from the desk of stinkpot

I’ve recently started my last (hopefully) thesis project on my way to my PhD. The project will be a study of the human gut microbiome; to analyze it, I’ll be embarking on an investigation of several months worth of human feces.  (And, if that high-level description grosses you out — be very afraid of the details that, in the name of basic human decency,  I’m witholding from this blog.)

In any case, I’ve been discussing this project a lot lately in the lab as I’ve tried to work out the logistics of this project.

I had no idea though how much notoriety I had gained until yesterday, after dinner with some friends.  As we were heading home, a labmate confessed, “Everytime I poop now, I think of you.”

Finally, my research is making a difference in someone’s life!

heard larry wall, creator and benevolent dictator for life of the perl programming language, speak today.

glad i went.  the first 15 minutes or so was a bizarre stream-of-consciousness race through about 100 1-word slides.  it was both profound and absurd, both celebration and diatribe.  equally fun was seeing MIT in its finest geek culture glory: in a room of approximately 100 programmers, there were maybe 15 women, 30 ponytails, 1 female ponytail, and a clear correlation between beards and BMIs.

real jewels of the talk:

• hearing someone trained in linguistics describe their philosophy to computer language design.  (noticed how he referred to variables as “nouns” and methods as “verbs.”)
• learning that hashes in perl are preceded with the “%” sigil, because the 2 dots in the percentage character are supposed to represent the key and value in a hash.
• hearing “we want perl 6 to be the martha stewart of languages — it’ll do everything everything better than any other language (except get incarcerated).”

Now that spring has sprung itself upon us, I’m hoping it’s safe to start posting pictures of what winters in Boston are like:

I gave a 20-minute talk today to about 200 grad students, post docs, and faculty at a departmental retreat. I think the talk went pretty well — I don’t think I rushed at all and I stayed on time. Folks I met afterwards also appeared enthusiastic about my material / delivery.

The relative ease I felt while giving speaking stood in stark contrast to how anxious I was leading up to it. I’d never spoken in front of so many people before and was frankly a little intimidated. So much so that it spoiled my weekend a bit — I was having trouble giving my attention to non-talk-related tasks Saturday and Sunday.

I thought I’d make a note of this, since one of the reasons I agreed to give this presentation was my hope that I’d get some ease speaking in front of large audiences. Now that the talk is over, I recognize that it’s not comfort with speaking that I’d like more of (although that’s always nice), but rather comfort leading up to the talk. It’ll be interesting to see if that comfort increases in the coming years …

wonderful transaction seen scribbled on a bathroom stall here at school:

i’m working on my thesis committee meeting slides under the loft bed in our bedroom.  christina is asleep “upstairs,” exhausted from the drain of med school.  fortunately for my blog, christina’s exhaustion and her penchant for sleep talking are on good terms.

christina: “yeah!”

me: “yeah what?”

christina: “the liver is filling inconsistently.”

me: “how should the liver fill?”

christina: “the food should go in all at once.”

christina: zzzzz.

it’s a little cute but also a little sad: even when she dreams, christina is in medical school.

i don’t think i’ve blogged about this topic yet; with the aid of some wonderful experimental collaborators and my advisor, i co-authored a paper in science this past summer on microbial ecology. my contribution to the project was an algorithm i named AdaptML. it’s a pretty cool algorithm*: i think it’s one of the first to gracefully combine genetic sequence information with the metadata describing which environments those data were sampled from, in order to ultimately produce a model of what environments bacteria hosting those sequences are adapted to living in. the algorithm can even predict environmental associations for the ancestral bacteria which gave rise to the present day ones you’re studying.

using a really nifty piece of online software called iToL**, i was able to plot the output of AdaptML in a very pleasing way. for instance, below is a sample figure used to help produce the science manuscript. the tree structure represents our best guess as to how a particular genus of bacteria named Vibrio evolved over hundreds of millions of years. (if Vibrio sounds familiar to you, it’s because one strain causes cholera.) the colors on the outer rings relate what kind of environment present day samples were found in; the inner balls tell you were we predict ancestral bacteria would have wanted to live.

adaptml figure

in any case, the reason i bring all of this up (besides to feel good about myself for getting a paper published in a good journal), is because i learned today that the above figure made it onto the cover of a very well known textbook in genetics. it lives on amazon, and will now forever provide proof of my programming ineptitude if some bugs in my code eventually emerge.

* for those comp bio geeks who might be reading this, what’s nifty is what AdaptML does under the hood. the idea is that it treats the environmental metadata like sequence information and runs a general markov model to infer ancestral environmental metadata. for instance, if you had present day genetic sequences all related by a phylogenetic tree, you could apply a jukes-cantor or kimura model to calculate the most likely ancestral sequences on your tree, by assuming that each nucleotide in your sequence has a certain frequency and that the probabilities of nucleotides transitions satisfy certain properties. AdaptML uses that same idea, except that instead of considering 4 possible character states (nucleotides), it can handle N states, where N is the number of observed environments.

