Tuesday, May 30, 2006


The AP has a story about a real-life Fight Club in Silicon Valley, a notion I find pretty funny, given the average physique of a techie. I can just see the billing: "The undercard fight tonight: Clash of the Michelin-Men ! And the title bout ... Stick Figure versus That Guy Who Keeps Talking About Kernel-Mode Network Drivers". I suppose that's why they resort to "Kicking, punching and swinging every household object imaginable -- from frying pans and tennis rackets to pillowcases stuffed with soda cans" -- it's difficult to hit somebody hard enough to make an impact when the only exercise you get is typing [although maybe that might lead you to develop the Fast-Typing Fingers of Death technique ...].

Oh, and I suspect the guy who skipped his first wedding anniversary to attend a fight got a taste of the real Fight Club when his wife heard about the reason he skipped their anniversary.

Saturday, May 27, 2006

Step One of Nerds Anonymous

I'm 32. I'm married, with a child on the way, and a mortgage. Clearly, I'm an adult [if you ignore the fact that I'm in school ...]. Yet, my birthday presents, by request, consisted of a math textbook, a comic and an Amazon gift certificate which I promptly used to buy more comics, among other things.

"Hi, I'm Alex, and I'm a nerd."

Friday, May 26, 2006


Another year gone by, marked by:

- a quite active summer
- classes in statistics and machine learning, and gaining a real appreciation of their use as lenses for interpreting the fuzziness inherent in the real world
- hands-on experience with the grind of daily experimental work
- a scientific conference here and there
- some [mostly administrative, alas] progress towards becoming Dr.Evil.

... and, of course, the absolutely coolest thing: creating our very own little person. I suspect that a lot of what I'll learn in the next year will revolve around thuddingly concrete things like how to change diapers and interpreting the urgent communiques generically encoded like this. Hopefully, this instruction manual will help.

My slogan for 32: "One-third more
action than '24' and 365 times as long !"

Browser wars

I'm considering helping out with a genome hacking project and would like a genome browser to facilitate this. It turns out that genome browsers are like C++ string classes: everybody's got one. Consider the following sample, just off the top of my head:

- Apollo: "
a Java-based application for annotating genomic sequences"
- Gbrowse: "
a combination of database and interactive web page for manipulating and displaying annotations on genomes" [from the same distribution as Apollo ....]
- Argo: "a production tool for manually annotating and visualizing whole genomes", from the MIT/Harvard Broad Institute
- The software underlying the UCSC Genome Browser
- A browser explicitly targeted at synthetic biology, with the drawback that the fellow developing it probably won't be spending much more time on it, because he's graduating and going back to a real job.

In other words, forget about Netscape vrs IE vrs Firefox vrs Opera -- now it's all about the browser within the browser. Maybe in a few years we'll have a browser-within a browser-within a browser war ...

In any case, I could just try them all out and see which one works the best. Or I could do what a "real" programmer would do: arrive at the foregone conclusion that all of them suck, that I can do better, and write my own, a thing I am sorely tempted to do, mainly because it's been years and years since I wrote any substantial chunks of code. The flip side is that this would involve having to write user interface code, something I've always avoided like the plague. Then again, learning a bit about all the AJAX hype would probably be a good thing in terms of keeping my technical knowledge reasonably current.

Going forth to TA no more

The final exam has been graded, all scores for the semester tallied up and the rest, namely assigning actual letter grades, is out of my hands: my stint as a teaching assistant is over. And, thankfully, I won't have to do it again, because it was pretty much zero fun. To be more accurate, I kind of liked the "teaching" bit ie answering questions and explaining stuff [with the beneficial side effect of giving me a better understanding of the material], it was the "assistant" bit, making up and grading problem sets and exams, that was a real drag. Especially the occasions when I spent hours coming up with a question [explicitly requested by a professor] for a problem set/exam only to have it discarded because it was too hard/made the exam too long/didn't fit in with the course emphasis after all. I suppose that's part and parcel of working for somebody, though -- god knows I wasted lots of time at Microsoft preparing material requested by my manager, or for "executive reviews", only to have it never looked at, or flipped through in a matter of seconds.

Anyhoo. That's all done, then.

