For example, as a notable and glaring omission, the book doesn't address the controversies over abortion at all. (Thus putting Haidt in a very odd position where he purports to have a general theory of moral psychology that explains the contemporary American ideological rifts, but nonchalantly refuses to apply it to the single most ideologically charged moral issue in the U.S. today.)
This blog author critiques an analysis of the abortion controversy that he or she attributes to Haidt. So Haidt evidently applies his theory to abortion somewhere.
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Using Amazon's "Search Inside the Book" feature, I found some discussion of abortion (along with birth control) on page 209 of Haidt's The Happiness Hypothesis. I wonder if that book is working with an earlier version of his theory, because he talks very explicitly about the importance of autonomy to liberals on those pages.
I haven't read The Happiness Hypothesis, but I've just read these pages on Amazon's preview. It seems to me that this was indeed an earlier phase of Haidt's thought, when he advocated a much more simplistic theory of the moral foundations and was still a partisan liberal. (I'm not just throwing around an ideological label here -- these days Haidt indeed describes himself as a "partisan liberal" in past tense.)
In these cited pages, Haidt gives some clearly biased and unrealistic statements. For example, we are told that "On issue after issue, liberals want to maximize autonomy by removing limits, barriers, and restrictions." But obviously, you only need to ask a libertarian for his opinion about this claim to realize that in fact "removing limits, barriers, and restrictions" applies only to a strictly circumscribed set of issues, and the liberal understanding of autonomy in fact has a more complex basis.
These days Haidt is far above such evident partisan biases, but I think he still hasn't come around to re-examining the issues of liberal autonomy in the light of his more recent insight, while at the same time he realizes at some level that it's incompatible even with his current view of the liberal moral foundations. I don't think he's avoiding these problematic discussions in a calculated way, so I think he simply has some sort of "ugh field" around these questions and thus fails to address them clearly and openly.