Ryan discussing Michael Eisen’s take on ENCODE. This is exactly my take on the matter (my emphasis).
It’s important to distinguish between the different views that one can have on function of non-coding DNA. The notion that “all non-coding DNA is functionless junk” is a straw man position that no one has ever seriously held. So, yes, there was already an expectation that some non-coding DNA would turn out to have function — and plenty of examples were already well known. This extreme “it’s all junk” idea did not need to be overturned, because no one claimed it and, as noted, other examples that refute it were already known. However, there is another claim that is coming out in these media reports and in quotes from the ENCODE authors — that the evidence indicates that 80% or more of the genome is functional. This is a claim that is based on the flimsiest of definitions of “functional” and is not one that likely to be unconvincing to many experts. So, the claim that “there is little or no non-functional DNA at all” is somewhat unique to ENCODE (John Mattick thinks so too). But it is a problematic claim because the evidence for this assertion is very tenuous.
Somewhere in the middle is what I believe to be the most reasonable view: a significant percentage of the non-coding DNA in the human genome is functional in the sense of being biologically meaningful, but most of it probably is not. This is certainly the view that is most consistent with the evidence, and it is, in fact, the one that the early proponents of the “junk DNA” concept actually held. As I noted in a previous post, the ENCODE authors have to work pretty hard to even get the 80% figure, which would still leave an awful lot of non-functional nucleotides in the genome.
Let’s also not forget about this, written in 1972:
These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.
Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.