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A Rejoinder to Part II of Stephen C. Meyer’s Response to Francisco Ayala

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March 11, 2010 Tags: Design

Today's entry was written by Darrel Falk. You can read more about what we believe here.

A Rejoinder to Part II of Stephen C. Meyer’s Response to Francisco Ayala

In Part 2 of Stephen Meyer’s response to Francisco Ayala’s critique of the Intelligent Design movement in general, and of Signature in the Cell in particular, Meyer focuses primarily upon Ayala’s statement that, “there are lots and lots of DNA sequences that are nonsensical.”

First, I would like to note that one cannot help but be impressed with how current Meyer is with regard to this literature. He cites ten articles from 2009 and three from this year. Clearly he and his colleagues are keeping up with the literature. This is just one example of why I have come to conclude that the ID movement ought to be considered a scientific movement.

Another example is Meyer’s book itself. In the book, Meyer, quite eloquently in my opinion, demonstrates that his approach fits within the bounds of how historical science is done. The fact that he spends time carefully analyzing the scientific literature for evidence of function is further indication that they are doing science. Their Intelligent Design model predicts that the DNA in the human genome (and other organisms) is fully functional, and Meyer and his colleagues are carefully scrutinizing the scientific literature to see if it is.

Although I am convinced they are wrong on many counts, I appreciate that they are doing science (however good or bad it is) and I hope the scientific community will engage them on the basis of that science and not on the basis of rhetoric (theirs and ours!). Elements of their work are clearly rhetorical, and I alluded to one example of that in yesterday’s post. Regretfully, there are times when I slip into that mode as well. I am trying my best to stay focused on the issues—if you catch me doing otherwise, you should feel free to call me on it.

Since Meyer used technical language unfamiliar to many non-scientists, I want to refer readers to an excellent new book, Inside the Human Genome: A Case for Non-Intelligent Design, by leading evolutionary biologist, John Avise. Like Ayala, Avise argues that biology informs theism, and most certainly does not negate it. If there is any one science-related book I would urge our audience to read in the upcoming year it would be this one. Avise clearly lays out the philosophical and theological work we Christians have yet to do, based on detailed but accessible descriptions of genomic data.

Meyer spends considerable time disputing what he calls “Ayala’s claim” that Alu1 sequences are distributed randomly. I’ve reread Ayala’s post several times trying to find what makes Meyer think Ayala claimed this. Put simply, he doesn’t say it nor does he imply it. He does say that on average there are about 40 copies of Alu sequences between every two genes, but this is simply a fact. Meyer spends considerable time trying to show Ayala is wrong about something he didn’t say. I don’t know why he does this and don’t consider to be helpful to the discussion.

There are about a million Alu sequences (see footnote) scattered around the human genome. They constitute about ten percent of all letters in the DNA code. Meyer points out that a number of functional regions have been discovered within Alu sequences. He’s right. But this comes as no surprise to biologists—evolutionary theory certainly predicts that some portion of these sequences would take on useful functions over time.

However, there is no question that many Alu sequences really have no function. As Avise explains in his book, and as Ayala mentions in his post, most of these elements are almost certainly of no value to cells. On the contrary, these extra sequences can cause serious problems. In Avise’s words, “To the best of current knowledge, many if not most of these repetitive elements contribute not one iota to a person’s well-being. They are well-documented however to contribute to many health disorders.”

Alu is only one of many kinds of repetitive elements in the genome. The actual number of DNA letters devoted to all mobile elements (those which move from one location in the genome to another) is at least 1.3 billion! That’s 45 percent of the genome. In addition, non-mobile elements represent another huge portion.

For sure, plenty of magnificent “sense” is scattered throughout the genome, coding for absolutely marvelous things—like how to make the brain, for example—but this still doesn’t negate the fact that almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful.

Since many of our readers are not experts and they depend upon authorities, I would like to conclude with a request. If you hold a faculty position in molecular biology at a research university (or you know of someone who does), and you think that my portrayal (or Avise’s and Ayala’s) of the current state of our knowledge about this is inaccurate, please send an email to info@biologos.org. We will post the names of any dissenting molecular biologists who hold faculty positions in research universities on our website. I am aware that ID folk will simply say that such scientists will not respond because of the need to be clandestine in order to protect their careers. However, my experience is that tenured faculty are not afraid to say what they think; indeed it is that quality that especially distinguishes the faculty I have known over the years.

1. Alu is a short stretch of DNA code. There are three billion letters of code in the human genome. One Alu sequence is about 300 letters long. There are about a million copies of this short sequence scattered throughout the genome.


Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.

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Bilbo - #6704

March 12th 2010

In the interest of starting an fight, Mike Gene has offered extensive arguments that both Alu elements and introns have played significant roles in promoting the evolution of metazoan life.  I think Nick Matzke needs to do more than dismiss Mike as an “excitable scientist” who hasn’t read enough evolutionary biology.  Arguments, Nick, arguments.


Mike Gene - #6708

March 12th 2010

Hi Nick,

“OK fair enough, I was over-interpreting.”

