Wednesday, December 13, 2006

Christina Mallet Photography is live !

Christina just unveiled her official website: Christina Mallet Photography, and is open for business. She's waiving session fees initially, so please go check out her portfolio, and if you, or people that you know in/around Seattle, need their pictures taken, consider utilizing her services.

Tuesday, November 07, 2006

Blog move

Update: The current location of my blog is

Like a good corporate citizen, I'm moving from Blogger to Microsoft Live Spaces; all further updates to my blog will be made at its new location: .

Sunday, November 05, 2006

A day at the office

Wednesday, November 01, 2006

Baby headrush

No, I'm not torturing our child. He actually likes it, at least if the huge smile he exhibits when he's right-side up again is anything to go by. Then again, maybe he's just happy to not be hanging upside down anymore ...

Curious uses of the word "acute"

From a post on Biology News Net [emphasis mine]:

Researchers led by neuropathologist Hannah Kinney, MD, and neuroscientist David Paterson, PhD, at Children's Hospital Boston and Harvard Medical School examined brain autopsy specimens from 31 infants who had died from SIDS and 10 who had died acutely from other causes, provided by the San Diego Chief Medical Examiner's office.

I was under the impression that death, in whatever form it occurred, was pretty acute, but apparently there are gradations even here. I suspect non-acutely is the way you want to go.

I've also always wondered about the expansion for SARS -- Severe Acute Respiratory Syndrome. Aren't "severe" and "acute" redundant here ? The only explanation I can come up with is that if the "severe" bit were left out, the pronunciation would be a bit embarrassing [though entertaining for the juvenile-minded, like me] whereas SARS minus the A would be unpronounceable ["I'd like to buy a vowel, Vanna".]

I assume there is a precise medical meaning attached to "acute" that merits its use in these circumstances, and that I'm just unaware of said meaning.

Return to the Emerald City

A few snippets, after being back in Seattle for a couple of days:

- Getting through the metal detectors at the airport was a lot like the "farmer, goat, wolf and cabbage" problem: both cats, and Zander, had to be taken out of their respective conveyances and carried through the detectors, and we could only carry one cat or baby at a time. After much head-scratching, the TSA folks bent the rules and allowed Christina to walk through the detector with one cat, drop it off, and then come back for the second cat by walking back through the detector [ie against the flow, usually a no-no]. The whole thing was such a spectacle that all the underemployed TSA folks also in the area crowded around to watch our menagerie make its way through. I wouldn't be surprised if a replica of our situation ends up being in a TSA "Advanced Security Conundrums" training video. [Side note: why on earth would a farmer have a wolf ? That seems equivalent to a cotton grower raising boll weevils ...]

- The flight itself was relatively uneventful. The cats were so terrified that they didn't emit a single peep, and Zander didn't fuss very much and slept through the last 3 hours of the flight. That said, there were plenty of other screaming kids on the plane, so he would have been in good company had he chosen to voice some displeasure.

- Seattle rolled out the "Welcome Home" carpet for us: after an initial day of rain, we've had 2 beautiful, clear and sunny [but cold] days, the sort you rarely get in Seattle. Driving across Lake Washington yesterday, we were treated to two of my favorite sights: mist on Lake Washington, and Mount Rainier. And I never realized until now how many deciduous trees there are around here, and that Seattle actually has some pretty nice foliage too.

- Fatherhood and zippy little cars are incompatible, as I found out during our car shopping expedition: you can't fit a rear-facing car seat and two adults into them, at least not comfortably. So, in another concession to the onset of maturity, we're getting grown-up, mom-and-dad cars. *Sigh*

-In two days, we've already had two "social" dinners [ie dinner with friends/family], which is about the number we would amass over an average 6 months in Boston.

Overall assessment: it's good to be home :-)

Saturday, October 28, 2006

Last day in Boston

As Christina has noted, we're almost outta here.

