There has been lots of talk (including some in the media; see here and here and here) about the Graur et al. (2013) paper in GBE which was critical of ENCODE, much of it focusing on the tone of the paper. While the Graur et al. (2013) paper certainly doesn’t pull any punches in terms of ENCODE’s outrageous claims and incredible media hype, it also contains a number of important criticisms of the science underlying the project. Graur et al. (2013) were not the only ones to publish peer-reviewed critiques, and I expect that the list will continue to expand.
Here is a list of the papers that have appeared to date:
Doolittle, W.F. (2013). Is junk DNA bunk? A critique of ENCODE. Proceedings of the National Academy of Sciences USA 110: 5294–5300.
Eddy, S.R. (2012). The C-value paradox, junk DNA and ENCODE. Current Biology 22: R898–R899.
Eddy, S.R. (2013). The ENCODE project: Missteps overshadowing a success. Current Biology 23: R259–R261.
Graur, D., Y. Zheng, N. Price, R.B.R. Azevedo, R.A. Zufall, and E. Elhaik. (2013). On the immortality of television sets: “Function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution 5: 578-590.
Niu, D.-K. and L. Jiang. (2013). Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and Biophysical Research Communications 430: 1340-1343.
Hurst, L.D. (2013). Open questions: A logic (or lack thereof) of genome organization. BMC Biology 11: 58.
Some of these authors have written blogs, in some cases to go after each other (stay tuned — there may be more debate coming).
Sean Eddy: ENCODE says what?