Francisco Ayala on “Signature in the Cell”

by Matthew Cobb

Jerry, on his way to the Galapagos, asked me to post this. Over at Biologos, “Science and the Sacred” has persuaded Francisco Ayala  to write a review of Stephen C. Meyer’s Signature in the Cell. Here it is. There’s a debate going on over there, too.

How should a person of faith respond to Signature of the Cell? I am an evolutionary scientist who would suggest the following considerations.

The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point? It is as if in a book about New York, the author would tell us that New York is not in Europe, and then dedicate most of the book to advancing evidence that, indeed, truly, New York is not in Europe.

Signature of the Cell offers Intelligent Design (ID) as the alternative explanation to chance in order to account for genetic information. This suggestion turns out to be no more convincing than a proposal by the author of the book about New York, who having exhausted all possible ways of telling us that New York is not in Europe, would now offer Peoria as the alternative city to visit. We would rather read about New York’s architecture, splendid avenues, and great parks; about the rich culture and ethnic diversity of the city; about its restaurants, concert venues, theatres, and wonderful sights in and around the city. But regarding natural selection, genetics, ecology, development, physiology, and behavior in the evolution of genetic information, there is nothing substantive in Signature of the Cell.

Christians and other people of faith should be troubled about Signature of the Cell for several reasons. One is that Meyer avoids consideration of the negative implications of ID as an explanation of the origin of genetic information, which is his main subject. According to Meyer, ID provides a more satisfactory explanation of the human genome than evolution does. ID’s explanations envision “discrete or discontinuous intelligent activity in the history of life” (p. 481). Scientists have now obtained the complete DNA sequence of the human genome. The genome has a length of about three billion nucleotides, the “letters” of the DNA alphabet. Scientists have also obtained the complete DNA sequence of the chimpanzee genome—also three billion letters long—and of several hundred other species of organisms. How can we envision the “discrete or discontinuous activity” of the Intelligent Designer? The human and chimpanzee genomes differ from each other in just a few percent of the DNA letters, less than two percent in the genes that code for proteins. Did the Designer tweak the chimpanzee genome to make the human genome? Or, perhaps more likely, did the Designer use a preexisting genome and tweak it a bit to make the human genome and tweak it a different way to make the chimpanzee genome? Did the Designer go on tweaking genomes a bit at a time to design the genome of the gorilla and other primates, and more and more tweaking for other animals, all the way down to mice, and even to fruitflies, with which we share a good fraction of the genome?

The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences, which turn on and off genes in different tissues and at different times and play other functional roles. There are also lots and lots of DNA sequences that are nonsensical. For example, there are about one million virtually identical Alu sequences that are each three-hundred letters (nucleotides) long and are spread throughout the human genome. Think about it: there are in the human genome about twenty-five thousand genes, but one million interspersed Alu sequences; forty times more Alu sequences than genes. It is as if the editor of Signature of the Cell would have inserted between every two pages of Meyer’s book, forty additional pages, each containing the same three hundred letters. Likely, Meyer would not think of his editor as being “intelligent.” Would a function ever be found for these one million nearly identical Alu sequences? It seems most unlikely. In fact, we know how these sequences come about: one new Alu sequence appears in the genome for every ten newborns, generation after generation. The Designer at work? Unlikely: many of these sequences damage the genome causing abortion of the fetus during the early weeks of life.

Perhaps one could attribute the obnoxious presence of the Alu sequences to degenerative biological processes that are not the result of ID. But was the Designer incompetent or malevolent in not avoiding the eventuality of this degeneration? Come to think of it: why is it that most species become extinct? More than two million species of organisms now live on Earth. But the fossil record shows that more than ninety-nine percent of all species that ever lived became extinct. That is more than one billion extinct species. How come? Is this dreadful waste an outcome intended by the Designer? Or is extinction an outcome of degeneration of genetic information and biological processes? If so, was the Designer not intelligent enough or benevolent enough to avoid the enormity of this waste?

