I had some more thoughts on the “too nice/too polite” problem. I think the other side of my problem is that I've been practicing on other grad students.
The reason why I decided to start with Journal Clubs was because the speakers aren't as intimidating as those at other departmental (meta-departmental) seminars. Additionally, we're encouraged to critically read all the General and Specialty Journal Club papers and the speaker is there not only to present the paper, but also to give out extra information (hence, all the extra research that goes into presenting one of these things). However, what didn't occur to me was that I'd be “breaking the code.”
Students don't tend to ask questions at these Journal Clubs. In fact, I think that the prevailing sentiment is that we're supposed to go easy on the students, because if we were up there wouldn't we want the same consideration? So, easy questions (eg. Can you define that negative control?) are ok, but the hard ones (eg. Those controls are very off. Can you still interpret the data?) are not. In other words, we, as grad students, should show some solidarity and help each other out in not looking stupid in front of the department. So, I feel like I've doubly hurt someone because not only did I ask a bothersome question, but it came from an unexpected source.
This thought came up because Advisor told me that he was glad that I asked that question. He told me that it needed to be asked and that he was pleased that I had gotten up the courage to ask it (he knows about my hesitancy to talk in public). I explained to him this feeling that perhaps that I should have waited for Dr. BigShot to ask. Advisor told me that was nonsense and that grad students should ask questions, Journal Club should lead to a lively debate, and it was a question for which the speaker should have been prepared. I acknowledged that in theory all of those things are probably true. He then said that perhaps I was taking this graduate student solidarity thing a bit too far. This led to a rather boring conversation (to anyone outside our department) about departmental culture and things that could make it better. In parting Advisor told me that it was good that I was coming out of my shell in the department and that other people could see his brilliance at picking me for a grad student.*
Advisor was being tongue-in-cheek there. We tend to joke a lot, so he wasn't being insulting to me.