"The controversy penalty can have a sudden and catastrophic effect on an article's ranking, causing an article to be ranked highly one minute and vanish when it hits 40 comments. If you've wondered why a popular article suddenly vanishes from the front page, controversy is a likely cause. "
I've heard it happens on HN but (as only an occasional commenter) I've never noticed it. It just went from #5 to nonexistent.
[1] excuse the IRC lingo