Meyer asserts that the theory of intelligent design has religious implications. “Those who believe in a transcendent God may, therefore, find support for their belief from the biological evidence that supports the theory of intelligent design” (p. 444). I do think that people of faith may find in the world many reasons that support their belief in God. But I don’t think that intelligent design is one of them. Quite the contrary. Indeed, there are good reasons to reject ID on religious grounds, in addition to scientific grounds. The biological information encased in the genome determines the traits that the developing organism will have, in humans as well as in other organisms. But humans are chock-full of design defects. We have a jaw that is not sufficiently large to accommodate all of our teeth, so that wisdom teeth have to be removed and other teeth straightened by an orthodontist. Our backbone is less than well designed for our bipedal gait, resulting in back pain and other problems in late life. The birth canal is too narrow for the head of the newborn to pass easily through it, so that millions of innocent babies—and their mothers—have died in childbirth throughout human history.

I could go on about human features that betray a design that certainly is not intelligent. I will add only one more consideration. More that twenty percent of all human pregnancies end in spontaneous abortion during the first two months of pregnancy. That is because the human genome, the human reproductive system, is so poorly designed. Do I want to attribute this egregiously defective design to God, to the omnipotent and benevolent God of the Christian faith? No, I don’t. It would not do to say that God designed intelligently the human genome and that it then decayed owing to natural processes. If God would have designed the human genome, surely He would have done it so that this enormous misfortune would not happen. Think of it: twenty percent of all human pregnancies amount to twenty million abortions every year. I shudder at the thought of this calamity being attributed to God’s specific design of the human genome. To me, this attribution would amount to blasphemy.

Before the scientific revolution of the sixteenth and seventeenth centuries, earthquakes, volcanic eruptions, and the like were attributed to direct action by God, so that the tsunami that five years ago killed two hundred fifty thousand Sumatrans might have been interpreted as God’s punishment. Now we know that these catastrophes are the result of natural processes. Similarly, people of faith would do better to attribute the mishaps caused by defective genomes to the vagaries of natural selection and other processes of biological evolution, rather than to God’s design.

h/t: Darrel Falk

29 Comments

  1. Posted January 7, 2010 at 5:19 pm | Permalink

    Stephen Meyer discovered this phenomenon while working late one night in the Disco lab: http://www.escape-to-the-seventies.com/images/sports/33-65933-F.jpg

    He soon discarded all other signatures in an attempt to reveal his manifesto entitled *The Selfish Signature*.

  2. Posted January 7, 2010 at 5:43 pm | Permalink

    The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point?

    Because religion relies upon repetition of its “truths” to convince the gullible of the truth where actual facts won’t support that “truth.”

    A subsidiary reason is that Meyer certainly can’t make a case for design, while 500+ pages that most religious people don’t really understand is impressive to these folk.

    And I think that repeating my first post at Biologos is not out of place here:

    Another way of asking Ayala’s questions is, was the “Designer” an adept computer programmer in giving us so many Alu segments, and in adapting Archaeopteryx quite incompletely from its reptilian ancestors, virtually guaranteeing its eventual extinction?

    I put it that way because, for public consumption, Meyer does not hesitate to claim an intelligent and competent designer of life, except that he puts it this way:

    the creator was not only capable of creating great beauty but he was a pretty adept computer programmer

    http://multimedia.play.it/m/audio/27941971/stephen-meyer-interview.htm

    [I checked the audio (starting around 3:20) first this time, and the transcript is quite good, though I improved its readability a bit]

    That’s coming uncomfortably (for IDists) close to a falsifiable, and falsified, prediction about life. No adept programmer put code into cells in order to produce the defects with which we live, and I rather suspect he knows the evidence fails to support such a claim.

    Glen Davidson
    http://tinyurl.com/mxaa3p

  3. Posted January 7, 2010 at 5:45 pm | Permalink

    The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point?

    Because religion relies upon repetition of its “truths” to convince the gullible of the truth where actual facts won’t support that “truth.”

    A subsidiary reason is that Meyer certainly can’t make a case for design, while 500+ pages that most religious people don’t really understand is impressive to these folk.