The movers came on Thursday to pack up our stuff and, while it's certainly nice to have somebody pack up your stuff, it is also not without its stresses. In our case, it was having to play a shell game with Zander, moving him from room to room in advance of the [literal] moving front, and making sure our cats didn't escape, terrorized as they were by strange burly men clomping through the house. Getting to our hotel on Thursday night was fun too. We had to transport:

- 1 baby
- 2 cats, in carriers
- 1 baby car seat + base
- 1 stroller
- 1 Pack-N-Play
- 1 large bag of baby accoutrements [clothes, diapers, bottles ...]
- 1 huge bag with our clothes
- 2 large bags of misc. other stuff [cat food, cat litter, disposable litter boxes]
- ... and of course our carry-on bags

... which made me silently vow to not move again with anything/anybody that must be carried, fed, or has special sleeping and excretory needs. And it got better:

- On the way to the hotel, one of the cats decided it really needed to do its business. In case you had any doubts, let me reassure you that

Freshly-minted cat business + car with windows that don't roll down = Totally Not Crazy Delicious

- I didn't have any cash to pay the cab driver, so we had to go find an ATM while poor Christina was left standing in the hotel lobby with a crying baby and a mountain of luggage
- After dumping all the luggage in our room, I was returning the luggage cart to the lobby and was mistaken for a hotel employee by a woman who wanted to know the location of a nearby hotel. I resisted the urge to give her an earful about not every black man pushing a luggage cart automatically being an employee and settled for a curt "Two blocks that way, and, by the way, I don't work here".

Friday was less stressful, as I just had to hang out in our apartment as the movers loaded all our stuff and clean up after them. There's nothing like emptying out your apartment to see all the hidden dirt that is missed during regular cleaning; in our case, I think I swept up enough cat hair to make a whole new cat.

And, so, today is our last day in Boston; we're getting on a 6:20pm flight to Seattle. My next worry is about spending 6 hours elevated 30000 feet above the ground in a small metal tube with 3 entities [2 cats and Zander] that are my responsibility but whose behavior I really have very little control over. All in all, I'll be glad when it's tomorrow :-)

I suppose the flip side of all this is that I don't really have much time to feel sad about leaving ;-)

Tuesday, October 24, 2006

"These are a few of my favorite things ..."

Since I've spent a lot of the last two years complaining about all the bits I didn't like about Boston, I figured it was time to to talk about the the positive aspects of being here. So, in no particular order, here's what I'll miss and/or liked:

- The Forest Hills cemetery: amazing "memorial sculptures" [aka big-@$$ gravestones] set in beautiful surroundings. Christina shot a few nice pictures here.
- Jamaica Pond: we must have circumnavigated the pond a few thousand times, for reasons like being bored, trying to induce labor, going for a run, and just wanting to take a walk.
- The Arnold Arboretum: another nice spot to take a walk.
- The Endy lab: a collection of very smart, creative, and funny people that I've had the privilege of calling colleagues over the last couple of years.
- All the interesting biological engineering, biology, CSBi and CSAIL seminars
- Zipcars: a pretty good alternative to owning a car
- The Weekly Dig: a really funny weekly paper with an irreverent, yet insightful, take on everything.
- The Wonder Spice Cafe, Royal Bengal, and Family restaurants: good food at reasonable prices, an all-too-rare occurrence.
- All the stuff Christina listed [although I'm not as big a fan of the "free stuff" as she is]

There are also a few things I wish I'd had a chance to do:

- Participate in one of the many [1K, 50K, 100K] entrepreneurship competitions held every year at MIT
- Watch a Robocraft competition
- Take a few more courses [like 7.03, 7.22, 7.23, 7.52, 7.86, 6.824, 6.829 and 6.852]
- Check out Cape Cod, Martha's Vineyard, Vermont and Maine
- ... and, of course, graduate with a PhD ;-)

Update: Another one of my favorite things was working out at the CW Taekwondo club, run by two friends of mine. They've managed to build one of the best Sport Taekwondo clubs in the country, with current and ex-national team members from various countries, including an Olympian, working out there. In other words, it's a great place to get your @$$ kicked ;-)

Monday, October 23, 2006

Advice to a young non-scientist

[Apologies to Peter Medawar]

With our impending departure from Boston, I've been thinking a lot about what I would change if I were to get the chance for a do-over. Below are the conclusions I've come to.

Making friends is hard: We didn't fully realize before we left Seattle how lucky we were to have so many friends and family close by, and how difficult it is to rebuild that sort of network in a new city.

The core of the problem was that neither Christina nor I had much exposure to people our age. Before starting classes, I hadn't fully internalized that I'd be surrounded by people who had, for the most part, just finished college, and were about eight years younger than me. An eight-year post-college difference is a pretty big gap in life experiences and expectations, one that made it hard for me to make many new friends. Christina's job was also pretty limiting in that respect in that it was, in some ways, tantamount to solitary confinement. And, since she worked at MIT, most of the few interactions she had were with students as well. Compounding these difficulties was the fact that most people in their early thirties have their social network in place and aren't necessarily actively trying to expand it, and so it's not easy to "break into" an existing circle of friends.

