Basically, the recent ENCODE findings just didn’t back up the “masses of junk in our DNA” thesis, so Darwin’s followers responded with a peer-reviewed tantrum.
We thought we knew why, but it is nice to hear someone else say it. Researchers John Matick and Marcel Dinger, in Springer’s HUGO, responding to ENCODE’s more florid critics:
There may also be another factor motivating the Graur et al. and related articles (van Bakel et al. 2010; Scanlan 2012), which is suggested by the sources and selection of quotations used at the beginning of the article, as well as in the use of the phrase “evolution-free gospel” in its title (Graur et al. 2013): the argument of a largely non-functional genome is invoked by some evolutionary theorists in the debate against the proposition of intelligent design of life on earth, particularly with respect to the origin of humanity. In essence, the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins 2006). This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells 2011).
Interestingly, they add (doubtless to protect themselves),
It is our position that these arguments are misguided. Indeed, we have refuted the specific claims that most of the observed transcription across the human genome is random (Clark et al. 2011; Mercer et al. 2012) and put forward the case over many years that the appearance of a vast layer of RNA-based epigenetic regulation was a necessary prerequisite to the emergence of developmentally and cognitively advanced organisms (Mattick 1994; Mattick and Gagen 2001; Mattick 2004; Amaral et al. 2008; Mattick 2009a, 2011). This case is, moreover, entirely consistent with the broad tenets of evolution by natural selection, although it may not be easily reconcilable with current population theory and current ideas of evolutionary neutrality.
Two things: Obviously, the “prerequisite” implies design, but none dare call it that. “Broad tenets of evolution” certainly does not exclude design.
Second, the very tantrum that Mattick and Dinger are addressing is evidence that Darwin’s followers do not think that “little junk DNA” is compatible with any theory they would accept. And that’s the main point these days. Note: Not “any theory that fits the evidence” but any theory they would accept. And not raise money to persecute whoever espouses it.