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”

Introduction

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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R Hampton - #16305

June 3rd 2010

Sternberg:

In the past two years several papers show that this progression of forms was more abrupt. If you look in the middle [transitional forms], (and I don’t question this progression of forms; I’m not a creationist) we have a taxa like gaveocetus, protocetus, georgiacetus—these are called protocetids—and they’re depicted as having rudiments of tale flukes, and reduced hind limbs and essentially look in between pakicetus and doradon.

...What’s interesting is that if you get a good text book on cretacion anatomy and embryology and look at the development of some of these structures, just the soft tissue parts, what you could never discern from look at the bones, to have a basic fully aquatic whale in and of itself is a feat of engineering (by that I do not mean intelligently designed).
-continued


R Hampton - #16307

June 3rd 2010

(cont.) ...I have a simple question: can this geological pattern that I accept and that I’m not going to attribute to outside intervention, be explained by the processes of population genetics. In other words, can neo-Darwinism alone provide an adequate causal explanation for the dramatic reorganization? [To which he eventually concludes, “it doesn’t add up”]


beaglelady - #16313

June 3rd 2010

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

Rich, that’s not exactly true. Over on this thread, I noted that one of Sternberg’s requirements to change a land mammal into a
whale actually seemed to betray faulty knowledge of how the mammalian spine moves.

What I said was,

I am not a whale expert, but one thing I did notice: near the beginning he [Sternberg] says (speaking of what’s required to turn a land mammal like Pakicetus into a whale),
“Unlike a dog’ tail that wags from side to side you have to have a tail that moves up and down.”
Well, a dog’s tail CAN move up and down.  Watch a dog or horse run—you won’t see the spine moving vertically.


beaglelady - #16314

June 3rd 2010

oops—sorry— let’s try that again:

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

Rich, that’s not exactly true. Over on this thread, I noted that one of Sternberg’s requirements to change a land mammal into a
whale actually seemed to betray faulty knowledge of how the mammalian spine moves.

What I said was,

I am not a whale expert, but one thing I did notice: near the beginning he [Sternberg] says (speaking of what’s required to turn a land mammal like Pakicetus into a whale),
“Unlike a dog’ tail that wags from side to side you have to have a tail that moves up and down.”
Well, a dog’s tail CAN move up and down.  Watch a dog or horse run—you won’t see the spine moving vertically.


Rich - #16316

June 3rd 2010

R Hampton:

I know what Sternberg said as well as you do.

Your first two sets of bolded words are redundant, as I already made it clear from the beginning that Sternberg is an evolutionist.  I never denied “evolution”, and I never said Sternberg did, either.

His remark about “neo-Darwinism alone”, however, does *not* imply the words you invented.  His remark is just as compatible with “neo-Darwinism can explain only 10% of the transformation, and is not the major driving force” as with “neo-Darwinism can explain 90% of the transformation, and only needs a bit of supplementation”.  Your invented words about what Sternberg “would be comfortable saying” go beyond what his statements warrant, and leave the impression that he’s far less critical of neo-Darwinian pretensions than he is.

In any case, you are evading the question.  Here is my claim on the table:  “Neo-Darwinian explanation has come nowhere near to providing a satisfactory account of how a land mammal could have become a whale”.  True or false?


Rich - #16321

June 3rd 2010

beaglelady (16314):

There would be many physiological changes necessary to turn a dog’s tail into a whale’s fluke *other than* the capacity for vertical motion, and you need to provide the genetic explanation for how those physiological changes would occur.  So, though I’ve already given you the dog’s tail (and by the way, you never responded to my further argument on the other thread where I showed that this concession was irrelevant to my overall argument) , you still have several hundred or thousand physiological changes to list, and you still have to provide genetic causes for each of them.  If you can do it, then go ahead.  If you can’t, then answer “True” to the claim I posed for R Hampton immediately above.


Gregory - #16331

June 3rd 2010

“Do you really *not understand* that he [Richard Sternberg] is mounting a slashing attack on neo-Darwinism and on Biologos-TE, or are you misrepresenting his argument willingly?” - Rich

Another fanatical untruth, Rich?! They are mounting.

Please show where Sternberg claims to ‘attack’ BioLogos.

“Sternberg is an evolutionist.” - Rich

And Rich is also an evolutionist. Just not a Darwinian or neo-Darwinian evolutionist. Right?

(You really must be forgiven for misrepresenting BioLogos time and time again, ad nauseum,  Rich, given that BioLogos clearly states it is *not* a theistic evolution Foundation.)

Do you really champion R. Sternerg as being at the vanguard of biology? Funny how you bet on horses, Rich.

Does Sternberg use the concept duo ‘designed evolution’?

p.s. I am *not* an ‘evolutionist.’


beaglelady - #16336

June 3rd 2010

Rich,

you still have several hundred or thousand physiological changes to list, and you still have to provide genetic causes for each of them.

Oh, I do?  Do you know exactly how many changes there are?  Why don’t you list them?

