NoMoreMalletrivia

Christina Mallet Photography is live !

2006-12-13T22:49:00.000-05:00

Christina just unveiled her official website: Christina Mallet Photography, and is open for business. She's waiving session fees initially, so please go check out her portfolio, and if you, or people that you know in/around Seattle, need their pictures taken, consider utilizing her services.

Blog move

2006-11-07T18:07:00.000-05:00

Update: The current location of my blog is http://mallet.typepad.com/malletrivia/.

~~Like a good corporate citizen, I'm moving from Blogger to Microsoft Live Spaces; all further updates to my blog will be made at its new location: http://alexmallet.spaces.live.com .~~

A day at the office

2006-11-05T00:15:00.000-05:00

"A case of the Mondays"

"You're fired !"

"No more TPS reports ?"

Baby headrush

2006-11-01T22:05:00.000-05:00

No, I'm not torturing our child. He actually likes it, at least if the huge smile he exhibits when he's right-side up again is anything to go by. Then again, maybe he's just happy to not be hanging upside down anymore ...

Curious uses of the word "acute"

2006-11-01T19:03:00.000-05:00

From a post on Biology News Net [emphasis mine]:

Researchers led by neuropathologist Hannah Kinney, MD, and neuroscientist David Paterson, PhD, at Children's Hospital Boston and Harvard Medical School examined brain autopsy specimens from 31 infants who had died from SIDS and 10 who had died acutely from other causes, provided by the San Diego Chief Medical Examiner's office.

I was under the impression that death, in whatever form it occurred, was pretty acute, but apparently there are gradations even here. I suspect non-acutely is the way you want to go.

I've also always wondered about the expansion for SARS -- Severe Acute Respiratory Syndrome. Aren't "severe" and "acute" redundant here ? The only explanation I can come up with is that if the "severe" bit were left out, the pronunciation would be a bit embarrassing [though entertaining for the juvenile-minded, like me] whereas SARS minus the A would be unpronounceable ["I'd like to buy a vowel, Vanna".]

I assume there is a precise medical meaning attached to "acute" that merits its use in these circumstances, and that I'm just unaware of said meaning.

Return to the Emerald City

2006-11-01T01:17:00.000-05:00

A few snippets, after being back in Seattle for a couple of days:

- Getting through the metal detectors at the airport was a lot like the "farmer, goat, wolf and cabbage" problem: both cats, and Zander, had to be taken out of their respective conveyances and carried through the detectors, and we could only carry one cat or baby at a time. After much head-scratching, the TSA folks bent the rules and allowed Christina to walk through the detector with one cat, drop it off, and then come back for the second cat by walking back through the detector [ie against the flow, usually a no-no]. The whole thing was such a spectacle that all the underemployed TSA folks also in the area crowded around to watch our menagerie make its way through. I wouldn't be surprised if a replica of our situation ends up being in a TSA "Advanced Security Conundrums" training video. [Side note: why on earth would a farmer have a wolf ? That seems equivalent to a cotton grower raising boll weevils ...]

- The flight itself was relatively uneventful. The cats were so terrified that they didn't emit a single peep, and Zander didn't fuss very much and slept through the last 3 hours of the flight. That said, there were plenty of other screaming kids on the plane, so he would have been in good company had he chosen to voice some displeasure.

- Seattle rolled out the "Welcome Home" carpet for us: after an initial day of rain, we've had 2 beautiful, clear and sunny [but cold] days, the sort you rarely get in Seattle. Driving across Lake Washington yesterday, we were treated to two of my favorite sights: mist on Lake Washington, and Mount Rainier. And I never realized until now how many deciduous trees there are around here, and that Seattle actually has some pretty nice foliage too.

- Fatherhood and zippy little cars are incompatible, as I found out during our car shopping expedition: you can't fit a rear-facing car seat and two adults into them, at least not comfortably. So, in another concession to the onset of maturity, we're getting grown-up, mom-and-dad cars. *Sigh*

-In two days, we've already had two "social" dinners [ie dinner with friends/family], which is about the number we would amass over an average 6 months in Boston.

Overall assessment: it's good to be home :-)

Last day in Boston

2006-10-28T09:06:00.000-04:00

As Christina has noted, we're almost outta here.

The movers came on Thursday to pack up our stuff and, while it's certainly nice to have somebody pack up your stuff, it is also not without its stresses. In our case, it was having to play a shell game with Zander, moving him from room to room in advance of the [literal] moving front, and making sure our cats didn't escape, terrorized as they were by strange burly men clomping through the house. Getting to our hotel on Thursday night was fun too. We had to transport:

- 1 baby
- 2 cats, in carriers
- 1 baby car seat + base
- 1 stroller
- 1 Pack-N-Play
- 1 large bag of baby accoutrements [clothes, diapers, bottles ...]
- 1 huge bag with our clothes
- 2 large bags of misc. other stuff [cat food, cat litter, disposable litter boxes]
- ... and of course our carry-on bags

... which made me silently vow to not move again with anything/anybody that must be carried, fed, or has special sleeping and excretory needs. And it got better:

- On the way to the hotel, one of the cats decided it really needed to do its business. In case you had any doubts, let me reassure you that

Freshly-minted cat business + car with windows that don't roll down = Totally Not Crazy Delicious

- I didn't have any cash to pay the cab driver, so we had to go find an ATM while poor Christina was left standing in the hotel lobby with a crying baby and a mountain of luggage
- After dumping all the luggage in our room, I was returning the luggage cart to the lobby and was mistaken for a hotel employee by a woman who wanted to know the location of a nearby hotel. I resisted the urge to give her an earful about not every black man pushing a luggage cart automatically being an employee and settled for a curt "Two blocks that way, and, by the way, I don't work here".

Friday was less stressful, as I just had to hang out in our apartment as the movers loaded all our stuff and clean up after them. There's nothing like emptying out your apartment to see all the hidden dirt that is missed during regular cleaning; in our case, I think I swept up enough cat hair to make a whole new cat.

And, so, today is our last day in Boston; we're getting on a 6:20pm flight to Seattle. My next worry is about spending 6 hours elevated 30000 feet above the ground in a small metal tube with 3 entities [2 cats and Zander] that are my responsibility but whose behavior I really have very little control over. All in all, I'll be glad when it's tomorrow :-)

I suppose the flip side of all this is that I don't really have much time to feel sad about leaving ;-)

"These are a few of my favorite things ..."

2006-10-24T05:26:00.000-04:00

Since I've spent a lot of the last two years complaining about all the bits I didn't like about Boston, I figured it was time to to talk about the the positive aspects of being here. So, in no particular order, here's what I'll miss and/or liked:

- The Forest Hills cemetery: amazing "memorial sculptures" [aka big-@$$ gravestones] set in beautiful surroundings. Christina shot a few nice pictures here.
- Jamaica Pond: we must have circumnavigated the pond a few thousand times, for reasons like being bored, trying to induce labor, going for a run, and just wanting to take a walk.
- The Arnold Arboretum: another nice spot to take a walk.
- The Endy lab: a collection of very smart, creative, and funny people that I've had the privilege of calling colleagues over the last couple of years.
- All the interesting biological engineering, biology, CSBi and CSAIL seminars
- Zipcars: a pretty good alternative to owning a car
- The Weekly Dig: a really funny weekly paper with an irreverent, yet insightful, take on everything.
- The Wonder Spice Cafe, Royal Bengal, and Family restaurants: good food at reasonable prices, an all-too-rare occurrence.
- All the stuff Christina listed [although I'm not as big a fan of the "free stuff" as she is]

There are also a few things I wish I'd had a chance to do:

- Participate in one of the many [1K, 50K, 100K] entrepreneurship competitions held every year at MIT
- Watch a Robocraft competition
- Take a few more courses [like 7.03, 7.22, 7.23, 7.52, 7.86, 6.824, 6.829 and 6.852]
- Check out Cape Cod, Martha's Vineyard, Vermont and Maine
- ... and, of course, graduate with a PhD ;-)

Update: Another one of my favorite things was working out at the CW Taekwondo club, run by two friends of mine. They've managed to build one of the best Sport Taekwondo clubs in the country, with current and ex-national team members from various countries, including an Olympian, working out there. In other words, it's a great place to get your @$$ kicked ;-)

Advice to a young non-scientist

2006-10-23T08:01:00.000-04:00

[Apologies to Peter Medawar]

With our impending departure from Boston, I've been thinking a lot about what I would change if I were to get the chance for a do-over. Below are the conclusions I've come to.

Making friends is hard: We didn't fully realize before we left Seattle how lucky we were to have so many friends and family close by, and how difficult it is to rebuild that sort of network in a new city.

The core of the problem was that neither Christina nor I had much exposure to people our age. Before starting classes, I hadn't fully internalized that I'd be surrounded by people who had, for the most part, just finished college, and were about eight years younger than me. An eight-year post-college difference is a pretty big gap in life experiences and expectations, one that made it hard for me to make many new friends. Christina's job was also pretty limiting in that respect in that it was, in some ways, tantamount to solitary confinement. And, since she worked at MIT, most of the few interactions she had were with students as well. Compounding these difficulties was the fact that most people in their early thirties have their social network in place and aren't necessarily actively trying to expand it, and so it's not easy to "break into" an existing circle of friends.

All this is not to say that we didn't make any new friends, but there were few enough of them, and we saw them so infrequently, that being in Boston was a pretty lonely experience. All that said, short of joining some sort of social club [*shudder*], it's not clear to me how we could have changed this bit of our stay here.

The high activation energy of mobility: When we moved here, we decided not to buy a car, but instead use Zipcars as necessary. On one hand, that worked out reasonably well, in that we didn't have to think about insurance, parking etc, but still had access to a car when necessary. On the other hand, it also stopped us from doing things that would have made our stay in Boston more pleasant, because there was always a very definite cost associated with using the Zipcar: for any activity, the question became "Do we want/need to do this enough that we're willing to pay the Zipcar fee for the necessary period of time ?". At $7-$8/hour, that sort of calculus brought with it the pressure to make every trip extra-worthwhile, which made us much less willing to try trips with uncertain payoff, like, say, exploring Massachusetts. It also made it hard to be spontaneous, because each trip required reserving the car a few days in advance, and we needed to plan our trips down to the hour to stay within our reservation window.

All in all, the delta between what we paid for Zipcar rentals on a monthly basis and what it would have cost to own a car was probably small enough that the additional freedom would have been worth it.

Going big sometimes considered harmful: I had two conflicting impulses when I started graduate school. One was to take the safe route to getting the necessary credentials: pick a research area that played to my strengths [ie purely computational work], pick an interesting but reasonably safe project, do a solid job on it, and get out quickly. The other impulse, based on the reasoning that since I was making such a large switch anyway, I might as well do it properly, was to become equally at home doing experimental biology and computational work, and pick a thesis project based purely on being the coolest thing I could think of, with little or no regard to safety. In other words, choosing the "go big" option of the "Go big or go home" philosophy espoused by a friend of mine.

I tried to chart a path through the middle, by looking for a thesis topic that would allow me to develop the computational skills that I figured would make me the most employable in industry [namely, machine learning/data mining] and applying them to the area of biology I find the most interesting [synthetic biology]. That took about a year, and still wasn't totally satisfactory, as is usually the case when you try to force a compromise between two incompatible bedfellows. In the meantime, I also figured out that I really don't like experimental work -- the slow, repetitive, everything-takes-forever-to-do, debug-by-semi-randomly-trying-stuff nature of it drives me crazy. In other words, I realized that I really should have taken the safe route; unfortunately, 2 years in and with a new addition to the family, doing that sort of a reset really wasn't in the cards.

I wish somebody had sidled up to me a couple of years ago, gently tapped me on the shoulder, and quietly said "Uhm, dude ? You already went big by going back to school; there's no need to get even crazier. Play it safe." Or, as a professor who switched over from "pure" computer science to CS applied to biology put it recently: re-orienting your vector takes time, and the important part is getting pointed in the right direction, not trying to get to the endpoint as fast as possible.

The lesson: sometimes you go big and you go home ;-)

There are probably a couple of other little bits and pieces that could have gone better, but I think the stuff above covers the biggest chunks. Now all I need to do is build a time machine so I can go back a couple of years and give myself the benefit of all this experience, thereby creating an alternate universe in which I become a mad scientist and destroy the earth via my green goo run amuck. Wait, maybe that's not such a great alternative...

Happiness, in 3 acts

2006-10-17T16:02:00.000-04:00

Here.

More ads that make no sense

2006-10-17T11:42:00.000-04:00

Time for another installment of "Ads in the subway that Alex has issues with".

In the last few weeks, I've seen a bunch of ads that have the tagline "Kids with asthma can ... [perform activity X]" and then say something like "Is asthma preventing your child from [performing activity X] ? Talk to your doctor !". Choices of [activity X] are playing, sleeping, learning, and doing sports.

Here's the thing I don't get: is the assumption behind these ads that people whose children have asthma -don't- talk to their doctors about trying to provide their kids with some relief, and need to be encouraged to do so ? Maybe that there is a subset of parents who regard asthma as the inescapable result of Divine Will, and are not aware that it's treatable ? The ads aren't sponsored [at least not directly] by a pharma/biotech company that just happens to make asthma medication; it's underwritten by a bunch of generic "benevolent" organizations. That seems to rule out the profit motive, so I'm left wondering why anybody would roll out such content-free advertising.

Maybe the next ad campaign these folks will come up with will be targeted at people with serious injuries and say something like "Have you just lost a limb and are geysering blood ? If so, you may want to consider consulting a medical professional."

And while we're on the topic of meaningless ads, there was one I saw last year, promoting this lady's candidacy for sheriff, that said "Actions have consequences. Think before you act.", to which the only appropriate response, I think, is "No sh!t, Sherlock".

One thing I will miss about using Boston's subway system is the opportunity it afforded me to be curmudgeonly about it. A friend of mine performs a similar service for the Seattle bus system, with the difference that she likes public transport, so her observations tend to be much more positive than mine. Or maybe that's just because Seattle is superior to Boston in this respect as well, leading to less opportunities to gripe ;-)

Leaving the hallowed halls of academe

2006-10-13T21:55:00.000-04:00

I've decided to leave my PhD program and return to Microsoft. A lot of reasons contributed to my decision, but the end result of summing over all of them is that the [certain] downside of staying in school finally outweighed the [mostly uncertain] upside, especially in light of my newly-acquired responsibilities. So, I'm currently trying to pull together a coherent Master's thesis, a task made somewhat difficult by the fact that I've bounced around a lot over my two years here. I think I have enough stuff that sort of fits together get by, though :-) ["Small pieces, loosely joined" ...]

We're heading back to Seattle in pretty short order -- the plan is to be gone from here in about 2 weeks, and I'm slated to start work on November 6th. Christina is very happy about our move and, while I'm bummed that I won't be finishing up the PhD program, I'm definitely also looking forward to being back in a city I like, close to friends and family, and living an "adult" life again. And it doesn't hurt that I'm going back to what promises to be a really cool job, writing code for large-scale distributed systems and working with people I know and like. One bit that I haven't quite figured out yet is what to do about my still-existing interest in biology, but I expect that keeping up somewhat with what's going on through a subscription to Science or Nature will help scratch that particular itch.

