from the desk of stinkpot

as usual, we had an eventful weekend. stephanie, my younger and only other sibling, graduated from high school in new york city. i’m really proud of her – she’ll be chemE in the fall at upenn and she won the science medal at her graduation. what more does an older brother / engineer need to warm his heart?

our house was packed for a couple of days, with relatives from california and the philippines. amongst them were my youngest cousins, whom i had hitherto met. i’m quite positive that they are the cutest children i’ve ever seen. even for asian children with bowl haircuts, they were ridiculously cute. obscenely cute even.

i’ve got proof:

stephanie herself looked quite pretty in her graduation / wedding dress. i got a good carrie-esque photo of her in the cathedral her school held its ceremony in:

later, at her graduation party, i was pleasantly surprised to see my cousin francis along with his fiancee, her sister, and another friend of theirs. christina, stephanie, and i all had a good time hanging out with the four of them; they spent the night and we watched a cheesy horror flick. like almost all of my cousins, i only knew francis from when i was about 5-7 years old (much of my extended family shipped off to california in the late 80′s). francis, however, recently moved back to new york a year or two ago and we’ve hung out a couple of times since then.

which has made for some confusing memories: it’s strange to suddenly laugh, drink and joke like friends with someone whom, in the majority of my memories, i regarded as much much older and mature than me (i’m 7 years his junior – that’s quite a bit of time when you’re 5 years old).

it’s also downright disturbing how much francis looks like my father minus 35 years of age:

so as usual, good weekend. except for the part where i screwed up and got christina and myself caught in traffic and subsequently lost, deep in the heart of new jersey, on our way to a 5K race. sadly, we were unable to start the race with all of the other runners.

gawsh, i’m starting to appreciate how difficult it is to develop algorithms. it seems that the function representing the novelty & utility of an algorithm vs. effort exerted looks like 1-exp(-x): the first couple of breakthroughs in a field come easily, but improving on them can be quite hard. in my case, i’ve been working a lot lately on how to go about inferring evolutionary events and phylogenies from sequence data. initial methods for phylogeny learning (like parsimony and distance matrices), at least in hindsight, appear relatively obvious but still completely changed the way people thought about evolution [this is the initial, sharply sloped part of the curve]. a little more work (maximum likelihood and bayesian approaches) yielded nearly as large gains [the function's slope is starting to decrease]. i feel like i’m in the terminal end of the curve, where a huge amount of effort may yield only marginal benefits.

that is, if i make any gains at all. this is what i think makes grad school much harder than med school: going into grad school, you have no idea how in the world you’re going to get yourself out. at least in med school, you know that if you can sit through a couple more exams, you get to add to your parchment collection. grad school possesses all of these wonderful uncertainties, like: what happens if your experiments don’t work? or your ideas are all wrong? or as i’m beginning to fear right now, you simply lack the mental chops to solve the problems you’ve bitten off? no lambskin for you.

bah, less than two months into my doctoral work and i’m already stressing myself out

i’ve decided to post some photos i took over the past weekend, to take my mind off of the sub-problem that’s triggered all this angst. (in case you’re curious, the problem is: given a phylogenetic history of a gene – the gene tree – and the phylogenetic history of several species – the species tree – how do you efficiently enumerate the minimum number of gene duplications and losses in the species tree that produces the given gene tree. the problem’s actually been solved before … no one explains it well, however, and i feel forced to reinvent the wheel).

in any case, christina and i met up with my good friend andrew, his siblings, and another on sunday out on the far eastern tip of cape cod. we took a bike trip from a town named brewster to a tidy little place called nauset beach.

throughout the day, we did new englandy things like see a lighthouse:

play on the beach:

swim in 50 degree (fahrenheit!) water [photo credit: andrew and his un-watersealed and anti-anti-fogging camera enclosure]:

and frolic in provincetown, which undoubtedly boasts one of the world’s highest drag queen-per-capita ratios:

and, of course, here are the obligatory artsy photos i took:

oh, who am i kidding. i try and make all of the photos i take artsy. some just suck less than others.

the rest of the cape cod photos cower here.

in any case, the beautiful weather on the cape provided conclusive proof that research & productivity are inversely proportional to how sunny it is outside. christina and i couldn’t get enough of being outside that day.

ok, missioned accomplished – a bit less stressed and ready for bed!

holy crap! the script i wrote about here actually came through – christina and i got world cup tickets to see the usa’s first match!!! they’re playing in some town i’ve never heard of: gelsenkirchen.

argh, figuring we’d shoot first and apologize later, we grabbed the tickets immediately. (my script has alerted me to available tickets about two dozen times before; this has been the first time i’ve actually made it through to the ticket shop.) of course, flights to the nearby city of dusseldorf are insane: $1000 a head.

it’ll kill me if we have to put these tickets back up for sale ….

gosh, there has to be a more economical way to get to germany.

the world is a mighty confusing place. it seems that there are two kinds of christina cruzes.

