from the desk of stinkpot

craigslist is our travel agent for boston; following used bike listings keeps taking us to new parts of the city. a couple of weeks ago, in the hopes of finding a $100 bianchi road bike, we made our way to hingham, on boston’s south shore.

[unfortunately, we were out of luck. the nice old woman who invited us out had mistaken her hybrid bike with slick tires as a road bike. we were a little bummed but had a contingency plan; we had brought along two bikes and went for a bike ride on some nearby trails in wompatuck state park. (the old lady totally made up for misadvertising the bike, by informing us of said park.)]

the bike paths there took us by what looked to be an abandoned army base. it was creepy: most of the concrete structures remained in place, but just hollowed out and covered in thick vegetation and graffiti. i took some pictures, of course.

those pictures demand appreciation; we originally set off without a camera, but those decrepit old buildings were so compelling that i forced christina into doubling-back to the car for a camera. in the process of snapping photos while riding my bike, i got my tire stuck in a set of train tracks and fell down. luckily, christina broke my fall. and luckily for christina, the pavement broke her fall.

we drove home along the shoreline. along the way, we came across the most delightful fried seafood shop — the hingham lobster pound. the boxcar restaurant made up for its lack of tables and chairs with sweet cholestorally goodness — their menu basically consisted of anything found off the eastern seaboard, fried in batter. we ate a delicious dinner of fried clams and fried haddock in the backseat of our car. some hot backseat action.

Do I really want to make a career out of being in academia?  Grad school, a post-doc, tenure-track faculty positions — not only does the whole process seem overwhelmingly competitive and anxiety-racked, but the very notion of academia seems a little contrived.  I think one of the reasons I became a grad student was because I could and many others couldn’t; my good grades and undergraduate research background afforded me an opportunity only a minority of students receive.  Anything selective must be good right?

Not that I’m feeling overly negative about grad school; it’s just interesting sometimes to step back and really think about the important decisions you make in life.  [It's especially appealing when you've been sitting in a hospital bed for the past five days].

So … in the welcome event that I have a successful doctoral thesis, will I pursue a professorship, in part because so few grad students get that chance?  Hopefully, I’ll at least be a little less cynical by then

In any case, cue the quote I read the other day that triggered my pretentious introspections:

“If you’re totally obsessed with Shakespeare and James Joyce and go to the ends of the earth researching them, we call you an English professor,” Thompson said. “This guy has chosen his body of art to consume, it just so happens he can’t make a living off of it. The only fundamental difference is he doesn’t have tenure.”

i’ve been in the hospital for the past 5 days. there’s no internet here and i’ve got two IVs in my arms. i’m not really in the mood to write code. i figured i might as well fill in all the blanks in my blog over the past couple of months — scroll down to see some new old posts.

june 29: passing quals [posted 07.17]

july 9: long weekend [posted 07.11]

july 3: butt exam [posted 07.11]

june 1: shingles [posted 07.11]

june 22: camping [posted 07.10]

this whole bleeding escapade was really poorly planned. going to the hospital effectively ruined what i had been looking forward to throughout my thesis proposal/shingles-racked summer: a trip to LA to see my cousin get married, followed by 3 weeks of backpacking through thailand, cambodia, and burma. my disappointment in missing those trips officially cinches this summer’s title as my “worst summer ever.” (even worse than that summer my mother enrolled me and my younger sister in a baptist day camp, where we had to compose skits about noah’s flood and play kickball in a basement with 8-foot ceilings.)

still, things somehow got even worse this week, after i was discharged from the hospital.

a little background: christina’s mcat was scheduled for yesterday, the 13th. for those of you who don’t know what the mcat is, it’s basically the most unholy test conceived — a four-hour long exam whose outcome largely dictates what tier of medical school you attend. studying for it took christina 2 months of daily practice exams and reviewing biology and chemistry lectures; the allied landing on normandy probably took less preparation.

