[PatrickHenry]

... the idea that retrovirus material is in there still competing with the original host DNA for replication is new to me and fascinating. Intramural competition within the DNA strand!

This isn't my field, but it seems to me that once the material gets established in the DNA, it's no different from a mutated portion of the DNA. The DNA chain doesn't care where it came from.

[VadeRetro]

I'm still absorbing it. The idea involves a tug-o-war for the regulatory stuff. Like authors fighting for a publisher, that sort of thing. It's beyond that, in fact. It's like a war for the genome space.

I can't tell if the theory is tinfoil or "widely accepted." Brain hurt!

[Nebullis]

...it seems to me that once the material gets established in the DNA, it's no different from a mutated portion of the DNA.

The difference is in the particular sequence, as you can well imagine. The HERV sequences carry instructions for transcription, translation, and reintroduction into other parts of the genome (like "jumping genes"). Those events would be as invasive as any new virus entering the cell.