Thursday, October 28, 2004

More Sox ruminations

A few more thoughts that occurred to me last night:

- The story of the Sox winning the World Series this year is a picture-perfect American story: rag-tag team of carefree, ne'er-do-wells are up against the buttoned-down, professional team [the Yankees], are almost out of the running and then manage to look deep into their own hearts and somehow dig up the courage and skill to come back from a 3-0 deficit and go on to win the World Series [beating the Cardinals is almost an afterthought]. The underdogs win and the world is a brighter, happier place, at least for a while. Revoltingly saccharine, isn't it ? I wonder how long it'll take before somebody makes a movie about this ...

- Now that the Curse of the Bambino has been broken, what are people in Boston going to complain about ? There's nothing like having a common enemy and the sense that you're struggling against fate to pull people together. Now, the Sox are just another baseball team, with nothing particularly mythic about them. Is that going to diminish the fervor of Red Sox fandom a bit ?

Wednesday, October 27, 2004

Boston Red Sox are World Champions

'nuff said.

I'm going to worship at the Cathedral Of Speed

... in about 9 months. The weekend of July 8th, 2005, the MotoGP motorcycle racing series is coming to Laguna Seca and, courtesy of my super-swell friend Brandon, we have kick-ass tickets to go watch this spectacle of speed and insanity on two wheels. Allow me to wax lyrical: the MotoGP class is the equivalent of Formula 1 in car racing -- insane motorcycles, ridden by insane men. The bikes are custom-manufactured, cost a million dollars or so a year to rent [you can't actually buy one from the factory, you can only rent them, and only about 20 teams get to do so], put out about 230-240 hp and regularly achieve speeds over 210 mph. That's just stupid fast, especially when you consider that they don't just get to slow down leisurely from those speeds but rather have to brake hard enough to almost get their rear wheels off the ground and then slam the bike on its side so they can make it through the next corner. From personal experience, I know how quickly things come at you at 150 mph [that's about as fast as I ever went on a racetrack], and how quickly they can go badly wrong [Turn 5 at Seattle International Raceway holds many bad memories for me ...] so I am in awe of anybody who can string together 20+ laps at such an insane pace without turning themselves into an ugly case of road kill.

Anyways, I'm very excited about this. The last time Brandon and I went to something like this was when we went to a round of the World Superbike Championship, Brandon almost ran over Mick Doohan [5-time 500cc class World Championship winner] in our rental car and we were so tongue-tied when we got a chance to take a picture with "King" Carl Fogarty [4-time World Superbike Championship winner] that all we could say was "wow", several times in a row [and we're not usually at a loss for words, especially Brandon]. Hopefully this time we'll be more suave.

[PS: Strictly speaking, Assen is considered the "Cathedral" of bike racing; Laguna Seca is more on the level of a parish church ...]

It's a special night ...

I just watched a full lunar eclipse [first time I've ever seen an eclipse of any sort] and the Red Sox are well on their way to a clean sweep of the Cardinals for their first World Series title in 1918. Not your run-of-the-mill night.

The not-so-special part of today was the fact that one of our cats peed on our bed. Again. And if you've ever had cats, you know that for such ostensibly clean animals, they have pretty damn pungent urine. The most annoying bit about it is that there's no way of knowing why he did it -- you yell at him and he just sits there and blinks at you before rolling over and going back to sleep.

Thursday, October 21, 2004

Christina and I Reverse The Curse

Could it possibly be a coincidence that the year Christina and I move to Boston is the year the Red Sox make it to the World Series, beating the hated Yankees in the process ? I think not. I think Christina and I are solely responsible for Reversing (Part Of) The Curse. And we did it without really thinking about it, only getting sucked into the Red Sox frenzy slowly. Imagine what we could do if we really put our minds to it ...

It's been pretty interesting being in Boston over the last couple of weeks.
A couple of weeks ago pretty much all I knew about baseball was that there was a guy with a club (yes, yes, I know technically it's called a bat) trying to hit a small ball travelling in excess of 80 miles an hour. Now, I actually know what it means when the "bases are loaded" and other such esoteric terms. That increase in knowledge is due to the fact that the entire city, and I do mean entire city, is insane about the Red Sox, and not just since the playoffs started. We noticed it when we first moved to Boston -- every second person was wearing some bit of Red Sox paraphernalia, and it's only gotten more intense. We were at a restaurant a couple of days ago where somebody had brought in a portable radio to listen to the game and the waiter kept coming by and announcing the score. That kind of enthusiasm just sucks you in so that you can't help but start being interested. Over the last week, I think pretty much everybody has had a continuous string of late nights, staying up until all hours to watch the games against the Yankees; this morning even my professor looked a bit tired and rumpled.

