“I would question if Thomkins’ methodology used on humans would still show us 99.9% the same genetically?”
I think it would, actually. The issues of synteny and differencing chromosome numbers would not come in to play.
His method may or may not be more accurate than others. But it doesn’t change anything vis-a-vis common descent.
Phylogenetic results wouldn’t change, I don’t think. In other words, apes and humans would still be closest whether 98% or 85% etc... Down the line.
Right, the numbers themselves are not so important except possibly when different methodologies are used to produce them.
Also we see such words as "identical" and "similar" used more-or-less interchangeably.
So now Thomkins thinks he's made an important point by emphasizing the mismatches between human & chimp DNA.
He suggests it means the actual average rate of mutations must be much impossibly higher than most scientists now figure.
But if scientists are not measuring mutations in the areas where Thomkins finds differences, then his point is, well... pointless, is it not?