If you look at the way the Wikipedia article on “Noncoding DNA” has settled after much to-ing and fro-ing after the ENCODE papers were published, you’ll see that the final “consensus” is that ENCODE’s figure of 80%+ function for DNA means little, since mere transcription is a poor indicator of function. Naughty ENCODE was careless in playing into the Creationists’ hands.
Uncommon Descent has just pointed to a paper by Mattick and Dinger who clearly belong to that increasing “lunatic fringe” of people with excellent credentials who cast doubt on that wisdom.
Mattick, a geneticist, has been suggesting for years (eg here and here) that advanced life could not even have evolved without the prior necessity for a sophisticated system of RNA control networks, such networks having themselves been positively selected because, not to put too fine a point on it, evolvability is a huge advantage to life.
This emphasis on the development of evolvability, you may recall, is shared by James Shapiro – and like him, Mattick’s view affirms that, but doesn’t explain how, ordinary natural selection has accomplished it. He is, like Shapiro, distinctly sharp with defenders of Neodarwinian orthodoxy, and yet shows little antagonism to Intelligent Design, even though he specifically rejects its core tenet – the need for a designer. Indeed, secular theorists like him seem to lack the disapprobation given to ID by the TEs associated with BioLogos, which must tell us something sociologically, I suppose.
Mattick, then, would say that ENCODE’s “80% functional” slogan is entirely realistic – being a reasonable projection on to what we don’t know from what we do now know of noncoding DNA’s many functions. Indeed he proposes that such DNA, the source (as I’ve suggested in a recent post) of most genetic innovation, has evolved by positive selection, which runs directly contrary both to orthodox Neodarwinian ideas and, specifically, to the dominant neutral theory.
What attracted my attention in the first article cited was his critique of his opponents’ claim that non-coding DNA is demonstrated to be “junk” by its lack of conservation. His paper is short and easy enough to read for yourself, but basically he is pointing out that the arguments used in “establishing” selection and non-selection are circular:
Here we challenge these arguments, showing that conservation is a relative measure based on circular assumptions of the non-functionality of transposon-derived sequences and uncertain comparison sets, and that regulatory sequence evolution is subject to different and much more plastic structure-function constraints than protein-coding sequences, as well as positive selection for adaptive radiation.
The real test of functionality, he says, is the evidence for organised differential use of non-coding DNA in different cell-types, which would seem to be self-evident. In his conclusion, having drawn attention to the ideologically motivated opposition of the “orthodox” to ID’s critiques, he plants his own flag in the sand in defence of natural selection as a general principle:
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.
The thing that strikes me here is those last few words, for they are actually an attack on two of the few branches of evolutionary science that possess a mathematical basis, and which therefore link biology to the hard natural sciences like physics rather than the world of Just-So Stories it often occupies.
Population genetics was the first field to put maths into evolution, albeit hedged about with a number of simplifying assumptions that largely divorce it from the real living world, though population geneticists wouldn’t accept that.
And neutral theory, remember, began not so much with a positive claim than non-coding DNA looked functionless, but that it must be so mathematically, because of real constraints on the ability of natural selection to operate effectively on large genomes in relatively small populations.
So if, as more and more of the data suggests, most of the genome is truly functional, and if maybe most of it subject to natural selection (despite this and the following couple of pieces), what is there left in evolutionary theory that one could say is hard science rather than narrative interpretation of history? And how could what maths there is prove to rest on such an insecure foundation?
Meanwhile, if nothing else, the existence and work of people like Mattick are good reminders that the impression one gets from the internet and the media generally, that the biological world is divided into “real scientists” and “pseudoscientific creationists” is nothing more than a myth, with far more power and influence than it warrants.