I don’t think that the retrovirus that gets incorporated into the DNA of its host is necessarily active and capable of generating RNA copies. The translation process generates mutations and irrespective of that the packaging of the RNA, infection of a host and (after reverse transcriptase) integration into the host DNA can take place. So, the thing that gets integrated may be dead or barely alive on arrival. And that could well be the case for a majority of the cases because of selection pressure. Killing the host cell (egg) would not result in offspring.

Pheromones, as we now know, are the chemicals that control nutrient chemical-dependent reproduction in all species. It seems likely that ERVs, including human ERVs (HERVs) cause the changes in intracellular signaling and stochastic gene expression that allow us to use olfaction and odor receptors in the clear evolutionary trail that can be followed from unicellular organisms to insects to humans.

The HERVs, for example, need only alter a cell’s ability to metabolize nutrient chemicals (food) to cause downstream effects on every cell of any organism. The metabolism of the nutrient chemicals to pheromones does the rest in the context of adaptive evolution.

When one looks at archaeal communities, viruses are often permanently linked to them from without, yet don’t destroy their erstwhile hosts. They are probably helping to transfer genes that convey the ability to get along in their resource-poor environments, both to locals as well as to newcomers. Bacterial viruses tend to be much more selfish and destructive, but then bacteria tend to be as well, all other things being equal (being opportunists of rich pickings that archaea apparently are not- there are few hints they cause disease (and if some do its unusual)).

In eukaryotes it may be the case (as some theorize) that nucleated cells come from a fusion of archaeal and eubacterial parents (along with their viruses one has to guess)- is there some continual give and take with external agents as well? The archaeal viruses, if benign and regulatory, would have formed the basis for much of the more cooperative executive machinery of the cell, while more opportunistic types would keep scaling the walls looking for entry. Some can be tamed. Can some of the ancient domesticated control genes mutate into fresh opportunists? My guess would be yes. Genetic dialectic. Lysenko would be proud- no, wait, he would have rejected all of this. Just as Marr would have rejected modern linguistics. God I miss the good old gulag days.