In light of the recent ENCODE papers, several researchers have questioned some of their conclusions and the way the authors have described their findings (“These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions” -that’s from one of the articles….-), not only in the primary articles, but also in interviews and press releases.
Michael Eisen has discussed some of these issues on his blog, and this is a brief extract from one of his posts:
But if you think about this, you will realize that this simply can not be true. As we and many others have now shown, molecular interactions are not rare. Transcripts, transcription factor binding sites, DNA modifications, chromatin modifications, RNA binding sites, phosphorylation sites, protein-protein interactions, etc… are everywhere. This suggests that these kind of biochemical events are easy to create – change a nucleotide here – wham, a new transcription factor binds, an splicing site is lost, a new promoter is created, a glycosylation site is eliminated.
And, as I’ve mentioned before….
Rather than assuming – as so many of the ENCODE researchers apparently do – that the millions (or is it billions?) of molecular events they observe are a treasure trove of functional elements waiting to be understood, they should approach each and every one of them with Kimurian skepticism
Thank you, Michael.