance than I.

Rich - #16405

June 4th 2010


Thanks for your kind comments.  I won’t have time to blog in the near future, but I’ll keep your offer in mind.

pds - #16411

June 4th 2010


Up to you.  I don’t have that much time either.  But you are spending a lot of time commenting here.  You should not waste your knowledge and logical reasoning abilities driving more traffic to Biologos.  Your insights deserve more prominence.  The thoughtful Christian community needs a more philosophically sophisticated alternative to Biologos.  If interested at all, leave a comment and I will email you.

Rich - #16416

June 4th 2010


I have to reduce my time here as well, but give me an address or link where I can send a message which will reach only you.  Maybe something is possible down the road.

pds - #16419

June 4th 2010

If you leave a comment on my blog, I will get your email without anyone else seeing it.  I will then email you and give you mine.

beaglelady - #16434

June 4th 2010

It’s not my responsibility to provide any lists.  I’m not the one with the theory.  You’re the one who is defending neo-Darwinism.

And you are the one with objections. You keep throwing out numbers for required changes. What’s behind those numbers?

What is your alternative theory to evolution (as the term is used by biologists)?  If it is design, why are cetaceans occasionally found with hind limbs? Why all the vestigial structures, such as the hind limb buds that develop on embryonic dolphins, only to disappear?  If that is purposeful, then the purpose must be to confuse and fool us. If the designer is a capricious magician, then every frog in the world could be an ex-prince, for all we know.  Are modern whales really enchanted land mammals?  (Please see Disney’s The Princess and the Frog.)

beaglelady - #16435

June 4th 2010

So I can’t promise you a theory of whale evolution from every ID proponent; what I *can* promise you is that any ID proponent who *does* offer such a theory will offer one much more complex and subtle than the chance-driven rubbish you’ll get Dawkins, Gaylord Simpson, Ken Miller, etc.

So what ID theorists do offer theories of whale evolution?  Are they published anywhere at all?

R Hampton - #16439

June 4th 2010

“uncritical acceptance of neo-Darwinism and “randomness” that I’ve objected to”

That’s false on both accounts. First, the science supporting “neo-Darwinism” has been (and continues to be) subjected to critical analysis since the publishing of “On the Origin of Species.” The example I used yesterday, Epigenetics, is a rather recent addition to Evolutionary Theory. Less then a decade ago (2001), the journal Science dedicated an entire issue to, “recent discoveries in the field of epigenetics ... are changing the way researchers think about heredity.”

Second, as I have demonstrated to you time and time again, randomness is not a theological problem because it simply does not exist for God, a being with perfect knowledge unbound by time or causation. Furthermore, randomness exists at all scales within this universe, not just at the level on genetic mutations or copying errors. Because quantum fluctuations, the motion of molecules, conception (the meeting of sperm and egg), etc, all factors into the development of life, even a “designed” genome can not escape probability. If ID truly has a problem with randomness, then it has a problem with Creation itself, not just Evolution.

R Hampton - #16440

June 4th 2010

But what if evolution occurred, but *not* primarily through neo-Darwinian mechanisms?  What if it occurred either through subtle divine guidance, or through elegant pre-planning, working through a built-in genomic intelligence, so to speak, which steered evolution in certain directions, so to speak?  In other words, what if evolution is teleological?

You can not accept that randomness IS divinely guided AND pre-planned - hence evolution IS teleological - because you insist that God is subservient to randomness rather.

Flip a coin. Flip it again. Then flip it a third time. The probability that I will be able guess the correct outcome is 1 in 8. Do you agree? What of God, is his “guess” also only as good as 1 in 8? Of course not, God knew in advance the exact sequence (he had to, if you believe in an omniscient being). In fact, it was part of his plan from the beginning. God also knew in advance every random mutation that will occur. How could he not?

Your fear of randomness betrays a doubt of God’s omniscience.

Gregory - #16468

June 4th 2010

*You’ll see many books written by strong ID supporters attacking this invasion of the humanities and social sciences and human life in general by “Darwinism” or “evolutionary” perspectives.* - Rich

Yes, I´ve read John West and spoken with him at some length on these issues. It is mainly Darwinism, not ´evolutionary perspectives´ that they attack. There´s a difference.

It is not BioLogos´ mission to ´attack Darwinism´. That is an explicit ID goal, which is why it is all but impossible to separate ID from the ´culture war´ mentality. You say you are not part of such a ´culture war,´ Rich. Yet you write like a warrior trained by the DI itself.

You seem to have no problem identifying with ´revolutionary ID´. But I prefer Mike Gene´s approach, which has led him to distance himself from the DI´s ´culture war´ mentality, though he knows much more than most about the ´psychology´ of the ´culture warriors´.

Rich - #16472

June 4th 2010


The numbers in question come from Sternberg, who spoke of hundreds (at least) and probably thousands of morphological changes.  Despite the fact that you are a dog-owner, I do not think you know more about animal morphology than Sternberg, an evolutionary biologist, does.  (I’m a dog-owner, too, and I wouldn’t on the strength of that presume to correct Sternberg.)

