IHOP, we have to stop meeting like this

quantitativeimagining is trapped in purgatory jury duty, so it seems I’ve primarily got myself to talk to this week. This might make a great opportunity to get back to semi-anonymous whining blogging.

I may have made a mistake when I planned my schedule for this semester.

As a graduate student, my funding (stipend + tuition) for the last few years has principally come from teaching-assistantships. The theory is you have a ‘half-time’ teaching position (~20 hours of work a week), which pays the bills, and leaves ‘half-time’ (~20 additional hours) for research. I’ve been intending to TA an intro biology lab for a while, and this semester finally got the opportunity. However, one of the intro-biology lecture professors requested me specifically as a TA, and I’m a sucker for that kind of flattery, so I’m splitting my time. Theoretically I’m 1/4 time (10 hours) for the lecture, and 1/4 time for the biology lab. In reality, I have more responsibilities for the lecture than I did last semester, when I was 1/2 time for that position, and TA work is consuming close to 30 hours a week. It also has been more stressful and less fun than some of my previous teaching experiences– lots of circumstances outside of my control (people not communicating with me, technological quirks) that have been setting me up to look stupid and incompetent.

This schedule also leaves 10-20 hours for research, about 5-10 of which gets sucked into my own class/meetings/chores/etc. I end up having maybe one to two afternoons during the standard work-week to actually devote to research, which puts a fair amount of pressure on me to be productive on evenings/weekends. As it happens, I’m not someone who works well under that kind of pressure. Have I mentioned that I’m in the fifth year of my PhD, and research progress this semester is non-optional? I haven’t been able to sleep on Sunday nights since the first week of the semester. All-nighters and I are old acquaintances– we go way back, but I’m twenty-six and I’m starting to feel a little weird about this lifestyle.

These are all purely first-world problems, causing only minor frustration. It’s also absolutely a situation I created for myself, eyes open. I should still have enough time to accomplish all that I need, especially if I stop psyching myself out.

The spooky grad-student hell dream

I few months ago I saw a production of “The Book of Mormon”– the musical written by the creators of South Park. I didn’t really like the (ethnocentric and racist) storyline, but some of the songs were catchy and fun. One of these was “The Spooky Mormon Hell Dream”, link here: http://www.youtube.com/watch?v=hNEh4bm6rNQ

It’s Hell for Mormon-specific minor sins (it features dancing coffee).

I waste a fair amount of mental energy feeling guilty for grad-student sins.

Things I’ve felt guilty about over the last week:

-losing productivity in late afternoon

-not getting to lab until 11:30am (after staying in lab until 3am the night before)

-working on projects that should have been complete several months ago

-outlining a NaNoWriMo novel during office hours

-doing homework the same day it’s due

-gchat and other internet while in lab

-not working on the weekend

-not being conscientious about lab chores

-complaining about my advisers

-not paying attention during talks

-not appreciating graduate school

-being more excited about books/fun than science/work

and last but not least…

-blogging in lab 🙂

Forgive me Science, for I have sinned…

I’m always working on being a better student, and not all weeks are as bad as last week. Still, it’s unusual to go more than a week or so without some failures, and the resulting disproportionate guilt. Graduate Student Hell probably includes angry committee members, rancid seminar coffee, dead specimens, and eventual unemployment. Hopefully that stays a spooky dream, and doesn’t become reality.

Greetings from IHOP

Late night pancakes and coding…fun times.

So much for a regular blogging schedule!

Shanah Tovah, everyone, a few weeks late.

For a couple weeks I was very busy, and then I fell out of the habit.

I’ve also written a second short story, and read…way too many books. It’s funny– I used to work so hard as a graduate student. I had to instill personal boundaries like “no bench work after midnight”, and “if you need to be in by 8am, make sure you’re out by 8pm”, because otherwise that sort of thing happened all the time. These days I have my books, my creative writing, my pets, and a few other hobbies lurking in the background. I sleep every night, I shower every day, and I’m a lot happier. It feels a little like cheating. I have the sense that if I’m not miserable in graduate school, I’m probably not working hard enough.

However, I finally finished Mistborn: The Final Empire. In the space of a couple days, I also read the two sequels. Brandon Sanderson is probably the top name in the epic fantasy genre these days (excluding George R. R. Martin, of course). This Penny Arcade comic isn’t entirely wrong: http://www.penny-arcade.com/comic/2013/09/30/sanderfuge

His prose is decent, his characterization is not extremely convincing, and large parts of his books get redundant and long winded. By the end of the trilogy, I’d find myself skipping pages at a time, because they were covering old (or annoying) ground.

That said, he can *nail* an ending! Any complaints I had about writing quality consistently disappeared in the last hundred pages of his books. They were all fast paced, surprising, and for lack of a better word, awesome. After finishing the Final Empire, and book 2 “Mistborn: The Well of Ascension”, I was ready to take back anything negative I’d ever said or thought about his writing. They more than make up for other weaknesses.

Starting the thesis

In the last week I’ve made a folder on my computer titled ‘Thesis’. I wont be graduating for another ~2 years, but I’ve started some outlines. I’m supposed to send an outline of one of my thesis chapters (not the imaging chapter, a different project) to my committee. I was supposed to have done that a couple weeks ago, but I think I’ve got about a month’s leeway. It’s exciting having that folder– it’s the light at the end of the tunnel. I’m also happy to be working on this project again– it’s the kind of biology that brought me to graduate school.