All this is not to say that we didn't make any new friends, but there were few enough of them, and we saw them so infrequently, that being in Boston was a pretty lonely experience. All that said, short of joining some sort of social club [*shudder*], it's not clear to me how we could have changed this bit of our stay here.

The high activation energy of mobility: When we moved here, we decided not to buy a car, but instead use Zipcars as necessary. On one hand, that worked out reasonably well, in that we didn't have to think about insurance, parking etc, but still had access to a car when necessary. On the other hand, it also stopped us from doing things that would have made our stay in Boston more pleasant, because there was always a very definite cost associated with using the Zipcar: for any activity, the question became "Do we want/need to do this enough that we're willing to pay the Zipcar fee for the necessary period of time ?". At $7-$8/hour, that sort of calculus brought with it the pressure to make every trip extra-worthwhile, which made us much less willing to try trips with uncertain payoff, like, say, exploring Massachusetts. It also made it hard to be spontaneous, because each trip required reserving the car a few days in advance, and we needed to plan our trips down to the hour to stay within our reservation window.

All in all, the delta between what we paid for Zipcar rentals on a monthly basis and what it would have cost to own a car was probably small enough that the additional freedom would have been worth it.

Going big sometimes considered harmful: I had two conflicting impulses when I started graduate school. One was to take the safe route to getting the necessary credentials: pick a research area that played to my strengths [ie purely computational work], pick an interesting but reasonably safe project, do a solid job on it, and get out quickly. The other impulse, based on the reasoning that since I was making such a large switch anyway, I might as well do it properly, was to become equally at home doing experimental biology and computational work, and pick a thesis project based purely on being the coolest thing I could think of, with little or no regard to safety. In other words, choosing the "go big" option of the "Go big or go home" philosophy espoused by a friend of mine.

I tried to chart a path through the middle, by looking for a thesis topic that would allow me to develop the computational skills that I figured would make me the most employable in industry [namely, machine learning/data mining] and applying them to the area of biology I find the most interesting [synthetic biology]. That took about a year, and still wasn't totally satisfactory, as is usually the case when you try to force a compromise between two incompatible bedfellows. In the meantime, I also figured out that I really don't like experimental work -- the slow, repetitive, everything-takes-forever-to-do, debug-by-semi-randomly-trying-stuff nature of it drives me crazy. In other words, I realized that I really should have taken the safe route; unfortunately, 2 years in and with a new addition to the family, doing that sort of a reset really wasn't in the cards.

I wish somebody had sidled up to me a couple of years ago, gently tapped me on the shoulder, and quietly said "Uhm, dude ? You already went big by going back to school; there's no need to get even crazier. Play it safe." Or, as a professor who switched over from "pure" computer science to CS applied to biology put it recently: re-orienting your vector takes time, and the important part is getting pointed in the right direction, not trying to get to the endpoint as fast as possible.

The lesson: sometimes you go big and you go home ;-)

There are probably a couple of other little bits and pieces that could have gone better, but I think the stuff above covers the biggest chunks. Now all I need to do is build a time machine so I can go back a couple of years and give myself the benefit of all this experience, thereby creating an alternate universe in which I become a mad scientist and destroy the earth via my green goo run amuck. Wait, maybe that's not such a great alternative...

Tuesday, October 17, 2006

Happiness, in 3 acts


More ads that make no sense

Time for another installment of "Ads in the subway that Alex has issues with".

In the last few weeks, I've seen a bunch of ads that have the tagline "Kids with asthma can ... [perform activity X]" and then say something like "Is asthma preventing your child from [performing activity X] ? Talk to your doctor !". Choices of [activity X] are playing, sleeping, learning, and doing sports.

Here's the thing I don't get: is the assumption behind these ads that people whose children have asthma -don't- talk to their doctors about trying to provide their kids with some relief, and need to be encouraged to do so ? Maybe that there is a subset of parents who regard asthma as the inescapable result of Divine Will, and are not aware that it's treatable ? The ads aren't sponsored [at least not directly] by a pharma/biotech company that just happens to make asthma medication; it's underwritten by a bunch of generic "benevolent" organizations. That seems to rule out the profit motive, so I'm left wondering why anybody would roll out such content-free advertising.

