From Genome Technology Online:

Perhaps They Should’ve Called It “One Man’s Treasure” DNA
September 17, 2007

It seems people are a little touchy about the use of the term “junk DNA.” On his Genomicron blog, TR Gregory attempts to put an end to the debate by harking back to the origins of the term, along with an exegesis of how it has been used over time and in various settings.

While GTO doesn’t doubt the accuracy of Gregory’s information, we have to say: his argument that scientists referred to these genomic regions as “junk” all while understanding how very important they were leaves us a little, well, dubious. But maybe we’re just naturally cynical.

Let me help you out. Comings (1972), who provided the first detailed exposition of the “junk DNA” idea (his article appeared in print before Ohno’s), wrote: “Being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.” Orgel and Crick (1980), who developed the idea of “selfish DNA”, wrote: “It would be surprising if the host organism did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another. This seems more than plausible.” Both approaches emphasized non-function based on proposed mechanisms of non-coding DNA increase. And both sets of authors noted that some of it would be functional.

Why people seem incapable of a) understanding a mildly complex history, and b) reading the literature is inexplicable to me. Given how much interest there is in non-coding DNA in the press and among anti-evolutionists, I think it is worth getting it straight.