Science and Culture Today | Page 1229 | Discovering Design in Nature

I have long questioned the assumption that most genomic DNA sequences are “nonsensical” or “junk.” And given the data that have emerged over the past seven or so years, a functionalist view of genome has robust empirical support. It is for this reason that I think many of the arguments presented by the Biologos Foundation are “wrong on many counts,” to borrow a phrase from Darrel Falk.

Here is an example. While reading the “critique” of Steve Meyer’s book, Signature in the Cell, by Francisco Ayala, a number struck me that I know to be incorrect. The integer that I am referring to is “25,000” and it is claimed to be the known tally of genes in our chromosomes:

The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences…

Now, the problem with such a statement is this: While there are ~25,000 protein-coding genes in our DNA, the number of RNA-coding genes is predicted to be much higher, >450,000.¹ Some of the latter range in length from being quite short–only 20 or so genetic letters–to being millions of letters long. Since 2004 we have learned that over 90% of our DNA is transcribed into RNA sequences at some developmental stage, in different cell and tissue types.^{2, 3, 4} (Our brain cells are unusually rich in these non-translated RNAs.) These RNAs are then processed into regulatory and structural sequences of all sizes.^{2, 3, 4}

For over a decade, mathematician Jeffrey Shallit has been an outspoken critic of intelligent design. Recently, in a series of blog posts, he has attacked Stephen Meyer’s book Signature in the Cell (SITC) for what he sees as a variety of shortcomings. Some of Shallit’s criticisms merit careful attention, which we’ll present here in weeks to come.

Other criticisms, however, are fluffy confections, failing to achieve even the slightness of what Hume called “mere cavils and sophisms.” Let’s look at one such bonbon of sophistry, Shallit’s claim that weather forecasting represents a devastating counterexample to SITC’s argument that complex specified information is, universally in human experience, produced by a mind or intelligence.

I’ve followed the back and forth between Francisco Ayala and Steve Meyer with interest. I happened to have just read Meyer’s book Signature in the Cell when I first saw Ayala’s commentary/review on it at the Biologos Foundation website. My initial response was that Ayala obviously hadn’t read the book, and, as a result, made some embarrassing mistakes that any reader of the book would recognize.

Darrell Falk at the Biologos Foundation was apparently responsible for inviting Ayala to comment on Meyer’s book, and has been drawn into the debate.

He published the first part of Meyer’s response to Ayala, but not without first offering his “background comments” about the debate. (I think David Klinghoffer has said what needs to be said about that.) The Biologos Foundation is committed to the “science-and-religion dialogue.” In my opinion, however, they have a peculiar way of fostering dialogue.

Earlier this week, the Biologos Foundation posted part of Stephen Meyer’s response to a review of his book Signature in the Cell by evolutionary biologist Francisco Ayala. Because Biologos decided to introduce its partial posting of Meyer’s response with a misleading and inaccurate preface, and because Biologos further decided to rebut part 1 of Meyer’s response before readers had a chance to read his entire response, we have decided to make the rest of Dr. Meyer’s response available on his website immediately. Just as readers were allowed to read Dr. Ayala’s critique in its entirety before reading Dr. Meyer’s response, we think it only fair that readers should have the opportunity to read Meyer’s entire response (which was written in Read More ›

The Discovery Institute has invited Dr. Francisco Ayala to debate the thesis of the book Signature in the Cell: DNA and the Evidence for Intelligent Design with the book’s author, Dr. Stephen Meyer. Those who’ve been following the debate between Meyer and his critics know that there has been a bit of back and forth since Ayala was invited to critique SITC on the Biologos website. Meyer has responded this week, with the first of two parts on the Biologos site. iscovery Institute would like to initiate a full-fledged, official debate between the two, and so we have already sent the following invitation to Dr. Ayala. Dear Professor Ayala: I am writing to you in my capacity as the Director Read More ›

Last updated 3/9/10, 7:00 pm.

