Today I picked my topic for my Preliminary Qualifying Exam (PQE). The PQE is none of the above. It is not preliminary; in fact, it is the last requirement in the program before dissertation. It is not a qualifying exam (“quals”), since this term refers to a test given at the beginning of a doctoral program in order to confirm that entrants have the required basic knowledge. Moreover, it is not an exam at all.

The PQE consists of a grant proposal, in written form, and an accompanying oral presentation. Each student may write on a topic in any field of their choosing, and will be judged by a panel of professors in that field. Note that this is a mock grant proposal. Although the paper is intended to include the full scope and detail of a true grant proposal, it is not intended to be submitted to an actual grant agency. Most students do not ever attempt the project proposed in their PQE. However, on rare occasions, students have gone on to write their dissertation by completing their PQE proposal, or even submit their PQE years later to an actual grant agency.

Tentatively, my PQE topic is on MRI Microscopy. The proposal is to perform a complete theoretical and simulational study to answer the question “how high a resolution can possibly be achieved by scaling down an MRI?”. If the answer is 5 microns, then MRI is not widely useful for microscopy. If the answer is 5 Angstroms, then MRI could be the future of microscopes.

Note that this is a very indirect project. I am not actually going to determine the maximum possible resolution of MRI. Rather, I am going to write an argument that a project to determine the maximum resolution of MRI would be worth funding. I have to show that:

  • The answer to this question is unknown.
  • It would be valuable to know the answer to this question.
  • This question is possible to answer, given what is already known.
  • I am the right person to answer the question, so you should give me money.

It’s quite an interesting challenge. I suspect that topic may evolve somewhat by the time the proposal is complete, which I hope will be in late spring.


Tomorrow morning is the first lecture for the class I’m TA’ing. We (the instructors) will get our first glimpse of how many students are taking the class, and try to determine things like when we should hold sections and office hours.

Tomorrow afternoon is my meeting with Jim (the chairman of the Biophysics department). I’m supposed to describe my proposal for my Preliminary Qualifying Exam (a mock grant proposal). I have no idea what I’m going to do.

So it’s going to be quite a day, tomorrow.

State of the Union

Tonight was Bush’s last S of the U. It was very well planned, and well-delivered. If I weren’t familiar with the full debate on these topics (guest worker programs, border fences, warrantless wiretaps, telecom immunity) I might well have been convinced that his was the voice of reason.

In contrast, the “Democratic response” was unbelievably bland, absolutely soporific, to the point that I literally could not stand to pay attention to it. I don’t think they said anything of any interest, or rebutted any of Bush’s implied claims, but if they did, I surely missed it. Are there really no Democrats who can read off a teleprompter with some hint of emotion, and aren’t running in the primary?

Darwin’s Nightmare

Last night, after Darwin’s Nightmare at the Civic Defense Film Festival. It was astonishing.

The movie is a documentary about the Tanzanian fishing industry in Mwanza City on Lake Victoria. It is composed entirely of camera-forward interviews; the production staff is never seen. The effect is to immerse the viewer in this world where Russian pilots transport arms into Africa and bring back fish, prostitutes are stabbed to death by their clients, fishermen dive into crocodile-infested waters to grab perch, and street children fight over scraps of food, then go to sleep by inhaling the fumes from melted styrofoam. It is hard to believe, and yet absolutely undeniable.

Brains are blue

At least, by the time they come our way. The folds are especially blue, and much of the surface is also gray or brown. There’s a surprisingly wide range of sizes, and one can easily get a sense that certain brains are diseased by their shape and color.

The brains are donated by participants in the Framingham Heart Study, which started in 1948. Participants in the study are interviewed and examined thoroughly every two years, so each brain (actually, we only get one hemisphere) comes from someone whose lifestyle and medical history are known in unusual detail.

Hopefully, I will be able to produce high resolution maps of these brains, and we will be to connect features of those maps to each donor’s medical history.


This morning, after a meeting with the professor for the course I’m TA’ing, I saw a funeral procession go past.

As I was leaving work in the evening, one of my coworkers walked by with a big cooler. I inquired, and she explained that we are getting a brain tomorrow morning from the Framingham study.

This sort of work definitely alters one’s perspective.

The worst street

I went out to dinner tonight at Grasshopper, a vegan restaurant in Allston. This is my second time there, and I have concluded that their trick is to make their food enticing by adding a huge amount of sugar syrup to almost every dish.

One of the other guests was a fellow bicyclist, and we concurred that Cambridge St is possibly the worst street for bicycling in the whole of Boston. It has 3 lanes each way, no bike lanes, superhighway-style offramps, and is terribly lit, especially on both of the steep overpasses, one of which crosses an 8-lane interstate, and the other a railyard. Also, the potholes are bad.

Thankfully, this 6-lane highway seems to have very light traffic, and very narrow lanes. They should really reduce it to two lanes each way and add a bike lane. They could also fix the broken streetlights, while they’re at it.

Video Games

I went out to dinner tonight with a bunch of nerds. It’s a regularly scheduled event, and fairly open. It’s almost like attending an official meeting of nerds. Anyway, lots of fun.

Of the eight people at dinner, one was a professor of video games at MIT, and many of the others were video game aficionados, so I availed myself of the opportunity to ask about two video games I recalled from watching my brother Jeff. I had vivid memories of both games, but didn’t know the names.

The first game was on the Apple IIe, and consisted of the player driving a yellow disk-like hovercraft over a sea, with the horizon visible in the distance and sky above it. Based on this description, the professor identified the game as AirHeart. I found some screenshots here, and even though I haven’t seen the game since I was 4 years old, I recognized it immediately.*

The second game ran on a PC, and was a side-scroller. I recalled a dark atmosphere, with a very distinctive, beautiful visual style, a small character, and dangerous black leeches. From this description, someone else identified the game as Out of This World, which is definitely correct. I might have been 9 the last time I saw this game.

So it was a very impressive, and fun, evening for me.

*: I might have been as old as 7. I can’t be sure.


How do you get white cat hair off a black sweater?

EDIT: With my roommate Simon’s rolly thing. Thanks Simon!

How do you get dayshifted, so as to wake up before noon?

EDIT: I got to work before 11:30, which is ok. Actually, it’s good, since otherwise I might have left before the very fun, unplanned dinner party.


Yesterday was another OLPC demo day. I brought in my software to show it off to all the visiting dignitaries from foreign countries and such. Unfortunately, the distance measurement didn’t work, due to an unknown, mysterious technical issue that I am quite convinced is not my fault. Luckily, I had something else to demonstrate, so that was fine. I must have been somewhat convincing. I’ve never been asked for my business card so many times in my life, and I kept having to write down my e-mail address for people (because I don’t have a card).

The gathering was followed by a send-off party of sorts for an OLPC engineer who’s leaving the country temporarily due to visa issues. The party quickly turned into everyone sitting around the TV, watching the guest of honor play Portal, a new video game, on the PlayStation 3. I got a chance to play some, and it was quite fun. Portal is an amazing video game, and part of the fun is that it is relatively short. We were able to play through the entire thing between 7:30 PM and 1:30 AM.

Late-night videogame parties full of major professional nerds are definitely fun. It’s less clear if Wednesday nights are the best time for them.