Thanks for saying this.  And no, I wasn’t trying to imply evolutionary theory should be able to predict from scratch exactly what proportion of DNA will be functional, without any input data etc., and that this is a flaw if it can’t.  I’m just pointing out that it is not very impressive to predict we will find both functional and non-functional sequence.


Mike Gene - #6709

March 12th 2010

Hi Nick,

You write, “And then the whole idea of Alus or other elements having “evolutionary functions”—i.e. “their function is in helping species to evolve”—is, at the very least, tremendously controversial, even though it is popular with various excitable scientists who haven’t read enough evolutionary biology to know that panselectionism is bad and we always have to consider non-adaptive hypotheses along with adaptive hypotheses for organismal feature X.”

Your point about panselectionism and non-adaptive hypotheses is a good one.  At least three things fall out of this point.

First, Wikipedia describes panselectionism as “the idea that selection is the only force strong enough to explain evolution, relaying random drift and mutations to minor roles.”  So where did this bad idea come from?  Let’s just say that I think one can make a reasonable case that panselectionism emerged naturally from the Modern Synthesis (which some people, even today, equate with the “theory of evolution”).


Mike Gene - #6711

March 12th 2010

Second, the rise of non-adaptive hypotheses and the decline of panselectionism helps us see the whole junk DNA debate in a more interesting light than the creationist debates – the existence of junk DNA helps to illustrate that natural selection is not always in play during evolution.  Natural selection, which is the only viable designer-mimic, is not omnipresent.


Mike Gene - #6712

March 12th 2010

And that leads to the third, and most interesting, point.  If we step back and consider evolution as function to generate more complex life forms, then it’s becoming more clear that the success of evolution is dependent on selection and neutral forces alternatively working in series.  In fact, this is what scientists have also found to be true when it comes to designing new protein activities by using in vitro evolution.  Paradoxically, this means that that if evolution is to spawn something like mammals, it needs to go through phases which suspend the role/reach of natural selection.  Those non-adapative processes, seen in the context of life’s architecture, may be a very clever (and non-intuitive) aspect of a design strategy.  The intelligent use of chance.


Mike Gene - #6720

March 12th 2010

Hi Dennis,

You write, “It is for this reason that I tend to focus on unitary pseudogenes when I present to non-specialists - especially examples like those devoted to non-mammalian life (e.g. the vitellogenin pseudogene in the human genome - click my name above for a link to a paper on this pseudogene).”

Indeed.  In fact, if I understand the basic argument that is being proposed by Meyer, it is that there is no such thing as junk DNA.  If that is the argument, one counter-example will suffice, in addition to being more easily communicated.


Edward T. Babinski - #6726

March 12th 2010

Does Meyers discuss the evidence for common ancestry of humans and apes as found in our genes? Does he discuss retroviral and other pseudogenes shared by humans and great apes? Or the hundreds of genes for smell that are no longer functioning in both humans and great apes, but still function in monkeys?

Meyers must FIRST discuss the human ape ancestry issue, since the evidence there is even clearer than in the case of “uses for junk DNA.” 

If Meyers does come to agree with Behe that the evidence is strong in the case of humans and apes sharing a common ancestor, then let Meyers admit is as Behe eventually came to admit outright. This is a very important question that the Discovery Institute needs to discuss amongst its own members. Todd Wood, as someone else pointed out, has also admitted creationism’s failure to account for the evidence of genetic common ancestry between humans and great apes. In fact, there are species of cats with greater genetic divergence than humans and chimpanzees, and in fact, there are near-identical sibling species of fruit flies with more genetic diversity between them than there exists between humans and chimpanzees.


Edward T. Babinski - #6728

March 12th 2010

Two former senior members of the Discovery Institute left it. One of them even wrote a detailed rebuttal to the film, Expelled. The other, Michael Denton, seems to have been the great-grandfather of the I.D. movement itself with his first book, by the time of his second book he’d learned so much about genetics that he could no longer reject the genetic evidence in favor of common ancestry, and he was also dissatisfied with the Discovery Institute’s continuing pandering to young-earth creationist arguments concerning the age of the earth and cosmos.


Edward T. Babinski - #6729

March 12th 2010

To sum up: The Discovery Institute cannot agree on whether science can tell us the age of the cosmos is a couple thousand years old or over 10-billion years old.  I guess science is just one mixed up enterprise according to the Discovery Institute!  What does Meyers say about the age of the earth? Surely the pirma facie scientific evidence is far more conclusive concerning the earth’s vast age than it is concerning such matters as “hypothetical uses for junk DNA.”

Likewise concerning creationism. Can the Discovery Institute agree on whether or not new species popped into existence whole out of thin air by the Designer’s will and power, or whether species were molded one gene or gene sequence at a time?

Can the Discovery Institute people agree on what the prima facia scientific evidence favors concerning the above two matters? Certainly the weight of all the scientific evidence stands for something relatively plain concerning the above two matters, far more plain that the question of “hypothetical uses for junk DNA.”

How USEFUL or USELESS is the Discovery Institute itself when it comes to even agreeing among themselves what the prima facia evidence is concerning the weight of scientific evidence today?


Bilbo - #6735

March 12th 2010

Hi Edward,

1) I would say the “great-grandfather” of ID was Sir Fred Hoyle, who argued that the first cells were intelligently designed, in his book, Evolution from Space.