    And I think that repeating my first post at Biologos is not out of place here:

    Another way of asking Ayala’s questions is, was the “Designer” an adept computer programmer in giving us so many Alu segments, and in adapting Archaeopteryx quite incompletely from its reptilian ancestors, virtually guaranteeing its eventual extinction?

    I put it that way because, for public consumption, Meyer does not hesitate to claim an intelligent and competent designer of life, except that he puts it this way:

    the creator was not only capable of creating great beauty but he was a pretty adept computer programmer

    multimedia.play.it/m/audio/27941971/stephen-meyer-interview.htm

    [I checked the audio (starting around 3:20) first this time, and the transcript is quite good, though I improved its readability a bit]

    That’s coming uncomfortably (for IDists) close to a falsifiable, and falsified, prediction about life. No adept programmer put code into cells in order to produce the defects with which we live, and I rather suspect he knows the evidence fails to support such a claim.

    Glen Davidson
    http://tinyurl.com/mxaa3p

  4. KP
    Posted January 7, 2010 at 6:03 pm | Permalink

    Not bad, but a) what’s with dissin’ Peoria? My mom grew up not far from there! and b) he needed to add a statement to pre-emptively stomp on the lame YEC argument that follows from the “bad design” argument that the minor defects occurred after the fall of Adam.

    • ritebrother
      Posted January 7, 2010 at 9:30 pm | Permalink

      But ID is a scientific theory, right? Specific theological arguments are off limits.

  5. bobo
    Posted January 7, 2010 at 6:11 pm | Permalink

    “It is as if in a book about New York, the author would tell us that New York is not in Europe, and then dedicate most of the book to advancing evidence that, indeed, truly, New York is not in Europe.”

    More to the point, it’s as if the author dedicated the book to arguing that New York is in Africa. (I like this better than his “Peoria” example.)

  6. Posted January 7, 2010 at 6:16 pm | Permalink

    All good stuff, I guess, but Ayala is mistaken if he thinks that God is off the hook for the predictable evils of the evolutionary process merely because he doesn’t micromanage it. God supposedly set up that process, on Ayala’s account, but even a less-than-omnipotent being could foresee the kinds of evils that would inevitably arise. Why not just create a world without those evils in a blink of time, which is well within the capacities of an omnipotent being?

    • Tulse
      Posted January 7, 2010 at 9:31 pm | Permalink

      Why not just create a world without those evils in a blink of time, which is well within the capacities of an omnipotent being?

      Blah blah free will, blah blah Original Sin, blah blah fallen world.

      At least that’s one response that would be offered to Ayala’s argument about the imperfection of Design. The problem with his approach as I see it is that he is ultimately attacking apologetics, which is pretty much playing the other side’s game. The arguments he offers aren’t, for the most part, scientific, but instead theological. Once you go onto their turf, you’re at a disadvantage, especially because the Problem of Evil (and Imperfection) has a long history that started well before evolutionary theory showed up.

  7. DGS
    Posted January 7, 2010 at 6:30 pm | Permalink

    I for one am very glad Ayala noted the rate of spontaneous abortions; that’s long been one of my favorites, it’s so shocking.

  8. Posted January 7, 2010 at 7:03 pm | Permalink

    That first “omipotent” in my last comment should have been “omniscient”. Silly me. The point is that an omniscient God would have known very well what evils would result if it created a universe in which the emergence of intelligent life would depend on an evolutionary process. Why not just create it right, without such evils, from the beginning? God didn’t lack the requisite power or knowledge.

    And that, of course, is the natural expectation of what an all-wise and all-powerful being would do; it’s not at all surprising that that is how Genesis portrays things.

    • KP
      Posted January 7, 2010 at 7:21 pm | Permalink

      …except that things get out of hand anyway. Enough evil crops up that God has to flood the entire world, killing everything in it. Humanity can barely catch its breath and then the Tower of Babel incident forces God to scatter everyone to the four corners (sic) of the earth with mixed up languages. And on and on and on…….

