from the desk of stinkpot

I attended an all-boys Jesuit high school in Manhattan named Regis, an experience that couldn’t have been more incongruous with what Saved by the Bell promised me for years. Still, going to high school in New York City was memorable; taking Driver’s Ed in Chinatown during rush hour is downright terrifying and smells delicious.


I loved being in Manhattan so much that I did my undergrad at Columbia. There, I earned a degree in biomedical engineering, a major I recommend highly. It’s fascinating to see how many organ systems and tissues you can mathematically describe using simple DC circuit diagrams. And as a bonus, I found that my department was a national powerhouse in the assignment of macabre student projects; I once got to spend 3 continuous weeks modeling how many synthetic erythrocytes a hemorrhaging soldier would need for transfusion before he or she bled to death. Down on the Morningside range, I was also fortunate enough to get mentored by Chris Wiggins and Barclay Morrison III, who both taught me a lot about science gets done.

I spent my PhD thinking about how to leverage computational tools like hidden Markov models, and binary tree reconciliation algorithms against problems in evolutionary microbiology. I was particularly fond of microbial ecology and comparative genomics. With the help of my advisor Eric Alm, I graduated with a doctorate in Computational & Systems Biology from MIT in 2010.  I am presently a Junior Fellow at Harvard’s Society of Fellows.  You can read more about my research at my academic webpage.


Now, those paragraphs were all very academics-centric (I cribbed them from an application I submitted some months ago). Here are some other things I enjoy and don’t take place at school: tennis, squash, photography, backpacking, and travel. I also hang out a lot with my wife, Christina, and wish I could hang out much more with my little sister in Philadelphia, Stephanie.


In conclusion, if you’ve read this far, say hi in comments below or shoot me an e-mail on over to Ldavid AT mit DOT edu. It makes my day to get letters from strangers on the internet.

I’ve finally had enough with blogger and it’s lack of categories / dependency on the ponderous and fickle blogger.com server. Hello Word Press!

Already, I’ve got a positive view of Word Press. It was astoundingly easy to move my blogger blog (including comments!) here onto Word Press. If you’re so inclined, here’s the guide I used.

i think i am in love with dr. laura garwin (pictured above).

i half-heartedly agreed to go to a talk she gave today at school. the biological engineeers here had arranged for dr. garwin to speak about post-doctoral careers outside the sphere of pure research. specifically, she was to talk about her own experiences in scientific editing and research administration.

to be perfectly frank, i anticipated her talk to be a snooze-bucket. my love of loose deadlines, loose dress codes, and occasionally blurting out, “eureka!” has me convinced that i’ll be a lab rat for the rest of my life. i doubted that i’d find a call to paper-pushing even mildly compelling. nevertheless, as things usually go with risky talks, i went anyway to score some free cookies and soda.

lucky me. dr. garwin’s gavethe most enjoyable mentoring talk i’ve heard in years. with a good deal of humility, she quickly chronicled her life: bachelor’s in physics from harvard; rhodes scholarship; phd in earth science from cambridge; top editor at the journal nature; administrative director at harvard’s genome research center.

all very shiny, but what really blew me away was her wonderfully zen approach to life. “don’t fear not knowing what you want to do with your life – i still don’t and i’m 49,” she confessed. a bit cliched, but she did walk the walk (heh, more cliches!) – science editing and research administration were due to serendipitous job openings. and amazingly, dr. garwin professed that she was about to undergo another career change: she was to quit her directing job to … return to cambridge and do a post-bac in trumpet! how cool is that?!

