from the desk of stinkpot

arthur c. clarke passed on today.  i just read his obituary and learned that he was the original author of the aphorism:

“Any sufficiently advanced technology is indistinguishable from magic.”

the next time i try and explain microbial evolution to someone, i think i’m going to quote mr. clarke.

auntie danielle, my sister’s godmother and my mother’s best friend passed away last night.  i thought i’d leave a photo here of danielle that i took on our way to the philippines two years ago.

meet hubert, my octopus.  he came to visit last week while i waited for some particularly long modeling jobs to execute on the darwin computing cluster (more on that later).

hubert’s timing couldn’t have been better, as his visit coincided with ned ruby‘s to mit.    here’s a picture of ned:

ned is a microbiologist from wisconsin who studies the symbiosis between the doe-eyed 3cm-long cephalopods above and a bacterium named vibrio fischeri.  the talk ned gave on that symbiosis was fascinating — it was filled with precisely the kinds of wondrous stories and unbelievable facts about the natural world that convince naive students to forego the median tax bracket and become phd candidates.

he began, as microbiology talks often do, by explaining why folks shold care about microbes.  in particular, he highlighted the applications of studying microbial symbioses.  to paraphrase:

there are roughly 10 bacterial cells in the human body for every 1 human cell.  folks estimate that each person harbors around 25,000 unique bacterial species.  the human genome consists of roughly 20,000 genes; the microbial pan-genome within us consists of approximately 3,000,000.

this begs the questions: how are 3,000,000 genes simultaneously regulated in the human body?  how are millions of unique metabolites and enzymes produced, transported, and employed in any coherent way?

tackling a symbiosis problem on that scale would be like trying to build a model of how individual cars affect the american nation.  so, ned decided to simplify the problem.  the squid he studies, euprymna scolopes (they look remarkably like ned above), enjoy the unique ability to selectively screen which bacterial species colonize certain regions of its body.  specifically, the squid possesses an organ on its belly that only vibrio fischeri can live in.

and here’s where things get amazing.  it turns out that the squid are nocturnal and feed near the ocean’s surface.  this makes them easy prey; predators in deeper waters can easily find the squid by looking upwards and pouncing on the shadows in the moonlight.  in response, the euprymna have evolved an ingenious trait known as counter-illumination.  while they swim at night, the euprymna’s vibrio-filled organ glows, thereby camouflaging their shadows in the moonlight.  by manipulating various muscles in the light organ that act as lenses, shutters, and filters, the squid can even control the intensity and dispersion of its anti-shadow.

how and why the vibrio bioluminesce is its own fascinating question in of itself that has already bestowed doctorates and macarthur fellowships on several researchers.

what ned talked about was studying how the euprymna and vibrio have evolved to interact with one another.  now, it took him an hour to explain what he’s learned over the past decade and i haven’t got the blogging fortitude to transcribe thirty slides worth of information.  besides, my memory has got the fidelity of a game of telephone.  so here’s the most salient points from the presentation:

• the euprymna are actually born aseptic.  within hours of being born, however, a handful of vibrio fischeri will colonize the light organ.
• over the course of the day, the vibrio make like calculators and rapidly multiply, eventually filling the light organ to capacity.
• after the evening feeding session, the euprymna contract the muscle surrounding the light organ and expel virtually all of the vibrio.

“huh?” i thought, as i heard that last bullet.  why kick out beneficial bacteria?

no one’s totally certain, but a leading hypothesis is that the bacteria are actually driving the expulsion!  the vibrio, perhaps not unlike pathogenic strains of e. coli, release toxins that likely degrade the membranes of the light organ, ultimately compelling the euprymna to eject the vibrio.  and by getting the heave-ho, millions of vibrio are re-introduced into the water column, ready to populate new infant euprymna.

this ending to the fairy tale blew me away.  on the one hand, you’ve got a bug that’s basically like cholera: it desperately wants to spread and effects that transmission by irritating mucosal membranes until the point of host expulsion.  but, unlike human-affecting cholera, these vibrio are profoundly beneficial to their host in some ways, thereby providing enough incentive for the euprymna to not evolve a comprehensive mechanism for complete vibrio fischeri clearance.  just a wicked cool example of how an apparently mutually beneficial symbiosis in nature can actually be a struggle between two completely opposing forces.