      Seems like God should have been able to forsee all this and create a world in such a way as to prevent it.

      In other words, Meyer’s argument reduces to the YEC argument… Too bad for him.

      • Notagod
        Posted January 7, 2010 at 7:53 pm | Permalink

        You guys are so rude. Come on, can you truthfully say, if you were one of the christian’s gods, you wouldn’t spend a few billion human lives for the opportunity to swing on a stick for a few days?

  9. Posted January 7, 2010 at 7:44 pm | Permalink

    wow, that was great. Ayala’s wildin’… thanks.

    • Posted January 7, 2010 at 10:07 pm | Permalink

      The Galapagos Islands are the most incredible living museum of evolutionary changes, with a huge variety of exotic species (birds, land and sea animals, plants) and landscapes not seen anywhere else.

  10. Posted January 7, 2010 at 11:58 pm | Permalink

    Went digging in the BioLogos blog this appeared on (glutton, yes?) and found this precious comment from Karl Giberson:

    We are actually using the term “BioLogos” so we can avoid constantly having to refer to “evolution,” which has become such a loaded term. The narrow scientific meaning of evolution has been lost as the word has come to include a fully materialistic worldview for many. If Darwin were alive today, I think he would be horrified to see what sorts of meanings have been attached to evolution.

    Theologically, evolution is simply the collection of secondary causes through which God works to create. And we accept the conclusions of science as to how that has happened. But we reject the conclusion that, because science lacks the tools to discover “purpose” that there is no purpose.

    Why can’t he figure out that until science shows there is a “purpose,” you shouldn’t conclude that there is one? Is that so hard?

  11. Ian
    Posted January 8, 2010 at 4:53 am | Permalink

    ‘Before the scientific revolution of the sixteenth and seventeenth centuries, earthquakes, volcanic eruptions, and the like were attributed to direct action by God, so that the tsunami that five years ago killed two hundred fifty thousand Sumatrans might have been interpreted as God’s punishment.’

    Interestingly enough shortly after the tsunami several Iranian Imams went public and said that it was the ‘wrath of Allah’ as a punishment for not being Islamic enough.

    With the next two months Allah dropped a mosque on several heads. I think that was His way of telling them not to so stupid.

  12. Torbjörn Larsson, OM
    Posted January 8, 2010 at 9:18 am | Permalink

    I experience several reactions to this.

    First, Ayala has a terrific simile in the city analogue. Then it goes downhill fast into apologetics as Tulse notes. Apologetics that isn’t as persuasive when you know that the same Biologos site is a collection house for theistic biologic propaganda (aka “theistic evolution”).

    Second, about that collection house. Maybe we should have a discussion about strategy, as ID has become marginalized in the media and theist propaganda remains. It serves no good purpose to shore up media responses to ID if it isn’t important in media.

    In fact, it is likely counterproductive as people thinks it is worth arguing, _and_ IIRC measurably tend to remember the subject, not the argument. I.e. they may end up remembering you as creationist or at least positive.

    One can still work against designism’s insidious tricks to wedge religion into science and education of course. This is one of those cases, I believe.

    But perhaps a better focus of resources now would be to take the general stand against apologists like Ayala and Collins/Biologos. FSM knows that what they lack in balls is made up for in tacking sauce and gravy onto theist “science”. Even their chosen name “theistic evolution” is an appalling misnomer, it is neither evolution as in natural process nor even valid theory (as it is rejected by parsimony in testing against evolution). It is, as I noted above, purely accommodationist propaganda based on apologetics.

    Third, on this topic did you all note the press release on the observation of bornavirus genetic material in human DNA [Tomonaga et al material in Nature]? Apparently these viruses have the same capability to insert genetic material as retroviruses. By now 8 % of human DNA is viral elements: “Retroviruses are the only group of viruses known to have left a fossil record, in the form of endogenous proviruses, and approximately 8% of the human genome is made up of these elements1, 2″

    I think this adds nicely to the apologetic “gods aren’t messy designers” ‘argument’. At least it should annoy designists. “Hello, I’m Torbjörn and I’m 1/10th viral.”