Overall, for all my whining and moaning about Boston etc, it's been a good two years, in a variety of ways. I learned a ton of interesting new stuff, met some good people I plan to stay in touch with, and don't have to live with the "If I'd only tried it" specter that would have haunted me if I hadn't taken the plunge and gone to graduate school. Oh, and I'm [hopefully] getting a Master's degree without having racked up any debt ;-)

So, that's that.

The coolest labs at MIT

2006-10-12T19:55:00.000-04:00

... are clearly the Endy and Knight labs, as this video shows.

Something not to do with your baby

2006-10-06T20:29:00.000-04:00

... is described here. The boy has serious pipes, made all the more emphatic when enclosed in the small space of a car. If the volume of his protestations is any measure of his willpower and stubborness, we're in for a world of hurt once he becomes mobile, agile, and hostile, and learns the word "No".

Academic follies, encore

2006-09-23T04:59:00.000-04:00

I know this is a horse of indeterminate liveness, yet I cannot resist flogging it some more.

Over at the Daily Transcript, there are two posts [1, 2], and associated comment threads, about "The Academy", at least in the life sciences, that are worth reading in their entirety, especially the comments.

[What, you're still reading this ? Fine.]

The summary: postdocs complain about the long hours, low pay, and lack of a life outside the lab required to even have a shot at a faculty position, never mind the insanity then required to achieve tenure. The response of a couple of professors, stripped down to its essentials: "Stop whining and suck it up, because we've got plenty more people where you came from that are willing to sacrifice everything. You should be grateful that you get to work on what interests you, with other smart people".

The first bit of the response is amazing not only in that it's addressed at highly educated, skilled people [not that it's something that should really be said to anybody] but also that they're willing to be spoken to and treated that way. And the defenses of academia in the second bit of the response are the standard "But look at the benefits !" justifications for the insane state of affairs, and stick in my craw every time I hear them.

"You get to work on what you want": Well, really, you get to work on what the funding agencies will give you money to work on. And, increasingly, these agencies are funding not individual investigators, but rather large, multi-investigator projects; see these posts about the decrease in funding rates and funding inequities between Big Biology and individual investigators, leading to what has been called a lost generation of individual researchers. So, it seems like there's a pretty good chance that, to survive, you may have to attach yourself to one of the mega-grants and end up working on something that's not exactly what you want to be doing. That's probably even more true if you're a junior faculty member, in which case you'll probably end up somewhere fairly low down on the author list of the published papers, which in turn isn't great for your career.

"... work with other smart people": Yes, that's definitely nice. But I'm always reminded of a simple numerical fact: most of the smart people in the world work somewhere else than wherever you currently happen to be. So that's not a good enough reason to put up with the execrable conditions.

... and from what I've seen, there are at least the same amount of bureaucracy and stiflingly boring tasks and meetings in academia as there are in industry. The only difference is that they're called "committee meetings", and probably drag on forever because nobody really has the final say over anything.

The other thing that I don't understand is why there is such an oversupply of PhDs [at least in the life sciences] who want to become academics. The possible reasons I've come up with so far are:

- a lack of awareness of alternatives, maybe due to being given bad career advice
- that the vast majority of them think of themselves as the PhDs of Lake Wobegon: all Above Average, and so the grim statistics don't apply to them
- such a pure, burning desire to explore the mysteries of Nature that, damn the torpedoes, any other course of action is inconceivable [and that word means what you think it means]. In which case, hey, go for it. But is that really the case for the majority of people ?

Don't get me wrong: I strongly believe that we need research universities and institutions, and basic research. I'm just amazed at the self-flagellation people are willing to inflict on themselves in order to join the academic club. And I wonder how long this pyramid scheme can keep going.

More baby goodness

2006-09-19T19:56:00.000-04:00

First smiles, cheeky monkey, and meeting the maternal and paternal grandparents.

[Someday soon, I'll post something other than baby pictures. No, really. I mean it. In the meantime, you might as well enjoy them ;-)]

"Abandon reason, all ye who enter here"

2006-09-10T23:14:00.000-04:00

From a NYT article:

MUNICH, Sept. 10 Pope Benedict XVI attracted some 250,000 people to an outdoor Mass on Sunday, urging his largely secular home country not to let science and reason make it “deaf” to God.

Hmm. Does that imply that it's not possible to be reasonable and religious [at least not all the time] ?

Shock and Awe, baby-style

2006-09-02T11:45:00.000-04:00

Shock:

Awe:

Daddy, there's a monster next to the bed

2006-09-01T20:28:00.000-04:00

... and his name is Zander. I say this not because he attempts to bodily devour Christina every 2-3 hours, starting with her chest, but rather because of the noises he makes. He is a veritable orchestra of monster noises while he's sleeping: grunts, gurgles, moans, sighs, crying, heavy breathing and, of course, the occasional, entirely unabashed, sound of a waste product download. Sometimes, he's so loud that I have to put a pillow over my head to drown him out. I always thought pre-verbal children either cried, made nonsense sounds, or were quiet ... little did I know they could easily find work as extras in "Where The Wild Things Are".

Showing off the captured Zandermonster:

Fatherhood, week 1

2006-08-24T20:07:00.000-04:00

[Baby stuff, probably non-interesting unless you're family =)]
Miscellaneous notes, after being a father for a whole week:

- Baby swing = Crazy Delicious Baby-Sleep-Inducing Machine.
- When changing diapers, it's generally a good idea to cover "the equipment" with a wipe, otherwise you may be treated to an in-house version of the Bellagio Fountains. With yellow water, and without the lights and music, though. That said, it's worth -not- taking that precaution just once, to see the look of surprise when he pees himself in the face [No, I didn't do so intentionally, it happened when I accidentally forgot to cap the waterworks.]
- Zander will soon be ready to challenge the strongest boy in the world to a wrestling match and utterly dominate him. Why ? Because, in my unassailable dad logic, I note that he can already lift his head up and turn it while lying on his stomach, something that apparently generally doesn't happen until the second month, and conclude that he must be extraordinarily strong.
- The lack of sleep, and overall stress level, hasn't been as bad as I feared ie we haven't been reduced to bone-tired bundles of nerves [yet]. That's attributable entirely to the fact that Zander is a great "starter baby" for rookie parents -- he sleeps quite a bit, doesn't fuss very much when he's awake, nurses well, and is pretty forgiving of clumsy parents who take a bit too long to change his diapers or clothes.
- One of our strollers has been named Optimus Prime, in view of the fact that it can be transformed from a full-fledged, large stroller into a fairly compact cuboid with the simple press of a button and a small amount of leverage applied in the right direction. It might be possible to turn it into a tandem bicycle with the right series of pushes and pulls. I suspect it was designed by origami masters capable of accessing hidden spatial dimensions.
- My man's got flair even when he's asleep:

In summary, it's pretty cool being a dad. How could you not love a face like that ?

A description unlikely to lead to future interview requests being granted

2006-08-19T15:18:00.000-04:00

From a NYT Magazine article describing the rivalry in competitive surfing between Kelly Slater and Andy Irons:

"Irons is considerably bigger, with a hint of baby fat and the blank, open-mouthed stare of a healthy young animal."

Ouch.

Alexander (Zander) Foli Todd Mallet

2006-08-18T19:21:00.000-04:00

The eagle has landed. I repeat, the eagle has landed.

DOB: 9:41 AM EST, 8/16/2006
Weight: 9 lbs 2 oz [4138 g]
Length: 21 inches [52.5 cm]
Feet: Huge
Cute Factor: Off the scale. Cutest baby in known universe, confirmed by several leading independent baby cuteness research institutes.

Pictorial evidence for above claims:

Other items of note:

- Driving down an extremely windy, narrow road with no median between the two directions of traffic [the Jamaicaway in Boston], at 11:30 at night, with your wife writhing in labor-induced agony beside you is a little ... nerve-wracking.
- Christina is an absolute champion for pushing out a baby weighing quite a bit more than the average [Yes, I know it's the distribution for Norwegian babies, but if it's good enough for the NIH, it's good enough for me ;-)]. Pushing, for all men who, like me, had no clue what it really involved goes like so: contract all the muscles in your body as strongly as you can, while holding your breath for 10+ seconds; take one breath; repeat muscle contraction + holding breath 4-5 times. Relax for a minute. Do it all over again. For several hours. Oh, and by the way, while doing this you're in a ridiculous amount of pain, drugs or no drugs.
- We have verified full function of Zander's food input and waste output ports.
- Yes, I've changed diapers. Most of them so far, actually. And I've already been christened -- he peed on me the very first time I changed his diaper. Nice to meet you too, dude.
- Do not, I repeat, do not put toothpaste on your baby's butt instead of vaseline. I almost made that mistake because, in the fog of diaper war, the two tubes looked pretty similar. Thankfully, I realized the error of my ways before actually slathering minty-fresh toothpaste all over his little posterior.
- Zander currently has only two states: eating or sleeping, with very quick and easy transitions between these states [Thankfully ! Let's see how long that lasts ...]. He is also not a man to let a full breast go to waste -- he nurses like a champ.
- Your ob/gyn may be gay if, in talking to you about your labor, he quotes lines from Barbara Streisand songs, namely: "What's too painful to remember, we simply choose to forget." Simply outstanding.
- I was under the impression that the good folks at the hospital will assist you in installing a baby car seat base into your car. Not so. All they do is tell you how to do the easy part: strapping your baby into the car seat, which is about as necessary as the little recorded message at the beginning of a flight telling you how to fasten your seatbelt. To get a "certified" car seat installation, you have to go by a police station. After driving to the two nearest police stations with a jury-rigged installation and finding out that we needed to make actual appointments, we decided to call it a day and just head for home. Parents for only two days and we're already being cavalier about our baby's safety...

In any case, we're back home and settling in. More dispatches as deemed relevant.

A perspective on science-induced pain

2006-08-15T18:20:00.000-04:00

I've been reading some of the early papers about T7, starting with papers published almost 40 years ago. Apart from the "Oh, so that's how & when they figured that out" factor, an equally interesting facet is that reading these papers with the benefit of the current state of knowledge means seeing science in action, so to speak -- watching the transition from early ideas [with varying degrees of "correctness"] to our current understanding, with various course corrections along the way.

Certain paragraphs also serve as a sharp reminder of the fact that, not too long ago, scientists had to walk barefoot, blindfolded, through snow, uphill both ways, to figure things out. Consider the following excerpt [from here]:

"Weiss and Richardson (1967) have shown that the 5' end of the poly-G-binding strand terminates in pApG----, and the 5' end of the complementary strand terminates in pTpC----. It is also known (as discussed extensively by several workers in the Cold Spring Harbor Symposium on The Genetic Code, Volume 31, 1966) that RNA chains grow in the 5' to 3' direction, protein chains grow from the amino terminal to the carboxyl terminal end, and translation of messenger RNA proceeds from 5' to 3'."

In other words, around the time this paper was published:
- Determining the last/first 2 nucleotides of a DNA sequence was considered a genuine scientific achievement. Systematic sequencing was still almost 10 years in the future, and the sequence of the first bacterial genome was 20 years away. In contrast, nowadays if you're not determining [and analyzing] millions or billions of nucleotides, you're not doing anything noteworthy.
- The details of how proteins are encoded in DNA, and the direction in which DNA and RNA are "read", had only been established 3 years ago, and was worth discussing at scientific conferences. This is stuff that kids learn in high school today.

Summary: biology was Really, Really Hard back then, and we didn't know very much, which must have meant a lot of fumbling around trying stuff. And yet people kept at it. I suppose the lesson is that I should stop whining about lab work and just get on with it, so that 40 years from now, my grandkids can say "Wow, you guys didn't know that back then ? How did you manage to do anything ? Hardcore !" before flapping their bio-engineered wings and flying away.

But it also brings up questions: is science-induced pain conserved ? In other words, are we now trying to do things/answer questions that are so much more complicated than what folks X years ago were doing that, despite our increased knowledge and technical capabilities, the work is still just as difficult ? Is there a minimum level of knowledge and technical capability below which doing stuff is order-of-magnitude more difficult, and above which the pain stays pretty constant or even decreases ?

D-day has arrived

2006-08-14T08:48:00.000-04:00

Today is Christina's "official" due date. Unfortunately, due dates are just another instance of seemingly-precise data that actually have fairly low information content, because a due date is very loosely correlated with when the baby will actually be born -- 90% of first-time mothers deliver after their due date. It's looking reasonably likely that Christina will be among those 90%, although maybe our midwife will say something different when we go see her later today.

This brings me to a more general point about pregnancy that I didn't fully appreciate earlier: nothing is certain. Pretty much the only thing that's guaranteed is that the mother-to-be won't sprout an extra limb [externally, at least], but everything else is up for grabs -- whether she has morning sickness or develops weird food cravings, how much weight she gains, what size the baby is going to be etc. In retrospect, we might have been able to spare ourselves a few prenatal visits because the vast majority of the answers to our "Is this normal ?"-type questions boiled down to "Everybody is different", which in plaintext means "We're not really sure. Call us if she wakes up one morning and is suddenly 7 feet tall and has a beard." In more fancy words, the probability distribution of just about every phenomenon associated with pregnancy has heavy tails.

Another lesson learned over the last few months: there's nothing like a prenatal visit for making a man feel invisible/irrelevant. It starts out in the reception area: every available magazine has a title made up of some combination of the words "Baby", "Parent[ing]", "Healthy", "Happy", "Infant" or "Mother". Men, when they are mentioned, usually occur in phrases like "How to make sure your husband doesn't drop the baby". I'm not saying I'd like them to have a bunch of issues of "Trucks, Guns and Hot Chicks" lying around, but it sure would be nice to have magazines other than ones that are so obviously not meant for men. And it gets worse when you see the actual midwife/nurse/doctor -- generally, I wasn't even acknowledged via a "hello" when this person came into the room, they just looked straight through me and started talking to Christina. Again, it's not that I want a cookie and a pat on the head for accompanying my wife to a prenatal visit, but it sure would be nice to be treated with an attitude conveying something other than "Oh, so you're the one who did this to her. Are you happy now ?"

And the final take-away from the last few months: it's a good thing I wasn't the one who had to be pregnant, because I don't think I'd have had the patience to deal with all the attendant aches and pains. Christina, in contrast, has been an absolute saint -- never once did she become the bitchy, moody person that pregnant women are so often portrayed as. But even sainthood wears thin -- she's very ready for the baby to arrive, and so am I.

So: time to leave the cocoon, little man ! The wide world, warts and all, awaits.

OMG, that crazy president totally has a blog !