oh and two sidenotes:

1.  ned ruby raises something like 10^5 euprymna a year in aquaria in his lab.  i was dying to ask him how they tasted.
2. in case you were wondering, poor hubert the hand-octopus was indeed sick with smallpox.  he passed  only a day after his photo was taken.

my body is officially in decline.

up and through college, i would not exercise for months, suddenly go for a run or play some tennis and not feel any aches.

today, i ran 4 miles for the first time since the fall and now feel like my knees are going to push right through my skin and explode.  it took me thirty seconds to climb a flight of stairs just now to get to my desk.

sigh — it’ll be the glue factory for me by next winter.

i’m really behind in sorting through the photos i’ve been taking.  here’re some from a trip i took with my family to the caribbean over the christmas break.  the trip was quite lovely — i can’t remember the last time my family was together, just the four of us, for an entire week.  i had an especially good time hanging out with my little sister, who i unfortunately see quite rarely nowadays.

i sat next to a fascinating lady on the plane ride down.  she was in her 80s, a self-published poet, and mother to twins who died sudden deaths within a year of each other recently.   she had also had cataracts removed a couple of months ago, which gave her a nifty hipster meets grandma look.  i’m completely blanking on her name; i know i wrote it down somewhere though.

we stayed at a rather ritzy resort (at least by my usual backpacking standards), replete with courtyard (and parents walking through):

big fancy rooms:

and finally, lots of signs keeping the locals out:

and the tourists safe from themselves:

we spent a lot of time on the beaches:

which also had lots of photogenic things, such as scary pieces of driftwood:

and awesome little coral formations.

in fact, a naturalist down there told me that the island (grand bahamas) is basically a 2-mile thick coral fossil, formed over the course of millions of years.  i wonder if that was true.

we also went kayaking (we went out to that small island in the distance):

where we struggled to put on wet suits:

and went snorkeling:

another day, we went to a national park and visited a network of limestone caves:

i was told that, indigenous carib families used these caves to hide from the conquistadors.

when not exploring the island, we also found ways to keep busy at our hotel.  shuffleboard, namely, was a popular game:

finally, we did do some walking around and exploring at night:

we’d go out for dinner, where the menu never changed: fried fish, fried conch, or macaroni.  by the end of our trip, i had nearly resolved to become a vegetarian when i returned to the states.  i certainly didn’t fall off the fried food wagon for weeks.  below is a particularly expansive bahamian dinner selection:

although it wasn’t the chronological end to our trip, new year’s eve i think is the appropriate thematic end to this post: a big, flashy, close.

pictures from the trip worth significantly less than 1000 words / photo can be found here.

maybe someone should get christina an slr soon.  i’m digging her photos.

petsi pies.  jacob, chris and i went over to the shop on beacon for a warm & delicious apres-brunch snack.  there, i discovered two things: 1) petsi’s mixed berry pie is heavenly — tangible proof of a benevolent, pie-adoring god.  2) the name petsi comes from the renee’s (the proprietress) childhood nickname.  renee’s parents really wanted a son (they ultimately had 5 children, all of whom were daughters).  during one pregnancy, to show fate they really meant business, they  promised to name the unborn child peter.  fate either didn’t care for her parents’ plans, or the name peter, as a girl (renee) was born.  still, her parents remained attached to “peter” and the nickname “petsi” was born soon thereafter.

2)   federal tax assistance software is the primary counter-example that any benevolent deity governs this world.  i spent 3 hours wrestling with turbo tax and it’s incredible repertoire of software glitches today.  i could actually feel my soul being squeezed out of me, as tech support had me re-enter my 1099-misc forms for the fourth time into their tax wizard.

i think a reasonable approximation of how interesting your day was can be gained by looking at the changes in your meal timing. dinner on schedule == nothing new. waiting an extra hour for dinner signifies something moderately unexpected (maybe good, maybe bad) came up. today, chris and i scored about +5 hours on my “meal surprise” scale.

