Of course, I don't have any answers. But, I don't find the idea of hotspots surprising. Snowflakes (at least as an analogy) form randomly. They accrue molecules of water in a haphazard way. Nevertheless, it can only form certain combinations of shapes (allowing for many many forms, of course). Why? Because of the chemical properties of water.The paper tries to explain something that's long been known: there seem to be mutation "hotspots" in areas of the genome. It proposes a model to account for this. It is interesting, but hardly likely to "shake things up majorly" as the author claims in an act of blatant self-promotion. It also doesn't address the issue of randomness of the mutations in regards to fitness.
So, perhaps DNA can accrue (to crudely extend the metaphor) changes only in certain ways. Seems a reasonable area of research.
You can't roll a 7 on a standard 6-sided die.
(That is to say, I agree with your post.)
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