“i’ve always wondered what it’d be like to be a professional musician,” dr. garvin admitted. “so i thought i’d give it a shot.”

of course, that kind of radical life changes are likely to be less challenging given all the money she’s probably saved up from two past successful careers.

nevertheless, to do things as impressive as leading world class scientific journals or research institutes i’m sure takes incredible passion. so to simply disengage one day in the name of the trumpet must mean two things: 1) she really likes the trumpet; 2) she’s not wedded to the ideal that you must become the absolute best at whatever you choose to do. rather, life is about doing the things you love doing.

i really liked that second message. i can already feel grad school’s pressure-cooking influence, encouraging me to bury myself in my work. which really, isn’t that bad of a thing, considering that i love my job and my research. yet, i’d be terribly disappointed if i only did work during grad school, and rarely travelled, made new friends, or even pursued my photography.

so thank you dr. garwin for your perspective, your wisdom, and the free soda and cookies.

this week has been full of long days.

i looked in the mirror on monday and saw stains on the edges of my teeth. these stains were both toothbrush and fingernail resistant. even worse, the stains were mildly conspicuous since they were on my front teeth. concerned, i asked christina if she had noticed them before.

“yea, you’ve had that for about a week. i thought you saw them when you smile at yourself in the mirror.”

i temporarily forgot about the teeth thing and thought about what chris was implying. either she thinks of me as being vain enough to constantly smile at myself, or that i’m simply indifferent about my appearance. or perhaps she somehow thinks both?

either way, i refocused and began to freak out. i might have cavities. that would be bad, since i hate seeing the dentist – i’ve successfully deferred an oral checkup for 3 years running. nevertheless, i decided that part of entering adulthood means you do things that you don’t like doing. such as seeing the guy who puts his fingers in your mouth for a living.

due to a last-minute cancellation, i was able to see a dentist just 3 hours later. instant dental gratification, you might call it. and, like so many things in life, there was good news and bad news. the good news: “those stains were probably due to coffee, tea, or soda.” relief! the bad news: “you’ve got a cavity.” angst!

apparently, it’s because i don’t floss. call me lazy or un-hygenic, but i don’t think it’s very fun to stick thread between my teeth until my gums bleed. then again, it’s also not very fun to have a cavity filled, i suppose.

actually, it wasn’t so bad. fate destined me to sort out my dental troubles quickly; someone cancelled there appointment today and i was able to see my dentist around noon.

things, thankfully, went swimmingly. dr. reid is a sweet middle-to-late aged man who hummed along to the music while he drilled holes in my tooth. i found it endearing that he also quietly apologized to me each time he bored a little deeper. here he is, performing probably his 5467th filling, and he’s still a little contrite.

to take my mind off of the dremmel rotating a couple thousand rpm and constantly passing by the soft tissue of my eyes and tongue, i spent most of the surgery reflecting on my anaesthesia. oddly enough, its injection was the most unpleasant part of the surgery. i swear that needle was poked so deeply into the roof of my mouth that i half expected it to pop out of my nose. just thinking about it again makes me cringe.

but, of course, i’d have bawled like a [insert noun here that's not those poor, cliched "babies" or "little girls"] had i not gotten my fixin’ of anaesthesia. what a stunning discovery anaesthesia was. internet, dishwashers, jello – i can imagine living in the sorry time when those inventions didn’t exist. but an age before anaesthetics? how uncivilized! being forced to see a surgeon must have been like a watered-down version of the death penalty. even minor surgeries, like my cavity filling, would have been, for lack of a better phrase, like pulling teeth. i can’t begin to imagine the horror.

hmm, the snappy finish i eagerly anticipated when i started this entry has failed to materialize. here’s the best i’ve got: “the only downside to anaesthesia is that it’s so difficult to spell correctly.” yuck, that was pretty weak sauce.

priceless quotes overheard from the hilarious portuguese family having a picnic in our backyard:

• i am republican, bitch! [unknown voice]
• well, it doesn’t matter [if you'll tolerate gay marriage] because i’m gonna become president first. i’ll be president first because i’m gonna work my ass off. [the 8-year niece of our landlord, yelling to her college-age cousin]
• the only reason they like obama is because he’s black. and he’s only black by injection! [the college-age cousin]
• thank god gore didn’t get elected. he woulda sat on his ass and bam! – we’d have had a nice nuclear bomb in our laps here in massachusetts.

this stuff is better than fox.

these freshly designed websites have been stinging the ego of my webpages’ collagen-filled, handwritten html code.

but rather than wallow in a tub of self-pity, my site has instead decided to get itself into shape. i’m so proud of its can-do attitude.

she’s looking better already. go see for yourself!

