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"Junk DNA," "Non-Coding DNA," and Larry Moran's Hyper-Pedantry

Earlier this week, David Klinghoffer posted an article responding to Larry Moran's claim of contradiction between myself and Jonathan Wells on "junk DNA." Larry Moran has now posted a follow-up on his blog. He writes,

We seem to have a bit of a problem here. I'm certain that David Klinghoffer would like to think of Richard Dawkins, John Avise, Ken Miller, and Jerry Coyne as "credible scientists" otherwise why bother attacking them?

Jonathan McLatchie probably thinks they are credible scientists as well. I've read lots of books and articles by these credible scientists and I can assure you that none of them think that all noncoding DNA is junk. McLatchie is correct.

junk-dna-cover.jpgOn this, Moran and I are agreed -- scientists like Richard Dawkins, John Avise, Ken Miller and Jerry Coyne certainly don't think that all non-protein-coding DNA is without function (although they do claim that most of it is). I think Moran is being a touch overly pedantic here, however. Promoters, enhancers, operators and transcription factors are all non-protein-coding DNA: Is Larry Moran seriously suggesting that Jonathan Wells doesn't think that those biologists have heard of those?

Readers may recall PZ Myers's attempt to excuse himself from my criticisms of his lecture on junk DNA (where he essentially implies that all introns and transposable elements are "junk DNA") by claiming that he was "simplifying for a lay audience." When pressed, PZ Myers qualified the equation of introns & TEs and junk. Likewise, if one were to press the aforementioned biologists (Dawkins, Avise, Miller and Coyne), I am sure that they would make a similar qualification with respect to their equation of non-protein-coding DNA and junk.

Indeed, in Chapter 2 of Jonathan Wells's The Myth of Junk DNA, he writes that

In 1972, biologist Susumu Ohno (at the City of Hope National Medical Center in Los Angeles) published an article wondering why there is "so much 'junk' DNA in our genome." The same year, his City of Hope colleague David Comings wrote that only about 20% of the human genome appears to be used; the remaining 80% seemed to be "junk" -- though Comings did not necessarily think it was entirely useless. [emphasis added]
Or consider Jonathan Wells's citation of Douglas Futuyma:
Although Futuyma acknowledged that some "noncoding DNA is unlikely to be 'junk' (as was postulated in the early 1970s)," nevertheless only Darwinian evolution can explain why the genome is full of 'fossil' genes: pseudogenes that have lost their function -- a phenomenon that is "hard to reconcile with beneficent intelligent design." [emphasis added]
Wells even quotes Francis Collins as acknowledging that "some small fraction of [ancient repetitive elements] may play important regulatory roles." He further quotes John C. Avise conceding that,
...several instances are known or suspected in which a pseudo-gene formerly assumed to be genomic "junk" was later deemed to have a functional role in cells. But such cases are almost certainly exceptions rather than the rule.
It seems that we have yet another case where the words of ID proponents have been twisted and misrepresented. But, sadly, this is something that we have come to expect.