Mike's Third Try

Sunday, August 20, 2006

Gradual Transitions

I've been thinking about some of the major transitions in my life, and how I've somehow managed to make them all relatively gradual. I came to Boston to work at IBM -- for a summer, when I knew my same old life in high school would be waiting for me after a couple short months. Then when I started MIT, I was already familiar with the area from having worked in Cambridge for two summers. I remember exactly how I started: I was at work one day and realized it was the first day of orientation, so I took a stroll from the office over to the student center and signed in. And I've been around here ever since -- including the summers.

The end of my college life has been even more gradual. First there was getting my bachelor's in '05, after which many of my friends left but my life stayed essentially the same. I spent a term after that as an alum at the Sigma Nu house (which means I didn't have to go to any meetings, or really participate in any of the fraternity activities) before I moved into an apartment and started living on my own -- so that was also a gradual transition. Then I got my master's, and a few more of my friends left, but I kept working on the same research in the same group. To keep my funding going, my professor had to hire me. And here I am, a professional with a job title and a salary and a dental plan.

What I'm getting at is that even though I know I've matured a lot in the last five years, I wonder how much I've missed out on by almost never having had the experience of changing my life to a completely new and unfamiliar place. I suppose orientation and rush at MIT were the closest I've had to this kind of experience, and it's probably telling that I remember that period as one of the most exciting parts of my life. I remember the exhilirating sense of having no habits or routines to restrict me; nothing at all to do but to explore and to meet the thousand other people in the same situation. And even though it seems quaint now that I know how those unlimited possibilites were ultimately determined into all the classes and degrees and friendships and rivalries and hookups and heartbreaks since then, I'm saddened to know that I might never have that feeling - of unlimited possibilities - again.

I really love it in Boston. But maybe I should get out of here, for my own sake.

Wednesday, August 02, 2006

Are there really any functional pseudogenes?

This paper purports to thoroughly explode the existing evidence for a model in which retrotransposed pseudogenes regulate the real gene. Was there really only one example that gave rise to this model?

Thursday, July 20, 2006

Resurrecting Neanderthals

Reconstruction of Neanderthals� Genome Planned - New York Times

The Times has a very well-written article about efforts at the Max Planck Institute to use 454 machines to sequence Neanderthal DNA. Interviewing some of the researchers, it describes very fairly some of the interesting science that will come out of this: three-way comparisons of human, Neanderthal, and chimp DNA to better understand human evolution. They're particularly interested in FOXP2, a so-called "language gene". Great so far. Then, at the very end of the article, the reporter seems to completely pull this out of his ass:

"If the Neanderthal genome were fully recovered, it might in principle be possible to bring the species back from extinction by inserting the Neanderthal genome into a human egg and having volunteers bear Neanderthal infants. There would, however, be great technical and ethical barriers to any such venture."

Wednesday, June 21, 2006

Neurons grown from ES cells restore function in paralyzed rats

Holy crap: I had no idea the field was this far along. Wow...wow

Thursday, May 18, 2006

Genome Biology | Large-scale and high-confidence proteomic analysis of human seminal plasma

Well, through the wonders of modern science, namely state-of-the-art mass spectrometry, we now have comprehensive knowledge of the proteomic composition of human semen.

The amazing thing about the paper, and perhaps to its credit, is that it's not really asking any specific question or testing any specific hypothesis; it's just, hey, for what it's worth, here's what semen is made of. Or maybe it was just a couple guys with an idle mass spec machine: the ultra-leading-edge incarnation of balls copying.

Materials and methods
Sample collection and SDS-PAGE
Fresh ejaculate was collected from a healthy, 27-year-old Caucasian male and immediately spun down at 13,000 g for 5 minutes at 4°C to separate seminal fluid from spermatozoa. Phenylmethylsulphonylfluoride (PMSF, 0.2 mM), benzamidine (0.1 mM), and 1 μg/ml each of aprotinin, leupeptin, and pepstatin (Sigma, St. Louis, USA) were added to the sample to avoid digestion by powerful proteases present in seminal fluid. To ensure complete separation of cell debris or occasional spermatozoa from seminal plasma, the sample was centrifuged at 100,000 g for 30 minutes at 4°C...

Wednesday, May 17, 2006

Google Web Toolkit

Google Web Toolkit - Build AJAX apps in the Java language

When they explain how it's supposed to work, you think to yourself, this is total bullshit. But it actually does it: you write your web application in Java and this tool compiles it to JavaScript and DHTML. I wonder if anyone there saw Sash, a now-defunct web application development platform I worked on at IBM five years ago. It hosted the web browser inside platform-native "locations" (such as standard window frames or the explorer bar) in such a way as to allow you to write normal desktop applications with web technologies. Cool stuff, heady days...

Saturday, May 13, 2006

I'm wrapping up my visit to Cold Spring Harbor Laboratory for the big genome biology meeting. It's the biggest conference in my field, and it's been a lot of fun to meet all these people whose publications I've been eating up in the last couple years.

I presented a poster on my comparative gene identification project, and it went pretty well. People seemed to be most impressed just by the introduction to the poster, which was just the idea that once you pile up enough genomes, the signal is so strong that you can actually eyeball the alignment to distinguish protein-coding sequence. Relatively few people cared about the actual algorithm that follows from that observation :-) I had some skeptics too (mostly competitors), but on the whole I didn't embarass myself.

Some highlights:

  • James Watson (as in Watson & Crick) falling asleep and snoring during a talk
  • David Haussler's talk. Stunning stuff about a noncoding RNA that has accumulated an extraordinary number of changes since human/chimp divergence, and is expressed in a certain type of brain cell during neurodevelopment.
  • Blowing off a session to drive into the city and visit friends
  • Housing at the Seminary of the Immaculate Conception...yeah.
  • The food: it's like being on a cruise
  • KFC buffet on the drive down
  • Meeting the editor of Genome Research...

CSHL has a beautiful campus, on the northern shore of Long Island. Unfortunately, the weather has been lousy for most of the conference, but it finally turned sunny today and I took a few nice photos. Tonight, we have a lobster banquet, and then I'm driving back to Boston...