[ckayatek]

I'm inclined to agree with the ENCODE scientists. You could argue that even protein binding sites that have no biological outcome titrate away transcription factors from other "active" regions. The system would have evolved with these sinks in place and therefore they constitute an active, useful part of the genome. Another way to look at it is that if you were trying to generate a computer model of the entire genome, you would have to account for the extra binding sites, even if they had no output in terms of protein or even RNA.