Oh dear. Greg Laden reviews a paper from John Mattick's group and he falls for the hype, hook line and sinker. Here's what Greg says [Genes are only part of the story: ncRNA does stuff].
The "Junk DNA" story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don't know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of "non-coding DNA." It does really seem that scientists assumed for too long that there was no function in the DNA.I hate to break it to you Greg, but junk DNA is not a myth. It really is true that a huge amount of our genome is junk. It's mostly defective transposons like SINES and LINES [Junk in your Genome: LINEs]. It's a lie that we don't know what most non-coding DNA is doing. We do know. It's not doing anything because it's mostly screwed up transposons and pseudogenes like Alu's.
Mattick may have found a few bits of DNA that encode regulatory RNAs but that's only a small part of the total genome. He, and you, have fallen for excuse #5 of The Deflated Ego Problem.
Ryan Gregory has already tried to teach Greg some real science about junk DNA so I won't pile on any more than I have [Signs of function in non-coding RNAs in mouse brain.].
UPDATE: RPM chimes in to expose the flawed thinking of Greg Laden [How Easy is it to Write About Junk DNA?]