What happened to junk DNA?

Isn’t a lot of DNA “selfish”, “parasitic”?

One of the standard defences of the selfish gene view is based on the discovery that, in humans and many other organisms, only a few per cent of the genome codes for proteins and can therefore be classified as ‘genes’ in the usual sense. The rest was described as ‘junk’ DNA, the ultimate example of ‘selfishness’ since it was seen as DNA ‘hitching a ride’ with no function, a bit like a virus that has become permanently resident in the body. The strong implication is that this discovery favours the selfish gene view.

I think that is a confusing way of viewing genomes. There are several ways in which the confusion can be unravelled.

The words ‘selfish’, ‘junk’, etc. are, of course, metaphors. More importantly they are empirically empty metaphors when applied to sequences of DNA. No conceivable experiment could validate or invalidate them. The reasons are fully explained in Noble (2011).  See also the answer to ‘what is wrong with The Selfish Gene?’ in this document.

That the metaphors are empty, however, does not mean that they have no impact. On the contrary, they have had, and still have, very persuasive impact on the way in which many people think about biology. The Selfish Gene sells in millions of copies. Its impact extends way beyond biology, into economics, politics and business studies.

A more persuasive counter-argument is therefore needed, and what might persuade most people is experimental evidence favouring a different view. Fortunately, recent experimental work has provided us with precisely that. The more we examine non-protein-coding DNA the more evidence we find that an overwhelming 80% is transcribed to form RNAs, and that around 20% are already known to have function (http://www.genome.gov/10005107).

Mobile genetic elements have also been characterised as “ selfish” and “parasitic”. Yet they account for nearly 20% of “all conserved (i.e. positively selected) differences between eutherian mammals and marsupials (Lindblad et al , 2011).” For further debate on these issues the reader is referred to the series of articles (July 2013) in Physics of Life Reviews.