2006-08-14T06:41:00.000-04:00

Iranian president Ahmadinejad apparently now has a blog [via BoingBoing]. Between this and his letter to Bush [awesome typo in the translation: the Bush slogan is supposedly "War and Terror"], he's certainly using heretofore non-presidential forms of communication. It almost seems like he's watched one too many movies of the sort where a common-sense "man of the people" who tells it like it is winds up as a politician and then proceeds to turn the established order upside down by departing from precedent and doing things his way [examples: 1, 2]. Maybe he'll set up a MySpace page next so people can "friend" him.

One thing I know for sure after watching an interview with him on 60 Minutes: not a man who should have a nuclear weapon. [Not that I really want anybody to have nuclear weapons ...]

Year II: lessons learned

2006-08-09T13:03:00.000-04:00

The last couple of weeks have been full of milestones: the second anniversary of our move to Boston, my qualifying exam, Christina's birthday a couple of days ago, and 2 years since my first blog post. And, of course, our very own little person will hopefully arrive in the next few days. With that, I figured it might be worth to put together another summary post of the past year, though this one will be much shorter than the multi-installment summary [1, 2, 3, 4] that I did last year. So, here 'tis.

"Shhh, be vewwy, vewwy quiet, I'm hunting theses"
... and I had almost as much trouble finding a thesis topic as Elmer has with that wascally wabbit. I looked into working on microRNAs, tried to come up with a good reason to rebuild a yeast chromosome, started working on investigating transcriptional feedback in the yeast pheromone response, and finally settled on working on T7.

One obvious question is why I had such a hard time finding a topic. The answer is also fairly obvious: my first choice [working on malaria] wasn't an option, and it took me a while to find an acceptable alternative that coupled my other two main interests, synthetic biology and high-throughput [HT] data generation and analysis. Those two areas are not natural bedfellows because most work in synthetic biology is currently focused on building single instances of relatively simple systems [which don't generate much very much data]. This meant that there were relatively few examples of research that I could use as inspiration, and so it took me a while to formulate a topic that fit my desires, addressed interesting questions, and fit into the overall research direction of Drew's lab.

In retrospect, I thought finding a thesis topic would be one of the easier parts of grad school. Guess I was wrong.

"It's what you don't know that's important"
A large part of getting a grip on a given field is having an idea of what the current limits of the field are ie what isn't known, what the interesting questions are, what's difficult etc. These aspects are, of course, the very bits that aren't covered in class: you're told in excruciating detail what is known, but nobody dwells on the "Hic sunt dracones" areas, even in graduate classes. I think a large part of the point of grad school is precisely that you figure out where the boundaries of knowledge are in your attempts to push them a bit further.

In any case, when I started school, I lacked the basic "this is what we know"-type knowledge and had no big-picture perspective of the current challenges in biology either, beyond a fuzzy "Biology is hard, because, well ... people tell me that it is. If it were easy, we would have created a dragon by now." Lacking this mental scaffold made it difficult to get more than a superficial understanding of the papers I read and talks that I attended -- not only did I struggle to fully understand the claims/results contained in the paper/talk, I also didn't have a framework in which to evaluate the overall impact of what I was being told. The end result was that my takeaway was generally "Uhm, ok, if you say so", and a few isolated facts that didn't really connect to the bigger picture.

The biggest intellectual transition for me over the last year was moving beyond the "just the facts, ma'am" stage, and towards a better meta-level understanding of at least a couple of the sub-areas of my new field. The largest contributor to that increased understanding was actually my thesis odyssey. In the process of trying to formulate a thesis topic, I had to think really hard about various areas of systems/computational biology -- what questions were being asked [and why], what tools were available to answer them etc. Doing so helped me tie together a lot of the loose strands waving around in my head into a semi-coherent overall picture.

The negative aspect of all this cogitatin' and meditatin', of course, is that I'm not as far along as I would have liked to be after two years of school -- I haven't done anything yet. That said, probably the main reason that I'm [theoretically, at least] "behind schedule" is that my envisioned timeline radically underestimated the switching costs of moving from computer science into biology -- remnants of the instinctive "Oh, how hard can it be ?" programmer's reflex, possibly.

Integrating over everything
At the end of the day [or year], though, the high-order bit is that I [still] like what I'm doing and think I made the right choice in leaving MS. That's not to say I didn't have a few "It'd be so nice and easy to go back to software" moments during and after our trip to Seattle -- things like hanging out with friends and family, going by the motorcycle shop where I spent many a dollar buying unnecessary stuff for my bike, and checking up on our house in Seattle served as sharp reminders of everything we gave up when we moved here. I'm sure I'll have similar sentiments each time we go back, but hopefully/presumably their intensity will decrease as I get closer to the end of grad school and can see the light at the end of the tunnel.

Next up, year III: try to get some real work done while being dominated by a tiny lifeform halfway based on me.

The ultimate rejoinder

2006-08-07T16:27:00.000-04:00

... to skeptics of science [via Pharyngula].

Just for the record ...

2006-08-01T20:45:00.000-04:00

... and in case I haven't clearly expressed my opinion on this matter before: Boston sucks.

Why ? Because we've had to spend all day cooped up inside due to a heatwave. And it's not about to get any better:

Tonight: Widespread haze after 3am. Clear, with a low near 80. West wind between 14 and 16 mph.

Wednesday: Widespread haze. Sunny and hot, with a high near 101. Heat index values as high as 111. West wind between 14 and 20 mph.

Compare that to the weather in the Promised Land, with daytime highs in the 70's.

Yup, signs point to "Definitely sucks".

Time to really get cracking on the research front, so we can leave this godforsaken place asap.

Benefits I was previously unaware of

2006-07-31T13:37:00.000-04:00

For the last few weeks, I've been trying to make sense of a new ad in the subway here. It's an ad for the Telephone Workers Credit Union and its tag line is "Now you don't have to be a telephone worker to benefit like one".

I don't understand the slogan. Are telephone worker benefits that great ? You'd think that if they were, it would have been reflected in popular lingo by now, as in:

"Man, that guy is benefitting like a telephone worker !"
"Dawg, I'm just tryin' to get some of them telephone worker benefits, na mean ?"

A visit to the website of the Telephone Workers Credit Union doesn't shed any light on the issue, beyond promising once more that you too, despite not actually being a member of this [apparently] blessed category, can benefit like one. No mention of what actual goodies await you, though.

Shame on those telephone workers for holding out on us about how great their benefits are !

"Got quals ?"

2006-07-30T09:15:00.000-04:00

Yes, I do -- I passed.

Or, rather, my thesis committee is recommending that I pass, but I won't have "officially" passed until their recommendation has been approved by the overall graduate committee for my PhD program.

As is often the case, the actual event was a lot less painful than I feared it would be. I think the main reason for this was that I managed to establish a reasonable amount of credibility early on by being able to answer most of the questions they asked about the biology of T7. After that, the questions were less of the explicitly probing "Do you have enough background knowledge ?" sort and tended more towards discussion of why I'd chosen the research plan I outlined in my proposal, and whether it was the best approach. Classwork didn't really come up, even after the chair of my committee explicitly proposed redirecting questions from my proposal to more general issues. So, the overall recommendation was that I pass.

[My favorite bit of the whole thing was when TK, bless his heart, started to answer a question that was meant for me and had to be dissuaded from doing so by the other members of my committee frantically waving at him to stop talking.]

The only [minor] fly in the ointment is that my committee wants another meeting in 6 months, rather than the usual 12 months. That's because, basically, after only 2 months on my project I don't totally have it under control, so they figured having a follow-up meeting sooner rather than later was a good idea. While it's kind of annoying to have another deadline of that sort [I was anticipating a year of being left alone], I suppose it's a good forcing function and will probably result in me making more progress in the next 6 months than I normally would have.

In any case, now I get to mentally prepare for a much bigger milestone: having our first child. Two weeks till estimated first contact, sooner if Christina's wishes are fulfilled.

'Tis the night before quals ..

2006-07-27T20:57:00.000-04:00

... and I am ... not relaxed, shall we say. And the bit I'm the most not relaxed about is the prospect of being asked a bunch of probing questions about the classes I've taken. I'd originally planned to start reviewing class material a couple of months ago, which theoretically would have given me plenty of time to clear up the bits that I never got too firm a handle on [EM, anyone ?], make the connections that I missed, re-read certain papers etc -- basically, really get my head around all the totally-new-to-me stuff that I've been exposed to over the last couple of years.

Needless to say, that didn't happen. After my thesis project switch, it took me the last month and a half to learn enough about T7 to put together a coherent proposal and do enough preliminary work to justify even having a thesis proposal meeting. [Of course, all that preliminary work was computational -- I haven't done any experimental work with T7 yet, so if the subject of experimental technique comes up, it's likely to be followed by a strained silence.]

So, I've basically spent maybe 3-4 days reviewing the 8 classes I've taken and feel like the best I can say about the vast majority of stuff covered in those classes is "Yes, I've heard of that and can, in a hand-waving sort of way, tell you about it. However, should you have questions about specifics, I will be forced to resort to the Chewbacca Defense."

In short, I feel like a dilettante. Not a good position to be in when you're about to be asked to demonstrate a "sufficient depth of knowledge across a broad set of areas", and that you're ready to start doing some [mostly] self-guided research.

Time to start collecting stamps

2006-07-19T16:27:00.000-04:00

... because apparently the new stamps are super. I have to say, though, the descriptions of each character seem rather anachronistic, as if they'd just been recycled from when the characters were first introduced. And it's weird that the female character descriptions say nothing whatsoever about their powers.

Anyway, now I finally have a legitimate reason to plaster Batman all over stuff without being accused of being juvenile.

The Neverending Proposal

2006-07-17T17:32:00.000-04:00

... has finally ended: I've been heads-down the last few weeks writing my thesis proposal and, after about 2 million drafts, I finally submitted it to my thesis committee members. And none too soon -- I don't think I could have taken another day of staring at the damn thing without going totally insane.

Now I have a week and a half to prepare for my actual qualifying exam, scheduled for July 28th, where I'll have to walk my thesis committee through a presentation of my proposal. This is when I can expect to be asked questions designed to make me squirm, not just about the proposal but also about "... more general topics in the field of computational and systems biology related to the research or course-work preparation of the student" [per the official description of the qualifying exam]. In other words, pretty much anything is fair game, so there's no point in going insane about it -- que será, será. My plan is to read through the notes from my classes, hope for the best and be prepared to deploy the phrase "That is known, but not by me" at the appropriate times.

Should anybody have time to kill and/or want to bore themselves by reading a copy of my proposal [with the ever-so-tantalizing title "Whole-genome re-engineering in service of systems biology"], consisting of 20 pages of fevered dreams, tarted up with learned references to papers I probably didn't read as thoroughly as I should have, and lightly sprinkled with dollops of "It's so crazy, it just might work !", let me know and I'll be happy to send you a copy.

Heartbreaker

2006-07-04T19:34:00.000-04:00

That's what you call something like this: holding it together for 120 minutes and then giving up 2 goals in the last 2 minutes. That said, Italy was definitely the better team. Ah well, no more chuckling at the announcers on Univision yelling " .... el alemán Lehmann !"

Au revoir, Brazil ...

2006-07-01T17:00:00.000-04:00

Lots of unhappiness in Brazil right now, after being outplayed by France. It was a deserved loss -- the Brazilian passes were sloppy, they didn't hustle for the ball, Ronaldo kept taking dive after dive ... and Zidane looped the ball over the head of many a Brazilian and made him look silly.

As a meta-comment, take a look at the French squad as compared to, say, the German squad, and see whether anything strikes you as odd about the demographics of the French team. Christina's mot juste: "Yeah, the French are good at getting other people to do their work for them."

"Deutschland vor, noch ein Tor !"

2006-06-30T13:57:00.000-04:00

I refer of course, to this, which led to a sound presumably not often heard in the Stata Center, the local home of the Comp Sci intelligentsia: lots of cheering and groaning from people huddled around a TV showing a [gasp !] sporting event.

Of course, there was also a typical MIT aspect to it: two of the folks watching the game were German and had set up a Linux server in Cologne that was streaming a synchronized version of the Gerrman-language broadcast of the game to their laptop, so they plugged in their headphones and listened to the German commentary while watching the game being broadcast in Spanish on Univision. Talk about merging media streams ...

Bye-bye, Black Stars

2006-06-27T15:23:00.000-04:00

Well, the expected happened. Despite the lopsided score, I think Ghana played well -- they out-hustled the Brazilians and created lots of opportunities to score but just couldn't convert them. Not to take anything away from the Brazilians [they showed the requisite flashes of offensive skill to make sure things went their way], in the end, I'd say Ghana was more a victim of bad luck than being outplayed.

Xxxtreme cancer therapy

2006-06-27T15:13:00.000-04:00

Fight cancer with radioactive scorpion venom. [Further studies have shown that the efficacy of treatment is increased if patients also get a concentrated dose of Red Bull at the same time as they're being injected with ... radioactive scorpion venom !!! Extreme to the max !!!]

It pays to have rich friends

2006-06-26T08:32:00.000-04:00

... even if you're already sitting on a pile of loot, because sometimes these friends will give you a truckload more money, making your foundation ridiculously well-funded.

I suppose it's only a question of time before Bill will once again be accused of being a monopolist and stifling competition in the charitable foundation market via underhanded practices like giving away too much stuff for free.

Next stop: round of 16 !

2006-06-22T12:02:00.000-04:00

Ghana beats US, 2-1. Suh-weet. Brazil, here we come ! [And I don't want to hear any guff about the penalty -- without it, the score would still only have been 1-1 and Ghana would have advanced.]

Public transport child discipline

2006-06-21T10:13:00.000-04:00

Oh, if only this were truly an option ... I would gladly try out various child control techniques, both in order to have a more peaceful ride, and as practice for my own upcoming challenges in this area.

Sushi Mallet, 11/1998 - 6/18/2006

2006-06-18T17:36:00.000-04:00

We had to put one of our cats, Sushi, to sleep yesterday.

He'd been lethargic for a few days, so we took him to the vet [a friend of ours, thankfully], who, after a chest x-ray, diagnosed him with having fluid around his lungs, making it hard for him to breathe. Apparently, the poor little guy had so much fluid in his chest cavity that he was only using 20-30% of his lung capacity. After reviewing the possible causes [heart disease, cancer, an infected puncture wound and, the cover-all, "fluid accumulating in the chest cavity due to unknown causes"], it became clear that getting a clear-cut diagnosis would be a long and very expensive process [ultrasound, blood work, hospital stays, chest punctures and draining], and that he would, in all likelihood, be diagnosed with something incurable.

So, with heavy hearts, we had him euthanized.

My eugoogly for the little furball:

Sushi was complicated, even for a cat. He liked the idea of being petted -- he'd follow me [and just about anybody else] around, striking seductive "wouldn't you like to pet me ?" poses. However, the sensation of being petted apparently often fell short of his desires, judging from his propensity to give you a reproachful look and make a quick, squirming exit, or, if he was in a particularly ornery mood, depart with a paw-swipe. This gap between theory and practice was possibly due to the fact that he would only tolerate a very specific way of petting him: smacking or rubbing the bit of his spine just in front of his tail, and, very occasionally, rubbing his ears. Anything else was just no good. Picking him up and/or trying to hold him was also a no-no -- definitely not a lap cat, much to Christina's dismay. However, when he was in the right mood and you got that ear-scratch just right, you were rewarded with an amazingly loud purr.