Maybe the next ad campaign these folks will come up with will be targeted at people with serious injuries and say something like "Have you just lost a limb and are geysering blood ? If so, you may want to consider consulting a medical professional."

And while we're on the topic of meaningless ads, there was one I saw last year, promoting this lady's candidacy for sheriff, that said "Actions have consequences. Think before you act.", to which the only appropriate response, I think, is "No sh!t, Sherlock".

One thing I will miss about using Boston's subway system is the opportunity it afforded me to be curmudgeonly about it. A friend of mine performs a similar service for the Seattle bus system, with the difference that she likes public transport, so her observations tend to be much more positive than mine. Or maybe that's just because Seattle is superior to Boston in this respect as well, leading to less opportunities to gripe ;-)

Friday, October 13, 2006

Leaving the hallowed halls of academe

I've decided to leave my PhD program and return to Microsoft. A lot of reasons contributed to my decision, but the end result of summing over all of them is that the [certain] downside of staying in school finally outweighed the [mostly uncertain] upside, especially in light of my newly-acquired responsibilities. So, I'm currently trying to pull together a coherent Master's thesis, a task made somewhat difficult by the fact that I've bounced around a lot over my two years here. I think I have enough stuff that sort of fits together get by, though :-) ["Small pieces, loosely joined" ...]

We're heading back to Seattle in pretty short order -- the plan is to be gone from here in about 2 weeks, and I'm slated to start work on November 6th. Christina is very happy about our move and, while I'm bummed that I won't be finishing up the PhD program, I'm definitely also looking forward to being back in a city I like, close to friends and family, and living an "adult" life again. And it doesn't hurt that I'm going back to what promises to be a really cool job, writing code for large-scale distributed systems and working with people I know and like. One bit that I haven't quite figured out yet is what to do about my still-existing interest in biology, but I expect that keeping up somewhat with what's going on through a subscription to Science or Nature will help scratch that particular itch.

Overall, for all my whining and moaning about Boston etc, it's been a good two years, in a variety of ways. I learned a ton of interesting new stuff, met some good people I plan to stay in touch with, and don't have to live with the "If I'd only tried it" specter that would have haunted me if I hadn't taken the plunge and gone to graduate school. Oh, and I'm [hopefully] getting a Master's degree without having racked up any debt ;-)

So, that's that.

Thursday, October 12, 2006

The coolest labs at MIT

... are clearly the Endy and Knight labs, as this video shows.

Friday, October 06, 2006

Something not to do with your baby

... is described here. The boy has serious pipes, made all the more emphatic when enclosed in the small space of a car. If the volume of his protestations is any measure of his willpower and stubborness, we're in for a world of hurt once he becomes mobile, agile, and hostile, and learns the word "No".

Saturday, September 23, 2006

Academic follies, encore

I know this is a horse of indeterminate liveness, yet I cannot resist flogging it some more.

Over at the Daily Transcript, there are two posts [1, 2], and associated comment threads, about "The Academy", at least in the life sciences, that are worth reading in their entirety, especially the comments.

[What, you're still reading this ? Fine.]

The summary: postdocs complain about the long hours, low pay, and lack of a life outside the lab required to even have a shot at a faculty position, never mind the insanity then required to achieve tenure. The response of a couple of professors, stripped down to its essentials: "Stop whining and suck it up, because we've got plenty more people where you came from that are willing to sacrifice everything. You should be grateful that you get to work on what interests you, with other smart people".

The first bit of the response is amazing not only in that it's addressed at highly educated, skilled people [not that it's something that should really be said to anybody] but also that they're willing to be spoken to and treated that way. And the defenses of academia in the second bit of the response are the standard "But look at the benefits !" justifications for the insane state of affairs, and stick in my craw every time I hear them.

"You get to work on what you want": Well, really, you get to work on what the funding agencies will give you money to work on. And, increasingly, these agencies are funding not individual investigators, but rather large, multi-investigator projects; see these posts about the decrease in funding rates and funding inequities between Big Biology and individual investigators, leading to what has been called a lost generation of individual researchers. So, it seems like there's a pretty good chance that, to survive, you may have to attach yourself to one of the mega-grants and end up working on something that's not exactly what you want to be doing. That's probably even more true if you're a junior faculty member, in which case you'll probably end up somewhere fairly low down on the author list of the published papers, which in turn isn't great for your career.

