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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Rich - #16516

June 5th 2010

Un. Catholic:

There is no reason why I should waste my time looking up your references again.  I’ve caught you in a literature bluff before, which has earned my distrust in your intellectual honesty.  See:

#13840 and #13851, “Would You Like Fries with that Theory?”

So I don’t intend to waste one minute looking up what are probably irrelevant references again.  And if I’m wrong, and they’re good references, too bad.  Read the story of the boy who cried wolf, and learn the moral of that story.

Oh, and by the way, how would you be qualified to tell whether or not anyone had demolished Sternberg?  Your scientific training, if any, is not apparent to me.  You seem to speak not out of personal knowledge, but out of Google searches.  And that seems to be common around here, that people take a hard-line stance, without sound knowledge of a subject matter, and then run off to the internet to justify their prejudice after the fact.


Rich - #16519

June 5th 2010

Well, I’ve enjoyed my rodomontade inside the fortress of TE land.  I see the armor, mounts and weapons of beaglelady, R. Hampton, Un. Catholic and a few others strewn all over the cobblestones of the courtyard.  I have yet to find the Ruggiero who can slay me.  So I’ll take my leave of the whale evolution discussion, leaving those filled with Sternberg-envy to deal with the inner demons that make them incapable of ever saying “I stand corrected” or “You’ve got a point there” or “I never thought of that”.
 
Till we meet again.


Rich - #16540

June 5th 2010

Dr. Falk:

Your introduction to this article describes Dr. Ayala as a “philosopher”?  Can you please tell me the basis of this designation?  Does Dr. Ayala have any academic training in philosophy?  Or, if not academic training, does he have any philosophical publications, e.g. books of philosophy, or articles in philosophy journals?  And either way, what exactly is his field within the subject matter generally known as philosophy? 

I am asking this question because (a) I have never seen or heard Dr. Ayala’s name mentioned in philosophical circles, and (b) I have not seen anything resembling philosophy in any of Dr. Ayala’s writings.  Where can I find information regarding Dr. Ayala’s philosophical accomplishments and activities?


beaglelady - #16577

June 5th 2010

Unapologetic Catholic,

Thanks for posting the peer-reviewed papers on whale evolution.  Why can’t Sternberg bring himself to write anything on whale evolution for the scientific community to review?


unaplogetic catholic - #16645

June 5th 2010

“Why can’t Sternberg bring himself to write anything on whale evolution for the scientific community to review?”

As Rich often claims about other, he’s literature bluffing and knows it.  He’s restricted himself to YouTube so he avoids direct challenges.

But you already kknew that.

“There is no reason why I should waste my time looking up your references again.”

I know you woudn’t ever be bothered reading the vast number of peer reviewed articles by THE recognized expert in cetacean evolution, J.G.M. Thewissen and the folks at Thewissen Labs.  The entire team’s work addresses each and every one of Rich’s claimed concerns: the evolution of marine mammal nursing, reporductive organ placement, teeth development, skull and vertebrae alignment, molecualr genentics—to to identify a just a few areas.

I do encourage anybody who is interested in the subjec to review the lab site and the many published papers on the various issues relating to cetacean research..


beaglelady - #16675

June 5th 2010

u.c.,

Yes, I knew that.  We are scolded for using the internet and then he directs us to watch internet videos! 

And he offered no ID alternative to evolution (as scientists understand it).

On some ancient seashore, did the intelligent designer really chase the Pakicetidae around so he could poof new information into their their germ cells?


Neal - #17208

June 11th 2010

So what would evolutionists seriously accept as falsification for Evolution??? 

The theory is more flexible than gumby and has been a poor model in making hard predictions. 

The only successful predictions are the ones where the the targets are drawn around evidence that seems to support it… at least until further evidence unsupports it. 

More people are asking the right questions of evolutionists and they will no longer be able to hide behind the shell games.

Ask the tough questions: 

          1. What evidence directly contradicts evolution?

              Every theory has some support, but a good theory should not contradict the evidence.

        2.  Dispense with the hand-waving generalities and just-so stories… give me the detailed evolutionary pathways of organ development.

            The human mind loves good stories and a good story teller can really drive the imaginations of the audience to fill in the details on their own.  Good evolutionists are great story tellers and their rhetorical skills are first class…  But ask the tough questions and understand that your audience is begging for details.  That’s where the rubber meets the road.  The rest is hogwash.


beaglelady - #17252

June 12th 2010

So what is your theory, Neal? Poof?


defensedefumer - #17334

June 13th 2010

Dear Neal,

Evolution is falsifiable. See http://www.talkorigins.org/indexcc/CA/CA211.html

Evolution has made predictions. See http://www.talkorigins.org/indexcc/CA/CA210.html

As an undergraduate biologist, I did study the evolution of organ development. While we do not know enough to comment on ALL organ development pathways, the theory of evolution has proven suffice the organs we do know, such as the insect leg and wings.