Occasionally, he'd get the cat crazies and charge up and down the hallway, sounding and looking like a tiny cat-pony. He loved chasing a feather on a string; when he finally "caught" it, he'd put it in his mouth and drag it away head held high, as if to say "Behold the mighty hunter !"

He was also a pain in the ass, due to the fact that he sometimes thought outside the box, specifically, on our bed and couch, when he was upset about something. Our first experience with this was when we came home from our honeymoon and found that he'd been using our bed as a litterbox for a few days. Mattress, comforter, sheets -- all ruined. We're still sleeping on the futon mattress we had to use that first night back from our honeymoon. As a result, we had to Sushi-proof the house: never allowing him inside the bedroom without one of us, always closing the bedroom door [after making sure he wasn't hiding under the bed], putting pillows on the couch at night etc. It also meant that anytime we wanted to go away for a couple of days, we had to find somebody to stay in our apartment [not just drop in once or twice a day] who was willing to follow a long list of rules -- he didn't do well with no human company, and would make his displeasure very clear.

He loved drinking out of cups and glasses. He viewed glasses of water anywhere near him as an open invitation to drink out of them, or dip his paw into them, thereby ensuring that you had to go get yourself another glass. Feeding him was also not entirely straightforward -- he didn't like eating with our other two cats, so we had to set his plate down a few feet away from them, and he'd only eat dry food if it was sprinkled on top of his wet food.

For all his quirks and oddities, though, he was a good cat, and I'm glad we had him.

Rest easy, Sushi. I'll miss having to close the bedroom door.

Catch-as-Cech-can

2006-06-17T18:15:00.000-04:00

After today's Ghana-Czech Republic game, the Czechs better pay their goalkeeper Cech a tidy bundle, because he was the only thing that kept the score from being totally lopsided. I hope the US goal is a bit more ... permeable during Thursday's US-Ghana game.

Oh, and it'd be nice if, the next time Ghana plays, the commentators have more insightful things to say than a continuous permutation of:

- "Wow, what an upset it would be if Ghana won"
- "This could be great for the Americans"
- "Teams that score first in the World Cup have a 26-2-2 record [of going on to win the match]"
- "Ghana seems to be playing much better than they did against Italy"

I mean, seriously, there was an utter lack of technical commentary about what was going on on the field, besides the occasional computer-generated statistic about shots-on-goal or number of fouls. The last time I actually watched more than 5 minutes of a football match was during the '98 World Cup [I know, I'm a bad German-Ghanaian for not keeping up with football], and I could have announced that game equally well.

In any case: go Black Stars !

Obligatory BillG post

2006-06-16T08:03:00.000-04:00

Well, it's finally happened: BillG announces that he's leaving "The Soft" ... in a while.

I think it's telling that Ray Ozzie, a relative newcomer to the company, instead of an old-timer, is taking over as Chief Software Architect. It seems to indicate that enough people have finally agreed that a breath of fresh air is needed as far as the company's technical strategy goes, and that this would be best served by not promoting from within. I only hope that there is enough internal goodwill towards Ozzie, and that he has the political savvy to manoeuver effectively through the intricate political web at MS, to get a fair crack at turning things around.

Predictably, the "I remember when Bill ..." stories are starting to emerg e. So, in that spirit let me share mine:
- My friend Brandon and I almost got "arrested" by the Microsoft security guards for rollerblading in circles around Bill's car in a Microsoft garage for a few minutes and waving at the cameras trained on the car. This was our way of attracting the attention of campus security on a weekend [when we'd failed to find them by any other means] because we wanted to give them an employee badge that somebody had lost. Needless to say, they were not particularly pleased with the manner in which we chose to locate them -- their parting words were something like "Next time, just pick up a phone and call xxxx" [the extension for campus security, which is written on every phone ...], with the unstated ending "... you @#$#@ retards."
- On another occasion, I was bombing around campus on my rollerblades [again], gathering speed in order to jump across a stretch of grass, and noticed a man walking towards me, coming at the bit of grass from the opposite direction. As I was accelerating, my train of thought was something along the lines of "That looks like ... nah, it can't be ... but it sure does look like ...", at which point I hit my take-off point, jumped and realized that it was indeed Bill, that I was flying through the air 3 feet away from him, and had just barely missed taking down the richest man in the world hard. I almost wiped out on my landing and looked back at him with a "Dude, so sorry !" expression, but he just shook his head slightly and kept on walking.

I did have a couple more "official" interactions with him, once as a member of a small group of folks who got to talk with him for an hour, and once by sitting in on an executive review he was a part of. Neither of those was particularly memorable, though -- in the first case, the conversation confined itself to fairly neutral topics, like "How big a threat is Linux really ?" and in the second case he didn't have any of his famed "That's the stupidest f@@#$ng thing I've ever heard" moments.

As I've said before, I think Bill's philantropic legacy may very well end up being as big as, if not bigger than, his contribution to "putting a computer on every desk". The bit I admire most about him is his sense of noblesse oblige [or, in SpiderMan terms, that "with great power comes great responsibility"], and his willingness to act on that. I've occasionally though that his wealth and influence must, in some ways, be a burden, because he basically has no excuse to not try to fix things that are broken in the world. And, short of giving away all his money, there's always the "... but you could be doing more" accusation. The average Joe, on the other hand, can hide behind the "What can I, a nobody do, to fix XXX ?" excuse. Bill doesn't have that escape hatch, and the impressive thing is that he realizes that and doesn't try to half-step by semi-randomly giving away money here and there -- instead, he's opting to devote all his time to fixing large problems.

Meanwhile, the Slashdot Linux/Unix fanatics, much like the US military and intelligence agencies after the fall of Communism, are starting to realize that they're going to need a new mortal enemy. My favorite comment from the few I read:

"Let's see:

Gates - creates world's most successful company, becomes world's richest man, leaves day job to spend billions on charity.
Us - Made lame borg jokes for 5 years, finally released a browser that's better than IE if you ignore all the unfixed copy/paste bugs. Convinced a few people that Unix sucked less than Windows.

Dude, I think *he* won."

Yes, he did.

Thesis Odyssey: Ithaca in sight

2006-06-12T16:09:00.000-04:00

Due to reasons I previously alluded to [to wit: "not feelin' it"] , I decided over the last couple of weeks to radically reconfigure my thesis project. No more yeast for me -- I'm a proud phage man now. More specifically, phage T7, a little critter that infects E.coli. I'm going to be mucking around with its genome, as described here -- v1 of the new genome was completed a while ago [and was the first official paper of the Endy lab at MIT] and work is now underway on v2, which is what I'm picking up and going to make the focus of my thesis. It's full-on, non-apologetic synthetic biology and will even give me a chance to write some code [because existing tools for genome redesign are non-optimal/non-existent], both of which are things I'm pretty excited about.

Of course, this means I have to learn a bunch of new biology [i.e. read about 2,567 more papers] and experimental methods, disband my existing thesis committee and form a new one, and reschedule my qualifying exam, so it's not all gravy.

Now, if you were too smart for your own good and wanted to upset me, you could ask impertinent questions like "Gee, Alex, how come you've been whining and moaning about not being able to find a decent thesis project when this one has been right under your nose for the last 9 months -- wasn't that a bit of a waste of time ?". And I would give you an answer involving the phrases "target fixation" and "too much action, not enough thought".

But you're not going to ask me questions like that, right ?

Christina: marine apex predator

2006-06-12T07:40:00.000-04:00

At 31 weeks, Christina's pregnancy has progressed to the point where she's like a shark: once she's on her feet, she has to keep moving, or she becomes extremely uncomfortable.

This shark metaphor extends into other areas of life, like going to the bookstore. I like to leisurely wander through the store, stopping for extended periods of time to examine the contents of a bookshelf. Christina, on the other hand, can't stand still, so she paces around, which in turn makes me feel like I'm in one of those Discovery channel programs that show sharks swimming around, coming close to the camera and showing their teeth, before moving on with a lazy flick of their tail ... and then circling back around again. After a few such circles yesterday, I snapped at her and told her that I felt like I was at the bookstore with a little child, and to knock it off. Without missing a beat, she responded "You are at the bookstore with a little child."

Touché. And a sign of things to come.

[In her defense, I was dawdling a bit, and we'd been walking for a while before we got to the bookstore :-)]

Geekfightclub

2006-05-30T18:16:00.000-04:00

The AP has a story about a real-life Fight Club in Silicon Valley, a notion I find pretty funny, given the average physique of a techie. I can just see the billing: "The undercard fight tonight: Clash of the Michelin-Men ! And the title bout ... Stick Figure versus That Guy Who Keeps Talking About Kernel-Mode Network Drivers". I suppose that's why they resort to "Kicking, punching and swinging every household object imaginable -- from frying pans and tennis rackets to pillowcases stuffed with soda cans" -- it's difficult to hit somebody hard enough to make an impact when the only exercise you get is typing [although maybe that might lead you to develop the Fast-Typing Fingers of Death technique ...].

Oh, and I suspect the guy who skipped his first wedding anniversary to attend a fight got a taste of the real Fight Club when his wife heard about the reason he skipped their anniversary.

Step One of Nerds Anonymous

2006-05-27T10:40:00.000-04:00

I'm 32. I'm married, with a child on the way, and a mortgage. Clearly, I'm an adult [if you ignore the fact that I'm in school ...]. Yet, my birthday presents, by request, consisted of a math textbook, a comic and an Amazon gift certificate which I promptly used to buy more comics, among other things.

"Hi, I'm Alex, and I'm a nerd."

32

2006-05-26T11:36:00.000-04:00

Another year gone by, marked by:

- a quite active summer
- classes in statistics and machine learning, and gaining a real appreciation of their use as lenses for interpreting the fuzziness inherent in the real world
- hands-on experience with the grind of daily experimental work
- a scientific conference here and there
- some [mostly administrative, alas] progress towards becoming Dr.Evil.

... and, of course, the absolutely coolest thing: creating our very own little person. I suspect that a lot of what I'll learn in the next year will revolve around thuddingly concrete things like how to change diapers and interpreting the urgent communiques generically encoded like this. Hopefully, this instruction manual will help.

My slogan for 32: "One-third more action than '24' and 365 times as long !"

Browser wars

2006-05-26T11:11:00.000-04:00

I'm considering helping out with a genome hacking project and would like a genome browser to facilitate this. It turns out that genome browsers are like C++ string classes: everybody's got one. Consider the following sample, just off the top of my head:

- Apollo: "a Java-based application for annotating genomic sequences"
- Gbrowse: "a combination of database and interactive web page for manipulating and displaying annotations on genomes" [from the same distribution as Apollo ....]
- Argo: "a production tool for manually annotating and visualizing whole genomes", from the MIT/Harvard Broad Institute
- The software underlying the UCSC Genome Browser
- A browser explicitly targeted at synthetic biology, with the drawback that the fellow developing it probably won't be spending much more time on it, because he's graduating and going back to a real job.

In other words, forget about Netscape vrs IE vrs Firefox vrs Opera -- now it's all about the browser within the browser. Maybe in a few years we'll have a browser-within a browser-within a browser war ...

In any case, I could just try them all out and see which one works the best. Or I could do what a "real" programmer would do: arrive at the foregone conclusion that all of them suck, that I can do better, and write my own, a thing I am sorely tempted to do, mainly because it's been years and years since I wrote any substantial chunks of code. The flip side is that this would involve having to write user interface code, something I've always avoided like the plague. Then again, learning a bit about all the AJAX hype would probably be a good thing in terms of keeping my technical knowledge reasonably current.

Going forth to TA no more

2006-05-26T10:03:00.000-04:00

The final exam has been graded, all scores for the semester tallied up and the rest, namely assigning actual letter grades, is out of my hands: my stint as a teaching assistant is over. And, thankfully, I won't have to do it again, because it was pretty much zero fun. To be more accurate, I kind of liked the "teaching" bit ie answering questions and explaining stuff [with the beneficial side effect of giving me a better understanding of the material], it was the "assistant" bit, making up and grading problem sets and exams, that was a real drag. Especially the occasions when I spent hours coming up with a question [explicitly requested by a professor] for a problem set/exam only to have it discarded because it was too hard/made the exam too long/didn't fit in with the course emphasis after all. I suppose that's part and parcel of working for somebody, though -- god knows I wasted lots of time at Microsoft preparing material requested by my manager, or for "executive reviews", only to have it never looked at, or flipped through in a matter of seconds.

Anyhoo. That's all done, then.

SB 2.0 report

2006-05-22T13:29:00.000-04:00

Came back this morning [on another red-eye flight, aaargh] from Synthetic Biology 2.0. Overall, it was a pretty nifty conference, with talks covering a lot of different topics. Thankfully, several people have saved me the trouble of trying to remember details from each talk by blogging about the conference: Mackenzie Cowell has a bunch of short posts giving high-level summaries of all the talks, whereas Oliver Morton [an editor at Nature] and Rob Carlson have slightly longer posts about various "meta" bits surrounding the conference. With that, my personal take:

Favourite phrases/words from talks:
- "Cyanobacillus generates ugly cells at low frequencies": from a talk by the author of a paper I've written about before. Apparently, beauty is only cell-deep.
- "Retrosynthetically": I still have no idea what that means, but it sounds cool.
- "Aza-ylide": an intermediate of an apparently well-known reaction [well-known to a segment of the population I am clearly not a part of]. What I liked about this word is its pronunciation: "eza-illid", [where the initial "e" is pronounced like the "a" in "age"] which makes it sound like Snoop Dogg's contribution to science.
- "What we're doing here is preposterous": from David Baltimore's talk about the Grand Challenge in Global Health that he's involved with. This statement referred to the fact that they're trying to do gene therapy, stem cell therapy and immunotherapy all at once, and none of those three therapies has worked [satisfactorily] yet, in any other setting.
- "Counting to 2 in a scaleable manner": one of the "Future challenges" listed in the concluding slide of a talk.
- "Don't laugh, Drew, if you had a pair of silk underwear, you'd be a lot less irritable": [slightly paraphrased] from Chris Voigt's talk about getting Salmonella to secrete spider silk, and why silk is such a wonderful material.

Moment of Zen
- Craig Venter showing a video [from the Discovery Channel, I think] whose main theme was "Craig is cool. He is travelling around the world in his yacht, collecting seawater and trying to sequence the DNA of critters he finds in it." As entertaining as the idea is, and as much as I'd like to be trawling around the world on a yacht, the video contributed absolutely nothing to the actual scientific content of his talk [as far as I could tell, but maybe I'm missing something]. At first I found it cringe-inducing, as in "Is he really so oblivious that he's showing an ad for himself ?", and then I transitioned to a state of awe at the sheer Zen-master chutzpah of the man.