Monday, May 22, 2006

SB 2.0 report

Came back this morning [on another red-eye flight, aaargh] from Synthetic Biology 2.0. Overall, it was a pretty nifty conference, with talks covering a lot of different topics. Thankfully, several people have saved me the trouble of trying to remember details from each talk by blogging about the conference: Mackenzie Cowell has a bunch of short posts giving high-level summaries of all the talks, whereas Oliver Morton [an editor at Nature] and Rob Carlson have slightly longer posts about various "meta" bits surrounding the conference. With that, my personal take:

Favourite phrases/words from talks:
- "Cyanobacillus generates ugly cells at low frequencies": from a talk by the author of a paper I've written about before. Apparently, beauty is only cell-deep.
- "Retrosynthetically": I still have no idea what that means, but it sounds cool.
- "Aza-ylide": an intermediate of an apparently well-known reaction [well-known to a segment of the population I am clearly not a part of]. What I liked about this word is its pronunciation: "eza-illid", [where the initial "e" is pronounced like the "a" in "age"] which makes it sound like Snoop Dogg's contribution to science.
- "What we're doing here is preposterous": from David Baltimore's talk about the Grand Challenge in Global Health that he's involved with. This statement referred to the fact that they're trying to do gene therapy, stem cell therapy and immunotherapy all at once, and none of those three therapies has worked [satisfactorily] yet, in any other setting.
- "Counting to 2 in a scaleable manner": one of the "Future challenges" listed in the concluding slide of a talk.
- "Don't laugh, Drew, if you had a pair of silk underwear, you'd be a lot less irritable": [slightly paraphrased] from Chris Voigt's talk about getting Salmonella to secrete spider silk, and why silk is such a wonderful material.

Moment of Zen
Craig Venter showing a video [from the Discovery Channel, I think] whose main theme was "Craig is cool. He is travelling around the world in his yacht, collecting seawater and trying to sequence the DNA of critters he finds in it." As entertaining as the idea is, and as much as I'd like to be trawling around the world on a yacht, the video contributed absolutely nothing to the actual scientific content of his talk [as far as I could tell, but maybe I'm missing something]. At first I found it cringe-inducing, as in "Is he really so oblivious that he's showing an ad for himself ?", and then I transitioned to a state of awe at the sheer Zen-master chutzpah of the man.

Moment of "wha' happen ?"
Jef Boeke talking about his lab's plans to rebuild chromosome III in yeast, and generating "genome swarms" of lots of yeast strains with different genomes. This is exactly what I was working on doing last year [based on an idea supplied by Drew], as described here and here. I eventually ended up bailing on this project because I couldn't figure out how to generate lots of genome variations via synthesis and/or come up with a good enough reason to ask Drew to spend the money it would have taken to do this project. Boeke has figured out a high-throughput way of generating genome variations, and figuring out what variation has been created, which isn't that surprising, given that:
1. he's been working with yeast since the mid-80's
2. he's published a bunch of papers on large-scale yeast genomics
3. he's an expert in transposon biology, and transposons are one way to generate variation in a genome
4. he's associated with the Hopkins High Throughput Biology Center
In other words, if somebody was going to figure that bit out, he'd be a bad person to bet against. However, he hasn't quite solved the money and "why do this ?" issues: he estimated that it'd take about $10 million over 5 years (!) to do this project, and he didn't really have any more "Wow, that would be so cool/useful !" ideas for what modifications to make to the yeast genome, and why, than I did. He's taking an interesting tack on gathering input, though: he issued an invitation to the yeast community to give him feedback on what sorts of changes they'd like to see made to the yeast genome; one good place to get those kinds of suggestions will probably be the 2006 Yeast Genetics and Molecular Biology meeting.

All that said, I still think it's a really, really cool idea and one I'd love to work on, so I plan to talk to him some more about it and see whether there's room for a collaboration. Of course, the thesis idea that I used to gather my thesis committee has exactly zero to do with this, so that might lead to needing to do some "cabinet reshuffling".

... and that's all, folks.

Addendum: as I mentioned above, one of the speakers was David Baltimore, an insanely accomplished man -- he helped to organize the Asilomar conference on recombinant DNA, is now the president of Caltech, was president of Rockefeller University for a while, helped to found the Whitehead Institute at MIT, and, oh, by the way, won a Nobel Prize when he was 37. I think I can be forgiven, then, for the fact that the [slightly juvenile, granted] thought that kept going through my mind as we stood shoulder-to-shoulder at the urinals in the men's bathroom was "I'm peeing next to a Nobel laureate ! I'm peeing next to a Nobel laureate !". It's not often you get to say that ;-) I considered telling him that I thought he was a pretty cool guy, but that might have been a bit ... awkward, given the circumstances.

Addendum #2: one other thing that struck me was the breadth of biological systems that were talked about, and being used, to build synthetic circuits. The bit that I still don't quite understand is how the folks that described working with multiple different genetic sub-systems from other organisms knew about the existence of these sub-systems in the first place. Did they just do tons of literature searches, hoping to stumble onto something that was appropriate ? Was there a serendipitous conversation with somebody working on something totally different who said "Oh, I've got just the thing you need" ? As we start to think about building more complicated circuits, or circuits with wider functionality, that knowledge of what "parts" are available is going to become more and more important. The Biobricks Registry is an attempt to provide such a parts list, but it requires community contribution to really be useful, and I wonder whether its emphasis on "standardized" parts is going to turn away contributors who don't feel like doing the work necessary to make their genetic circuit standards-compatible. It would be a shame if synthetic biology became as lore-based as much of [experimental] biology is, requiring expert knowledge of the literature, word-of-mouth etc to know what parts are available to build a functioning circuit, instead of having a more systematic way to retrieve this information.