Today I also had my first meeting with Senior-Adviser in several months. He’s not impressed with my overall progress over the summer. He’s generally difficult to impress, so this isn’t the end of the world. He’s a very old-school scientist-late nights, long weekends, etc. He was just noticing that a manuscript I’ve been working on was projected to be done by now. However, he’s been gone for the summer, so he’s got the birds-eye perspective. He’s not aware of all the trouble-shooting and supplemental work I needed to do to make this manuscript happen.

Of course, his disapproval is not entirely unfair. There’s been times over the summer where I’ve been distracted (especially when my botanist-friend was visiting), or could have generally worked harder.

Either way, I’m not too upset. Even when Senior-Adviser is being critical (which is often), the criticisms are rarely personal, so they’re easy to take. He just wants the work to get done. I want the same thing. We’re always clearly on the same team.

meetings with advisers

I had a meeting with Adviser-Prime today, discussing the image-analysis project I’ve been working on for most of the summer. My interactions with Adviser-Prime have been somewhat rocky in the past, but they’re currently at a high point. I can’t remember ever having such a long stretch of positive meetings.  He commented today that he’s not sure what’s changed with me, but that it’s like ‘working with a different person’.

I haven’t changed, but I believe I can list some of the things that have given that impression.

1) We’re meeting semi-regularly, not too frequently (approximately once every other week).  Overly frequent meetings can give the impression of nothing changing.  However, we’ve usually had the opposite problem, which is…

2) We’re meeting semi-regularly, as opposed to not meeting at all.  In the past we’ve gone months without meeting, and that can really highlight the slowness of science.

To give an example, at the beginning of the summer we agreed I’d have a draft of one manuscript finished by the end of July, and an outline of a thesis chapter (unrelated to the manuscript) done by mid August.  Now in mid-August, the manuscript draft is only partly written, and I’m just getting started with the thesis chapter.  From a birds eye view, I didn’t meet either of the goals that seemed pretty reasonable at the beginning of the summer. However, because we’ve been meeting approximately bi-weekly, he’s seen where I’ve expanded the analysis section, and how I’ve been trouble shooting a few aspects of the project that went sideways. Every meeting, he’s seen me make good progress from the previous meeting, although not on the linear path we’d originally projected. The more frequent meetings have also allowed him to give me feedback, which has indubitably helped keep me on track.

3) I’ve begun bringing written agendas to our meetings, in which we discuss the goals we’d set on our previous meeting, how I’ve progressed with them, and what I believe should be the next steps. I usually include a few figures or tables of data to illustrate the results, and we write his comments into the document each week, and each keep a copy.

This was my idea, but Adviser-Prime has been very enthusiastic about the concept. This keeps us both accountable and on task.  It forces me to stay organized with my work, and also protects me from feeling ambushed about tasks I haven’t prioritized (our last confrontation was over a textbook I hadn’t read).

4) I’ve been developing a more assertive attitude.  This has been an ongoing effort– projecting a certain minimum amount of confidence seems to be extremely important.

If I tell people “I’m worried about my progress, I don’t think I’m getting enough done, I don’t really know what this result means”, etc., they will believe all of it and more. Taking control of the conversation means taking control of how I’m perceived, and it’s possible to do so without being pushy. These days, I try to make sure we stay in the frame of ‘we’re talking about interesting results’, and away from ‘justifying failure’.

5) I’m not currently teaching or taking classes (both can occasionally be big time-sinks, and really slow research down).

6) I’M NOT DOING BENCH WORK.  Computational work comes much more naturally.

My graduate work would probably have gone more smoothly over the last few years if I’d started a PhD already knowing these things. I frequently wish I hadn’t started a PhD directly out of college– some of this has less to do with ‘the pilgrimage’, and more to do with growing up.

Some of this is also just the wheel.  I hope it continues to stay up for a while (and that eventually I’ll graduate 🙂 )

My thesis is lost in a random forest!

The statistics term of the day is ‘truncated power basis’.

The less ironic stats term of the day is ‘knots’, in the context of spline regression. When you fit a spline, you set a different polynomial function for each value of X– ‘knots’ are where the different functions tie together.  Terms like that make the whole concept easier to understand and remember.
These methods are fun to read about, and the information is definitely going be helpful when I’m analyzing data over the next few months.
However, it can be frustrating how much time it takes up.  It’s not directly moving my phd along.  If I’m going to be reading for the sake of scholarship, I’d prefer if it was more closely related to genetics or biology.

My botanist-friend is visiting from Gondal over the next few weeks– he’ll be helping me move across town.  Between the reading, the move, and the visitor, this may not be a great week for research.

year of the blog

I’ve recently had a birthday, and made several personal resolutions.
One of these is to write something in this blog, every day, even if it’s just one or two sentences.
This will be the year of the blog.

I’m currently at an all night diner finishing up a statistics textbook, watching some data I’m processing eat up all my computer’s memory.
Sometimes I wonder about my decision to go to graduate school.
I wouldn’t say I’m not interested in ridge regression, but I think the fantasy novel I just downloaded might be more interesting.