This was at #1 on the front page like an hour ago, and now after almost 100 new comments it’s off the front page at #40. What happened?

The answer could be: (1) users flagged it; (2) mods downweighted it; and/or (3) it set off the flamewar detector, a,k.a. the overheated discussion detector.

In this case it was #3.

That's one of the ways the system autocorrects. A sensational/indignant post attracts upvotes because that's how upvotes work (this is a weakness of the upvoting system), and this triggers an overheated discussion, which trips the flamewar detector which penalizes the post. It's about as simple a feedback mechanism as a thermostat.

That's why it's not uncommon for something to be at #1 and have tons of upvotes and comments, and then suddenly plummet. We do review all the threads that get that particular penalty but sometimes it takes a while.

Edit: ok, I've reviewed it. In this case, the thread is actually pretty good. I'm not sold on the article*, but a good thread is enough to turn off the flamewar penalty in this case, and I've done so.

(* not a judgment about article quality in general, only about how good a fit it is or isn't for HN)

I don't know how this works. @dang might have an explanation?