Wednesday, October 20, 2010

"Junk DNA" and Science Stoppers

The Discovery Institute's Evolution News & Views has an article by one "Jonathan M." entitled, as approximately one Discovery Institute article per month is required to be, "Yet More 'Junk DNA' Not-so-Junk After All."   It concerns a paper in the journal Cell discussing how long non-coding DNA strands near genes could affect gene expression, and goes on to note that while creationism and ID are often condemned as "science stoppers," it is ID that leads us to suppose that non-coding DNA probably serves some sort of function and encourages scientists to look for it.

It is nowhere suggested, to be sure, that the authors of the paper are ID supporters or were motivated in their research by a suspicion that the genome is "rationally designed."  But what struck me was that one of the first intimations that non-coding DNA played an important role in the functioning of the genome was Barbara McClintock's (ultimately Nobel-Prize winning) attempts to make some sense of the vagaries of corn genetics.  She was not moved to find a function for transposable, non-coding elements after their existence was shown; she was moved to posit them and perform painstaking experiments to show they existed because she needed something like them to explain why corn didn't follow straightforward Mendellian rules.

Granted that McClintock had difficulty convincing fellow botanists of her theories, it remains the case that the discovery of noncoding DNA was more or less simultaneous with the demonstration that some of it did something.  And then, of course, there was Ernst Mayr's initial suspicion of the whole idea that there were significant amounts of nonfunctional DNA in the genome: if it had survived natural selection, he first assumed, it must do something.  "Pan-adaptionism" is at least as compelling an argument for the functionality of "junk" DNA as design (a Designer, after all, might indulge in nonfunctional decorations of the genome according to His own ineffable aesthetics), although as Richard Dawkins has pointed out, we always need to consider that some parts of the genome might be adapted to help those parts survive, not to help us survive, and as Stephen Gould was fond of insisting, we cannot assume that everything about living organisms actually is an adaption.

Some "junk" DNA is plainly vestigial (and note, of course, that "vestigial" is defined as exhibiting reduced function, not nonexistent function): the famous GULO pseudogene in old-world anthropoids, or the numerous disabled genes for smell in human beings.  The notion that such genes are "junk" was based not on the assumption that they must have no function, but on the observation that they clearly didn't have the functions one would normally expect of DNA.  That "junk" could turn out, on occasion, to serve functions for the organism is no more astonishing or contrary to "Darwinism" than is the idea that random mutations in general could, on rare occasions, be beneficial or bestow novel traits.

That some "junk" is in fact pretty nonessential, though, was demonstrated by another scientific paper, Nóbrega, et al.'s "Megabase deletions of gene deserts result in viable mice" (Nature 431, October 2004), which showed that a million or more bases could be removed from some segments of a mouse's genome without affecting development in any noticeable way (note that some attempts did result in nonviable mice, which shows that the deleted segments contained important segments, not that the entire segments were functional; if you can find a million bases in a row that serve no vital function, there are probably a lot more shorter segments interspersed among functional segments that really are nonfunctional as well as noncoding).

As noted above, given that we are entitled, per ID principles, to no assumptions about the aesthetic or design principles of the Designer, it does not follow that function-free "gene deserts" contradict the design hypothesis (indeed, it's famously difficult to think of any possible observation that contradicts the design hypothesis).  But one wonders if a commitment to the idea that the genome was rationally designed rather than opportunistically evolved would lead to this particular "fruitful research."


  1. Hi Steven,
    Can you suggest a book for the not-a-scientist- but-interested-person in ToE? Ideally one that I could find in a library. I have tried working through the Wikipedia article but I get bogged down in details I don't fully understand. So I'm looking for a book that is aimed a teaching the subject. I have been tempted to get Coyne's or Dawkin's recent books. Have you read them? Thoughts?

  2. I would suppose that depends on what aspects of evolution you are interested in. Coyne's and Dawkins' new books cover the evidence for common descent, which is not quite the same as a general overview of evolution (on the other hand, both are interesting and both a probably available at the library). Dawkins' earlier works (also widely available) focus almost exclusively on natural selection, which I suspect is a narrower focus than you'd want.

    For a general layman's introduction to evolution and evolutionary theory, you might do well to check out Carl Zimmer's new The Tangled Bank. The trouble, of course, is that I don't know whether that is in your local library (it is not in mine). I would recommend it over his older, more general Evolution: the triumph of an idea, which is in my local library and might well be in yours.

    Note that there are web resources specifically designed for interested laymen: the Talk.Origins archive, for example, which has a page title "Introduction to Evolution" and the "Understanding Evolution" page maintained by UC Berkeley.

  3. Orgel and Crick, in their famous 1980 paper on Selfish DNA claimed:

    "It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes."

    Not really about "junk" but selfish and junk have some relationship.