In fact, evolution of the reptilian jaw joint into the mammalian middle ear is seen clearly in the fossil record. That said, if you really want to observe the evolution of the bones, just look at the embryonic devlopment of the oppossum.

As a Christian, I find it hard to look at such evidences and deny evolution. For me to do so would be dishonest.


Rich - #18148

June 21st 2010

Neal:

Don’t mind beaglelady (17252).  I’ve asked her dozens of time to speak *out of her own knowledge of biology* and give us *her* evidence for the capacity of neo-Darwinian mechanisms to produce a whale.  She always changes the subject, either by asking “Well, how do you account for those vestigial legs in some whales?”, or by asking “Well, how do you think whales came about then—poof?”

Notice that the first stratagem evades admitting, “I have no explanation how neo-Darwinian processes alone could possibly create whales” by going on the offensive: “If you can’t think of any other explanation for feature X, neo-Darwinism processes must have generated it (even though I don’t have the slightest clue *how* they generated it).” 

Notice that the second stratagem falsely appeals to “God of the gaps” charges, when ID is in fact not committed to supernatural explanations.  I.e., it attempts to ridicule ID by appealing to existing prejudices against ID, instead of providing an argument to support neo-Darwinism. 

My guess is that it will snow in July in Arizona before beaglelady discusses the genetic mechanisms that can produce any part of a whale.  So I wouldn’t worry too much about her objections.


beaglelady - #18196

June 21st 2010

So if I, a non-scientist, don’t have all the answers at hand, it must be unlikely? Not knowable?  Nice.

Rich should know that a professional is attempting to discuss genetic mechanisms with him on
this thread right now..

My guess is that it will snow in July in Arizona before beaglelady discusses the genetic mechanisms that can produce any part of a whale.

Or when Dr. Sternberg writes something up about about whale evolution for scientists to peek at.


Rich - #18227

June 21st 2010

beaglelady:

Well, we finally have an admission that you are a non-scientist, which I had suspected all along.  And no, I didn’t say that anything was unknowable.  I said that the mechanisms of whale evolution hadn’t been shown.  And, unlike you, I don’t accept things that haven’t been shown, just on the authority of specialists.  Specialists have vested interests like everyone else, in fact, more so than everyone else.

Actually Dennis is not attempting to discuss genetic mechanisms with me at all.  He is refusing to discuss the mechanisms.  You don’t see that, because, as you’ve indicated, you’re a non-scientist.

Funny that you point to Dennis as “a professional”, but when I point to Sternberg, who is also a professional, you ignore him.  Dennis, by the way, has published *nothing* on whale evolution, yet has an opinion on it, so why aren’t you bashing him the way you bash Sternberg, for having an opinion without publishing?  Why aren’t you asking Dennis to produce a set of mechanisms for whale evolution?  Oh, I forgot, you think he *is* producing a set of mechanisms.  But perhaps you didn’t notice that he is talking about chimp-human evolution, on a thread that’s supposed to be about whale evolution?  Sigh.


glsi - #63393

July 17th 2011

To date, I’ve only finished about half of Signature in a Cell.  I love it and can’t wait to finish. 

So far this book is about matters of science.  There is very little in the first half which deals with  theology.  That’s why it’s so funny  that Dr. Alaya’s review is almost all concerning theology and criticizing the book and it’s author on this level.  He’s pretty much mute on the extensive and impressive science presented in the book.  I could venture a guess why:  Dr. Alaya is hopelessly stymied by the book and has no science of his own to refute it.  The tired old theories of  “RNA world”, etc. look more and more hilarious everyday.  You know, it seems like the proponents of those theories are getting quieter and quieter all the time.  They seem to not want to talk about it! 


John - #63412

July 18th 2011

gisi:
“So far this book is about matters of science.”

Hi gisi, I’d appreciate it if you’d comment on this matter of science from p. 128: 
“A protein within the ribosome known as a peptidyl transferase then catalyzes a polymerization (linking) reaction involving the two (tRNA-borne) amino acids.”

Is this true or false?

“He’s pretty much mute on the extensive and impressive science presented in the book.”

Why doesn’t Meyer DO any science? How do you know that Meyer’s presentation isn’t incredibly deceptive? Why don’t you check the veracity of Meyer’s claim above?

“I could venture a guess why:  Dr. Alaya is hopelessly stymied by the book and has no science of his own to refute it.  The tired old theories of  “RNA world”, etc. look more and more hilarious everyday.”

Interesting. Would you say that Meyer’s description of the RNA World hypothesis (not a theory) from p.298 is accurate?
“According to this [RNA-first] model, these RNA enzymes eventually were replaced by the more efficient proteins that perform enzymatic functions in modern cells.”

“You know, it seems like the proponents of those theories are getting quieter and quieter all the time.  They seem to not want to talk about it!”

I submit that you aren’t listening to the real science at all, gisi. They are doing things like winning Nobel prizes for data that support the RNA World hypothesis. Can you figure out to which particular Prize I refer when I point to the two hilarious Meyer quotes above?

glsi - #63417

July 18th 2011

John,


Actually, it’s those who claim a belief in chemical evolution who need to be answering the questions.  Rather than theological musings,  Dr. Ayala should instead put this debate to rest and relegate Dr. Meyer’s book to the dustbin with some hard science.

The basic problem is this:  There are lifeless amino acid (building blocks) that you can find in nature or even brew up in the laboratory.  Then there are living cells.  There is nothing in between and no pathway to get there.  This problem remains a problem no matter what mistakes or oversights might be in Dr. Meyer’s book.

  Scientists have proposed theories and searched for pathways for a long time now with no credible results.  Supplying RNA templates, contaminating samples and using human intelligence to edit out unwanted chemical reactions doesn’t count.  But hey, supply any chemicals you want in any laboratory conditions you want.  Chemicals still do not reproduce themselves.  DNA does not reproduce itself.  You need ALL the molecular machines working together in a living cell for these things to occur.  If somebody has some evidence to the contrary let them come forward and collect their prize.  Then we can skip this whole conversation.
 

John - #63421

July 18th 2011

gisi:
“This problem remains a problem no matter what mistakes or oversights might be in Dr. Meyer’s book.”


My dear gisi,

Your desperate evasiveness is amusing. 

There is absolutely zero evidence that the two passages I challenged you with represent mistakes or oversights, and significant evidence that they do not. 

If you strongly believe that they are, then YOU need to show how Meyer’s thesis can accommodate corrections to these blatant falsehoods.

We both know that it can’t.

“Scientists have proposed theories and searched for pathways for a long time now with no credible results.”

This is absolutely false, as you implicitly concede by your evasiveness.

“Supplying RNA templates, contaminating samples and using human intelligence to edit out unwanted chemical reactions doesn’t count.”

Meyer’s blatant falsehoods don’t relate to any of those things. He’s fudging the unequivocal evidence that neither you nor he can explain. Why not confront the truth, gisi?

“But hey, supply any chemicals you want in any laboratory conditions you want.  Chemicals still do not reproduce themselves.”

I respectfully suggest that you Google “vitalism Kornberg replication” to see how science trashed this view in the 1950s. All IDCreationists have done since then is move the goalposts.

John - #63424

July 18th 2011

Also, are you familiar with PCR? I supply chemicals under specific conditions, DNA is reproduced.


glsi - #63427

July 18th 2011

Like I said, using templates doesn’t count.   Kornberg not only used a template, but then added enzymes to do the work. And as we all know enzymes are produced in living cells in the first place.  So I wouldn’t call that DNA reproducing itself.

The reason that the onus is on  chemical evolutionists to come up with some answers is because they’ve been so successful in getting their stuff into my daughter’s textbook.  It’s on them to back up “RNA world” with some actual evidence.  Otherwise they should throw in  Genesis, Native American creation myths, Francis Crick’s spaceships and maybe even Dr. Ayala’s views on what a smart god would actually make.  But let’s not call it Biology anymore.

I read that when Stanley Miller died in 2007 the University of California threw out most of his still-in-progress origin of life experiments that he’d spent much of his career working on.  I don’t guess they thought he had any block-buster results in the making.  Hopefully, they kept a couple samples just for a good laugh. 


John - #63429

July 19th 2011

gisi:
“Like I said, using templates doesn’t count.”


You didn’t say that. You said that RNA templates don’t count. My PCR didn’t use RNA templates.

“Kornberg not only used a template, but then added enzymes to do the work.”

You wrote, “But hey, supply any chemicals you want in any laboratory conditions you want.  Chemicals still do not reproduce themselves.”

