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ENCODE’s ‘junk DNA’ claims spark biological bunfight

Define ‘functional’

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An overly-promotional – or perhaps merely badly-written – abstract in Nature has spawned a biology boffins’ bunfight.

It started with this item, “An integrated encyclopedia of DNA elements in the human genome”, which makes the startling claim that the ENCODE project (Encyclopedia of DNA Elements) had data which “enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.”

In the hands of science journalism, this became an even more startling fact. The New York Times said “Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role”; The Conversation said “Human Genome 2.0: ENCODE project debunks ‘junk’ DNA”; “Breakthrough study overturns theory of 'junk DNA'” in The Guardian (whose worst offence, to be fair, is in the headline rather than the story), and so on.

The accepted notion has been that 98 percent of the human genome is “noncoding DNA” – that is, not associated with encoding protein strings. If that figure were slashed to 20 percent, it would clearly be a genetic revolution.

Would it surprise any seasoned Register reader to think there’s more nuance in the story than appears at first glance? Of course not.

It boils down to defining what is “functional”. The layperson probably thinks “functional” DNA strings have a specific expression – that the functions discovered by ENCODE are, in other words, somehow analogous to the genes that give us blue eyes, red hair, that regulate melanin in the skin or whatever.

ENCODE, however, has used a much broader definition of function: if any specific biological activity could be tagged to a gene, it was described as functional. As Canadian biologist notes, that’s a broad stretch. It means that even being replicated counts as a “function” (that is, if this gene string gets copied accurately in the next copy of a human genome, it’s performed a function).

The authors of the Nature paper agree, in fact: they make the more conservative – and interesting – claim that a sizeable chunk (20 percent) of DNA thought to be inactive is actually involved in regulating that tiny proportion (two percent) of the human genome that actually encodes protein sequences.

Worst of all, according to sci-bloggers like Nick Matzke on his Panda’s Thumb blog: the inflated “80 percent” claim gives considerable aid and comfort to creationists. The study “provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA”, says Evolution News, for example.

It would be a pity if this argument distracted attention from the real value of the ENCODE work: the human genome is a huge and complex beast, and the better it's catalogued and understood - including the "junk DNA" - the better our tools for battling genetic disease will become. ®

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