What I said concerning ENCODE was simply that it ''opened up the possibility'' that the entire genome had a function.
To use the analogy I used before, this is like saying that since you can hear static on your radio that this opens up the possibility that there is a radio station on every part of the dial.
Therefore, all I'm saying is that when seeing how genetics has been unravelling the secrets of previously thought ''junk DNA'', and how more evidence comes to open the possibility that maybe the whole genome is functional, I think it is the idea that any part of the genome is junk that should be regarder with great skepticism, not the other way around.
At the same time, there are sections of the genome that have accumulated mutations at a rate consistent with neutral drift. These include processed pseudogenes which were the first to be called "junk DNA". If they do serve a function it is probably independent of the actual DNA sequence. The more we learn of genetics the easier it is to find junk DNA. Even more, scientists have removed over 2.3 million base pairs from the mouse genome with no visible change or loss of function. This is one half the size of the E. coli genome. Obviously, there is much more vestigial DNA in the eukaryotic genome than in the prokaryotic genome.
"We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis."
Megabase deletions of gene deserts result in viable mice - PubMed