I submitted a link yesterday which received some up votes, comments and spent some time on the front page. I had to go to bed while it was still there, as I'm on the other side of the world from most HN users. I woke up this morning and discovered I could no longer comment on the thread or reply to comments on it - though I could still vote them up.
I compared it to threads of a similar age and similar location on the top news list and commenting on those still seems to be open.
Is this a bug or by design? Did the thread get closed?