** i can’t rave about this software enough. i can honestly say it has changed the way i interpret my data; i never would have noticed patterns of evolution embedded in my datasets, had i not looked at them via iToL.

great moment #432:

you’re brainstorming in your advisor’s office and the conservation culminates in his declaration: “we’ll become the watson and crick of poop!”

i love grad school.

i had dinner with a good friend from high school — JD — last friday night.  we traded stories from high school, most notably reminiscing how he had actually dated lady gaga and brought her to prom.

JD is now studying architecture up the street at harvard.

it was insanely fun to talk to someone who devotes nearly all of his energy to being creative.  i had such a good time that i wanted to write down here some of the fun things we talked about:

• architecture students are told by their professors on day 1 that, “you’ve already been in architecture school your entire life.  every hospital, every school, every home you’ve been in — those structures have been slowly been informing your sense of space and design.”
• architects worry a lot about making “big mistakes.”  if you screw something up bad in science, no one reads your paper and it’ll get forgotten.  if you screw something up bad in architecture, evidence of your failure will stick around for decades …
• we talked a lot about photography and design.  both force you to walk around and constantly study what’s in front of you: light, shadow, depth of field, angles, foreground, vanishing points, right angles.  “so many people just use their eyes to not walk into things.

also, people like JD who can draw out on bar napkins how to get mollusk shells from the golden rectangle rock.

mollusk shell from golden rectangle

this is one of those days that i’m really glad i’ve got a blog, and can record somewhere (that i won’t lose) what i was thinking the day barack obama was inaugurated. decades from now, when i, or perhaps even my children revisit this, i’m sure it’ll make for pleasant recollections.

anyways, on to what was on my mind tuesday (besides bacteria and my thesis). of course, there was the excitement of finally having a president who is fabulously eloquent, intelligent, and capable of getting a wide array of people to work together. it’s a wonderfully refreshing change, and the news has been awash with these sentiments all week. (future-me: don’t look here for further discussion on those topics — i won’t bother wasting digital breath on something that’s already been written about to death.)

still, i think i harbor at least one unique perspective that’s worth recording, one that i have yet to see reported in any article or even have heard another person discuss out loud.

yesterday’s inauguration actually made me feel like i fit into this world just a little bit better.

i know that sounds a little melodramatic, but let me explain.

my parents were both born and raised in the philippines. they met in new york city in the early 1980′s; i was born the year after they married. both agreed to make a conscious effort to facilitate my assimilation into american culture by speaking only english at home. consequently, i never learned either of the filipino languages my parents are fluent in: kapangpangan or tagalog.

there were foreseen, and unforeseen, consequences of my parents’ linguistic policies. as expected, i got good at english and speak american english without a discernible accent. i almost certainly under-appreciate that latter benefit. but, what i think my parents didn’t quite foresee would be that not knowing tagalog would help cause a small tear in my sense of identity that i have still yet to mend.

i recall first trying to work out my racial / cultural identity in first grade, as i stood over one of those trough-style urinals in elementary school. a classmate had asked me in the bathroom if i was related to bruce lee. my thought process went something like this:

• of course not. he’s chinese and i’m filipino.
• wait, can i really call myself filipino if i was born in new york city and don’t speak tagalog?
• in any case, why would you even think i’m related to bruce lee. do i sound chinese to you?
• i guess bruce lee and i do have the same haircut and he is pretty badass.

“yes, i’m related to bruce lee.”

variations on this tune have played out innumerable times since then. the basic harmonies are: i walk, talk, and act like an american kid (+1 american); i don’t look anyone i see on TV (-1 american); i can’t truly consider myself filipino while lacking the fundamental component of filipino culture: language (-1 filipino).

even as i write these sentences, the liberal/hippie streak in me (i get it from mom’s side) wants to say something like: “it doesn’t matter what you look like, you’re whatever you consider yourself to be,” or “americans aren’t just white or black.” the problem is, those arguments wear pretty thin by the 16th time someone in polite conversation asks:

“where are you from?” [me: new york]

“no, where are you really from?” [me, slower: new york city]

“ok … where are your parents from?”

years of asides like that, as well as the thankfully rare, but still maddeningly subtle hints which belie strangers preconceived notions regarding my background (the slowly paced and overly annunciated greetings drive me crazy), add up. toss in the occasional awkward scenario where i’m the only asian person within a 300 person radius (usual offending locations: county fairs and country club tennis courts), and you start to see why i still can’t help but second guess how american i am.

so those preceding paragraphs are in a nutshell, why barack obama could have stood on the inauguration stage for 30 minutes without opening his mouth, and said something profound to me. clearly not white, debatably black, and perhaps even indonesian, obama is one thing for certain: not your average looking american. and yet, he now occupies the role of the foremost american in the world.

i don’t think i’ve ever felt so american.