Moment of "wha' happen ?"
- Jef Boeke talking about his lab's plans to rebuild chromosome III in yeast, and generating "genome swarms" of lots of yeast strains with different genomes. This is exactly what I was working on doing last year [based on an idea supplied by Drew], as described here and here. I eventually ended up bailing on this project because I couldn't figure out how to generate lots of genome variations via synthesis and/or come up with a good enough reason to ask Drew to spend the money it would have taken to do this project. Boeke has figured out a high-throughput way of generating genome variations, and figuring out what variation has been created, which isn't that surprising, given that:
1. he's been working with yeast since the mid-80's
2. he's published a bunch of papers on large-scale yeast genomics
3. he's an expert in transposon biology, and transposons are one way to generate variation in a genome
4. he's associated with the Hopkins High Throughput Biology Center
In other words, if somebody was going to figure that bit out, he'd be a bad person to bet against. However, he hasn't quite solved the money and "why do this ?" issues: he estimated that it'd take about $10 million over 5 years (!) to do this project, and he didn't really have any more "Wow, that would be so cool/useful !" ideas for what modifications to make to the yeast genome, and why, than I did. He's taking an interesting tack on gathering input, though: he issued an invitation to the yeast community to give him feedback on what sorts of changes they'd like to see made to the yeast genome; one good place to get those kinds of suggestions will probably be the 2006 Yeast Genetics and Molecular Biology meeting.

All that said, I still think it's a really, really cool idea and one I'd love to work on, so I plan to talk to him some more about it and see whether there's room for a collaboration. Of course, the thesis idea that I used to gather my thesis committee has exactly zero to do with this, so that might lead to needing to do some "cabinet reshuffling".

... and that's all, folks.

Addendum: as I mentioned above, one of the speakers was David Baltimore, an insanely accomplished man -- he helped to organize the Asilomar conference on recombinant DNA, is now the president of Caltech, was president of Rockefeller University for a while, helped to found the Whitehead Institute at MIT, and, oh, by the way, won a Nobel Prize when he was 37. I think I can be forgiven, then, for the fact that the [slightly juvenile, granted] thought that kept going through my mind as we stood shoulder-to-shoulder at the urinals in the men's bathroom was "I'm peeing next to a Nobel laureate ! I'm peeing next to a Nobel laureate !". It's not often you get to say that ;-) I considered telling him that I thought he was a pretty cool guy, but that might have been a bit ... awkward, given the circumstances.

Addendum #2: one other thing that struck me was the breadth of biological systems that were talked about, and being used, to build synthetic circuits. The bit that I still don't quite understand is how the folks that described working with multiple different genetic sub-systems from other organisms knew about the existence of these sub-systems in the first place. Did they just do tons of literature searches, hoping to stumble onto something that was appropriate ? Was there a serendipitous conversation with somebody working on something totally different who said "Oh, I've got just the thing you need" ? As we start to think about building more complicated circuits, or circuits with wider functionality, that knowledge of what "parts" are available is going to become more and more important. The Biobricks Registry is an attempt to provide such a parts list, but it requires community contribution to really be useful, and I wonder whether its emphasis on "standardized" parts is going to turn away contributors who don't feel like doing the work necessary to make their genetic circuit standards-compatible. It would be a shame if synthetic biology became as lore-based as much of [experimental] biology is, requiring expert knowledge of the literature, word-of-mouth etc to know what parts are available to build a functioning circuit, instead of having a more systematic way to retrieve this information.

Cyberpunk marketplace

2006-05-19T06:12:00.000-04:00

This sounds like something out of a William Gibson novel.

Tired just thinking about it

2006-05-16T20:30:00.000-04:00

In theory, our Seattle visit was supposed to be relaxing. In practice, because it was so short and we came back on the red-eye, I'm now about as tired, or more so, as when we left. And it's not about to get any better:

- I leave for Synthetic Biology 2.0 on Friday. Before then, I have to finish coming up with questions and a scoring scheme for a final exam, grade 60+ problem sets and update the poster I'll be presenting at the conference.
- Next week is finals week, so it'll be a mad scramble to grade the final exams and figure out final scores for everybody
- I'm going to the Biology Department retreat on June 1st and 2nd.
- Sometime between now and the first week of June, I have to start and finish writing the first draft of my ~20 page thesis proposal so I can give it to Drew for comments.
- June will be devoted to doing experiments to fill in the yawning chasm in the "Preliminary Results" section of my thesis proposal; this will involve learning some experimental protocols that are apparently rather finicky [in plaintext: easy to screw up], and will thus undoubtedly contribute to my prematurely graying hair. In addition, I'll be going over the material from all the classes I've taken so far, to further prepare for my qualifying exam.
- My qualifying exam is July 12th -- ~2 hours of being grilled on my thesis proposal and whatever else my thesis committee members feel like asking.
- As previously noted, I may have to deal with having to find new renters for our place in Seattle sometime in the next couple of months
- Our baby's due date is August 14th, but only 5% of babies are delivered on their due date, so who knows when he'll actually show up. In any case, I expect I'll be a total zombie for at least a couple of months after he's born.

... and with that, we're in November.

I see a lot of Mountain Dew and highly-caffeinated tea in my future.

Notes from the annual pilgrimage

2006-05-16T18:59:00.000-04:00

Christina and I just came back from an all-too-short visit to The Promised Land [aka Seattle]. Trip notes, in no particular order:

- The weather was perfect: sunny and dry in the 60's and 70's the whole time. In contrast, while we were gone, New England got so much rain that it led to the worst flooding in 70 years. Outstanding timing on our part, I'd say.
- The main reason we were in Seattle was a baby shower [for our little-man-to-be]. However, it wasn't the standard baby shower which [I've been led to understand] mostly consists of a group of women sitting in a circle, competing to see how often they can use the words "adorable" and "cute" in reference to baby outfits. Instead, we made it a combination "see all our friends" party/co-ed baby shower by inviting all our friends, male and female to ... sit in a circle and coo about baby stuff. Actually, the cooing was limited to a small part, it was much more a chance to catch up with everybody who came. That said, we did make out like bandits with respect to gifts of baby-related stuff, so a big "Thank You" to everybody who came [and gave us stuff ;-)]. And, of course, another big "Thank You" to Christina's mother and sisters for organizing the shower/party.
- Even after 2 years in Boston, Christina and I are still amazed by the amount of trash littering the streets. Christina kept insisting that Seattle was much cleaner, but I was skeptical -- I figured all cities have trash on their streets, so this time, I made it a point to notice how clean [or not] the Seattle streets are. And, what do you know -- Christina was right. The Seattle streets and sidewalks really are spotless, and not just in the upscale neighborhoods. Even the sidewalk and street outside a liquor store where shady characters tend to hang out were clean. Why the difference ? Do people just not throw litter on the street, does Seattle spend a much larger amount on keeping the streets clean, is it because Boston has had a couple more centuries to accumulate crud ?
- We ate ridiculous amounts of good food [Christina's mum made an amazing strawberry cake that I'll be demanding for my upcoming birthday], so much so that at the end of our visit I actually refused a slice of after-dinner cheesecake, which is pretty much unheard-of. It's time for a bread-and-water diet for a while, now, though.
- The amount of new construction is amazing -- new condos and townhouses are springing up everywhere, in conjunction with a general rise in real estate prices. Good news for us in that our townhouse has appreciated nicely in value, bad news in that it means we'll have to pay more when we want to move into a bigger house to accomodate an expanding family.
- On the subject of real estate, the folks who have been renting our townhouse are considering moving out, which would be a huge pain in the @$$. Trying to find renters from a distance is not something I'm looking forward to at all -- we're really attached to the house and so we want to make sure we don't rent it to bozos who will trash it. Thankfully, friends of ours have offered to help with interviewing renters, and hopefully it'll be relatively easy to find renters if we keep the rent the same as it has been for the last couple of last years [given the general increase in real estate prices].
- You know you're broke when your financial planner declines to charge you for financial advice because he says "Well, it'd be like trying to squeeze blood from a turnip". I think he files us under "charity work" and gets a tax deduction for it.

Pictures to follow once the photographer-in-residence releases them for public consumption.

Two computer-y items

2006-04-30T19:00:00.000-04:00

Item one: The keynote speaker at this weekend's CSBi retreat was Alan Crane, the CEO of Momenta Pharmaceuticals, who bears an uncanny resemblance to Bill Gates. The bit that gave me a "glitch in the Matrix" moment was when he started to talk about monopolies, anti-trust and the FTC. Except that, in this case, he was explaining why having the FTC around was a good thing for his company.

Item two: I received a letter from State Farm Insurance, dated 26th April 2006, to inform me that they were terminating automobile coverage for me as of August 3rd 2004. The only way I can explain this occurrence is that whatever passes for a computer system with them got a little ... behind in what it was doing and is finally getting around to cleaning out some old stuff. Talk about resource starvation ... I have this vision of a thread perpetually relegated to the background, getting thinner and thinner until finally, with its dying breath, it managed to get an old rattling printer, in a musty basement somewhere, to spit out the letter I received.

42'' x 32'' of postery blandness

2006-04-29T07:38:00.000-04:00

That poster I was complaining about having to put together ? Yeah. That. Against much internal resistance [and only because I had to], I finally dragged it out of myself, and am going to hem and haw my way through it today at the annual CSBi retreat. AMY, however, is not featured on it, besides a comment in the Conclusions section about having "constructed strains [that we are] characterizing" because AMY101.1 and AMY201.1 are still terra incognita at this point, only having come into being [accompanied by the obligatory maniacal laughter and triumphant "It's alive !" echoing down the halls] in the last couple of days.

The poster is, as I feared/expected, nothing except a list of "things I'd like to do and why they might be interesting." The bigger problem [ie besides the utter lack of results of any sort] is that I find myself rather ... non-excited by the proposed research described on my poster -- it's basically a bunch of standard DNA hacking to better understand the yeast pheromone response pathway. While that's a perfectly respectable line of research, there's nothing particularly "synthetic" about the biology in it, nor much of a computational aspect, especially of the "machine learning" type that I'd like to do.

I need to fix that, and fast, especially given that my qualifying exam and accompanying thesis proposal are in 2.5 months.

CSBi-cal cancer

2006-04-28T19:11:00.000-04:00

Tim Hughes gave a talk yesterday in which he made a comment about a "connection between CSBi and cancer". While he was probably referring to the fact that a couple of the most prominent faculty members that are part of CSBi work [in one fashion or another] on cancer, I couldn't help but think that his statement could also be interpreted as CSBi being a form of cancer slowly taking over MIT, as evidenced by the number of MIT faculty members "associated" with CSBi [where "associated" means "signed up on the CSBi website"].

I suppose it's a reflection of the fact that "systems biology" is the new hotness, despite the fact that nobody can define it [but presumably they know it when they see it...], and everybody wants to be associated with its incandescent light. Or something. In any case, it does make me wonder whether CSBi is becoming so diffuse that there's no point in thinking of it as a distinctive entity anymore. Not that that would necessarily be a bad thing -- as Tozier has pointed out, barriers between disciplines can be annoying. Presumably that'd be all the more the case if a new "discipline" whose guiding motto is "Throw all possible methods at the problem and see which ones stick" [the polite term for this is "interdisciplinary approach", I think] suddenly decided to get all exclusive and clubby in an "You're not interdisciplinary enough" sort of way.

A vexing question of nomenclature

2006-04-23T06:08:00.000-04:00

As I've said before, labeling is important when doing lab work. This is true not just for chemicals, but also for cells -- it's much more convenient to have a short label referring to a particular kind of cell than to always have to say "The cells containing genes X and Y, but without genes A and B ...". The convention [or maybe just -a- convention] in the field of yeast biology when naming cell lines [aka "strains"] created by a particular researcher is to give them a label of the form xxY.### where xx are the researcher's initials, 'Y' denotes the fact that it's a yeast strain and ### is some number, like 123. [Some might argue that this somewhat dry naming scheme, much like the very staid practice of naming yeast genes with a three-letter abbreviation supposed to encode something about their function, reflects the fact that yeast biologists just aren't as much fun as those wild and crazy Drosophila people. But I digress.]

This convention is at the heart of my problem: if I follow it, all my yeast strains will be called ... AMY.

Beyond the knee-jerk "Real Male Scientists (TM) don't create anything called 'Amy', they pick names like 'Crusher 11X' or 'BloodHammer 6' or 'RQZ2001.21' " reaction, this notion also disturbs me because I find myself coming up with anthropomorphic questions like:

- Am I creating a line of fembots, with model designations AMY001, AMY002 etc ? [Granted, they'll look much more like this than like that, but still ...]
- Will all the other AMYs be forever jealous of AMY001, because she was my first ?
- Will AMY007 be a yeast secret agent, mating somewhat indiscriminately and generally living a life of ill-repute ? On the plus side, that probably means she'll be impossible to kill ...
- Will AMY067 be a total b!tch, impossible to please, always dying or exhibiting weird behavior at the most incovenient times ?
- Will my cells, in general, be more fickle and inconstant than if they were called something more boring, like, say, RGY ?
- How will Christina take the news that I spend all my time at work with AMY ? Even worse, do I really want my son being told "Daddy can't spend any time with you right now because he's with that !@#$^$%@ AMY" ?

Some possible solutions I've come up with are:
- Buck the trend and put the 'Y' in front of my initials, so my strains will be called YAMxxx. Not great, but a little better.
- Use an initial from one of my middle names, which leads to the names KMYxxx or EMYxxx. Unfortunately, both of those still sound a lot like female names; it's the "MY" part that's the problem and trading Amy for Kimmy or Emmy doesn't seem like a net win.
- Spell out the letters when talking about my strains ie refer to them as A-M-Y. The drawback here is that it doesn't work in print [and hopefully, at some point, something about my strains will be in print :-)]

... or I could just accept that, in all likelihood, nobody other than me cares and resign myself to creating a numbered series of AMYs.

Don't upset the prisoners, they're very delicate

2006-04-11T11:13:00.000-04:00

Apparently an officer at the state's largest prison is going to be disciplined for screening "Brokeback Mountain" for the prison inmates. Money quote:

The problem isn't that the movie is about gay cowboys, but rather the "graphic nature of the sexually explicit scenes," a Massachusetts Department of Correction spokeswoman said.

Ok, so let me get this straight: they're worried about showing sexually explicit scenes. To a) people in prison who b) probably have more gay sex than the protagonists in "Brokeback Mountain" ever dreamed of.

What are they worried about, that the inmates have led such a sheltered life that they'll be traumatized by the sex scenes, or that their "re-education" will be set back ?

I continue to wonder how people can say such patently retarded things with a straight face.

You complete me

2006-04-11T10:07:00.000-04:00

..., at least my thesis committee. Sort of. As in: I've finally filled out my thesis committee, except for the one wildcard that's going to be assigned to it by the Powers That Be [aka the CSBi graduate committee]. The members are:

- Fred Winston, a "real" biologist and an authority on all things yeast, especially transcription.
- Ernest Fraenkel, with expertise in investigating transcriptional regulatory networks in yeast and whose lab, in collaboration with others, has generated oodles of genome-wide binding data for yeast transcription factors.
- Alexander van Oudenaarden, who, in addition to being a funny professor, has also done a bunch of really nifty "systems biology" research combining experimental and computational approaches.

