I know I’m beating a dead horse, but here’s a paragraph every single reporter writing on ENCODE should have read, and every single scientist from the consortium speaking to the media should have referred to:
The major goal of ENCODE is to provide the scientific community with high-quality, comprehensive annotations of candidate functional elements in the human genome. For the purposes of this article, the term “functional element” is used to denote a discrete region of the genome that encodes a defined product (e.g., protein) or a reproducible biochemical signature, such as transcription or a specific chromatin structure. It is now widely appreciated that such signatures, either alone or in combinations, mark genomic sequences with important functions, including exons, sites of RNA processing, and transcriptional regulatory elements such as promoters, enhancers, silencers, and insulators. However, it is also important to recognize that while certain biochemical signatures may be associated with specific functions, our present state of knowledge may not yet permit definitive declaration of the ultimate biological role(s), function(s), or mechanism(s) of action of any given genomic element.
This is the kind of language you hear at conferences – language that I’d say is not controversial at all. By this criterion, ENCODE has been a great success. And this paragraph makes it clear that ‘junk DNA is debunked’ cannot possibly, under any scenario, be the immediate conclusion of the experiments conducted by ENCODE.