Friday, March 1, 2013

Blank On The Map: The nature of publications

paper in the journal of Genome Biology and Evolution has been doing the rounds on the internet recently and was shown to me by a friend. It is titled "On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE", by Graur et al. The title is blunt enough, but the abstract is extraordinarily so. Let me quote some of it here:
A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. [...] This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. [...] The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.