Marginal Revolution outlines its comments policy:
Marginal Revolution: Comments policy: In response to a few inquiries, here is a reminder about our comments policy. Having "comments on" is neither a default nor a right for the reader. Usually the quality of the comments is excellent; I read them with learning and real joy. But some topics attract, or have attracted, poorly thought out or overly emotional comments. Some topics fall into very predictable debates. In other cases previous comments already have attracted significant and noteworthy discussion. Paul Krugman, free will, religion, Iraq, and yes immigration are a few examples of these tendencies. Once low-quality comments get started, they tend to feed upon themselves, sometimes for days at a time. We know that good comments attract readers to this blog, so we wish to maximize the average quality of comments. Sometimes this means no comments, but that is in the interests of good debate, stochastically speaking and properly construed over time.
Don't overanalyze this. Other times comments are turned off simply because neither of us is available to monitor for spam. There is also something to be said for randomization per se. We also do not favor off-topic comments, which tend to be deleted. "Comments off" is not an attempt to stifle debate; there are thousands and indeed millions of other outlets for your views and that is debate too.
I would like to know the algorithm they have for predicting when the average quality of comments on a thread will be negative...