Friday, May 19, 2006

Cyberpunk marketplace

This sounds like something out of a William Gibson novel.

Tuesday, May 16, 2006

Tired just thinking about it

In theory, our Seattle visit was supposed to be relaxing. In practice, because it was so short and we came back on the red-eye, I'm now about as tired, or more so, as when we left. And it's not about to get any better:

- I leave for Synthetic Biology 2.0 on Friday. Before then, I have to finish coming up with questions and a scoring scheme for a final exam, grade 60+ problem sets and update the poster I'll be presenting at the conference.
- Next week is finals week, so it'll be a mad scramble to grade the final exams and figure out final scores for everybody
- I'm going to the Biology Department retreat on June 1st and 2nd.
- Sometime between now and the first week of June, I have to start and finish writing the first draft of my ~20 page thesis proposal so I can give it to Drew for comments.
- June will be devoted to doing experiments to fill in the yawning chasm in the "Preliminary Results" section of my thesis proposal; this will involve learning some experimental protocols that are apparently rather finicky [in plaintext: easy to screw up], and will thus undoubtedly contribute to my prematurely graying hair. In addition, I'll be going over the material from all the classes I've taken so far, to further prepare for my qualifying exam.
- My qualifying exam is July 12th -- ~2 hours of being grilled on my thesis proposal and whatever else my thesis committee members feel like asking.
- As previously noted, I may have to deal with having to find new renters for our place in Seattle sometime in the next couple of months
- Our baby's due date is August 14th, but only 5% of babies are delivered on their due date, so who knows when he'll actually show up. In any case, I expect I'll be a total zombie for at least a couple of months after he's born.

... and with that, we're in November.

I see a lot of Mountain Dew and highly-caffeinated tea in my future.

Notes from the annual pilgrimage

Christina and I just came back from an all-too-short visit to The Promised Land [aka Seattle]. Trip notes, in no particular order:

- The weather was perfect: sunny and dry in the 60's and 70's the whole time. In contrast, while we were gone, New England got so much rain that it led to the worst flooding in 70 years. Outstanding timing on our part, I'd say.
- The main reason we were in Seattle was a baby shower [for our little-man-to-be]. However, it wasn't the standard baby shower which [I've been led to understand] mostly consists of a group of women sitting in a circle, competing to see how often they can use the words "adorable" and "cute" in reference to baby outfits. Instead, we made it a combination "see all our friends" party/co-ed baby shower by inviting all our friends, male and female to ... sit in a circle and coo about baby stuff. Actually, the cooing was limited to a small part, it was much more a chance to catch up with everybody who came. That said, we did make out like bandits with respect to gifts of baby-related stuff, so a big "Thank You" to everybody who came [and gave us stuff ;-)]. And, of course, another big "Thank You" to Christina's mother and sisters for organizing the shower/party.
- Even after 2 years in Boston, Christina and I are still amazed by the amount of trash littering the streets. Christina kept insisting that Seattle was much cleaner, but I was skeptical -- I figured all cities have trash on their streets, so this time, I made it a point to notice how clean [or not] the Seattle streets are. And, what do you know -- Christina was right. The Seattle streets and sidewalks really are spotless, and not just in the upscale neighborhoods. Even the sidewalk and street outside a liquor store where shady characters tend to hang out were clean. Why the difference ? Do people just not throw litter on the street, does Seattle spend a much larger amount on keeping the streets clean, is it because Boston has had a couple more centuries to accumulate crud ?
- We ate ridiculous amounts of good food [Christina's mum made an amazing strawberry cake that I'll be demanding for my upcoming birthday], so much so that at the end of our visit I actually refused a slice of after-dinner cheesecake, which is pretty much unheard-of. It's time for a bread-and-water diet for a while, now, though.
- The amount of new construction is amazing -- new condos and townhouses are springing up everywhere, in conjunction with a general rise in real estate prices. Good news for us in that our townhouse has appreciated nicely in value, bad news in that it means we'll have to pay more when we want to move into a bigger house to accomodate an expanding family.
- On the subject of real estate, the folks who have been renting our townhouse are considering moving out, which would be a huge pain in the @$$. Trying to find renters from a distance is not something I'm looking forward to at all -- we're really attached to the house and so we want to make sure we don't rent it to bozos who will trash it. Thankfully, friends of ours have offered to help with interviewing renters, and hopefully it'll be relatively easy to find renters if we keep the rent the same as it has been for the last couple of last years [given the general increase in real estate prices].
- You know you're broke when your financial planner declines to charge you for financial advice because he says "Well, it'd be like trying to squeeze blood from a turnip". I think he files us under "charity work" and gets a tax deduction for it.

Pictures to follow once the photographer-in-residence releases them for public consumption.