first, lunch was delayed by +1 hours. chris and i played tourist this morning, as we took a guided walk of mit’s tunnel network. the tour was a bit humdrum (it was led by a fellow from mit facilities, who very well couldn’t show us anything too mischievous), but still fascinating; virtually every building under mit sits atop a network of interconnected tunnels. there must be literally several miles of corridor winding and snaking their way underneath the campus, enabling students to cross almost the entire university while avoiding dangerous things like sunlight and breezes. things got even more interesting after the official tour, however, as christina and i did some exploring and found that another level of tunnels lives below mit’s first basement level. we saw all sorts of gnarly things: huge grids of intersecting and overlapping pipes knitted together; gigantic pieces of rusted machinery whose dials for appendages and loud buzzing reminded me of enormous metal dragonflies; the dozens of pieces of graffiti lining back walls, tagging who had previously found the rooms we chanced upon. i actually brought my slr along with me and took some pretty cool photos (which now sit very far back in a photo-processing queue).

second, dinner was delayed +4 hours for something even more special.  thanks to a labmate’s tip earlier in the day, chris and i scored sneak preview tickets to michel gondry’s new film, be kind rewind, which was being screened for free at mit.  and, as if my pair of free-ninety-nine tickets weren’t worthwhile enough, michel gondry was even going to come by after the movie for a Q&A.

i could hardly contain my excitement throughout the afternoon as michel gondry is probably my favorite director — i was blown away by eternal sunshine of the spotless mind, as well as the science of sleep.  his movies have this wonderful sincerity to them (that may even occasionally verge on the naive) that manifests itself not only in his characters but in how he shoots his films as well: long, unbroken scenes shot in single takes and the ingenious use of simple props and clever camera angles to avoid having to use special effects.  needless to say, i heart michel gondry.

remarkably, the evening lived up my own hype.  be kind rewind was just as marvelous and inventive as i had hoped it would be.  sure, the characters weren’t quite as well developed as in eternal sunshine, but some of the scenes were absolutely sublime — the 120-second-or-so montage midway through the movie where 5 classic movies are reprised using only one take and something like $20 in props and cheese pizzas was breathtaking.

yet, unbeknownst to me, i spent a year’s worth of karma sometime this afternoon — two things happened this evening whose excitement even manages to supplant a free advance screening to a michel gondry movie.

1) i got to meet michel gondry.  i ran into him at the top of a flight of stairs in the movie theater.  at least, i thought it was him — i saw a man who looked too old to be a student and uncomfortable enough to be an artist.  “are you michel gondry,” i recall blubbering.  and frankly, i can barely remember anything else i said after he nodded his head.  for the first time in my life, i knew what it meant to be starstruck.  all i could manage was a couple of stupid, incoherent words that may or may not have assembled themselves into sentences: “your imagination … beautiful … changed how i see the world … tuna fish.”  smooth move, ex lax.  i think i heard a sheepish “you’re welcome,” before i slinked away in a daze.

2) topping things off, i was able to steal out of the theater a little early, before the Q&A finished, and appropriate a 3 X 4 foot copy of the be kind rewind movie poster.  a little jog back to my lab here, some stalking of director gondry there, and i was actually able to corner him with the poster and a sharpie before his press conference.  michel gondry’s last words to me: “you just stole my poster and now you want me to sign it?”  of course, he then smiled and signed the poster, leaving me positively elated.

good day.

it’s now 2.30 am and i’m still up trying to program on my dying powerbook.  christina fell asleep hours ago on the futon next to my desk.

when it gets late, i try and take breaks to talk to subconscious christina. our conversations are usually very short and delightfully enigmatic. they’re like sleep haikus. slaikus, i think i’ll call them. tonight’s was a good one:

what are you dreaming about?
nothing.
how can that be? everyone dreams.
this person is boring.
so you’re boring?
no, this person i’m in.
where’s your body then?
sleeping.

gave christina her first squash lesson today.

holy crap she’s talented. within an hour, she was able to hold a rally with me.

of course, this was all to be expected. chris has got preternatural hand-eye coordination. last summer, i took her out to the baseball diamond across the street; she had never played baseball before. within a couple of pitches, she was belting balls into the outfield.

in any case, i look forward to having a new squash partner.  i used to play quite a bit of squash in college (i was on columbia’s varsity team).   squash is a wonderfully demanding sport: i get a much better workout “squashing” than i ever do on the tennis court — both mentally and physically.  you’ve got many more options for each shot in squash as opposed to tennis (due to four walls surrounding you), and the rallies between skilled players last on the order of minutes.  squash is like is like a vacuum for your body — you walk off the court completely empty.