.. and, of course, the inimitable Drew.

All in all, I'm very happy with it -- I think I have a good mix of professors with experimental and computational expertise, just what the doctor ordered. Add the fact that they're all very nice and hence liable to get along when put in a room together [ie "play well with others"] and I think I'll get some very good feedback and guidance from them.

"I will lash together a machine of bone and blood ..."

2006-04-11T10:02:00.000-04:00

Once again, the good folks at Penny Arcade had me in stitches with their latest comic. It's a perfectly-done pastiche of many of the conventions of the fantasy/horror genre. I especially like the concept of a fear engine.

Computational work is starting to look really good

2006-04-04T12:21:00.000-04:00

[More whining]
After fighting his way past the lair of contaminated reagents, getting stuck for a week in the swamp of non-growing cells and narrowly winning a long battle with yeastie beasties that refused to eat perfectly good DNA placed in front of them [despite repeated imprecations along the lines of "There are starving cells in the fridge next door ! Eat your DNA !"] , our hapless protagonist now finds himself facing yet another foe: the Plasmid That Is Not What You Think It Is.

Ok, that's enough talking about myself in the third person.

I obtained said plasmid [basically, a bit of DNA] from somebody in another lab and was counting on it to do great things for me, in terms of reducing the amount of work I had to do. Unfortunately, it turns out that there's a large-ish mismatch between what the plasmid is supposed to do [and the DNA sequence it's supposed to contain] and what it actually does. I initially became suspicious when some cells with that plasmid that shouldn't have grown [because I screwed up the experimental procedure] grew like crazy. And my suspicion was further heightened when I looked at the supposed DNA sequence and found it sorely at odds with what it was supposed to be. Further digging revealed that the person I got it from wasn't entirely sure how it had really been constructed and was a bit fuzzy on certain fairly basic aspects of how plasmids work. Not reassuring.

So at this point, I think the safest thing to do is not waste any more time trying to figure out what it actually is, but rather just make my own from scratch. There go another few weeks. *Sigh*

What makes it all worse is that I have to present a poster in ~3.5 weeks at the annual CSBi retreat and I think that pretty much the only thing I'll be able to put on that poster is a fancy-sounding abstract and some high-level ideas that trail off into "... but I don't actually have any results."

At this rate, I may have to acknowledge defeat sooner rather than later and go back to being a keyboard jockey.

Patently non-non-obvious

2006-03-31T14:02:00.000-05:00

Paul Graham has an interesting essay on whether, and how much, software patents matter. Snippet:

If you want to patent an algorithm, you have to frame it as a computer system executing it.
Then it's mechanical; phew. The default euphemism for algorithm is "system and method."
Try a patent search for that phrase and see how many results you get

Yup. Guilty as charged. These are issued patents that I was involved in filing for over 5 years ago and pretty much forgot about until a couple of months ago. I guess they finally made it through the labyrinth of the Patent Office and were actually granted. Look, ma, I'm an inventor !

[Just to be clear -- I don't think that the "systems and methods" described in these patents are particularly "non-obvious", but, hey, I was young and needed the money.]

The most fragile machine in the world

2006-03-27T15:42:00.000-05:00

... is apparently the escalator at the Downtown Crossing subway stop. About every 2-3 weeks, its innards are laid bare, and serious-looking, grizzled men, Men Who Know How To Use Tools, stand waist-deep in its guts, among gears, chains and other manifestly metallic, oily things, discussing the state of their patient in grave tones.

Why a machine that moves at the stately pace of 2 feet a second should require almost-weekly maintenance whereas another machine that revolves a few thousand times a minute, a machine driven by blowing sh!t up inside it, can go for years on end with no problems is baffling. Sure, I can see parts wearing out and needing to be replaced, but every couple of weeks seems a bit much. Is there a malevolent escalator gremlin that keeps gumming up the works ? Is the underside of the escalator continuously being sprayed with acid ? Is it shoddy workmanship, leading to a continuous case of "what had happened was ..." as the escalator repair company tries to explain the latest breakdown ?

Inquiring minds want to know.

An update from the experimental trenches

2006-03-25T08:46:00.000-05:00

It would seem that I'm being punished for my recent whistle-blowing description of the realities of lab work. Consider: since then, I've wasted a week trying to figure out why a boringly standard PCR reaction [a technique for amplifying DNA, kind of like a copier] wasn't working, only to find out that it was because one of the reagents was contaminated [and of the two tubes containing that reagent, I kept picking the contaminated tube ...]. And I've spent the last week trying to get run-of-the-mill yeast cells to grow in a medium that is the yeast equivalent of nutritional paradise, with no success.

In other words, I'm having trouble even with stuff that should be simpler than falling off a log. This does not bode well for my proposed thesis project, which involves making lots of changes to yeast DNA. On the other hand, maybe I'm just frontloading all the experimental woes and once I get past the startup issues, everything will go swimmingly ... yeah, that's it.

Kickin' like Bruce Lee

2006-03-24T06:31:00.000-05:00

After a couple of weeks of false alarms, when Christina could feel the baby moving and kicking but I couldn't, I finally felt him kick. Very cool. Borrowing a turn of phrase that seems to be popular in scientific papers, I think that it's fair to say that "this evidence, taken together with earlier pictorial evidence, argues convincingly for the presence of another human being inside Christina".

That said, I still think the whole person-living-inside-another-person bit is ... strange. It's one thing to know about the process in an abstract sort of "Oh, yeah, babies grow inside their mother's womb" way, but observing it on a daily basis definitely brings home the reality.

Creation of fire by unnatural means

2006-03-17T09:07:00.000-05:00

From a Driftglass rant [thanks to Tozier for the link]:

"Blame everyone who was screaming “Fire!” while the coming conflagration -- that you created by briskly rubbing stupid ideas together -- was containable"

Awesome imagery. And here's the appropriate soundtrack, courtesy of Beavis and Butthead.

Alternative uses of nuclear power

2006-03-08T11:37:00.000-05:00

As a big fan of comic books, I whole-heartedly agree with TJ Prima.

Panic-inducing, somewhat arbitrary, classifications

2006-03-05T09:00:00.000-05:00

Sometimes, the phrase "high risk", it does not mean what you think it means.

Case in point: standard prenatal testing usually involves an ultrasound at 12 weeks that measures things like the nuchal translucency of the baby, plus a maternal blood test that looks at the levels of various hormones and proteins. Passing this data, plus the mother's age, through the diagnostic meat grinder results in a number that tells you the risk of the baby having Down's Syndrome. This number is generally conveyed to you by your doctor/ob-gyn/midwife/initiate-in-the-healing-arts-of-your-choice.

Now, here's the way you don't want that person to start the conversation: "I'm afraid that you're at high risk of having a child with Down's Syndrome." [which is how the conversation started for us]

*Thunk*

That's the sound of our jaws and hearts hitting the floor. After the initial "Wha' happen ?" reaction, and a flurry of agitated questioning, it turned out that our kid apparently had a 1 in 130 chance of having Down's and the midwife suggested we go see a genetic counsellor to talk about what to do next. Needless to say, we were fixated on the "high risk" bit and dragged ourselves out of the door in a somewhat dejected manner.

About 30 minutes later, when my brain started working again, I realized "Wait a sec ... 1 in 130 ... that's less than 1% ... that's 0.8% ... that means the chances of the child not having Down's Syndrome are 99.2% ... sh!t, those are better chances than just about anything in life." Actually thinking about the numbers like that made us both breathe much easier.

It turns out that the phrase "high risk" means "greater than 1 in 250", and that cutoff is chosen because the risk of inducing a miscarriage by having amniocentesis, which can tell you for sure whether or not the child has Down's syndrome [as well as other chromosomal abnormalities] is about 1 in 250. In other words, the high-vrs-low risk classification is based on a cutoff that nobody without a screaming case of the OCD heebie-jeebies would consider "high risk", even taking into account the increased risk sensitivity induced by the thought of bringing a new person into the world.

You would think that part of the training given to people dealing with already on-edge parents-to-be would include helping them to see these sorts of diagnostic numbers in context. I mean, contrast a conversation that starts with

"Your child has a 99.2% chance of being OK, which is a bit lower than the 99.6% we usually like to see, so let's talk about what you might want to do"

with one that begins

"You're at high risk of having a child with Down's Syndrome."

It's hard to imagine a harsher start than the second one, other than maybe something like "Based on our tests, your child is doomed to a lifetime of pain and suffering -- an eagle will feast on his liver daily, he will be made to push a boulder uphill in perpetuity and, oh, let's see, it says here that ... every two days or so, he'll have to dive into a pile of razor blades, after which he'll be sprayed with salt dissolved in lemon juice. Any questions ?"

In any case, we opted to have amniocentesis to get rid of that niggling 0.8% of uncertainty and the child is fine and definitely a boy.

The moral of the story: when you hear a fuzzy phrase like "high risk", ask what the precise definition of that is before you get all wound around the axle.

Lineage

2006-03-04T12:48:00.000-05:00

We had an initial inkling based on ultrasound pics that were just a bit too early to be definitive, but it's now been confirmed: we're having a boy. And each time I think "I'm going to have a son", it stops my train of thought in its tracks because a first-born son has such ... mythical associations.

Wow.

Sweating the little things isn't always bad

2006-03-04T12:29:00.000-05:00

Arts and Letters Daily has links to two articles that debate the effectiveness of the "broken windows" approach to crime fighting, which is based on having the police pay more attention to misdemeanors, such as "loud parties, unleashed dogs, public drinking, and even littering".

I have no idea how effective this approach is in reducing serious crime. However, I think it's not a bad idea for the simple reason that it might make people more civil. And that's something that's sorely needed in Boston, where the pendulum of individual rights vrs communal obligation has definitely swung a bit too far to the "It's a free country and I can do what I want" side. Actually, it may not even have as much to do with people explicitly asserting their liberties as it has with them just being oblivious to the fact that, oh, dropping trash in the middle of the street when there's a garbage can 10 feet away, or singing [badly and loudly] on a crowded commuter train might just be, y'know, not very "considerate of other people".

I never knew I was such a "people suck" curmudgeon until I moved to Boston. At least I think of it in terms of "Back in Seattle ..." instead of "Back in my day ...".

Whole numbers in the range 1-10 only, please

2006-03-02T20:37:00.000-05:00

First object lesson in being a teaching assistant: do not make up a homework problem whose solution involves a lot of fiddly arithmetic with numbers that have to be accurate up to 4 decimal places. Or else you'll end up having to check that fiddly arithmetic for 60+ problem sets. And that's no fun for anyone.

Words worth a thousand words

2006-03-02T10:19:00.000-05:00

Every once in a while, you hear a new word or phrase that is so obviously le mot juste that it is immediately absorbed into your vocabulary. Here are two recent acquisitions of mine:

- If you've ever wanted a perfect way to describe the look that comes from kids wearing sweatshirts with the hood up, or a beanie/skull cap/knit hat, and their pants around their knees, forget "gangsta". A much more evocative term, courtesy of Christina: urban gnomes. It's brilliant. I mean, compare this and that and you'll see what I mean. I'll never be able to look at these kids again without giggling.

- If you want to convey how earnest you are, appropriate use of the word sinceriously will make your sentiments perfectly clear. Again, from Christina, but not one she coined; it was generated by somebody she works with for whom English is a second language.

The realities of lab work

2006-02-21T13:04:00.000-05:00

As I start to do more labwork, I'm gaining an appreciation for two things:

- The often-peddled view of "breakthrough" experiments obscures the fact that the majority of time needed to do experimental work is spent just making all the stuff you need for the experiment you really want to do. Doing the "final"/"breakthrough" experiment itself is often one of the quickest bits.
- A lot of experimental molecular biology is based on exceedingly unlikely events and making it up on volume.

Let's take the second bit first. An analogy, inspired somewhat by personal experience: suppose you have your windows open on a warm summer night and a bat flies in and starts flapping around in circles in your living room. You'd like to catch the bat and toss it back out on its ear, so to speak. One [admittedly batty, haha] scheme would be to reason as follows: a bat is sort of like a mouse with wings. Now, what catches mice ? Cats, that's what. Are there any cats on hand ? Yes, there are. So, how about tossing a cat into the air and hoping that it catches the bat ? [Assume, for pedagogical purposes, that the cat available to you is sufficiently composed to recognize the most important aspect of the situation, viz. that there is a mouse to be caught, and ignores such trivialities as the fact that it's being tossed into the air.]

Now, the chances of the cat catching the bat on any single toss are miniscule. However, if you toss the cat, say, a million times, the chances that the bat is caught start to rise into the realm of not-totally-improbable. And that's how a lot of experimental procedures in molecular biology work: you throw together a bunch of things that might snap together in the right way maybe once in a million times, but if you do this with bajillions of cells [and you can easily get a million cells in a milliliter of cell culture], the chances are good that you'll get a few instances where things snap together correctly.

Ok, so you get lucky occasionally, but given that lots of lab work consists of mixing colourless liquids together to make more colourless liquids and you can't really look inside cells to see what's going on at the molecular level [recent cool developments notwithstanding], how do you figure out when the desired event has taken place ? This is where the high art [and science, I suppose] of genetic selections comes in. A lot of genetic selections are predicated on arranging things such that if the right thing happened, the critter lives; if the wrong thing happened, the critter dies [or vice versa; both types of selections are used].

For example, a commonly used selection is antibiotic resistance: take cells that are normally vulnerable to an antibiotic like ampicillin, perform your experimental procedure on them and then looks for cells that have acquired resistance to ampicillin. If the right thing happened, a small fraction of the cells will have acquired a gene that makes them resistant to ampicillin and will grow on an ampicillin-containing medium whereas the rest of the cells that you used for your experiment will die. Genes like the ampicillin resistance gene are referred to as "markers", because they mark the cells that you want.

A concrete example of all this: one of the ways to insert foreign DNA into a yeast cell is to use a mechanism called homologous recombination. Pretend the yeast genome consists of actual text, like:

"Tonight I ask you to pass legislation to prohibit creating human-animal hybrids because I think they're the work of the devil"

If you now introduce a piece of DNA whose beginning and end are the same as some stretch of genomic DNA into the yeast cell, like:

"creating human-animal hybrids like me and other members of my administration because"

then, a few times in a million, there's a bit of "cut and paste" so the yeast genome becomes:

"Tonight I ask you to pass legislation to prohibit creating human-animal hybrids like me and other members of my administration because I think they're the work of the devil"

This sort of swapping is called homologous recombination. It's a rare event -- the new piece of DNA needs to "find" a stretch of genomic DNA that matches at the right spots and, even for something as simple as yeast, the genome is over 13 million letters long so there's lots of ground to cover; the cell is a pretty crowded place; the right protein machinery needs to be around to make the swap happen etc. And, of course, you have to get the details of the experimental procedure [mostly] right.