Sternberg argued that you have to get from vertical motion to horizontal motion. I merely explained that you already have horizontal motion.  Now you want me to explain the evolution of the fluke?  I suspect that flukes don’t fossilize well (I don’t think they have bones) and I’ve already explained that I’m not a whale expert. Besides, I don’t think we have any DNA from early whale ancestors. I’ve also explained that the complete story of the transition might not be recoverable.


beaglelady - #16337

June 3rd 2010

Therefore,  “no proof implies a poof” is not a reasonable assumption.

All scientific theories are incomplete and whale evolution is no different.  Why do you think scientists are busy in their labs?  I have no idea of the current state of our knowledge of whale evolution (as the term is normally used) or what evolutionary problems are currently being pursued.  You can bet scientists are working on the unknowns.  Sternberg looks for gaps in knowledge, but scientists seek to fill in those gaps.

If whales didn’t evolve (as the term commonly means), enchantment might better explain the occasional hind limbs found on living whales. What do you think?

What answers do you have for us—a sequence of intelligent design interventions?


Gregory - #16341

June 4th 2010

Hi beaglelady,

thanks for fixing the html problems. Always good to hear about/from Polkinghorne. Hope you enjoyed the dinner.

You surely know by now that Rich is not going to offer anything ‘positive’ in promoting ‘intelligent design’ on the topic of ‘whale evolution.’ There *is* no ID theory of ‘whale evolution,’ is there?

Rich’s goal is simply to doubt (how original?) ‘neo-Darwinian mechanisms’. This is valid in a way. In another way, of course, it is simply avoiding reality. 

In other words, Rich is a ‘wedge’ proponent. Negative, negative, and maybe at some rare times a positive prediction. Obviously not an ‘evangelical’ is Rich.

Doubt Darwinism, but don’t propose a better alternaive. Karl Popper would poof on Rich’s posturing.


Rich - #16342

June 4th 2010

Gregory:

I told you and others already about Sternberg’s articles at Discovery, reprinted electronically in *Signature of the Controversy*.  Read them, and tell me whether you think they show neutrality toward Biologos.  There are also some caustic (albeit pre-Biologos) remarks on Sternberg’s web site about one of Collins’s arguments about “bad design”.

Biologos states that it is not a theistic evolution foundation?  How foolish of me not to notice.  But tell me, how is it that almost every column posted here is directly or indirectly related to evolution?  (Even the very fine series of columns on the Bible by Pete Enns is there at least partly to clear away YEC objections to evolution.)  And how is that almost every argument made about evolution, ID, YEC, etc. is *identical* to the arguments made by TE/EC?  Can you name me one specific Biologos position that (a) was not held by many TEs; (b) is critical of any main argument of TE?

Re your question:  Not Sternberg alone.  Sternberg is one of a group of younger biologists whose work will relegate neo-Darwinism to a much lesser role in the overall scheme of evolutionary biology.


Gregory - #16347

June 4th 2010

Rich,

You wrote:
“But tell me, how is it that almost every column posted here is directly or indirectly related to evolution?”

BioLogos is seeking to convince Christians, mainly evangelical American Christians, that it is not ‘sinful’ to accept an old Earth and biological evolution.

Do you agree with this mission or not?

“Sternberg is an evolutionist.” - Rich

“Sternberg is an evolutionist.” - Rich

Sternberg is also a theist, i.e. a Christian theist.

So Sternberg qualifies as a theistic evolutionist.

Yes, it is foolish of you not to notice that BioLogos is *not* a TE foundation. Karl Giberson has made it crystal clear that BioLogos differs from TE in not wanting to accept the ‘baggage’ of the term ‘evolution’ or the ideology of evolutionism. You seem dumb to (& not able to hear) this.

Can you imagine why Giberson says this? Just give a care to offer support for once, will you Rich?


Rich - #16350

June 4th 2010

beaglelady:

I never said “No proof implies a poof”.  How many times do I have to deny holding the views that you and others here keep imputing to me? 

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.  How can you defend it, when you’ve just admitted that you have no idea how many changes would be needed, or whether the biologists know how they could have occurred?  Why aren’t you agnostic instead?

“The complete story of the transition might not be recoverable”?!?!  You missed your calling; you should have become a diplomat.  The fact is that *none* of the morphological changes has been causally accounted for. 

Sternberg doesn’t “look for gaps”.  He points out the inadequacies of certain mechanisms to achieve certain results.  That is not “looking for gaps”.  It’s perfectly good science.  Only people who propose feeble, wildly improbable mechanisms would object to it.  Oh, gee, I forgot, neo-Darwinians *do* propose feeble, wildly improbable mechanisms….


Rich - #16352

June 4th 2010

Gregory:

“BioLogos is seeking to convince Christians, mainly evangelical American Christians, that it is not ‘sinful’ to accept an old Earth and biological evolution.”