already, i put a bit of kink in chris’ study schedule, by going to the hospital the weekend before her exam. the poor girl slept for 2 nights by my bed in the hospital (thankfully, mom came up and stayed with me the next 2 nights, which gave chris a chance to get some real sleep back in our apartment.) i was already worried that the bloody mess i had gotten us into had undone some of her careful test preparation.

apparently, my colon felt no such remorse. thursday night, about 12 hours before her exam, i began to bleed again. (i feel like i should be canonized soon, given all this spontaneous bleeding.) the plot thickens, but sadly doesn’t clot: christina is already asleep and i’m beginning to get light-headed. i had already shed a third of my red blood cells the previous week — additional bleeding is likely unfavorable for little things like remaining conscious or continuing to oxygenate my vital organs. yet, waking christina to take me to the hospital will at the very least leave her exhausted for her behemoth test the next morning. even taking a cab to a medical clinic and leaving a note will likely stress her out and jeopardize her success on a test she’s studied months for. on the other hand, ignoring my bleeding and going to sleep runs the risk of me fainting from blood loss in my sleep. which, of course, is something that might be a bit tricky to extricate myself from …

[two cliche's spring to mind.  cliche #1: "talk about being stuck between a rock and a hard-place." cliche #2: "you can't get blood from a stone."]

maybe it was the excessive blood-loss talking, but i made a choice that in retrospect, might not have been the best one: i decided to take my chances and just go to sleep.

epilogue: christina got to her mcat with a mostly clean emotional slate and hopefully did ok. i even drove her, in an effort to prove that i was in good health. of course, that was a slight lie — i was still hemmoraging blood that morning (and probably shouldn’t have operated a motor vehicle — then again, i figured that if i got in an accident, well, i’d probably be bleeding anyway.)  thankfully, whatever was going wrong righted itself later on friday and i soon stopped passing blood in my stool.

still, even as i write this blog post, i can’t help but worry that some maroon-stained sword of damocles is dangling over my abdomen, waiting to slice back into my GI tract.  every ache or even stray muscle contraction in my lower torso has me worried that i’ve broken my merchandise.   dammit, it sucks being damaged goods.

it’s been a rough couple of days.

thursday morning, i get a call from my gastroenterologist. apparently, my polyp had a pre-cancerous adenoma in it. [bad polyp, bad!] that doubly sucks: 1) i had something with the word “cancer” in me (scary even with the prefix pre-). 2) i’ll have to start getting regular colonoscopies to see if polyps are coming back.

funny though, how his call wasn’t my biggest concern that morning.

instead, i was freaking out over the crazy amount of blood i saw during my morning bowel movement. it was a brilliant red, and it had diffused through all of the water in the bowl — it was perversely beautiful actually, like a sunset on a dusty evening. snap back to reality: i’d never seen so much blood in a toilet bowl before and it freaked the shit out of me.

i called the physician who had removed my polyp. concerned, he assured me he had “cauterized the hell out of” the vascular stalk that my polyp had been detached from. he thought it might have just been old blood finally being pushed out. but, he warned me that if i saw anymore blood … well, that’d be bad.

i decided to try and relax and just wait for my next bowel movement. i went to lab and even met with some collaborators. still, throughout my meeting, i felt that horrible feeling you get when you’ve eaten rotten mexican food and it’s passing straight through you — when the meeting ends, i dart to the bathroom and listen in horror as a prodigious amount of fluid spills out of me. i estimate it’s about 2 cups of blood, based on how long it takes.

i’m blanched (in horror, probably not from blood loss) by the time christina gets me to the ER at mount auburn hospital.

the next 24 hours are tortuous. it takes 7 hours for me to get through patient triage and be assigned a hospital bed. (meanwhile, i’m constantly expunging about 10 ounces of blood an hour.) as if things couldn’t get any worse, a nurse informs me at 1 AM that i’m scheduled for an emergency colonoscopy the next morning. that means i get to drink laxatives again but this time while attached to an IV and bleeding profusely. i’ve had better nights.

