Two great comments from T Ryan Gregory at E Birney’s Blog post on ENCODE.
He is replying to someone in the comments section. In the first quote, he again (and correctly) highlights that there was never a period when researchers supposedly dismissed all ncDNA as junk. I’ve quoted him before here stating that.
In the second one, he talks about intelligent design.
What I am talking about is what was actually being said in the primary literature. In that case, it is abundantly clear that there was no widespread dismissal of possible functions for non-coding DNA among the researchers working in the field. I have not been quoting selectively, either — I looked at the papers that first described each type of non-coding DNA elements, for example, or review papers from the period, or news stories in Science and Nature from that time. All of them show that function was a common expectation, or at least a serious question, throughout the supposed period of dismissal.
I personally don’t think non-functional junk DNA is all that relevant to the fight from either side. Why should “intelligent design” assume that nothing is non-functional? Our own intelligently designed artifacts often have crap in them. Who would argue that the computer code for Windows is flawless and without non-functional, redundant, sloppy, or otherwise unnecessary bits? I have never seen a clear articulation of the reason that ID predicts no non-functional DNA (other than the obvious “God don’t make no junk” — and even then, why not?).