[dekhn]

I'm not a bioinformatician. I'm a biophysicist (BS in Molecular Biology and Biochemistry) who works in computer science. That said, as I have worked closely with most of the world's genome experts (and parried with them on this very issue), I am an authority in this area.

Anyway, I don't mind that you're harsh. It's pretty hard for people to unlearn their years of misunderstanding the genome! There is a lot of misinformation. Basically, you're just insisting on this line of reasoning: http://selab.janelia.org/people/eddys/blog/?p=683 "ENCODE says What?"

In regards to the ENCODE project's "embarassment", a couple things happened: 1) the press attributed a number of overly aggressive claims to ENCODE. If you read the papers you'll notice they used very hedged statements. 2) ENCODE actually observed some very interesting things. We took their data, and worked on it some more, and we found that a number of their measured transcription tracks actually did represent functional biology. In particular, I can assure you, based on very solid evidence that your estimate that RNA genes make up only 4% of the genome is vastly lower than reality.