"... work with other smart people": Yes, that's definitely nice. But I'm always reminded of a simple numerical fact: most of the smart people in the world work somewhere else than wherever you currently happen to be. So that's not a good enough reason to put up with the execrable conditions.

... and from what I've seen, there are at least the same amount of bureaucracy and stiflingly boring tasks and meetings in academia as there are in industry. The only difference is that they're called "committee meetings", and probably drag on forever because nobody really has the final say over anything.

The other thing that I don't understand is why there is such an oversupply of PhDs [at least in the life sciences] who want to become academics. The possible reasons I've come up with so far are:

- a lack of awareness of alternatives, maybe due to being given bad career advice
- that the vast majority of them think of themselves as the PhDs of Lake Wobegon: all Above Average, and so the grim statistics don't apply to them
- such a pure, burning desire to explore the mysteries of Nature that, damn the torpedoes, any other course of action is inconceivable [and that word means what you think it means]. In which case, hey, go for it. But is that really the case for the majority of people ?

Don't get me wrong: I strongly believe that we need research universities and institutions, and basic research. I'm just amazed at the self-flagellation people are willing to inflict on themselves in order to join the academic club. And I wonder how long this pyramid scheme can keep going.

Tuesday, September 19, 2006

More baby goodness

First smiles, cheeky monkey, and meeting the maternal and paternal grandparents.

[Someday soon, I'll post something other than baby pictures. No, really. I mean it. In the meantime, you might as well enjoy them ;-)]

Sunday, September 10, 2006

"Abandon reason, all ye who enter here"

From a NYT article:

MUNICH, Sept. 10 ­ Pope Benedict XVI attracted some 250,000 people to an outdoor Mass on Sunday, urging his largely secular home country not to let science and reason make it “deaf” to God.

Hmm. Does that imply that it's not possible to be reasonable and religious [at least not all the time] ?

Saturday, September 02, 2006

Shock and Awe, baby-style



Friday, September 01, 2006

Daddy, there's a monster next to the bed

... and his name is Zander. I say this not because he attempts to bodily devour Christina every 2-3 hours, starting with her chest, but rather because of the noises he makes. He is a veritable orchestra of monster noises while he's sleeping: grunts, gurgles, moans, sighs, crying, heavy breathing and, of course, the occasional, entirely unabashed, sound of a waste product download. Sometimes, he's so loud that I have to put a pillow over my head to drown him out. I always thought pre-verbal children either cried, made nonsense sounds, or were quiet ... little did I know they could easily find work as extras in "Where The Wild Things Are".

Showing off the captured Zandermonster:

Thursday, August 24, 2006

Fatherhood, week 1

[Baby stuff, probably non-interesting unless you're family =)]
Miscellaneous notes, after being a father for a whole week:

- Baby swing = Crazy Delicious Baby-Sleep-Inducing Machine.
- When changing diapers, it's generally a good idea to cover "the equipment" with a wipe, otherwise you may be treated to an in-house version of the Bellagio Fountains. With yellow water, and without the lights and music, though. That said, it's worth -not- taking that precaution just once, to see the look of surprise when he pees himself in the face [No, I didn't do so intentionally, it happened when I accidentally forgot to cap the waterworks.]
- Zander will soon be ready to challenge the strongest boy in the world to a wrestling match and utterly dominate him. Why ? Because, in my unassailable dad logic, I note that he can already lift his head up and turn it while lying on his stomach, something that apparently generally doesn't happen until the second month, and conclude that he must be extraordinarily strong.
- The lack of sleep, and overall stress level, hasn't been as bad as I feared ie we haven't been reduced to bone-tired bundles of nerves [yet]. That's attributable entirely to the fact that Zander is a great "starter baby" for rookie parents -- he sleeps quite a bit, doesn't fuss very much when he's awake, nurses well, and is pretty forgiving of clumsy parents who take a bit too long to change his diapers or clothes.
- One of our strollers has been named Optimus Prime, in view of the fact that it can be transformed from a full-fledged, large stroller into a fairly compact cuboid with the simple press of a button and a small amount of leverage applied in the right direction. It might be possible to turn it into a tandem bicycle with the right series of pushes and pulls. I suspect it was designed by origami masters capable of accessing hidden spatial dimensions.
- My man's got flair even when he's asleep:

In summary, it's pretty cool being a dad. How could you not love a face like that ?