    • Torbjörn Larsson, OM
      Posted January 8, 2010 at 9:25 am | Permalink

      Er, to annoy designists that should be: “Hello, I’m Torbjörn, I’m 1/10th viral – and so are you!”

  13. ennui
    Posted January 8, 2010 at 10:47 am | Permalink

    I had the seriously bad sense to click through to the BioLogos site blog–that little TE coffee klatch run by Templeton–and it contained way, way, way too much Kwok to stay for long.

  14. Leigh Jackson
    Posted January 8, 2010 at 3:21 pm | Permalink

    I’ve not read Ayala’s book “Darwin’s Gift to Science and Religion” but he appears to see natural selection as the solution to the problem of natural evil.

    If he is a true NOMA believer then God must entirely disappear from the natural world. Well that’s better than trying to implicate Him/Her (male and female created he/she them in his/her own image) in quantum mechanics or the anthropic constants, as some have attempted in BioLogos land.

    He must presumably tend towards apophatic theology. I should read the book, I suppose.

  15. jose
    Posted January 8, 2010 at 6:56 pm | Permalink

    I don’t like that “God wouldn’t do that, would he?” kind of argument.

    The Christian God as described in the Bible is clearly a psycho. Of course he would do anything you can imaging for no reason. Maybe he did all the stuff Ayala describes just to fuck us up.

    In my opinion, biological arguments, like fulfilled predictions of hypotheses based on evolution, are much more effective.

    • jose
      Posted January 8, 2010 at 6:58 pm | Permalink

      **imaging–>imagine.

  16. Posted January 9, 2010 at 9:09 pm | Permalink

    I just can’t understand why he stopped there. By the same reason God can’t be the designer of DNA, he can’t be the creator of the universe either.

  17. Brian McCormack
    Posted February 12, 2010 at 6:44 pm | Permalink

    Once you concede, as most of you seem to,that the “information” in the genome isn’t the product of chance, there has to be another explanation for its being there. Meyer maintains that the observable constant conjunction of information and intelligence makes his explanation better than any of yours. I think he’s got you. That’s why most of you rant like village atheists who learn that no one in the village takes them seriously because they have no explanation for existence. Meyer has an explanation based on human experience. You’ve got nothing better. In fact, you’ve got nothing at all to counter his hypothesis but bristling resentment against all things spiritual. Expiate your anger and try to comport yourselves as real scientists!

    Oh,and have a nice day!

    • Mike McCants
      Posted July 9, 2010 at 1:07 pm | Permalink

      “Once you concede, as most of you seem to, that the “information” in the genome isn’t the product of chance”

      This is a typical creationist misunderstanding. The concession is that the emergence of life is not due to chance ALONE. That is why Meyer is seen as simply beating a strawman to death for a hundred pages. He is arguing that chance ALONE is not sufficient to explain the emergence of life. Scientists agree. So what?

      “there has to be another explanation for its being there”

      Of course. But a supernatural explanation (god did it) is no explanation at all. The scientific explanation is that there were certain “properties” of the “environment” that meant that chance was not working ALONE. Meyer wishes to trick you into thinking that life could not have originated naturally. But that’s a negative assertion. He can’t prove that.

      “Meyer maintains that the observable constant conjunction of information and intelligence”

      Such a “conjunction” is observed today with human intelligence. What “intelligence” existed 4 billion years ago when life originated? He has no evidence that any such “intelligence” existed 4 billion years ago.

      “Meyer has an explanation based on human experience.”

      Nope. He has nothing. “Human experience” does not apply to 4 billion years ago.

      “you’ve got nothing at all to counter his hypothesis”

      His hypothesis is not scientific, so it’s simply ignored. The scientific counter is that scientists continue to explore the question of the origin of life. Will they understand how it could have happened in another hundred years or so? Come back then and we’ll talk about their success or failure. But the point is – that we don’t understand this yet is no reason to jump to the conclusion that “god did it”.