Enzymes are chemicals. You were completely wrong, but you won’t admit it, just like you’ll never admit that Meyer deceived you about the strongest evidence supporting the RNA World hypothesis because he can’t explain it.

“And as we all know enzymes are produced in living cells in the first place.”

They are chemicals. Is peptidyl transferase a protein?

“So I wouldn’t call that DNA reproducing itself.”

I call it supplying any chemicals I want in any laboratory conditions I want.

“It’s on them to back up “RNA world” with some actual evidence.”

They have. Nobel Prize-winning evidence that Meyer can’t explain. Did you figure out what was blatantly false about Meyer’s claims about the RNA World hypothesis and the actual evidence yet, or are you impervious to reality?

“I read that when Stanley Miller died in 2007 the University of California threw out most of his still-in-progress origin of life experiments that he’d spent much of his career working on.”

Wanna bet? I’ll bet you $100,000 that the polar opposite is true. Where did you allegedly read that, gisi?

“I don’t guess they thought he had any block-buster results in the making.  Hopefully, they kept a couple samples just for a good laugh.”

They analyzed them and published the results in Science. You don’t guess very well, and you’re afraid of actual evidence. You cling to false hearsay. 

What does the Bible say about hearsay, gisi?

glsi - #63434

July 19th 2011

Ouch, you got me.  Guilty!  I read that in Discover magazine’s special issue on evolution.  It’s currently on the shelves at Borders.  And it’s true, they do publish a lot of very flimsy stuff on the subject of evolution.  But anyway, I ain’t a gamblin’ man.




John - #63440

July 19th 2011

“Guilty!  I read that in Discover magazine’s special issue on evolution.”


Read what? The falsehood or the truth?

“It’s currently on the shelves at Borders.  And it’s true, they do publish a lot of very flimsy stuff on the subject of evolution.”

Your falsehood wasn’t about evolution. Let’s talk about Meyer’s falsehoods about the RNA World hypothesis and how you determined that they were mistakes or oversights instead of deliberate lies.

“But anyway, I ain’t a gamblin’ man.”

You don’t believe in any of the falsehoods you are spreading. Nor does Meyer.

glsi - #63441

July 19th 2011

No idea what you’re talking about, John.  The pro-Darwinian Discover magazine published an interesting little piece about Stanley Miller that states exactly what I said it does.


John - #63443

July 20th 2011

The polar opposite is true, gisi. If you are correct, how do you explain the existence of the Science and PNAS papers?


And I find your refusal to engage me on the very subject you chose to bring up (the RNA World hypothesis) to be fascinating. It’s strong evidence of your lack of faith in Meyer.

glsi - #63504

July 26th 2011

I haven’t seen the articles you’re referring to.  Seems like it’d be headline news if they found out Miller had in fact ever succeeded in conjuring up any life in his jars.  Seems more like Stanley spent most of his career searching in vain for something that was never there.  At least maybe his failure can be instructive to the seekers of the RNA World.   That’s what I’d take from this month’s Discover article anyhow.  


glsi - #64292

August 27th 2011

Here you go John, this may be helpful to you:


from pg. 13 of Summer 2011 Discover magazine by Douglas Fox:

“Shortly after Miller finished his 25-year experiment, he suffered a stroke that ended his career.  His laboratory, with 40 years of samples, was emptied in 2002 to make way for a building renovation.   Experiments that had run for years or decades were discarded without ever being analyzed.”

I’m glad you challenged that!  It’s very doubtful to me that the author would have made that one up.  

John - #64591

September 8th 2011

“Seems like it’d be headline news if they found out Miller had in fact ever succeeded in conjuring up any life in his jars.”

Nice straw man! When did Miller ever state that his goal was “conjuring up any life,” gisi?

Why not examine the evidence?

Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment
Eric T. Parkera,1, Henderson J. Cleavesb, Jason P. Dworkinc,Daniel P. Glavinc, Michael Callahanc, Andrew Aubreyd,Antonio Lazcanoe, and Jeffrey L. Badaa,2
PNAS April 5, 2011 vol. 108 no. 14 5526-5531

Take note, gisi: because you lack sufficient faith to examine the evidence directly, the best you will do is pretend that what the authors say about the evidence is the actual evidence. You are driven by fear.

Then you quote hearsay:
“Experiments that had run for years or decades were discarded without ever being analyzed.”

That doesn’t support your explicitly quantitative claim, now, does it? And your explicitly quantitative claim is just designed to fool the reader into believing that there’s no new evidence out there, right?

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