A scathing review of the ENCODE project has just be published.
A set of select highlights is here
Here's my favorite:
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%.
There's also an excellent dig about rewriting textbooks. My own take remains the same. The encode project produced some valuable data and was well executed right up until publication time. Then it fell prey to overhype. The authors were excellent technologists but they were not good biochemists, geneticists, biologists or philosophers. Maybe it's archane to refer to the literary nature of the PhD degree but "Philosophy" is in there, and it's a shame that potentially good science gets such a bad rap due to a failure at the finish line. If a scientist is going to make a claim about function, they need to understand what function means (and what teleology is), even if that stretches them outside of their prior expertise. A bioinformaticist ought to know all about being stretched outside of their core competency. It happens to us all the time, and we all have to worry about stumbling at the finish line.
Oh, and if anyone wants a more sedate and scholarly treatment of ENCODE and the issue of Junk DNA, Sean Eddy produced a fine exposition in Current Biology. clicky clicky