Despite the old canard that the only people to question Darwinian evolution are evangelical Protestants (a canard regurgitated yet again last week by the New York Times), the fact remains that Darwin dissenters can be found among thoughtful scientists and other people from all religions and walks of life. There have been many Catholic dissenters from Darwin, from St. George Jackson Mivart and G.K. Chesterton a century ago to biochemist Michael Behe and philosopher/theologian Benjamin Wiker today. There also have been numerous Jewish dissenters from Darwin. David Klinghoffer writes about one of them in an essay for First Things on Rabbi Samson Raphael Hirsch (1808—1888): Hirsch insisted again and again that God must be understood as acting with complete freedom Read More ›
Brain Cancer Chromosomes. Chromosomes prepared from a malignant glioblastoma visualized by spectral karyotyping (SKY) reveal an enormous degree of chromosomal instability -- a hallmark of cancer. Created by Thomas Ried, 2014
In his recent response to Stephen Meyer’s Signature in the Cell, Francisco Ayala claimed that repetitive portions of our DNA called “Alu” sequences are “nonsensical.” Ayala wrote: “Would a function ever be found for these one million nearly identical Alu sequences? It seems most unlikely.” In his response to Ayala, Meyer showed that Ayala is factually wrong about this. According to recent technical papers in genomics, Alu sequences perform multiple functions.
In a rejoinder to Meyer, Darrel Falk defended Ayala and claimed although “a number of functional regions have been discovered within Alu sequences,” there “is no question that many Alu sequences really have no function.”
In my last blog, I showed that the vast majority of the genome is transcribed, either into protein-coding genes or into regulatory RNAs. The technical literature — some of which I cited in that blog — reports that the genome is an RNA-coding machine. Clearly, most DNA really does have function.
In this and subsequent posts, I will provide other sorts of evidence that so-called “junk DNA” is not junk at all, but functional.
We have all seen a variant of the plot in a movie. A strange signal appears–in one film it is a recurrent wireless telegraph code that is transmitted from San Diego after a global nuclear holocaust (On the Beach); in another it is radio transmissions from deep space (Contact); in still another it is crop circles (Signs). As we all know, the first signal turns out to be due to a Coca-Cola bottle: Wind blowing on a window shade next to the bottle results in the latter being occasionally nudged, which sometimes leads to a telegraph key being tapped by the very same. But in the second movie, the signals received turn out to contain a complex set of encrypted data with an intricate mathematical pattern — they are the specifications for building a device that can travel through space-time wormholes, sent from a friendly alien civilization. So also are the crop circles in the third film messages from an extraterrestrial race, except that the designs portend an attack on humanity.
Now, the reason we are drawn in by such stories is obvious: The signals have serious implications for the characters. It could mean the survival of mankind after a thermonuclear war; it could mean that there are other sentient beings in the universe. That is why we would quickly lose interest in the plot if, say, in every scene where a scientist appeared before an important governmental group and said, “The outer space signal contains over sixty thousand, multidimensional pages of complex architectural plans,” she were countered with, “This is exactly the predicted outcome of billions of years of cosmic evolution — you see, random interstellar events lead to just this kind of complex specified information…we are not impressed.” We would want our money back.
My purpose for bringing up this subject is that I have a mysterious genomic signal for you to see — which I will show you tomorrow. We detected it some time ago and it has aroused the interest of some genomicists, but you will find no mention of it books such as Francis Collins’s The Language of God — which is peculiar. But I have another aim in mind, too, for broaching this possible chromosomal code: A key first indicator of functionality is a distinctly non-random pattern. The persistence of a distinct signal in different contexts often suggests functional constraints are operative–that is why genomicists look for them. And since I want to focus on the global functions of such Short Interspersed Nuclear Elements (SINEs) as human Alus and their mouse and rat counterparts, their far-from-random placement cannot be elided. In fact, I will argue that it is a critical part of the genome story that the folks at Biologos aren’t telling you.