If that were *all* that Biologos were trying to do, I’d have no objection.  But you can’t possibly have read the columns closely and not seen that their claim is much stronger than that.  An old earth and biological evolution are not merely *acceptable theologically*; they are *required by scientific integrity*.  That theme is harped upon over and over again.  And the major cause of the evolutionary changes which “natural selection” selects?  Why, “randomness” of course—the theme of a number of columns lately, by a few different columnists.  In other words, Biologos *actively pushes* neo-Darwinian theory.  Gregory, you are smart guy.  How can you miss this stuff?  Have you deliberately put blinders on?


Rich - #16354

June 4th 2010

Gregory:

You are right, there is no ID theory of whale evolution.  Nor should there be.  Whereas YEC, OEC, TE, and Dawkins-Darwinism are all *theories of origins*, ID is a *theory of design detection*.  ID, as such, is interested in the question whether the whale body and genome shows evidence of design, not the question how the design was implemented.  Thus, there is no ID theory of whale evolution.  But those who accept premises that are, broadly speaking, “design” premises, can of course accept macroevolution as fact and then speculate about the genetic devices by which the design is transmitted, modified, etc.  So you won’t get a theory of whale evolution from Paul Nelson, who doesn’t think macroevolution happened, but you could get one from Sternberg (whom I’d call small-id), or Behe, or Denton (another small-id guy).  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.


Rich - #16357

June 4th 2010

Gregory (16347):

I’ve said—what, about a hundred times now?—that I have no objection to “theistic evolution” in the general sense, and that Behe, Denton, Sternberg and others who work within a design perspective can be “theistic evolutionists” in that general sense.  Why are you trying to get me to “admit” what I’ve already admitted, as if you’ve just trapped me on some crucial point?

It’s not theistic evolution that I object to.  It’s all the associated liberal theological dogmas and uncritical acceptance of neo-Darwinism and “randomness” that I’ve objected to.  No one who has read my comments carefully, and has even sophomore reading comprehension skills, could ever think I’ve argued anything else.

Taking the word “evolution” out of the *name* of Biologos, when the word “evolution” appears in just about every column on this site, is meaningless.  Everybody *knows* that every single member of Biologos endorses macroevolution and that they all regard anyone who doubts macroevolution as scientifically benighted.  Biologos is TE rebranded.  The same personnel, the same ideas, the same arguments, and most of all, *the same constant targets*—YEC and ID.  If it quacks like a duck…


Gregory - #16358

June 4th 2010

My eyes are clear, Rich. U r a generation or two older than me. Perhaps Ur vision is faulty from age? But I’m sure U’ve never considered that, have U?

“An old earth and biological evolution are not merely *acceptable theologically*; they are *required by scientific integrity*.” - Rich

U believe in/accept an ‘old earth’ and biological (micro-)evolution, don’t U, Rich?

“You are right, there is no ID theory of whale evolution.” - Rich

But U are wrong, there *should* be an ID theory of whale evolution *if* ID has implications (as Behe says it does) 4 zoology or comparative anatomy.

Intelligent design is anti-process theory. It doesn’t speak of how, who, when or where. Weak! It just speaks of *IS,* of origins. It looks like a duck, therefore it *IS* a duck. Quack, quack.

How shallow a philosophy of science this undeniably is! If U were *really* a PhD in intellectual history, Rich, (which U would have to display if U actually published anything @ ‘intelligent design’) U would easily understand this. As it is, I have no proof (because U shun experts, and continue to misread Giberson’s appeal to wisdom) that U are no more than an undergrad secretary of rhetoric.

ID is *not* a theory of origins. Reaaalllyy?


Rich - #16360

June 4th 2010

Gregory:

So Giberson and Biologos are opposed to “the ideology of evolutionism”?  What’s new about that?  ID has been leading the charge against “the ideology of evolutionism” for years.  It has ventured into subjects dear to your own heart—the use of “Darwinism” as the theoretical basis of horrible politics, horrible psychology, horrible sociology, etc.  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.  Look at John West’s attack on Larry Arnhart’s political Darwinism.  Look at Richard Weikart’s scholarly work on the connection between Darwinism and the Nazis, and Darwinism and eugenics.  On Uncommon Descent, columnists excoriate “evolutionary psychology”.  And ID’s attack on all these applications of Darwinism is much more effective than Biologos’s attack, because ID casts doubt not only upon the applications to the social world, but even upon the biological basis of the applications.
(continued)


Rich - #16362

June 4th 2010

Gregory (continued):

If human “evolution” is conceived in the way that Darwin described it in *The Descent of Man*, it’s very hard *not* to follow through on the social applications, both in theory and practice, as West shows against Arnhart in great detail.  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?  The moral and social consequence are quite different from those which follow from an evolutionary theory which is essentially “dog eat dog”.  This is where Biologos is crippled in its Christian mission.  It 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 - #16363

June 4th 2010

Gregory:

I won’t respond to any post that uses “U” for the word “you”.  We’re not two 14-year-old girls, “texting” each other.  If you want an adult, educated reply, put your message in adult, educated English.


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