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Some points. Sorry to not give references. I hope later to write up a lot of this stuff, but meanwhile I think a warning on Yudkowsky's warning is desirable asap.
From memory, Jerry Coyne is actually a fan of Gould - don't know where Tooby thought that he wasn't. Ditto David Jablonski.
Gould 'finished' his 1400 page plus magnum opus, The Structure of Evolutionary Theory, only a few months before he died of cancer. Yes, it is often woefully verbose, with repetitions and overlaps that would otherwise be imho inexcusable. And his various thoughts on different levels of selection are not well structured (but imvho these are quite difficult for non-mathematicians / programmers to think about - it takes a bit of practice before you think about them clearly). But there is gold buried in his sea of words.
Gould was fighting, inter alia, against biologists' inertia re 2nd order selection, and against Dawkin's earlier mistake (since recanted) re the Selfish Gene. See, e.g. Darwin in the Genome by Lynn Helena Caporale for a hint of what Gould was up against. And Mayr changed his mind during his long career re speciations. I groan at some of Gould's overstatement, but sorry Yudkowsky, at least on this topic, your overstatement is worse than Gould's.
I haven't read all Barkley__Rosser's comments, but at least the first few make a lot of sense to me - nice work Barkley.