To prepare for the mysterious genomic signal, though, I want to draw your attention to this figure:
What you are seeing are the relative densities of Long Interspersed Nuclear Element (LINE) L1s and SINEs along 110,000,000 DNA letters of rat chromosome 10.1 (From Fig. 9d of reference 1.) The x-axis represents the sequence of letters in DNA and the blue line indicates where SINEs occur — what Ayala calls “obnoxious sequences” that are supposedly due to “degenerative biological processes that are not the result of ID.” The red line indicates where LINE sequences occur.
By the way, Francis Collins is a principal author of the Nature paper where these results are published.
Both LINEs and SINEs are types of mobile DNA, namely, retrotransposons, and together they can comprise around half of the mammalian genome. As should be clear from the figure, LINEs tend to peak in abundance where SINEs taper off and vice versa (see the blue boxes). We have known about this pattern since the late 1980s, so it is no surprise to someone who has been following the subject. What should be surprising to anyone, however, is that the same machinery is responsible for the movement of both types of retrotransposon. A complete L1 element encodes the proteins necessary to “reverse transcribe” an RNA copy of itself back into DNA, and to insert the generated duplicate into some chromosomal site. SINEs, by way of contrast, rely on the L1-specified proteins for all their copying and pasting routines.
This compartmentalization of LINEs and SINEs along the mammalian chromosome can also be detected by using molecular probes for L1 or Alu(-like) sequences2:
For junkety-junk elements that can make up fifty percent of a mammal’s mostly junkety-junk genome, the rule seems to be: Location, location, location.
Interestingly, this higher-order pattern cannot be detected when small sections of DNA are examined. It only becomes evident when stretches that are millions of nucleotides long are studied. This banding pattern has been known for decades–but for some reason it is rarely (if ever) discussed by “junk DNA” advocates. The bands on the chromosome arms fall into two general categories:
If the intelligent-design side in the evolution debate doesn’t receive the support you might expect from people who should be allies, that may be because they haven’t grasped why the whole thing matters so urgently. I got an email recently from a journalist whom I’d queried on the subject. “All told, I’m on the ID side of the debate,” he wrote, “but it isn’t a pressing interest for me.”
Anyone who similarly doesn’t quite “get it” should read our friend and colleague Wesley J. Smith’s new and important book on the animal-rights movement, A Rat Is a Pig Is a Dog Is a Boy. If you follow conservative journalism, you’ve likely heard about the book from the contentious deliberation it has received in National Review and on NR‘s website. This started with a review by speechwriter Matthew Scully, similarly a friend and a gifted polemicist. Scully is the vegetarian and champion of animals who, for the 2008 Republican convention, wrote the best speech ever given by that great white hunter, Governor Palin.
As a reviewer for Wesley Smith’s book, Matthew Scully was a surprising choice. Scully’s own book, Dominion: The Power of Man, the Suffering of Animals, and the Call to Mercy, received a wounding review in The Weekly Standard some years back from none other than Wesley Smith and it comes in for criticism again in Smith’s book. I can’t understand NR‘s decision to match these two valued friends of the magazine against each other. Matthew wrote, I am sorry to say, a distorting and unfair review of Wesley’s book, to which NR then let Wesley reply, generating additional discussion on the website but less illumination than the subject deserves.
So let’s highlight Smith’s contribution to public understanding of why the Darwin debate matters. His recounting of terrorist and other heinous acts by animal-rights extremists (even grave-robbing!), his exploration of the wicked views of “personhood” theorist Peter Singer, author of A Darwinian Left and the manifesto Animal Liberation — these tell us about the leading edge of what you might call the animalist view, equating humans with animals.
A biology educator recently wrote me asking how we test intelligent design using the scientific method, how ID is falsifiable, and how ID explains patterns we observe in nature. These are very common questions that we receive all the time from teachers, students, and interested members of the public, and they’re usually legitimate, sincere, and thoughtful questions. In this case, they certainly appeared to be such, and below I post a slightly modified version of my response to the teacher, withholding any information about the teacher to protect his/her identity: We help many educators to better understand the debate over evolution. Contact us for more information!
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 ›
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. Discovery 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 of Read More ›
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.
