I've not heard of that book before but will have to check it out. Did it happen to mention any of the experimental research done showing that removal of 'junk DNA' makes organisms (microorganisms anyway) less capable of adapting to environmental change? As I remember it, some researchers took a bacteria (probably e. coli, that's usually the easiest to do this sort of thing with but I'm not certain) and separated out two populations. In one they let it be, and in the other they stripped out all 'junk' DNA that didn't play a role in protein synthesis. Then they introduced harsh conditions to both (I think something like high acidity or low availability of food or something like that) and while the 'junky' population adapted relatively quickly, the 'pure' population quickly died off and wasn't able to gain beneficial mutations quickly enough to survive.

No, most of the viral junk DNA is just repeating copies of non-coding regions (Alu and other repeats). This is an example of an actual coding gene from a virus, which is much more rare and sporadic.

Excellent book. It made the subject so readily accessible to the layman.