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i’m so sorry for beating that silly analogy into the dead horse. my brain is just fried – adobe makes such useful products, but ladens them with absolutely terrible documentation. that homepage took much longer to produce than it should have.

to atone for the terrible weight-loss wordplay, i’ll post another diet-related wrong (which of course makes things right). hooray!

those poor ivf surplus embroys. already headed for the trash. now, their chance to contribute to science and humanity has been delayed indefinitely once again. (that picture in the article, of bush surrounded by babies born of surplus embroys makes me want to throw up a little in my mouth.  don’t politicians feel any shame when they blatantly use human beings to abet their pandering?)

chris and i had a nice discussion last night about what happened yesterday. now that i’m a “biologist,” i thought it would be nice to play devil’s advocate, arguing that what bush did was the moral thing to do. and frighteningly, the more i thought about it, the more i could understand why our president would do something so silly.

recall, all the bill was asking to do was make excess ivf embryos (already slated for destruction) available for federally funded research. seems like an obviously good idea, especially given that so many people think stem cells derived from these embryos hold the key to all kinds of wacked out research.

but, as a friend of mine from high school pointed out to me a long time ago, just because the thing is going to die doesn’t mean it’s right to exploit it. for instance, let’s say a convicted criminal was going to be executed: would it be right to submit him/her to medical experimentation before the execution, just because he/she “was going to die anyway”? most people would say no.

christina countered: “well, that’s because the convict is capable of saying no to the research.”

that lead me to the favorite prop of the medical ethics class i took in undergrad: the terminally ill patient so mentally handicapped that they couldn’t possibly give medical consent to things. would it be ok to use them as human guinea pigs? again, probably not.

i’m having trouble thinking of an example where you can ethically prematurely end the life of a human being for the benefit of research. (an easy way out, though, would be to just admit that the embryo isn’t a human. this doesn’t strike me as too hard, since a human embryo at the time stem cells are harvested probably looks identical to at least any other vertebrate embryo.)

of course, right now, it’s legal to prematurely end the lives of human embryos … for ivf. i still don’t understand why the people who voted against stem cell research aren’t screaming bloody murder at clinics offering ivf. proponents of stem cell research should really sponser a bill to have ivf outlawed, thrusting senators’ crazy embryo double standards into the public eye.

i won’t hold my breath though. instead, i’ll just hope that it’s garbage like this though that gets congress shaken up this november. until then, you know what they say: “snakes on a plane, man.”

ughhh, it’s been so hot and humid lately here in boston. the woolly heat just blankets you as you step outside and into the sun.

christina and i have eschewed air conditioning in our apartment due to the following moral arguments:
1) we’re cheap.
2) having both descended from 100′s of generations of tropical island people, our egos can’t bear the thought that we’d be overcome by boston summers.
3) we’re cheap.

sadly, blood has already been shed for our noble, air conditioner-free cause. one of our giant danio fish committed suicide today, by jumping out of our fish tank. apparently, fish do crazy things when their water gets too hot. our three oscar fish also don’t look so good – they’ve stopped eating. poor guys. rather than invest in a water air chiller, we’re just going to see who lives out the summer and buy more of those kinds of fish. we’re darwinian monsters.

i do have a plan, however. when we were visiting the really nifty-looking reichstag:

i learned from our tour-guide that the architects engineered a huge water-based temperature regulation system beneath the building. in the summer, water was pumped near the ground’s surface and allowed to heat up. the water would then be stored until the winter, during which the water would be pumped through the reichstag, warming the place up. meanwhile, a parallel hydraulic system would be using the cold winter air to chill water; that water would be used to cool the building in the summer. pretty clever stuff.

