HN was originally largely in the "scientific conference" mode, with very smart people discussing areas in which they were experts. Now HN has much more "cocktail party" flavor, with smart people chatting about random things they often know little about. And certain subjects (e.g. economics, Apple, sexism, piracy) bring out the "debate team" commenters.
Any of the three types can carry on happily by themself. However, much of the problem comes when the types of conversation mix. The "cocktail party" conversations will annoy the "scientific conference" readers, since half of what they say is wrong. Conversely, the "scientific conference" commenters come across as pedantic when they interrupt a fun conversation with facts or "citation needed". A conversation between "debate team" and one of the other groups obviously goes nowhere.
I think the comment karma in HN encourages "cocktail party" conversation since you're as likely to get upvoted for trivial chitchat as a carefully-reasoned expert statement. (See http://news.ycombinator.com/bestcomments) Also, as I just found out, "expired link" on HN encourages quick comments rather than slowly written ones.
(And yes, I realize the irony that this is a "cocktail party" style comment of with my random opinion. I've actually considered ways of making this categorization quantitative, but it would take way too much time.)