In at least one of those cases (vaccination), there may have been no way for scientists to get out an engage in advance. Indeed, science had won. Vaccination was accepted as routine for decades. Then, panic emerged in the 1990s or so in various forms. And again, there's little discussion of how to deal with such flare-ups: "crisis communication" gets about half a paragraph.
Maybe those are good models. But it's still incredibly frustrating that they provide no insight on how to resolve issues where the science is as clear as it ever gets, and large numbers of nonscientists simply discount it. You know the issues: evolution, vaccination, climate change, etc. On subjects like these, Mooney all but throws in the towel:
Battle lines have hardened... and it may be far too late to “fix” the situation.
The word "fix" didn't need scare quotes in that sentence. The disconnect is a problem, and it does need to be fixed.
Additional: I rather like some of the commentary made by Evil Monkey here.