2)  Behe didn’t just “admit” to common descent.  He argued for it extensively in his book, The Edge of Evolution.

3) I think most of the other leaders in the ID movement reject common descent.  So things like the existence of shared pseudogenes between chimps and humans would be a problem for them.  Perhaps that is part of the motivation for rejecting the idea that there is much junk DNA.

4) I think Meyer accepts an old earth and “limited” common descent, whatever that means.  Some leaders accept an old earth.  Some don’t.

5)  Mike Gene, who does not consider himself to be part of the ID movement, has been developing his hypothesis of “Front-loaded Evolution,” which is the view that the first cells were intelligently designed and loaded with information to make evolution of metazoan life more probable.  Check out his site:

designmatrix.wordpress.com


Gordon J. Glover - #6790

March 14th 2010

In his book, Signature in the Cell, Meyer uses the sucess of Big Bang Theory, and the prdictions it made like cosmic background radiation and Hubble red shift, as examples of historical science.  He also uses the example of plate techtonics and radiometric dating.  So I would say that at least when it comes to the age of the earth / cosmsos, Meyer is not a history denier.


Bilbo - #6819

March 14th 2010

Richard Sternberg’s rejoinder to Darrel Falk’s rejoinder:

http://www.evolutionnews.org/2010/03/asking_darrel_falk_to_pick_a_n.html


Bilbo - #6820

March 14th 2010

From Sternberg’s reply:

“So the true number of genes in our DNA is probably >450,000 + 25,000 = >475,000. What is more, these >450,000 genes cover more than 88.5% of our 3 billion genetic letters. That’s right—most, if not close to all, of our chromosomal DNA consists of different types of genes that have only recently been discovered.

How do these facts square with this comment made by Falk?


  but this still doesn’t negate the fact that almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful.”

Is he right?


Nick Matzke - #6824

March 14th 2010

Sternberg is drastically overinterpreting his sources, the article he cites says that there *might* be *as many as* 450,000 genes, and Sternberg converts this to “probably” *more than* 450,000.  And the actual article does an analysis, and IIRC re-finds the few hundred known noncoding RNAs, and a few hundred more possible new ones, and doesn’t reach any dramatic conclusion about hundreds of thousands of others, and furthermore notes seriously the possibility that a lot of them are transcriptional noise.

In any event, the hypothesis that 85%+ of the human genome is actually RNA genes needs to explain why various vertebrates get by with only 10% as much.  Sternberg’s brain apparently doesn’t even have the bare capacity to acknowledge the existence of widely varying genome sizes, let alone the implications of this well-known fact for hypotheses like the idea that the genome is actually all genes even though it looks like half of it is derived from parasitic repetitive elements.


Mike Gene - #6840

March 15th 2010

Apart from the comment about Sternberg’s brain, I think Nick’s point about the variability in genome sizes, coupled with the mass of repetitive elements, is a very powerful one.  In fact, it should be the very focus of discussion if one is to deny the existence of non-functional sequences.  Nick is not laying out some side issue or knee-jerk criticism; he is spelling out the real, core roadblocks. He’s saying, “Step back from arguments about this sequence or that sequence, from arguments about gene numbers, and look at the big picture.”  Put it this way.  If the entire human genome plays a functional role in the cell/organism, then why in the world does the puffer fish get by with a much more compact genome that is missing huge spans of “junk DNA?”  And why do salamanders have something like 40X more DNA than humans (if I recall correctly)?


Arthur Hunt - #6884

March 15th 2010

the hypothesis that 85%+ of the human genome is actually RNA genes

Sternberg seems to be including two groups of “RNA genes” that are not consistent with his claims of function: 

1.  “RNA genes” derived from those parts of the genome that are transcribed, but whose RNA products are almost immediately broken down.

and 2. the parts of the genome that are actively silenced by small RNAs that are transcribed and converted to siRNAs and the like.

Remove these classes of “RNA gene” from the discussion and his 85% number is a large overestimate.

Also, I suspect he is double-counting, at least in the cases of non-coding RNAs that are derived from promoter regions but do not become canonical mRNAs.  Several of such cases have been discovered, but they are better viewed as a part of the corresponding protein-coding gene.

Some essays that touch on these matters to various extents:

http://aghunt.wordpress.com/2008/07/21/junk-to-the-second-power/

http://aghunt.wordpress.com/2008/12/13/strange-things-at-promoters/

http://aghunt.wordpress.com/2009/02/22/more-strangeness/


Bilbo - #7093

March 17th 2010

I’ve noticed that Sternberg is continuing to argue his case: 

http://www.evolutionnews.org/2010/03/ayala_and_falk_miss_the_signs.html


Bilbo - #7094

March 17th 2010

Bilbo - #7192

March 19th 2010

Glad to see the comment section is available again.  Sternberg continues his case here:


http://www.evolutionnews.org/2010/03/beginning_to_decipher_the_sine.html#more


Argon - #7265

March 20th 2010

Does anyone else find it odd that Sternberg seems to approach the genome from an almost pure selectionist point of view?


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