thankfully, the colonoscopy seems to go off without a hitch the next day. it seems the seal on the polyp’s stalk had actually held; what happened was that the stalk itself had filled with blood like some heinous over-filled water balloon. and eventually, it had popped.

the gastroenterologist who staunched the bleeding basically removed all of the stalk and sealed off the vasculature near the walls of my colon. i’m told that the risk of bleeding reoccuring is minimal. still, to be safe, my physician insists i spend the next four days in the hospital, under constant monitoring by nurses. to allow my wounds to heal, i’m also kept off of food for 2 days.

this last restriction is especially trying, as i hadn’t really eaten the day before i was admitted to the hospital. thus, i go about 72 hours without food, a fast which makes me painfully aware of how much of tv advertising is food related. bisquick pancakes, dark chocolate keebler brownies, buttery shrimp scampi from red lobster — i make a mental note to consume all immediately upon leaving the hospital. for god sakes, i spent an entire 30 minutes fixated on an infomercial advertising the “heat wave cooker,” which chef ron conclusively proves locks in flavor and allows harmful cholesterol to leak out of whatever fowl or small game you’re basting.

between the bleeding and the fasting, i lost 10 pounds in those 5 days. (that’s a lot when you weigh about as much as an chain-smoking anorexic czech supermodel to begin with.)

what’s really frightening, however, was learning that my hematocrit had dropped by about 30% in the first 24 hours of my bleeding. christina and i had been planning on backpacking in burma next week (to be covered in another blog post) … had my bleeding started only a week or two later, i could have been days from civilization, much less a hospital with a functional colonoscope. yet, the rate at which i would have lost blood meant that within 2 days, i’d be in extremely bad shape. i blurted out to chris this morning, “you know, had we been backpacking in burma, you might have watched me bleed to death.” that shook both of us.

ok ok, that was pretty morbid and a little over-dramatic as well. i’ll just end with some photos i took in the hospital (never too sick for photos!):

[ i had a great view from my room.]

[mom and dad got worried and drove up from new york to visit]:

[ i thought this was really cool -- the doctor should me a photo of my colon and the stalk they had clipped off. it used to be as thin as a pencil -- you can see in the first photo in the upper left that it had swollen up like a big leech. i'd advise scrolling away if you're squeamish ... and looking closely if you're one of my buddies in med school.]

my body is sorely confused — it must think i’ve joined AARP or something. last month, i’m struck by the bane of geriatrics: shingles. today, i underwent the universal rite of senior citizenhood — the colonoscopy (a fancy word for a butt exam).

you see, my quals weren’t the only test i took this summer. i also took a fecal occult blood test — and failed. i should have studied harder. in any case, my butt doctor thought it prudent that they go and inspect who spiked my punch.

—

the word “traumatic” doesn’t begin to describe how awful the whole ordeal was. i had the pleasure of:

• one night spent drinking a gallon of colyte and 10 ozs of magnesium citrate (advertised on the bottle as the “sparkling laxative.”) [when i asked the pharmacist who looked like mark paul gosselaar what the difference between the two was, he smiled and said, "the first one gets things going and the second one finishes you off." i know you might not want to have read that, but i feel like what i went through gives me at least the right to make other people squirm.]
• being assured by my physician (from behind his splatter-guard mask that covered him from neck to the crown of his head) that “i’d be heavily sedated,” only to burst out of semi-consciousness midway through the procedure in a paroxysm of abdominal pain. apparently, i’ve got an abnormally narrow colon and it didn’t appreciate 5 feet of tubing snaking its way through.
• being insanely disoriented and discombobulated after the exam. i barely recall my physician speaking with me before i was released. it seems that my sedatives were mixed into a cocktail with some valium-like drugs that have an amnesiac effect. [good lord, i got date-raped.]

