October 2006
Retreat
The biochemistry department holds a retreat once per year that all members of the department are required to attend. This year it's one day shorter than last year with the same amount of break time, so we have it a lot easier than last year but it's still a lot of science in very few days.
Every lab in the department has roughly an hour in which to present the work they have done over the past year. The PI speaks then typically one to three postdocs or graduate students give 15 minute talks on their research. In addition, poster sessions are held from 9 to 12AM for the two nights we stay there. Every member of the department who has been there for more than four months is required to present in some form or another at the retreat.
The retreat itself is held in a really beautiful place. Stanford owns a "hotel" near South Lake Tahoe towards the southern end of Fallen Leaf Lake. (It's at the end of fallen leaf lake road if you want to look at it through google maps.) Stanford Sierra Camp is basically a set of lodges with housing suites nestled around the edge of this lake. From here any number of outdoor sports are offered including tennis, basketball, sailing (a number of boats ranging from ~5 person boats to others more suited for individual sailing), waterski (in the summer) and of course hiking. But this is the Biochemistry Department retreat, so we only had a few precious hours on Thursday to explore these possibilities. The rest of the time was all science all the time except when eating and sleeping.
Not that this is a bad thing, I learned a tremendous amount in just three days. Further, I now have a good idea of what projects are going on in each lab. Most of the talks were very interesting, but some actually didn't really overwhelm me with interest. In these cases I often couldn't really see how what was being discovered was really important or particularly novel. Again though, the vast majority of the talks were fascinating and even though I'm not specifically interested in every last one of the projects being explored in the department, I would be very happy to find myself as close to the bleeding edge as these labs. Luckily, I'll have that chance.
On Thursday I decided to take a boat out sailing despite the drizzle. The scenery was still quite impressive and more importantly there was enough wind for me to go very fast. There's nothing quite like gliding along the water with no noise other than the rushing turbulence along the hull. In the morning I got up very early to see the sunrise and take a brief jump in the lake. Very brief. I'm not sure what the water temperature is except that it's very cold, but hey, it definitely wakes you up.
This past Sunday was the first football game for the Biochemistry intramural football team. Unfortunately we lost to the team from the graduate school of business. On the plus side, it's likely they're the best flag football team in the league with several championships under their belt. This upcoming Sunday will be the real test of our abilities. Also this Monday I learned that the finger injury I sustained two weeks ago at football practice is in fact a small fracture and a distended tendon in my middle finger. I'll be going 4 more weeks in buddy splints, basically velcro straps that act like tape connecting the middle and index fingers. Whatever, play hard, get injured. It would be nicer if we won though. Luckily, Sunday we'll do that.
On the non-retreat work side, we ended up missing two lectures of macromolecules, meaning when we returned on Monday we had a lot of catching up to do. Tuesday night, I did manage to finish watching both video taped lectures and the first half of the problem set. Rotation-wise today I ordered primers for my experiments so come Friday I'll be able to start doing some PCR-mutagenesis and getting the project moving. Meantime, I've got to figure out where I want mutations for the 30 amino acids following my DNA binding domain.
I'll conclude with some pictures from the retreat and football:
Sports and Pictures
I think it's fair to say that now the semester has reached a fairly regular schedule. I have homework, papers to read and today I met with Anne Brunet in the genetics department about the rotation project I'm doing in the Ferrell lab.
Basically I'm going to be working with a postdoc in the lab on the evolutionary origins of acetylation. He has a theory on how this regulatory mechanism came to be and we're interested in seeing whether acetylation sites in a protein called FOXO have different effects on a given protein. In other words, do all acetylation sites contribute equally to regulation or does one in particular matter more? Hopefully my rotation project will lay some of the foundations for answering this and other questions.
Classes are also starting to really get underway. We have our first problem set for the macromolecules course and yesterday we all met to discuss how to solve the stickier problems (more or less all of them). We got our first paper to review for the frontiers course as well. Frontiers is a course held by the genetics, developmental biology and biochemistry departments that basically reviews a paper from the current literature by that week's seminar speaker. We read the paper then on Tuesdays at 5:00 we review it as a group. On Wednesday the author of the paper gives a talk at Stanford and afterwards joins the students in frontiers for a separate question and answer session. We can then ask them about pretty much anything we'd like. How did they get into research? What does figure 4 in the paper we just read mean? Is there a flaw in their assumptions? How do you write a grant to get money for what you actually want to do as opposed to what institutions will fund? That kind of stuff. Trouble is the paper for this week was really dense genetics. Especially considering that I've never taken a genetics course in my life, a deficiency I hope to address at some point in the near future. Even the professor had a little bit of trouble making sense of it. Nevertheless once we got to the meat of the paper it was really quite interesting to get some exposure to the rather new kind of whole-genome genetic analysis it described.
It's not all classes and rotations here though, the biochemistry department graduate students have started a co-ed intramural flag football team. We practice once or twice a week and I feel we're getting pretty good, which is great. Unfortunately there have been some casualties of the game. Eric, a 3rd year in the Pfeffer lab, has torn or twisted or otherwise damaged the tendons in his pinkie finger pretty badly. Two practices ago, I also became a victim of football practice. I tried to catch a throw that was coming in low to the ground, but it was dark so my hand wasn't in the right place. The ball jammed into my right middle finger pretty badly. A few doctor's appointments and a set of Xrays later and my finger is now in a cast. I also have an appointment with a hand specialist next Monday to tell me whether or not I've actually chipped a bone in one of the joints. I may not be playing in the next couple of weeks. We'll see; hopefully it heals by the time we actually start playing games. It's still a little bit swollen and I can't fully curl the finger without it hurting. I think it's getting better though. Hopefully anyway.
But I don't need a finger to go biking. This past Saturday I took the nice bike out for its first intentional long distance ride since I got here. I say intentional because earlier I locked my keys in the car after getting my bike looked at. Luckily the bike was out of the car, so I had a way to get back to Stanford from Mountain View to get a set of spare keys (Escondido Village staff loaned me a key to get into my apartment). Total distance: 9.2 miles. Saturday though, that was intentional. I went for 15.4 miles up Page Mill road, which is actually fairly uphill for most of the ride traveling away from my apartment. The way back was much nicer. Now 15.4 miles isn't actually long distance by the standards of people who bike this way fairly regularly, but I'll get to some longer trips eventually.
I end here with some pictures I've picked up in the past couple of days. I'm trying to get better at remembering to take pictures, next entry I'll try to have some from the Biochemistry retreat. Tomorrow we leave for Lake Tahoe where Stanford has a kind of conference center. We'll stay there three days courtesy of the department. It's going to be really beautiful. During the day though, we'll be attending department talks and poster sessions. So on top of being nice place, we're going to get a thorough introduction to the state of research in all the labs in the department. It's going to be an intense, informative weekend.
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