As a former book review editor (at National Review), I take a professional interest in book reviews and all the things that can go right or wrong with them. I confess, though, I’ve never seen anything quite like the treatment of Stephen Meyer’s book, Signature in the Cell: DNA and the Evidence for Intelligent Design, on BioLogos, the curious website funded by the Templeton Foundation and specializing in Christian apologetics for Darwin. The site published what was clearly, unambiguously written to look like a review by biologist Francisco Ayala that, as Steve Meyer pointed out already, actually gave every evidence that Ayala had not read the book. (My colleague Dr. Meyer thinks Ayala did read the Table of Contents, but on this I must disagree.)

On what did Ayala base his views about Signature? This is a bit of a mystery. BioLogos president Dr. Darrel Falk is unstinting with fulsome praise for Ayala (“one of Biology’s living legends”). Falk claims he actually asked Ayala to respond to Falk’s review of Signature. Falk purports that in publishing Ayala’s review, he mistakenly failed to introduce it with the disclaimer that Ayala was reviewing Falk’s review, not Meyer’s book per se. Yeah, sure. Falk’s review did not provide Ayala with his absurd misrepresentation of Meyer’s argument. Instead Ayala gives every impression of having derived that from his own assessment of the book itself. As Ayala claims,

The keystone argument of Signature of the Cell [sic] 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?

Yet that is certainly not the keystone argument of Signature, and Meyer in fact spends only 66 pages (out of 613) on it. But that is not really the point here.

What’s notable is that Falk in his own review, whatever its other faults or merits, never claimed that Signature is all about proving that “chance by itself, cannot, account for the genetic information found in genomes.” Falk doesn’t mention the word “chance.” So where did Ayala get his mistaken notion? All one can say is, not from the book, which he patently didn’t read, and not from Falk. Indeed, Ayala in his essay does not mention Falk or Falk’s review. Clearly, Ayala wanted readers to think he was reviewing Signature in the Cell–or Signature of the Cell as he repeatedly calls it. Thus, for example, he commends Meyer for his “elegant prose.” The idea that Ayala was merely acting in good faith on Falk’s assignment of responding to Falk’s review is hardly believable.

Last week’s New York Times article on academic freedom legislation makes a false assertion that the Selman v. Cobb County Board of Education claimed it was illegal to single out evolution in a curricular policy. The NY Times article wrongly states: The legal incentive to pair global warming with evolution in curriculum battles stems in part from a 2005 ruling by a United States District Court judge in Atlanta that the Cobb County Board of Education, which had placed stickers on certain textbooks encouraging students to view evolution as only a theory, had violated First Amendment strictures on the separation of church and state. Although the sticker was not overtly religious, the judge said, its use was unconstitutional because evolution Read More ›

Earlier this year, evolutionary biologist Francisco Ayala critiqued Stephen Meyer’s book, Signature in the Cell, in an invited essay for the Biologos Foundation website. Dr. Meyer has now responded with the first part of a two-part response, “On Not Reading The Signature in the Cell.” In this first part, Meyer argues that Ayala unfortunately does not appear to have read Signature in the Cell, and so his effort to refute the book falls flat. Indeed, Ayala’s “review misrepresents the thesis and topic of the book and even misstates its title.” Read more here.

The evolution of antibiotic resistance is typically the result of small changes allowing for survival in a microbe or other organism under special circumstances where the organism faces extremely strong selection pressure due to the presence of some antibiotic drug. In other cases, it is the result of the transfer of pre-existing antibiotic resistance genes from one microbe to another, and the selection of such microbes in an environment containing antibiotics. Even in the first example, evolution does not produce a truly new function. In fact the change produced often makes the microbe less fit when the antibiotic is removed–it reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost Read More ›

The recent front page New York Times article on academic freedom legislation offers a stark reminder that the intelligentsia is very worried about the prospect of teachers gaining academic freedom, as a bill presently in the Kentucky legislature would allow, “to help students understand, analyze, critique, and review scientific theories in an objective manner, including but not limited to the study of evolution, the origins of life, global warming, and human cloning.” From 2008-2009, 12 academic freedom bills were submitted into state legislatures, including Florida, Alabama (2), South Carolina (2), Missouri (2), Michigan, Louisiana, Oklahoma, Iowa, and New Mexico. Now in 2010, there are 3 bills already, including bills in Kentucky, Missouri, and Mississippi. The Kentucky bill contains an excellent Read More ›