(above) the first kind of christina cruz. my adorable girlfriend.

(below) the second kind of christina cruz. northwest florida’s premier entertainer.

there is no adjective in elvish, entish, or the tongues of men, to describe the hilarity that ensues when standing next to christina cruz (my girlfriend) and browsing over to the website of christina cruz (the barrenness of breasts).

oh and what’s also confusing is trying to figure out how to pluralize “christina cruz.” i’m fairly certain you don’t “apostraphe-s” the thing, but “cruzs” doesn’t look right either. “cruzes” i guess is slightly better, but also serves to perpetuate the hoax that is the silent e.

i turned 23 on wednesday. i celebrated by taking my one final of the semester, which went surprisingly well. (i was pleased for two reasons: 1) i was able to put down a reasonable answer for each question; 2) my sense of academic apathy, first nurtured in senior year of undergrad, has finally blossomed this semester)

that afternoon, christina suggested that we should at least go out to dinner, to mark my getting older and the end of the school year. so we hastily put together some dinner plans, grabbed our neighbor jesse, and headed off to redbones – my favorite restaurant in these parts.

when we got there, i was surprised to see a bunch of friends i’ve made here at mit. apparently, over the past couple of days, christina and jesse had arranged for them to come and meet us for dinner. i was rather touched by christina and jesse’s effort, as well as by the fact that people even showed up. i’ve always considered myself to be shy and introverted; seeing a bunch of people take the time to come out for my birthday was really nice – it makes me feel much less socially incompetent.

given the good food and good company, dinner of course was fantastic.

afterwards, we meandered over to “the burren,” a nearby irish pub.

apparently, i had a bit too much to drink.

that last photo is my favorite. at first, since my recollection of the later stages of that night is a bit hazy, i thought jesse and i were doing some strange ninja/i-dream-of-genie dance. instead, i’ve been informed that we’re really flashing the gang symbol for “john f donnelly field,” the park we both live across from. the rest of the photos from that night made their way here.

one day, i’m going to be too grown-up for the whole drink-until-you-black-out bit. maybe by next birthday.

p.s. mom, if you’re reading this, don’t worry – stephanie will be fine next year in college. she’s already more mature than me.

does anyone know who blew up the boardinhouse?

not yet, but roomers are flying!

i yoinked this from the new york times. new yorkers who like taking photos should definitely get outside this sunday and on july 13th!

Q. I’ve heard about a “Manhattan solstice,” when the sun supposedly lines up along the streets. Is it for real? When does it happen?

A. Here’s the lowdown on the sundown, courtesy of Neil deGrasse Tyson, director of the Hayden Planetarium at the American Museum of Natural History. Next Sunday and on July 13, the sun will fully illuminate every Manhattan cross street (not the curved or angled ones) on the street grid during the last 15 minutes of daylight, and it will set on each street’s center line. The sight is breathtaking.

This is a special photo opportunity, with parts of Manhattan’s canyons getting illumination they normally don’t get.

If the Manhattan street grid ran north-south and east-west, the alignment days would be the spring and fall equinoxes, the two days when the sun rises due east and sets due west. But the Manhattan grid is angled 30 degrees east from geographic north, shifting the days.

There are two corresponding mornings of sunrise right on the center lines of the Manhattan grid, Dr. Tyson wrote in an e-mail message: Dec. 5, 2006, and Jan. 8, 2007.

Those four solstice days will shift no more than a day over four years as a result of leap days, Dr. Tyson wrote. But the shift is so small that if you went out only on these dates, you would see the effect just fine. “In fact the effect is good for a day on either side of the advertised days, typically offering a range of weather choices for the avid viewer,” he wrote.

As for the sunset next Sunday and on July 13, Dr. Tyson wrote, the sun will line up on the center lines just as its falls halfway below the horizon. The official sunset, when “the sun’s last smidgen sets below the horizon,” lines up on slightly different days, but this one makes for a nicer photo.

christina and i took an impromptu trip to maine 2 weekends ago. her firm was sponsering a convention for grants administrators in portland. (yes, even people who underwrite grants have symposia.) the convention was from monday-wednesday; we decided to go up on saturday and spend two nights camping and biking along the maine coast.

