[allmendream]

Indeed, it looks like this noncoding regulatory DNA; in addition to the other regulatory DNA already known about - might make up as much of the genome as the actual genes themselves!

Still no known function for the majority of the genome.

Not saying one won't be found, but a hypothesis of “junk” that might be beneficial to be kept around, and might be of use some day - is still a reasonable hypothesis. One which is strengthened by findings like the envelope protein of an ERV being used by placental mammals - not weakened by it.

[count-your-change]

Actually I wasn't referring to something that might be useful someday but more like along the lines of this article, and related ones at the same site:

ScienceDaily (May 21, 2009) — Scientists have called it “junk DNA.” They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature force the genome to carry so much excess baggage?”

The article goes on to discuss the answer to its own question.