Thursday, October 25, 2012

Planning Ahead and Writing As You Go

So even though I'm probably 2-ish years from graduating (plus some very large error bars on that number), I've started writing bits and pieces of my thesis. Not just in the sense that I'm writing manuscripts, which I'm also working on, but in that I'm trying to plot out the larger story I'm trying to tell. I also want to right everything down while I still remember why I did it in a particular way.

My advisor seems confused whenever I mention this approach. He's very strongly in the camp of write the papers, and copy-paste to make a thesis. Given his reading habits, it does mean fewer things he has to read, which is good for getting anything out the door. However, at this point, many of my results are of the "and this approach didn't work" variety. Not necessarily paper material, but things I feel should be documented for future students in the group. A quick poll of Twitter seems to indicate that the thesis is a good place to include this sort of thing, and it can always be deleted when you go to do the manuscript. Of course, according to the comments at GenomicRepairman, it seems unlikely hypothetical future students are going to read it anyway.

I also like looking at the bigger picture, because it gives me a sense of things I've *done*, not just the giant list of things I still need to do. When I'm in the writing mood, I'm trying to write up methods sections and working on piecing together background sections as I read. It also helps me plan, and find the holes in my story I need to fill.

What approach did you take (or are you taking) to thesis writing?

Tuesday, October 9, 2012

Being Smart Doesn't Mean You Can't Be Dumb Too

PLS has a post up, "I'm too smart to end up like that". Man, did that hit a little too close to home. As I've probably made abundantly clear, I am not in a good advising situation. It's one of the major factors that drove me into blogging. As of last week, more students from my group have quit grad school than graduated  which is NOT typical for my department. Nor were any of these of the "I just don't belong in grad school" variety. Two of the students had been here for 5+ years and had at least one paper before finally leaving, and they weren't subtle about their reasons.

In my second year, I was seriously contemplating leaving. Senior students (one of whom ended up leaving) told me to switch groups while I still could. I had fellowship money, anyone would take me. But I had what I thought was four papers worth of data, and I didn't want to leave that much data. Well, two years later, my advisor finally read the first manuscript, and the reviews come back with a reference which effectively killed the next three papers. It's very easy for me to look back and say I should have left then.

But when you join a group, you have to be optimistic. You have to assume that the students who are willing to voice issues have personality conflicts with their advisors, because many times, that's the truth. You can't start assuming failure, or it will become a self-fulfilling prophecy. Until you find conclusive evidence to the contrary, you assume things will work. And as time goes on, you know certain things are lies, but you hope for once they won't be. "I'll get to it next week." "We'll meet soon." "Our collaborators will send us the code later this week." Because the alternatives are depression, or leaving, and where are you going to go?

The realities of Ph.D funding and departmental politics can make it very difficult to jump ship by the time you've been in a group long enough to have real problems. There may be 30 professors in your department, but half of them are doing projects you are absolutely uninterested in or have no background in. Most of the remaining professors have no more funding, depending on the time of year, or have proposals submitted without any firm cash in hand. Then there's the professors who are too buddy-buddy with your old boss. If you take can take a Master's and change universities, you may have to go through course requirements and qualifying exams all over again. Sometimes, you can change departments within a university, but courses and quals still present a very large obstacle.

There are days when I think I am very, very stupid for continuing with my advisor. But there are also days when I look at the data, and realize that I've done good work, and if I can nag him into reading it, I will put out good papers. I enjoy my project (most days) and think my research is interesting. I'm not in a position that's threatening my safety. And frankly, I don't have the willpower to start over in another group.

Your advisor doesn't have to be blatantly abusive to end up in a very bad situation. It may not even be noticeable until a year or two in, when you notice the student who has to do "just one more experiment" or "just one more paper" before they graduate. It can be simply always having you as one of their lowest priorities. And it's much harder to notice until it's too late.

And maybe the students in PLS's course will scoff and say they're too smart to end up like me. Maybe they're right. But sometimes, being smart does nothing to prevent you from making bad or unlucky choices.

Tuesday, October 2, 2012

Finding Motivation

This weekend, there was a recruitment event for high school students looking at GiantU. Departments put on demonstrations and do brief presentations about why we're awesome. I volunteered to help with the demos, along with a bunch of undergrads. The undergrads were all very self-conscious, and asked me to do most of the talk.

When I don't do it for awhile,  I forget how much I really enjoy teaching. While TAing this year is out, because I'm still on fellowship, I'm going to try and convince my advisor to let me TA again in the fall (generally, students only teach once, unless their advisor has no money or they're switching groups).  Teaching reminds me why I'm doing this in the first place.

Another senior student has left the group instead of graduating. I've now seen more people walk out on my advisor than graduate. Needless to say, morale is low around here. But we're doing what we can to keep each other motivated. There be almost no overlap between projects, but having someone ask questions that make you think is still a source of motivation. There's a sort of grim determination of "it won't be me". Now, if I could just get code to do what I want it to do...