Chapter 3 is a bit daunting to comment on given its length and substance. The following are some initial reactions rather than a comprehensive analysis.
The discussion of compositional mechanisms is worthwhile. I can see the logic of grouping them together as qualitatively similar and qualitatively distinct from substitution; I wonder if all biologists would agree.
Several of them could be considered mutations in a general sense, which can muddy some discussions of evolutionary biology. If one tends to think of mutation as synonymous with substitution, then one will likely think of evolution largely in terms of gradualism (as Watson defines it) with all the limitations and caveats that come with it.
I found the discussion of recombination and the various models of how it might beneficial to be helpful. I’m not sure I’ve seen that particular topic covered so systematically. I also appreciated the discussion of crossover in genetic algorithms and why it can sometimes seem like just another form of mutation. As someone who has played around a little bit with basic GA programming, I’ve puzzled over that myself.
Somewhere around “Beyond Sex” I started to get bogged down more frequently. Possibly because the connections to biology came around less often, possibly because the chapter focuses a lot on surveying more than synthesis. I suspect I will need to revisit some of this material if the later chapters build on it.