[jonathansizz]

Why won't you answer my questions? It's not up to me to prove a negative, if such a thing were possible.

I wasn't referring to active or co-opted transposons, which make up less than 1% of total transposon sequence in the genome. I'm talking about dead, non-functional transposons. These were indeed active and functional in the distant past, but are long since dead. If you have an hypothesis that such sequences in fact have a function, then by all means let's hear it. Likewise with dead viruses, satellites, etc.

It's interesting you mention 'meaningless speculation in the absence of data', since your friends at ENCODE recently embarrassed themselves in just such a way with their pervasive transcription nonsense, as do those who claim function for repetitive, unconserved regions of the genome without any evidence or even an hypothesis, when we have every reason to believe that these are the remnants of formerly-active elements that were subsequently inactivated.

As I said above, it's clear that a small fraction of non-coding DNA has a regulatory role. We've known about this for decades. Recent discoveries don't account for much; RNA genes make up about 4% of the genome.

Sorry if I've been overly harsh in my replies, but from my experience many bioinformaticians have shown themselves to be ignorant about even basic biology, so I took the precaution of going over a few basics.

[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.