i figure we could use a similar system to climate control our apartment. we’ve got a huge vat already sitting beneath our apartment – our landlord’s brother-in-law has been using it to crush his own grapes in the fall. (if you’re wondering why, it’s for his basement winery … in the context of our portuguese neighborhood, we’ve learned that a basement winery makes perfect sense) christina has brought up the very valid point, though, that a giant tank of water under our house would probably give the blasted mosquitos, gnats, and fruitflies infesting our house the upper hand.

so, the backup plan is to force water through a series of tubes and ducts to my nearby and wonderfully climate-controlled lab. the water would be heated or chilled as it snaked through the labs; it would then flow back to us and surrender its thermodynamic bounty.

perfect.

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in other news, i came across a really crazy website the other day. 4shared.com. if they were able to kill napster and morpheus, it should be a piece of cake to sue this site into oblivion. nonetheless, the site has yet to go down …

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oh, and i just found out that avril lavigne and the lead singer from sum 41 got married two days ago! you’ll have to excuse my zeal and being a bit slow on the celebrity news lately – i’ve been completely out of touch this past year, since we don’t have cable and it’s raison d’etre, vh1. it’s funny: i always thought that i was above the whole celebrity gossip thing. but, the giddiness i felt when i married an avril lavigne and sum 41 playlist on itunes this morning obviously belies that belief. god, it’s really embarrasing admitting that i’ve got either of their songs on itunes. i’ll just console myself by remembering that admission is the first step to recovery.

it’s been a good summer so far. i’ve already done 2 of the 27 things i’ve hoped to do in my life.

the first was #23: backpacking for at least 2 weeks in a foreign country. check.

the second has been #16: learn c. i finally took care of this one last week.

not knowing c has been a real mark of shame for me over the past couple of months. i mean, here i am getting a degree in computation and i don’t even know one of the most famous computer languages in the world. what kind of programmer was i?

i’ve settled on an analogy to explain to non-programmers what it’s like to not know c: it’s like a rap artist not knowing how to freestyle. freestyling, like any improvisational art, isn’t easy. of course, a rapper recording a record doesn’t need to flex any freestyling skills – that’s what his/her crazy-ass lyrics are for. similarly, c, due to its crazy syntax and requirement that programmers think about wacky things like memory allocation, is less than straightforward. most programmers nowadays don’t seem to need c. for example, there are a bunch of other languages which are either much easier to learn (like python), nearly as powerful but less ornery than c (like java), or often just more convenient (like perl). [mind you, i'm certainly not an authority on programming - i just haven't had a hard time coming up with excuses as to why i could avoid writing programs in c.]

to finish my analogy: although a rapper need not be able to freestyle, freestyling’s difficulty makes it a hardcore skill. and isn’t being hardcore what rapping is all about? likewise, i’ve always considered people who can decipher c’s obfuscated code to be hardcore. (apparently, i’m not alone: 1, 2.) and therefore, since i didn’t know c, i wasn’t hardcore. so uncool.

well, last week, that all changed. my putative thesis took a wild new turn and forced me to, instead of writing my own program, modify someone elses. and, (gasp!), that other program was written entirely in c.

as usual, in the case of most dreaded scenarios, it turned out that learning c wasn’t nearly as difficult as i had psyched myself into believing. all it took was 2 good textbooks and about 36 hours of patience.

epilogue: do i feel like a better person for knowing c? sadly enough, i actually do. not so much for being able to add another language to my cv. but more for that general mushy feeling you get when you’ve motivated yourself to do something that you’ve avoided for quite some time.

[so i tried to find a suitable graphic for this post by searching for the string "hardcore" in google images ... good god some girls have humongous boobs. they were like giant tumors!]

tonight’s excuse for why i got no work done.