      • Brian
        Posted July 10, 2010 at 9:24 am | Permalink

        Mr. McCants:

        Maybe Myer doesn’t have proof of intelligence 4 million years ago. But this isn’t an argument about when intelligence appeared (and I don’t presume to speak for Myer on this.) For me, this is an argument about the nature of this intelligence. You know that, ultimately, that’s what this argument is really about! And you also know that there is a plausible inference of a self-aware creator that you can never accept as a matter of strict obedience to deep, left-wing religious fundamentalist dogma.

        Once you concede, as you do,that: “The scientific explanation that there were certain ‘properties’ of the ‘environment’ that meant that chance was not working ALONE” (Emphasis yours.),isn’t the scientific onus on you to support your hypothesis with empirical proof of the intelligence with which chance was “working” in the environment?. Or do you accept the chance-intelligence partnership as a matter of faith, because you can’t otherwise explain the complexity of life forms? Do you and your fellow members of the Faith-Based Science Community think that the powerful intelligence responsible for the dazzling diversity and complexity of life had self-awareness and lived in a kind of heaven, or was it brilliant, but unconscious, and lived on Earth (without knowing where it was)and then inexplicably vanished – leaving you and its partner “Chance” with confused looks on your faces?

        When, as you propose, in a hundred years, your Faith-Based Science Community fulfills the prophecy of its Book of Revelations, will I, at my quite advanced age, experience the “Rapture”?

        In sum, until you identify Chance’s partner, your non-explanation is no better than the supernatural one. In fact, its less intellectually satisfying, because its inertness is inelegant and intuitively unappealing, unlike the supernatural explanation.

        On what day of the week does your Church hold services? When do you observe your Feast of the (Groundless) Assumption?

        • Torbjörn Larsson, OM
          Posted July 10, 2010 at 10:52 am | Permalink

          I wouldn’t have ordinarily answered, since the original comment is such a strawman.

          No one is saying that the information in the genome, which we know is picked up from the environment, is a product of chance, but of evolution. No other explanation is needed, and we know that for a fact.

          Now the argument is expanded to “complexity of life forms”. What would that complexity be?
          While evolution isn’t simple due to all its contingencies it is simple in principle: it takes functional (surviving) populations to functional ones.

          Evolution can as well accumulate functional complexity (say, as multicellulars interconnected organs) as get rid of it (say, as parasites). Neither the process nor its substrate (populations) depends on any defineable complexity, nor does it need to result in such, nor is such a result unexplainable.

          That later is another strawman.

          Finally, not only is evolution an observable fact, but that it is a basic part of todays biology science is too. So we end with a third strawman. Not surprisingly, because that is all anti-scientists have on science.

          [That, and quotemining of course; preferably with a touch of gish gallop.]

  18. Daniel
    Posted July 20, 2010 at 4:28 pm | Permalink

    I’m afraid that Mr. Ayala must renounce his own evolutionist position based on his own professed belief that “chance, by itself, cannot account for the genetic information found in the genomes of organisms.” That is precisely what evolution espouses. Natural selection, it is true, is not random. Unfortunately, natural selection does not play a formative role in mutations. It merely propagates beneficial mutations. Mutation, not natural selection, is what presumably generates the information, and mutation is purely random.

    Stephen Meyer already demolished these counterarguments in a debate with Dr. Peter Ward of the University of Washington. You can watch the debate here:

  19. Bob O
    Posted August 22, 2010 at 4:23 am | Permalink

    Mr. Ayala has degrees, awards, and has written a great deal; yet rather than deal with Stephen Myers basic thesis that the cell shows evidence of design he falls back on sophistry. Most of us know about New York, but relatively few of us have any concept of how a cell replicates. Mr. Myers did not define the source of the design. Mr. Ayala does define the source and then goes on to offer proof that the source as he defines it is somehow inadequate in the design. It’s as though he’s arguing with himself kind of like cheating at solitaire. Now, for my opinion: I thought Signature in the Cell was long and as for the designer, I think there were likely many designers rather than one.


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