Even if we take a very low number of morphological differences between a whale and a putative ancestor, say, 300, neo-Darwinism can’t provide plausible genetic pathways to those 300 differences.  My challenge has been up here for a month now, and no commenter, and not a single Biologos Ph.D., has come up with a single scientific reference which fully explains even *one* morphological change.  Scientific honesty dictates that the claim (that ND mechanisms can explain the evolution from land mammal to the whale) be regarded as inadequately supported.  Note that I did not say “false”.  I said “inadequately supported”.  And I don’t adopt scientific claims that are inadequately supported.  You may, if you wish.

Gregory - #16473

June 4th 2010

[BioLogos] *insists that a Christian moral and social theory must be built on a fundamentally anti-Christian theory of human nature—Darwin’s.  If you’re into cutting off bad “evolutionary” conclusions in the social sciences, ID is your natural home, not Biologos.* - Rich

Darwin was more non-Christian than anti-Christian. His wife was a Christian [they didn´t divorce] and he £ supported church activities throughout his life.

I´m willing to give BioLogos a chance to show its colours, Rich. Maybe you should too? ID is primarily uninterested in forming *a Christian moral & social theory.* There is not one sociologist, anthropologist or psychologist listed among DI fellows. Why not?

BioLogos is acting responsibly wrt ´old´ earth & mutability of species, in contrast to the IDM, which seeks to involve non-natural causes in natural-physical sciences without identifying the Source of Intelligence or the Intelligence in action.

Biology will move forward with new discoveries & at some point ´Darwinism´ will be a term no longer used. In fact, many people don´t use it to self-identify any longer, Rich, even if you just assume based on your imagination that they do.

Rich - #16474

June 4th 2010


Your continued references to vestigial organs and so on indicate that, despite my repeated explanations to you and others, you do not grasp the distinction between evidence that points to common descent and evidence that points to neo-Darwinian mechanisms.  I have not challenged common descent; I’ve challenged neo-Darwinian mechanisms.  But having been a university teacher for over 25 years now, I’ve slowly (and sadly, given my optimistic nature) come to accept that some people are just not going to “get” certain points, no matter how many times you explain them, and no matter how many different approaches you take to explaining them.  It now appears to me that further repetition of the same definitions, distinctions, explanations, analogies, etc. will not do any good in your case, so I leave off further attempts to convince you.  Best wishes.

Gregory - #16476

June 4th 2010

*If you’re into cutting off bad “evolutionary” conclusions in the social sciences, ID is your natural home, not Biologos* - Rich

Let me go further with this. ID has made clear it is not simply anti-evolution, but also pro-ID. There is no need to shelter with ID to make criticisms of ´bad evolutionary conclusions in the social sciences´ because the IDM are not leaders in this area. They are among the best, if not *the best* at thrashing out at the scientific work and and extra-scientific implications of Charles Darwin´s research and writings. But biology is larger than Darwin and so surely too is social scientific theory and methodology.

Once an evangelical Christian *accepts* an old earth and mutability of species, which is what BioLogos, but *not ID* is outwardly promoting, there need to be support networks that validate the correctness of their decision and which help them integrate their theology with science and philosophy in a positive or coherent way. I don´t see ID trying to do this, but I do see that as a role of BioLogos. Francis Collins´ philosophy of science or theology of science may not be as deep as Mariano Artigas´, but BioLogos can offer help to Christians that neither ID nor YEC do.

Rich - #16477

June 4th 2010

R Hampton:

Regarding chance, omniscience, etc., your theological understanding is negligible.  If I had you as a student in one of my freshman religion courses, I could try to help, but unfortunately that is not to be, and certainly I am not going to spend time arguing with someone who does not know the basics of either philosophy or theology.

On the science side, you will not answer my True of False question (16316; see also 16302), and I take that as a win for me by default.

Best wishes.

Rich - #16478

June 4th 2010


Let’s end on a note of agreement.  Biologos and ID have quite different missions.  I see Biologos’s “mission field ” as:  (a) conservative Protestants who are hostile to evolution and (b) conservative Protestants who are open to evolution, but fear that their sympathies for it are ungodly and/or will be condemned by their conservative peers.  I see ID’s “mission field” as: (1) Christians who think that neo-Darwinian explanations are so solid that God’s omnipotence, providence, etc. are endangered; (2) secular people who won’t respond to arguments from revelation or authority, but are at least open to arguments for God’s existence that are based on the empirically verifiable facts of nature.  Because the two groups have two different mission fields, they behave differently.  I have no problem with that.  My problem is with the arrogance and condescension (usually veiled with politeness and a Christian smile, but quite evident to those on the receiving end) with which ID is treated by columnists and commenters here, and with the dogmatic statements (in both science and theology) which are made by many here.  As I said, my mission here is not to sell ID, but to refute lies about ID, and to combat dogmatism.

beaglelady - #16487

June 4th 2010


Why can’t you tell me how vestigial organs and atavisms could possibly square with design?  You haven’t explained it at all.

unapologetic catholic - #16507

June 5th 2010

“My challenge has been up here for a month now, and no commenter, and not a single Biologos Ph.D., has come up with a single scientific reference which fully explains even *one* morphological change.’

Not. True.

For those who want to know all about whale evolutio,there is ab entire lab devotedy to that subject.  http://www.neoucom.edu/DEPTS/ANAT/Thewissen/

It answwers all of Rich’s objections and questions and demolishes Sterberg (who can’t seem to count whales).  Peer-reviewed articles:


Thewissen’s 2009 article is especialy detailed. http://en.scientificcommons.org/52961215

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