Even though it happens so rarely, homologous recombination is one of the main ways used to modify the yeast genome. The selection that's often used to find the cells in which it happened is to use cells that can't make an amino acid that they need [and so they won't grow on medium without that amino acid] and, together with the new DNA, introduce a gene that allows them to make that amino acid. Cells that have successfully recombined the new DNA into their genome then acquire the ability to grow on medium lacking that essential amino acid, which ends up looking like this -- the white spots are colonies of yeast cells that are able to grow successfully.

Of course, there's now another complication: the number of easily usable marker genes is fairly small, certainly less than 10 for yeast. If you use up one marker gene each time you modify a cell, this means that you're limited to less than 10 successive modifications. So if you want to make lots of changes, you have to figure out a way to recycle your marker genes. Doing so often requires that you have what's called a "counterselectable" marker -- if you grow cells in one way, only cells that contain the marker survive; if you grow them in a different way, only cells that don't have that marker survive. So the entire procedure requires that you first do your experiment such that only cells in which the right thing happens acquire the marker and survive and you then take the survivors from the first step and grow them under different conditions so that only the ones that have now lost the marker stay alive.

Each such iteration takes, say, 1-2 weeks if you're good at it, have all the necessary raw materials [like the pieces of new DNA] readily available, and don't run into any trouble [which is, unfortunately, not a sufficiently rare event ...]. So, to make, say 10 changes in the genomic DNA of a yeast cell, you're talking 3-6 months until you have the yeast cells that you want to actually experiment on.
If, along the way, you've had to construct the new pieces of DNA yourself, a process that's pretty much the equivalent of self-flagellation, it'll probably take twice as long. Throw in a fudge factor of "I've never done this before, so I'll make lots of mistakes along the way" and you're up to about a year.

Now you can finally start doing things like checking how these cells respond to being poked with the molecular equivalent of a sharp stick. And, of course, if you're unlucky, they won't do anything interesting at all, so you've just spent a year of your life on mind-numbing work and constructed something that's about as exciting to watch as this. Congratulations !

All this is just a long-winded way of saying: this whole lab work thing is definitely 99% perspiration, 1% inspiration.

Throwing stones from the inside

2006-02-21T10:50:00.000-05:00

After recently reading "Off-Center", which presents some pretty persuasive evidence that the Republican party has managed to mostly stamp out dissent within its ranks and is heading hard-right to kookville at full speed, it's nice to see that there are still some Republicans who aren't afraid to tell it like it is [together with, of course, the obligatory administration shill ...]. The description of Bush [attributed to Bartlett's book] as a man not at all inclined towards thoughtful analysis resonates with me all the more because I just finished "The Survivor: Bill Clinton in the White House", which portrays Clinton as the diametric opposite: so interested in considering all the angles that he was sometimes paralyzed.

It's hard to imagine a worse match than this man, a personification of the adage "For every complex problem, there is a solution that is simple, neat and wrong" , with a world that's as complicated as ours.

Cheney, truly a minion of Hell

2006-02-17T19:42:00.000-05:00

Only a creature of dark aspect would be able to strike such fear in the hearts of men that they apologize for getting shot by him and are concerned about his well-being.

I mean, damn. That's a serious Dark Jedi mind trick.

[An alternative theory is that Whittington's statements are a consequence of the affection and love that Cheney inspires in all who meet him, but we all know that would just be crazy talk.]

Numbers, useless

2006-02-15T06:45:00.000-05:00

From a story about the man who was unwise enough to be around a Dick Cheney packin' heat:

Dr. David Blanchard, the emergency room chief, estimated that Mr. Whittington had more than 5 but "probably less than 150 to 200" pellets lodged in his body.

That really rules out only 1-5 pellets, but leaves the door open for, say, 20000 pellets because of the artful "probably" dodge in the second half of the estimate. Translation: "I have no clue, but since you insist on me giving you numbers, here they are. Satisfied ?". Kind of like Musharraf's recent take on the likelihood of terrorist fatalities.

[Not that I'm generally in favor of people getting shot but this whole thing still has me chuckling. It would have been even funnier if Cheney had been the one with the indeterminate number of pellets inside him.]

What I tell you four times is true

2006-02-10T10:44:00.000-05:00

Hmm. I've been tagged with the "4 things" meme, the blog version of a chain letter. At least it comes without the "If you don't pass it on, a friend of yours will be gored by a rampaging boar when he least expects it" threats that usually accompany such things.

Four jobs I've had:
1. Gardener, in a cemetery. Very laid-back patrons.
2. Programmer in a high-energy physics group. FORTRAN, I hardly knew ye ... thank god.
3. Footsoldier for the now-mired-in-bureaucracy, Not-Really-Very-Evil Empire. Nothing like some TPS reports, with accompanying cover sheet of course, for slowing down the inexorable rise of evil.
4. Stacker and general monkey boy in a college library. This allows me to scoff at the admonitions in a library not to re-shelf books myself because I know the secret code of Dewey.

Four movies I can watch over and over:
1. "Enter the Dragon"
2. "Crouching Tiger, Hidden Dragon"
3. "Princess Mononoke"
4. ... actually, I can watch [bits of] lots of movies multiple times, regardless of how good/bad they are, something that utterly baffles Christina.

Four places I've lived:
1. Wernau, Germany
2. Accra, Ghana
3. Philadelphia, PA
4. Seattle, WA

Four TV shows I like:
1. Arrested Development
2. Curb your Enthusiasm
3. House
4. Six Feet Under

Four places I've vacationed:
1. Namotu, Fiji
2. Itacare, Brazil
3. Sayulita, Mexico
4. Matapalo, Costa Rica

Four of my favorite dishes:
1. Haribo gummy bears [trust me, I can make a meal of them]
2. Sauerkraut and Spaetzle
3. Fried plantains and jerk chicken
4. Real German pretzels, with salami

Four sites I visit daily:
1. Superbike Planet
2. Surfermag.com
3. Arts and Letters Daily
4. NY Times

Four places I'd rather be right now:
1. Just about any MotoGP racetrack, on a dry, warm, sunny day, riding a motorcycle I don't have to worry about crashing
2. Sitting on a longboard in warm, non-sharky water, with very few other people out and consistent, glassy waves that are gentle enough that even I can surf them and no reef or rocks to worry about on the frequent occasions that I wipe out
3. At the Amazon website, with no spending limit
4. Seattle

Four bloggers I'm tagging:
1. Christina
2. Brandon Watson
3. John Miller
4. Lawrence David

Four books/series I like:
(arbitrarily restricted to fiction)
1. Anything by Iain M. Banks
2. Anything by Neil Gaiman
3. Richard Morgan's Takeshi Kovacs series
4. Ursula le Guin's Earthsea series

Four games I can (and do) play over and over again:
1. Scrabble
... and that's about it. Not much of a game player.

There. All of me, in 4-sized chunks.

Graphic violence

2006-02-08T16:35:00.000-05:00

For some reason, I think this headline would be funny if it weren't so tragic:

"Bush Urges World Leaders to Halt Violence Over Cartoons"

A month's worth of reading

2006-02-03T16:06:00.000-05:00

Well, the next semester is almost upon us -- classes start on the 7th and with that my responsibilities as TA begin [actually, they've already begun; we've already written the first problem set]. The last few weeks have been mostly marked by reading. To wit, I have devoured the following:

- "Birds Without Wings": Another Louis de Bernieres tragicomedy, more tragic than comedic. Not quite as entertaining as the triad that begins with "The War of Don Emmanuel's Nether Parts" but definitely larger in scope.
- "Dreams from My Father": This didn't do much for me, I must admit.
- "The Great Influenza": A well-written, if sometimes rather repetitive, account of the 1918 flu. What makes this more than just a long-winded version of "Lots of people died from the flu" is the account the book gives of all the social and cultural factors that influenced the course of the flu: the First World War, the recent emergence of science-based medicine, the state of [biological] science in general, Wilson's decision to devote all American resources single-mindedly to the war etc. The book even has an interesting thesis that indirectly pins World War II on the 1918 flu.
- "Anansi Boys": More gods-walking-among-us fare from Neil Gaiman, this time based on Ananse, a character I heard/read lots of stories about growing up in Ghana. An easier read than "American Gods", I thought.
- "Woken Furies": A good conclusion [maybe ?] to Morgan's Takeshi Kovacs novels. Less predicated on Takeshi being faster/smarter/stronger than everybody else and much more "internal", so to speak.
- "Market Forces": Capitalism taken to the extreme, plus legalized road rage. Entertaining, but the ending left me a bit flat.
- "The Algebraist": More Iain Banks goodness, with the usual Banks ending -- the story is [ostensibly] over, but you can sense that a new interesting tale is being born and so you wonder what happened to the characters next.
- "The Republican War on Science": The title pretty much says it all and the book makes a convincing case for it [on the off chance that anybody is seriously still in denial about the issue].
- "Lamb: The Gospel According to Biff, Christ's Childhood Pal": Very funny satirical account of the first thirty years of Jesus' life. Kind of like "The Satanic Verses" [or recent cartoons], minus the accompanying fatwa and insanity.
- "Fluke": Another comedy by the author of "Lamb", but not quite as funny.
- "Off Center: The Republican Revolution and the Erosion of American Democracy": Viewed in a disinterested way, a very interesting handbook of how one party has managed to ignore the pressure to remain close to the center and instead moved extremely far to one end of the spectrum, without having an overwhelming majority anywhere. From a less detached perspective [eg you think the leaders of said party are bunch of scumbuckets], well, it's just plain scary and somewhat disheartening.
- "Superman: Red Son": What if Superman's rocket had landed in the Soviet Union instead of the middle of America ?
- "Marvel 1602": The X-men set in, well, 1602, period costumes and all. Nicely done.
- "Batman: The Dark Knight Strikes Again": A 60-year old Batman once again comes back and cleans house, putting the hurt on Superman [who just isn't very bright, despite being "super" in all other respects -- if he'd stayed on Krypton, would he have been considered a bit slow ?]

... and several hundred pages worth of scientific papers as I try to nail down my thesis project.

Somehow, I suspect I'll be doing less pleasure reading for the forseeable future.

The jesters speak truth

2006-02-01T22:28:00.000-05:00

Here. There's more I want to say about the State of the Union speech ~~and the smarmy f!ck who gave it~~ but let's not even go there.

Bottom-up loss of autonomy

2006-01-31T07:32:00.000-05:00

I used to think that electric toothbrushes were just another sign of laziness; after all, how much energy is it to move the brush yourself ? However, after Christina convinced me to get over my initial bias and try using a Sonicare, I became a convert. Intuitively, it does seem like having something whirring around in your mouth at semi-relativistic speeds will probably get your teeth cleaner than a purely manual process. In addition, Sonicare toothbrushes, quite apart from sparing you the muscular exertion of having to actually move your hand, also shoulder the burden of telling you when to switch mouth quadrants and when to stop brushing, by dint of beeping at the appropriate recommended-by-9-out-of-10-dentists times.

Sometimes, though, all this automation can backfire. While brushing my teeth this weekend, I caught myself thinking "Hmm, it sure seems like I've been brushing for a long time, how come it's still going ?" ... and then realized that I was using a good ol' non-electric toothbrush and, oh horror of horrors, was entirely on my own when it came to deciding when to stop brushing -- no benign machine overlord was going to guide my actions. [I'm happy to report that after only a few moments of confusion at the immense responsibility thus bestowed upon me, I was actually able to stop brushing.]

Maybe this is how the rise of the machines begins -- not with Skynet, but with a humble toothbrush and a loss of our ability to do the simplest things.

[Aside: as further proof that, no matter how ridiculous an idea is, somebody will have done it: I thought to myself "I wonder whether you can overclock your toothbrush ?", consulted the oracle and, lo and behold, here is an instructional video on exactly that.]

We're bringing in reinforcements

2006-01-25T09:14:00.000-05:00

... or, more specifically, -a- reinforcement: Christina is pregnant.

We're very excited about it and looking forward to all the things we've been told about [with some Schadenfreude =)] by our friends with kids -- sleep deprivation, thinking that baby talk is an acceptable form of communication, being able to have entire conversations revolving around the activity of the baby's digestive and excretory systems etc. Actually, no, we're not really excited about those bits but it seems like there's no way to get around them, so we'll just have to grin and bear them as the price of getting our very own little person who we will mold into, like, the best person, ever. [Really. Trust us. We're professionals, we know what we're doing.]

More details, provided by the person doing the heavy lifting right now [ie Christina] here.

Football fan for a day

2006-01-23T15:45:00.000-05:00

Generally, I don't care about the Superbowl, other than hoping that it generates some cool commercials. This time, however, it's different -- the Seattle Seahawks are going to the Superbowl, for the first time. Come February 5th, I may have to adopt the time-honored tradition of laying in a large supply of junk food and a bunch of [candy-ass] bee r and settling down on the couch to actually watch a full-length football game.

Truth in advertising

2006-01-17T15:00:00.000-05:00

The subway cars here are plastered full of ads from colleges and job training programs that promise to help you get those skills you need to make your dreams come true, fulfill your potential etc -- basically, they all promise to make the world your oyster. In general, I'm all for inspirational messages but the wide-eyed wonder of it all gets a little tiring after a while.

Today, I finally saw an ad that [sort of] tells it like it is -- its tagline was "With the right tools in the right environment, almost anything is possible." [emphasis mine], which reminded me of my favorite motivational poster.

Unfortunately, I suspect that, unless a "Crazy People"-like situation unfolds in the advertising business, whoever approved that ad isn't going to make it very far in the business.

Best bookstore name ever.

2006-01-16T11:16:00.000-05:00

BLMF.

Sometimes, you just gotta violate those rights a little bit

2006-01-15T09:21:00.000-05:00

Last year was a pretty bloody one for Boston: the homicide rate was the highest it's been in 10 years [and a lot of those homicides happened in an area we were initially thinking about living, but that's a whole different story ...] and police identified suspects in only about 20% of them, a 10-year low. Part of the problem with solving these crimes is apparently an increase in witness intimidation, such as gang members wearing T-shirts that say "Stop Snitching", a move that led Boston's mayor Tom Menino to consider banning the sale of these T-shirts in Boston, a notion that aroused the ire of the local civil liberties union, which is understandable.

I didn't really pay much attention to the dust-up about these T-shirts until I saw somebody wearing one yesterday. That's when it really struck me that wearing a shirt like this, especially given the current atmosphere in Boston, is like hanging a sign around your neck that says "Attention law-enforcement officers: I'm probably involved in something shady you'd like to know about". If I were a police officer, I'd make myself a T-shirt that said "Start Talking" and devote an inordinately large share of my attention to anybody wearing a "Stop Snitching" shirt, outraged claims about "profiling" and civil rights violations be damned.

