I just read a marvelously snarky critique of the ENCODE papers (which most of the bioinformaticians I know considered flawed in their over estimates of how much of the human genome is “functional”). Perhaps the best of the critiques is this one: On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE.
The article accuses the ENCODE authors of several academic sins:
Oddly, ENCODE not only uses the wrong concept of functionality, it uses it wrongly and inconsistently.
Sadly, the authors of ENCODE decided to disregard evolutionary conservation as a criterion for identifying function.
Some of their comments are marvelously snarky:
According to Eric Lander, a Human Genome Project luminary, ENCODE is the “Google Maps of the human genome” (Durbin et al. 2010). We beg to differ, ENCODE is considerably worse than even Apple Maps.
The article provides solid reasoning for why the estimate that about 80% of the genome is functional is completely bogus, and provides more reasonable estimates:
Ward and Kellis (2012) confirmed that ~5% of the genome is interspecifically conserved, and by using intraspecific variation, found evidence of lineage-specific constraint suggesting that an additional 4% of the human genome is under selection (i.e., functional), bringing the total fraction of the genome that is certain to be functional to approximately 9%. The journal Science used this value to proclaim “No More Junk DNA” Hurtley 2012), thus, in effect rounding up 9% to 100%.
The ENCODE project produced a lot of good data, but some of the hype surrounding it irritated a lot of biologists and bioinformaticians, who are pleased to see the ENCODE hype so amusingly and accurately skewered.