still, i suppose the whole procedure was worthwhile — my gastroenterologist removed a “large” (his adjective, not mine) polyp from my GI tract. talk about bad meat. it’ll take a couple of days for a lab tech to biopsy my polyp. i tried to talk the doctor into letting me keep my polyp in a jar, but he ignored me and probably thought it was the drugs talking.

worst. night. ever.

i narrowly passed my thesis proposal defense the other friday. it wasn’t catastrophic or anything like that, but it certainly didn’t go as well as planned.

for one thing, the oral examination was much more serious than i had anticipated. i hadn’t been so naive as to think my orals would be fun — a fellow second-year grad student, who had considered opening his proposal defense with a joke had been advised by a more senior student, “it’s best not to start your talk with a joke. actually, it’s best not to have any jokes in your proposal. in fact, try to spend the entire two hours like you’re on the verge of tears.”

still, i hadn’t anticipated how much of an “exam” my qualifying exams would be. [stupid, i know.] from my graduate program’s advisory guidelines, i knew i’d have to convince a group of faculty that the research i intended to pursue over the next few years was both feasible and valuable. what i didn’t appreciate, however, was that my general knowledge of biology and computation would be tested. for instance, i was tossed questions so fundamental about biology that i was thrown off balance. the worst was: “what’s a gene?” — i fell into the trap of trying to offer some overly profound answer (and floundered long enough to look like i had no idea what a gene was).

in the end, i received a “tentative pass” for the oral portion of my quals. although not having a sharp answer for what a gene was probably didn’t help, what proved much more damaging was my spotty understanding of how the data i work with was collected and my sparse thought on the experimental implications of my research. getting called out for that of course wasn’t fun, given that the faculty i had invited onto my committee: ed delong, drew endy, and manolis kellis … saying these guys do science is like saying lance armstrong rides bikes or bostonians like their baseball team.

thankfully, however, it occurred to me midway through getting upbraided for not knowing enough about promoter region detection was how special the whole qualifying experience was. here i was, explicitly being mentored by 4 world-class scientists on how to do good science: how to become an active consumer of data; how to influence the progression of a particular subfield. to be taught those lessons by research giants is a wonderful privilege and a very welcome compliment — some people must think i’m worth grooming.

+5 points for lawrence’s fragile ego.

while making slides for my thesis proposal this friday, i came across this beautiful triptych of a macrophage attacking an e.coli cell. this painting definitely needed to shared; it does a fabulous job of illustrating how remarkably dense a living cell is. (the fact that interacting biomolecules find one another amidst this mess is proof that magic is real.)

i should also point out that the fellow who painted these watercolors, david goodsell, is also a professor of molecular biology at scripps. in other words, the man is a first-rate scientist and a first-rate artist. needless to say, as a third- or fourth-rate biologist and a forty-seventh-rate photographer, i’m blue-green with algaenvy.

i saw a terrific bike today on mass ave. in cambridge, right by city hall.

what set this bicycle apart was its electronic wiring.  it had 2 headlights and 2 tail lights.  each was homemade: the designer had taken some translucent salt and pepper shakers and studded their ends with LEDs from radioshack.  i followed the leads from the shaker lights down to the front wheel hub — there was a generator enclosed within the oversized hub.  nifty!

but, what was really rad was how the whole circuit was completed.  i could only find one lead from each light to the hub-generator.  the negative leads from each light were either just soldered to the bike’s frame or to it’s metal mesh basket.  and then it hit me: the entire bike was the ground!!  sure enough, there was a lead soldered from the bike fork to the hub’s ground lead.

how cool is that?!

seeing that bike made me want a camera phone for about the 3rd time in my life.  (first two times involve “thoth,” the g-string-wearing, viola-playing, opera-singer/yodeler who used to show up in grand central station during my morning commute to high school.)  everything happens for a reason my mother tells me; maybe this episode is an sign that i should buy an iphone?