Feel-good company slogans

2006-01-11T07:32:00.000-05:00

Generally, company slogans are designed to inspire trust and make you think that they will share your pain if something goes wrong. The folks at Godfather Racing seem to be aiming for something different; their slogan is "If we lose, you die !". Granted, their target market demographics are skewed towards people who think that "If you're not crashing, you're not riding fast enough !" is actually good advice, but even so, the risk asymmetry in that particular motto should give pause to the most gung-ho racer when deciding whether to buy something from them. Then again, maybe they should be commended for brutal honesty ...

[And, as a minor nit, what's with the machine gun logo ? Were they thinking "What's that movie with the swarthy, Italian-looking guy going crazy with a machine gun and yelling about his 'leetle friend' ? That was 'The Godfather', right ?" Wrong.]

Random funny stuff

2006-01-04T16:39:00.000-05:00

Newly discovered today: The Chronic Of Narnia.

And my favorite video from last year: The Old Negro Space Program.

Useless, yet strangely deity-like, knowledge

2006-01-03T15:53:00.000-05:00

Over 80,000 digits of pi have been memorized. When will people start to memorize genomes ? For example, the genome of bacteriophage T7 is only 40,000 bases long, so it should be possible to memorize the complete genomic sequence of T7 [unless memorizing sequences of only 4 distinct letters is way harder than memorizing sequences of the numbers 0-9].

Useless ? You bet. But it'd be pretty cool to be able to say that you personally, if only in an exceedingly abstract sense, know everything there is to know about another living creature [assuming you'll grant that a virus is alive, something that is debatable].

In search of something Spreadably Delicious (TM)

2006-01-02T15:35:00.000-05:00

Something insidious is happening, if not across America, at least around me: quietly, stealthily, without public outcry, Nutella, that truly Spreadably Delicious (tm) paste, is disappearing from the aisles of the grocery stores I frequent.

It started in Trader Joe's: available one week, gone the next. Replaced by a home-grown version, "Trader Joe's Hokey Alternative To Nutella" [or something along those lines], an entirely insufficient substitute. [I tried it. I know.] A decision probably driven by some misguided attempt to enhance the Trader Joe's brand, or cut costs, or some other such corporate decision made without thought for its effects on the man on the street [like me].

Nutella was also available in the co-op grocery down the street from us, albeit at a higher price than from Trader Joe's, and hence we'd avoided buying it there. But, driven by necessity, I attempted to fill the gaping hole left in my breakfast by going to the co-op. This, too, ended in despair: no more Nutella. In its stead, a noisome potion made by Loacker, Johnny-come-latelys attempting to crowd in on the turf so ably filled by Nutella for the last 60+ years.

Driven beyond the endurance of any reasonable man, I invoked the awesome, other-worldly powers of the Nutella Locator to find a store close to us rumored to be trading in the embargoed good.

Today, we visited that store. True, there was a sticker on a shelf that said "Nutella". But, like an empty tooth socket, it too was achingly unfilled. Mockingly empty. And, as if to rub it in, a jar of another pretender to the throne, the Milky Way spread, right next to it. In a last-ditch effort, I asked one of the store employees whether they had any more of it in the back. After initially not quite comprehending the question, she disappeared for a while and then returned to tell me something that haunts me yet: "They tend not to have it." And while my brain was still trying to interpret this sentence, she disappeared and I did not have the heart to go after her and ask her what she meant.

What to make of this gnomic utterance ? That sometimes this store has Nutella, but, on average, it tends to be sold out ? That interpretation seems rather too complex and philosophical. I would like to think that she simply meant that they are currently sold out, and was not making a statement about the availability distribution of Nutella being somehow ... skewed, since that would mean I might have to adopt a more sophisticated sampling strategy than simply returning periodically to check on its availability.

What, then, to make of this disappearance ? Is it simply the result of the troubles of Kobe Bryant [who used to be the face of Nutella in the USA] ? Is it a conspiracy by enemies of mine in high places to rob me of a cornerstore of my diet ? I don't know. What I do know is that the search will go on, and I will not rest until I can once again enjoy the many forms of Nutella Usage.

Programming languages as options

2005-12-31T11:49:00.000-05:00

Two related posts about programming languages, which, together with operating systems and programming style guidelines, are the Holy Trinity of "Things Most Likely To Cause Computer People To Turn Into Religious Fanatics":

- Joel Spolsky's post about the perils of JavaSchools
- The QofW take on Joel's post

My personal take on this is that there's no perfect programming language, you should always pick the language most appropriate for your task and knowing more languages and programming paradigms just increases the tools you have in your toolbox. Expanding on this relatively content-free platitude and applying it to the question at hand:

I took the version of the Penn CSE course that Joel describes, where you're taught Scheme and ML before C/C++. It was definitely hard to wrap your head around Scheme when you were already used to an imperative style of programming, and lots of people said "Never mind" and dropped out of the major. For years afterwards, I reflexively recoiled from anything to do with AI because I'd been told that Scheme/Lisp was extensively used in AI and I never wanted to go near anything with that many parentheses again. And I've never had to use Scheme or ML again. So, on one hand, I agree with the argument that, for the most part, any reasonable language has all the facilities you're likely to need, that Java is a perfectly reasonable thing to teach and that teaching people Lisp [and, to a much lesser extent, C] is a lot like forcing people to learn Latin.

On the flip side, though, I do think that, right now, starting out with languages like Scheme and C is actually a better way to go, in the long run, but for somewhat different reasons:

- Scheme, and functional languages in general, are just a totally different way of doing things than imperative languages are. You think about your data structures differently, you manipulate them differently and there are facilities in functional languages that just make them an easier fit to certain tasks than imperative languages [the same, of course, is also true the other way around]. So learning a functional language increases your awareness of alternative approaches to tackling a problem, which, I claim, is always a Good Thing.

- C, more than anything else, just forces you to get closer to the machine and, in the process, be careful and be aware of what you're doing. It's been argued that being close to the machine [eg having to do your own memory allocation, treat strings as null-terminated character arrays etc] is also becoming obsolete because it promotes buggy code and reduces programmer productivity, so it's much better to rely on innovations like garbage collection and the ready availability of class libraries etc. That's a reasonable argument, for the most part, but it's subject to the Law of Leaky Abstractions -- sometime, somewhere, something is going to break in the abstraction layer you're sitting on top of and if you don't know how to go down to the appropriate level, figure out what's going on, and fix it, you're hosed. Also, if you ever get into really hardcore systems hacking/optimization, the chances are that you're going to have to break your abstraction layer and dive down into the guts of the system. So while using languages like Java that relieve you of some of the more mundane aspects is the right thing to do a lot of the time, you're better off learning something lower-level, like C/C++, first. You could, of course, extend this argument and say that everybody should learn assembly language; while not entirely unreasonable ;-), my general rule of thumb would be to stop one level down: learn something that's one level lower than the currently most-used level of abstraction [eg C instead of Java, at the moment]. That way, you have the option of choosing the right tool for the job.

So, in the end, I agree with Joel that it's better to start off with Scheme and C than with Java, but not for the reasons he gives -- it's not about pointers and recursion specifically, it's about having a wider range of options than the least common denominator.

Updates:
- Thanks to Cosma for pointing me at Ook.
- Another reason it's really not about recursion specifically: in practice ie when building a real-world system, using recursion isn't that great an idea anyway, at least not unless it's tail recursion, which is just iteration by another name. Because otherwise you blow your stack space, and that's no fun for anybody.

The end of larnin'

2005-12-21T17:06:00.000-05:00

... or at least the end of having to larn' stuff and answer pointed questions about it.

As of noon today, my semester is over. And, with that, I'm pretty much done with the classes I'm required to take. So, no more professors asking me invasive personal questions about things like max-margin classifiers, or what the picture of an electrophoresis gel allows me to conclude about the position of restriction sites on the plasmid etc. At least, not unless I choose to take more classes. [which I probably will because, hey, somebody else is paying for it]. Or until my qualifying exam, which I'll have to take sometime between June and August next year [and whose nature is still rather nebulous -- it's never been administered because my PhD program is brand new ...].

My only other required contact with classes will be when I have to act as a teaching assistant next semester. That's something I'm looking forward to about as much as a root canal, given that I have zero aspirations of ending up as a professor or teacher in any official capacity. That's not to discount the beneficial effects of the fact that it forces one to understand the material better, or because I think it's not an important job. It's just one of those important jobs and/or forcing functions that I wish I didn't have to deal with ;-)

Of course, now I don't have any more excuses to not make any progress on actual research ...

Labeling considered important

2005-12-19T12:36:00.000-05:00

If:

You are in possession of: two identical bottles containing the same volume of colorless liquid. Bottle 1, labeled "A" contains liquid A; bottle 2, labeled "B" contains liquid B [ie the only distinguishing marks are the labels].
And you are not in possession of: a photographic memory that remembers little details like the spatial ordering of the bottles and labels
And you want to: rewrite the labels to make them more legible
Do not: rip off both labels at once, wad them up and throw them into the trash
Because you will: not have any clue which bottle contains which liquid. And you will have to remake said liquids, which may or may not be a huge pain in the posterior. Especially if you have, 10 minutes previously, spilled most of your supply of one of the necessary components, all over your lab bench.

This concludes today's lesson in "Short Non-Protocols in Molecular Biology". Thank you for your attention. You may now return to your regularly-scheduled cloning.

Spy Vs Spy

2005-12-18T09:37:00.000-05:00

MIT uses SpamAssassin to help filter spam email and, for the most part, it does a good job. However, it seems the SpamAssassin is sometimes outwitted by another assassin: Jason Bourne. I say this because the last couple of spam emails that have made it into my inbox have contained segments from Robert Ludlum's Jason Bourne series of novels, like:

"slumped in the rear seat waiting to hear the words. The nun comes out, monsieur! cried the driver. She enters the first taxi! Follow it, said Jason, sitting up. On the avenue Victor Hugo, Laviers taxi slowed down and pulled up in front of one of Pariss few exceptions to tradition-an open plastic-domed public telephone. Stop here, ordered Bourne, who climbed out the instant the driver swung into the curb. Limping, the Chameleon walked swiftly, silently, to the telephone directly behind and unseen by the frantic nun under the plastic dome. He was not seen, but he could hear clearly as he stood several feet behind her. The Meurice! she shouted into the phone. The name is Brielle. Hell be there at noon. ... Yes, yes, Ill stop at my flat, change"

I guess the inclusion of random innocuous text like this in addition to the usual pitches for Cialis etc is enough to throw off the spam filter, at least for a while.

Is the use of segments from this particular series of novels, with their theme of sneakiness of various sorts, a knowing wink on the part of the spammers ? Who knows, but I found it amusing all the same.

Finals, my favorite part of the year

2005-12-16T12:55:00.000-05:00

Classes are over, and all that stands between me and some downtime are two finals. Unfortunately, these finals illustrate two of the extremes encountered in classes.

- For my statistics final, we're not allowed to bring any sort of notes, so I have to memorize what amounts to ~13 pages of formulae. The entire class was basically an exercise in chug-and-plug: figure out what the right formula is, stick in the appropriate numbers/symbols and, voila, you get an answer. Very little emphasis on a deeper understanding of the material, so the only thing that really gets tested is how well you can pattern-match between what you've memorized and what the problem demands.

- For my machine learning final, we can bring whatever we want, short of a computer or another person. Unfortunately, if the midterm, past problem sets and the final practice problem set [which explicitly says "Some of these problems are very hard"] are any indication, that's not going to help much because this class actually requires a pretty deep understanding of the material and the professor has no qualms about making us squirm. An issue that is not helped by the fact that we covered lots of material, but generally not in very much depth.

Somewhere, there has to be a happy middle ground.

All whining aside, I thought both classes were [or will be] useful, which, in the end, is what counts.

Wikipedia: good, bad or indifferent ?

2005-12-16T07:48:00.000-05:00

Two somewhat opposing viewpoints on Wikipedia:

- Nature magazine says that Wikipedia's science entries are, on average, not bad [but not great either]. That squares with my experience with Wikipedia, which has been mostly confined to looking up science-type stuff.
- The Penny Arcade take on Wikipedia, which I find pretty funny [especially the "quantum encyclopedia" bit] and also agree with, for the most part.

I can definitely see how there can be lots of editing and re-editing and inchoate debate about entries on subjects that are, well, open to debate. That's something that Wikipedia's science entries probably have to contend with less -- the equation is either right or wrong, there isn't a gray area -- which may lead to higher-quality entries.

I suppose the results of the Nature survey are a good sign for OpenWetWare (OWW), which is a Wiki-based attempt at allowing folks doing research in all areas of biology to easily share information. [Full disclosure: I'm a big fan of OWW, have used it a ton myself, and am a member of a team of MIT folks that just got an iCampus grant to spread the word about OpenWetWare and get more labs/people to join up, so my sympathies are definitely with the Wikipedia style of doing things.]

Virtual laziness

2005-12-09T06:48:00.000-05:00

Apparently, playing videogames is too much work for some people, so they're outsourcing it. I'm sure it's only a matter of time before somebody makes a videogame in which your character plays somebody sitting on a couch playing a videogame. Because, y'know, all those "active" videogames are too physically demanding.

How lazy can you get ? We're well on the way to finding out.

Anti-abstract

2005-12-06T17:50:00.000-05:00

The abstract for a scientific paper is kind of like the elevator pitch for the paper: it should make you want to read the whole paper or, failing that, at least give you an idea of what the paper is about, and the major results contained in the paper. Either way, it's supposed to increase the amount of information you have.

However, sometimes there are abstracts like this:

"We describe the use of the matrix eigenvalue decomposition (EVD) and pseudoinverse projection and a tensor higher-order EVD (HOEVD) in reconstructing the pathways that compose a cellular system from genome-scale nondirectional networks of correlations among the genes of the system. The EVD formulates a genes x genes network as a linear superposition of genes x genes decorrelated and decoupled rank-1 subnetworks, which can be associated with functionally independent pathways. The integrative pseudoinverse projection of a network computed from a "data" signal onto a designated "basis" signal approximates the network as a linear superposition of only the subnetworks that are common to both signals and simulates observation of only the pathways that are manifest in both experiments. We define a comparative HOEVD that formulates a series of networks as linear superpositions of decorrelated rank-1 subnetworks and the rank-2 couplings among these subnetworks, which can be associated with independent pathways and the transitions among them common to all networks in the series or exclusive to a subset of the networks. Boolean functions of the discretized subnetworks and couplings highlight differential, i.e., pathway-dependent, relations among genes. We illustrate the EVD, pseudoinverse projection, and HOEVD of genome-scale networks with analyses of yeast DNA microarray data."

This one achieves almost the opposite effect; it reads like something generated by SCIgen. It's like a finely-crafted mind virus that enters your brain via your optic nerve, scribbles over some perfectly good empty memory cells and fills them with gobbledy-gook. After reading it several times, trying to figure out what it meant, I feel like I actually know less now. It's sort of like Snow Crash, but for scientists.

Things like this shouldn't be called abstracts, they should be called obfuscats.

[Disclaimer: I haven't actually read the paper. For all I know, it might be a masterpiece of clear exposition and cutting-edge science, but with an abstract like that I suspect not many people will ever find out. ]