Recently in Junk DNA Category

“The Selfish Gene.” “Selfish DNA.” Oh, how such phrases can get people bent out of shape.  Stephen Jay Gould hated such talk (see a little book called The Panda’s Thumb), and Richard Dawkins devoted more time to answering critics of his use of the term ‘selfish’ than should have been necessary. Dawkins’ thesis was pretty straightforward, and he provided real examples of “selfish” behavior of genes in both The Selfish Gene and its superior sequel, The Extended Phenotype. But there have always been critics who can’t abide the notion of a gene behaving badly.

Leaving aside silly bickering about the attribution of selfishness or moral competence to little pieces of DNA, let’s consider what we might mean if we tried to imagine a really selfish piece of DNA. I mean a completely self-centered, utterly narcissistic little piece of DNA, one that not only seeks its own interest but does so with rampant disregard for other pieces of DNA and even for the organism in which it travels. Can we imagine, for example, a piece of DNA that deliberately harms its host in order to propagate itself?

Of late the IDists have been complaining about the dearth of reviews by ID skeptics of Stephen Meyer’s book Signature in the Cell. I agree, it would be nice if there were more reviews out there, but (a) the arguments boil down to the same old fallacious “improbability of assembly of functional sequence all at once from scratch by brute chance” creationist argument that dates back to at least the 1960s creation science literature, and (b) the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. I.e. information comes from intelligence and is too improbable to explain by chance, therefore intelligence! The actual known origin of the vast majority of genetic “information” – DNA duplication followed by mutation and selection is (1) almost completely ignored by Meyer and (2) directly refutes Meyer’s key claim, which is that the only known explanation of new information is intelligence. So in one sense, there is not a heck of a lot to review in Meyer’s book. If you are a sufficient wonk about the ID debate, there is some interesting stuff about Meyer’s highly revisionist account of his own history and the history of the ID movement, and there is an interesting study to be made of the science that Meyer left out of his book, but that makes for a big project, so it will be awhile before I or someone else get it out there.

But, while reading across the book, you do occasionally come across some examples of truly bizarre argumentation. Here an example which I just posted in response to a Telic Thoughts challenge:

By Don Prothero http://faculty.oxy.edu/prothero/index.htm

Don Prothero is a paleontologist and Professor of Geology at Occidental College in Los Angeles, and Lecturer in Geobiology at the California Institute of Technology in Pasadena, and author of Evolution: What the Fossils Say and Why it Matters, in my opinion the very best book on fossils and evolution for the general reader. Last night, Monday, November 30, Prothero debated (along with Michael Shermer) ID advocates Stephen Meyer (longtime head of the Discovery Institute’s Center for the Renewal of Science and Culture) and Richard von Sternberg (the former editor who in 2004 published Meyer’s pro-ID article in the last issue of the Proceedings of the Biological Society of Washington (D.C.) which Sternberg was scheduled to edit, despite the article being wildly off-topic for an alpha taxonomy journal, substantially copied from other Meyer publications, badly inaccurate, and just weird in several ways). Sternberg is now, I believe, an employee of the Discovery Institute.

Prothero wrote these remarks directly after the debate and emailed them to me. I have added links where relevant. — Nick Matzke

My mind is a bit fuzzy from the loss of sleep, and the two hours of “debate” went by very quickly, so I cannot recall all the details, let alone recount them. Here are my morning-after thoughts about last night’s “Battle in Beverly Hills.” I don’t know when they’ll release the video recording of the event, but when it does come out, hopefully it will be possible to post it so you can all see for yourself how it went. My subjective summary of it is that our side did very well: I caught them off-guard with new arguments they had no answer for; Shermer pushed them hard repeatedly to state who the “Designer” was (and Meyer finally conceded it was God), while we both pushed them hard on the fact that neither of them ever addressed the topic of the debate, “Origins of Life.” I could tell that they were rattled a number of times, and I definitely shook up Meyer and got under his skin with my answers. Several times Meyer and Sternberg were arguing with each other, leaving the moderator, our side, and the audience wondering who runs their show. The best sign of my effect on them was Meyer trying to challenge MY credentials, or dodging a tough question by playing the sympathy card and calling me “condescending” — and the virulent post on the Discovery Institute site this morning, full of lies and spin. Of course, the event is staged so that no one will really “win”. Their supporters turned out and dominated the audience, but I had a LOT of people come up to me during the book signing (we sold a LOT of books) and congratulate me, or discuss points further with me. And we got just as much applause and sympathetic laughter at our well-turned phrases as they did.

As a last treat for the 150^th anniversary of the Origin, have a look at young-earth creationist creationist Cornelius Hunter [Update: Hunter has stated he is not a young-earth creationist on his blog, so I guess he’s not, although that position directly follows from his stated theology/philosophy], author of the “Darwin’s God” book and blog. Hunter’s basic argument against virtually any common pro-evolution argument is, basically, “But you evolutionists are claiming that God wouldn’t have done it this way! You’re making an unscientific theological argument!”

In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents. The means by which these genes arise are many. One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons. This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA. In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.

The ID blogosphere is much agog, and has been for some time, about recent (and not so recent) results that suggest some sort of functionality in what has long considered to be nonfunctional (junk) DNA in eukaryotes. The most recent buzz centers on studies (such as ENCODE ) that indicate that large swaths of so-called junk DNA are “expressed” by RNA polymerase II. Apparently, the fact that RNA polymerase transcribes alleged junk DNA is a blow to Darwinism, and a feather in the cap of ID. Their excitement in this regard, I suspect, will wane greatly once they learn some of the true implications of these results. For the matter of “expression” in junk DNA is one wherein ID meets, and gets swallowed by, the Garbage Disposal.

What follows is a discussion of a relatively recent report that rains on the ID parade. As is my habit, I’ll summarize the essay for those with short attention spans – the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk.