from the desk of stinkpot

for all you emacs junkies, i’ve found a carbonized (looks prettier on a mac) emacs package here that plays well with tiger. server’s a bit slow, though.

i thought i’d post another one of those “dangerous ideas” because they’re so darn interesting.

this one is courtesy of steve strogatz: pimp of non-linear dynamical systems and author of probably the most widely-read textbook on the subject.

steve-o sez:

I worry that insight is becoming impossible, at least at the frontiers of mathematics. Even when we’re able to figure out what’s true or false, we’re less and less able to understand why.

An argument along these lines was recently given by Brian Davies in the “Notices of the American Mathematical Society”. He mentions, for example, that the four-color map theorem in topology was proven in 1976 with the help of computers, which exhaustively checked a huge but finite number of possibilities. No human mathematician could ever verify all the intermediate steps in this brutal proof, and even if someone claimed to, should we trust them? To this day, no one has come up with a more elegant, insightful proof. So we’re left in the unsettling position of knowing that the four-color theorem is true but still not knowing why.

Similarly important but unsatisfying proofs have appeared in group theory (in the classification of finite simple groups, roughly akin to the periodic table for chemical elements) and in geometry (in the problem of how to pack spheres so that they fill space most efficiently, a puzzle that goes back to Kepler in the 1500′s and that arises today in coding theory for telecommunications).

In my own field of complex systems theory, Stephen Wolfram has emphasized that there are simple computer programs, known as cellular automata, whose dynamics can be so inscrutable that there’s no way to predict how they’ll behave; the best you can do is simulate them on the computer, sit back, and watch how they unfold. Observation replaces insight. Mathematics becomes a spectator sport.

i found his worries noteworthy because i’ve noticed similar ones creeping into biologists’ heads – especially computational biologists (i’m supposed to be one of those when i grow up). some people (not me) are predicting that if you take the technology common today (dna sequencers, microarrays, etc) and combine them with the right future breakthrough (say the ability to measure protein levels on the cellular scale and in high throughput) you’d have enough data to train a black box; this black box would take as input some cellular condition and output a prediction of cellular behavior – things like future gene expression, protein levels, cell growth … the works. obviously, this would be tremendous breakthrough – it’d be a phenomenal tool for doing things like drug discovery.

people are of course working on stuff like this already, feeding mountains of microarray, protein-protein, mass-spec, and gene sequence data into a bevy of machine learning algorithms, hoping to produce some kind of program that can produce useful predictions of what a biological system will do. (it’s really hard though – biology is one gnarly wombat.)

but, assuming this approach does work, part of me would still be sad. what does this kind of approach teach us about biology? i’m not sure you can argue that just having the capability of predicting what a system will do implies that you’ve learned anything (see here how bill gates figured out how to win at “petals around the rose”). for many scientists (including strogatz it seems), what matters more than obtaining the result is that somehow, along the way, you’ve sated the curiosity that drove you to ask questions in the first place.

(i’d be thrilled if someone came up with a more scientifically “pleasing” method of understanding complex biological systems. i’m not holding my breath though – i’m constantly stunned by how complicated (read: how much math you need to predict) even the most simple biological processes, such as how the lambda phage decides its fate or even stochastic treatments of simple biomolecular interactions.)

i’m really trying to curb the number of things i steal from boing-boing, but i couldn’t help myself on this one: “a contemporary version of the traditional irish wedding ring.” this is for real – it can be yours for the measly sum of $25.

if you have no idea why i’d post something like this, the magic word is goatse. don’t google it though if you value your eyeballs. seriously – if you’ve never seen it before, don’t – i repeat – don’t look it up. it’s just sick and i’m never going to forget that damn picture. (of course, i’m sure my repeated warnings haven’t picqued your interest in the slightest.)

a bunch of really nifty idea nuggets here (“today’s most dangerous ideas,” put forth by some of the brightest people i’ve ever read/heard speak/heard about); richard dawkins, a biologist who likes to think about how evolution shaped human behavior, has some especially interesting things to say:

Retribution as a moral principle is incompatible with a scientific view of human behaviour. As scientists, we believe that human brains, though they may not work in the same way as man-made computers, are as surely governed by the laws of physics. When a computer malfunctions, we do not punish it. We track down the problem and fix it, usually by replacing a damaged component, either in hardware or software.

Basil Fawlty, British television’s hotelier from hell created by the immortal John Cleese, was at the end of his tether when his car broke down and wouldn’t start. He gave it fair warning, counted to three, gave it one more chance, and then acted. “Right! I warned you. You’ve had this coming to you!” He got out of the car, seized a tree branch and set about thrashing the car within an inch of its life. Of course we laugh at his irrationality. Instead of beating the car, we would investigate the problem. Is the carburettor flooded? Are the sparking plugs or distributor points damp? Has it simply run out of gas? Why do we not react in the same way to a defective man: a murderer, say, or a rapist? Why don’t we laugh at a judge who punishes a criminal, just as heartily as we laugh at Basil Fawlty? Or at King Xerxes who, in 480 BC, sentenced the rough sea to 300 lashes for wrecking his bridge of ships? Isn’t the murderer or the rapist just a machine with a defective component? Or a defective upbringing? Defective education? Defective genes?

people love to dump on evolutionary biologists because they’re so reductionist. nonetheless, if you buy the idea that the brain really is just a kind of computer, adhering to some set of processing rules, dawkin’s ideas become awfully interesting.

christina and i have finally returned to cambridge after spending the last few days home in new york. we celebrated the new year by making shrimp tempura rolls and watching danny deckchair and the skeleton key. the skeleton key was especially frightening, since it combined two of my deepest fears: old people and the south. kate hudson (playing a nurse from hoboken) was defenseless against the pair of evils.

it was nice to be home for christmas. as usual, we all went to church; this year, however, was the first year that both the david kids went as atheists. i’m not sure what dad’s take is exactly on the whole jesus thing. nevertheless, steph, dad, and i certainly stuck out as the only 3 people not taking communion in the entire church. i’m not sure whether or not to be glad that steph’s declared herself an atheist. on the one hand, i’m glad that she’s rejecting the whole faith deal – i can’t help but see it as a kind of emotional crutch. yet, i can’t help but feel guilty (score one for my catholic upbringing) that poor mom didn’t end up with at least one of her kids a devout catholic. she did try her best though – both steph and i went to catholic high schools.

and speaking of steph, i should mention that she got a terrific christmas gift: an early acceptance at UPenn! she already looks the part:

dad had trouble containing his excitment when he heard the news:

(more pictures of christmas at home here).

i’m glad that i also had a chance to meet up with andrew while i was home. i spent a night at his digs down in the east village. if you’re not familiar with new york, that’s an awesome part of town; nothing seems to close and there are a phenomenal number of bars, pubs and restaurants on each block. sadly, that also translates into astronomical rent prices. andy and his roommates pay about 2.5X our rent for only maybe 75% of our space. yikes. nonetheless, given that you’re only young once, i think it’s worth it.

in any case, we had a good time hitting up mcsorley’s (the oldest pub in america, apparently) and a japanese restaurant whose sushi bar was meant only to serve sushi. nevertheless, we sat down and had a fun time doing some sake bombs, to sate one of andy’s shady shady online friends whom he had lost a bet to. (i blame this whole sordid affair on this region of the internet.) andy’s friend required photographic proof of the sake bombs:

more photos from the night here.

i’m a big fan of the kind of music that doesn’t get played on the radio (the good kind). unfortunately, that means that i usually have trouble finding new bands that i like.

i’ve just come across this awesome site, however, that looks like it’ll change that. pandora takes as input a song or artist of your suggestion and uses some learning algorithm to suggest other songs that have similar characteristics (such as tonality, beats per minute, instrumentation, etc). i’ve been having fun with it for sometime now; this is really really exciting software. and, it appears to be free!

[photos taken from kevin freitas' journal]

this is sad: it appears that the fellow who assembled this house is being forced to dismantle it. Vladimir Deriugin, an artist from Tacoma, Washington decided that his canvas would be his house. From here on the East Coast, I must admit that his house looks crazy (damn you lazy sunday) delicious. Nonetheless, I can understand why a neighbor or building code inspector would be feeling litigious.

[seen on gizmodo]
some poor kid in hawaii thought he was getting an ipod video this christmas – boy, he must have been surprised to open apple’s sleek packaging and find a piece of wrapped meat inside. it seems that a disgruntled employee (one of the world’s greatest resevoirs of hilarity) decided to stick it to walmart by repacking ipod boxes with slices of meat. to the employee’s credit, he did at least have the decency to wrap the meat in plastic.

personally, i’m hoping that this story has its facts garbled and that this isn’t the work of a disgruntled employee. instead, here’s to hoping that santa has grown environmentally conscious and is moving away from distributing fossil fuels. instead, while awaiting advancements in clean energy research, santa has decided to temporarily dispense cold meats to bad little children. because cold meat doesn’t release greenhouse gases.

i’ve just posted some photos from the sushi night christina and i hosted on tuesday night here. that night was especially exciting for me, since it was the first time that i’ve ever hosted a party at my own place. the party was also a much-needed spin down from the ass-whooping my BE.420 final handed out earlier in the day. (it was a 3-hour exam; we were allowed to choose 6 of 10 questions – i think i only completed 2 correctly and 2 more i left partially blank. but, because everyone else had trouble sitting down after the exam, i’m thinking the curve should be generous.)

in any case, a good, botulism-free time appeared to be had by all, in spite of the fact that neither christina nor i had ever prepared sushi prior to that night. luckily, jesse (is there anything he doesn’t know?) helped out with finding sashimi grade fish and showed everyone how to make a sushi roll. people hung around for a while and we made quite a ruckus until well after our landlord manny came home. since manny sleeps right above our living room, this suggests that either our ceilings our very soundproof (unlikely, since i hear them yelling all the time upstairs), or that manny is a bit hard of hearing. or maybe, he likes going to sleep to the sound of grad students loudly chatting with one another below him.

oh and here’s a photo of hillary asking google why it is that hasidic jews on the subway have such strong personal odors. (turns out it engenders a “palpable sense of community” – something the hasids are big on.) that hillary – always so inquisitive.

most people grow out of their lego phase. solid geeks don’t grow out of theirs – they simply learn that it’s not socially acceptable to spend more time with legos than with the opposite sex.

nonetheless, it’s still awesome to see what happens to those few lego geeks who stay the course.