(being a graduate student has got to be one of the best “jobs” in the world. i can simply disappear from the lab for days, not give anyone advance warning that i’ll be leaving, and not get chastised when i get back. unbelievable.)

in any case, we spent our first night camping in what was really a gloried backyard. the campground turned out to be in a grove of trees alongside a crop of freshly constructed houses. nonetheless, christina and i still had a great time – we cooked tacos for dinner using the stove we bought at the nearby 24-hour ll bean store. that night, for the first time, i built a campfire by myself – i had previously only done so with my dad or with camp counselors. it’s good knowing that i learned how to do at least one useful thing during my first year of grad school.

making good use of the campfire, christina had her first-ever campfire-cooked smore for dessert. she liked them so much that she also had them for breakfast:

we then set off on a super-hilly 25-mile bike loop from freeport to brunswick and back. along the way, we got to chill out on some awesome rock outcroppings on the maine shore:

we also had a fantastic lunch in brunswick at a very cleverly named seafood joint. deep-frier + seafood = crazy delicious.

brunswick was also home to a couple of absolutely huge indoor flea markets:

later that day, we settled into our next campground, a site we found during our bike tour. recompence campgrounds was situated right on the maine shore, on a set of low bluffs overlooking a narrow, gravelly beach. we were in luck – altough the campground was not yet officially open, the owner let us spend the night anyway. we had the entire 200-tent-site to ourselves.

we pitched our tent behind a small shock of trees blocking the winds coming off of the ocean:

this picture doesn’t do the tent-site justice; it had to be the most beautiful place i’ve ever pitched a tent. down a staircase hidden behind those trees, we found a pair of canvas chairs just waiting for us to relax in:

that night, we went into town and treated ourselves to dinner at a thai restaurant quite incongruous with rural maine. back at the campsite, i made another fire, we cooked some more smores, and turned in early. we couldnt’ stay out too late, since temperatures had dropped into the 40′s by nightfall. luckily, our mummy-style sleeping bags proved nice and toasty.

i got up at about 4.30 the next morning to watch the sunrise. i dragged christina out of her sleeping bag about 20 minutes later; both of us agreed that waking up at the ungodly hour was worth watching the sun creep up and over the maine shore. needless to say, dawn’s shadows make daybreak-maine very photogenic:

we spent the remainder of the morning on the beach. life has fewer pleasures more simple than throwing huge rocks into the water and watching them go splash.

we were pretty sad to leave such a tranquil place.

we spent the final two nights of our trip through maine at a somewhat dull hotel in portland. neither of us were too upset to leave the camping behind, however, since it poared both nights we stayed in the hotel. dripping-wet camping is not a lot of fun. in fact, the hotel wasn’t bad at all, since it had cable (something we’ve cheaped-out on getting here in cambridge). we also had a great time at the conference, mooching off of corporate lobster dinners and getting absolutely smashed with another attending couple who happened to also be from new york. good times.

the rest of the photos from maine live here.

sadly, it looks like we won’t be buying a house after all this summer. everything just didn’t come together, which is too bad, since christina and i were both excited to have our own place. fortunately, things probably worked out for the best.

one of the reasons for my sanguine outlook is that we’ll have disposable income this summer.

of course, that’s completely unacceptable for a graduate student. reading jennie’s blog today, christina and i’ve decided that we should attempt to remedy the situation by heading to germany to see the world cup this summer.

unfortunately, all 3 million! seats are sold out already. however, starting tomorrow, it looks like fifa will be offering for resale returned tickets.

since i don’t feel like constantly reloading their site every 5 minutes at work, i’ve written a little shell script to check the website for available tickets. if you too would like to head over to germany in june, stick the following into a cronjob and wait for an email notification!

curl -s -o fifa.txt “http://tickets.fifaworldcup.com/cgi-bin/ds_wme?fun=pksbyeventreihe&doc=ds_einzel1&id=WME_NO_SESSION&affiliate=wme&key=0″
soldcount=`cat fifa.txt | grep “soldout” | wc -l`
if [ $soldcount != 512 ]
then
echo `date` | mailx -s “there’re world cup tix!” me@gmail.com
fi

[ of course, modify the email addresss on the last line. oh and i make no promises that this will work, since i had only negative controls in my test set - i had no example of what an available ticket looked like ]

this is the entrance to the new apple store on 5th ave, across from the plaza and right in front of the fao schwartz. i don’t think i’ve ever come across such a unique door. it’s encased in a giant glass cube – you step through the door and descend a glass spiral staircase down into the store. this apple store will also be open 24 hours a day.

and people wonder why we’re cultists.