I wonder whether it's going to be the same once the World Series actually starts or whether the city is so emotionally drained from the Yankees games that the actual World Series will be anticlimactic. Personally, I've become a Red Sox fan -- any team that refuses to quit as much as these guys did is my kind of team, so I hope they fully Reverse The Curse and win their first World Series in 84 years. Take that, Bambino !

Tha H-Dog keeps it real

Herbert Kornfeld, the Accounts Receivable Supervisor at Midstate, is my favourite Onion "columnist"; the sheer absurdity of it just makes me laugh every time. In his latest column, "A Day Off ? Sheeit", he writes what is perhaps his funniest line ever:

"Bitchez," I shouted from my hoopty. "Give up some numbahz 2 Daddy H so's he can krunch 'em."

That just had me rolling.

Tuesday, October 19, 2004

"Crossfire" hosts get caught in crossfire

Or, more accurately, in sniper fire, coming from the phenomenally accurate Jon Stewart [the host of the "Daily Show", a satire news show] when he appeared as a guest on their show a couple of days ago. He tore into them, telling them that they had a responsibility, being on a real news channel like CNN, to stop playing the partisan hack game and actually have reasoned debate about the political issues. Of course the hosts bristled at this but he pretty much reduced them to tears, especially Tucker Carlson, who just got handed his @$$ on a silver platter. The amazing thing about this is that he managed to be funny while handing out a verbal good ol' behind-the-woodshed beating to people who are presumably supposed to be pretty good at repartee themselves.

The best way to appreciate how brilliant he was is to go find one of the many videos of this segment floating around on the net [google "jon stewart crossfire"]; be warned, however, that it's 36Meg and may take a while to download. If you don't have the patience or bandwidth for that, check out the transcript on CNN.

Jon Stewart is my hero.

Zen koan, MIT-style

A few weeks ago I was sounding off about the fact that one of my classes isn't a whole lot of work and the math isn't that hard. Well, that was, uhm, ... premature. Very premature. In the meantime, the professor has opened up a whole new can of mathematical whup-ass -- pretty much every lecture in the last few weeks has consisted of him doing math on the board for an hour and a half and I just handed in a problem set that consisted of close to 30 pages of handwritten math.

Given this, I had to laugh today when he started the lecture today by saying "The next couple of lectures are going to be rather math-intensive", as if he thought that so far we'd been taking it pretty easy on the math. What really made me snort, though, was his next comment: "The math isn't hard, you just have to know how to do it."

This struck me as a very Zen statement -- it says nothing and a lot, all at the same time. It's content-free from the perspective that obviously if you know how to do something it's not really hard [modulo some things that are tricky because they're not fully under your control, like performing a tricky surgery]. On the flip side, it's also a very positive statement if you look at it as "You don't have to be a math genius to be able to do it, as long as you're not intimidated by it."

I'm choosing the second option. We'll see how that works out for me ;-)

Monday, October 18, 2004

Shocking revelation: Ghana not good place for biotech ! Street riots ensue.

Imagine my surprise when I learned today that Ghana lacks the capacity for genetic engineering. And here I thought that it was akin to the San Francisco Bay Area in terms of technical sophistication.

The reason articles like this piss me off is because they illustrate the stupid grandstanding that still goes on in the country, with bureaucrats pretending that Ghana is on par with industrialized nations and hence saying that it lacks the capacity for genetic engineering is considered a "disclosure". No shit, Sherlock, anybody who's actually been there could have told you that, you didn't need the Director-General of the Council for Scientific and Industrial Research for that.

Sunday, October 17, 2004

Ok, evolution is not evil, it's just not the whole story

Thanks to David for clearing up my confusion with respect to whether Creation Scientists believe all evolution is bunk [apparently they don't]. This ties in nicely with an article just published in Wired about the new assault on evolution, which is based on the "Intelligent Design" argument: existing organisms contain many highly complex systems which couldn't have evolved through pure chance and so point to the existence of a "supernatural" designer.

I must admit that I too have a really hard time believing that the types of finely-tuned systems that exist in biology evolved purely by chance -- I suppose if somebody showed me the probability calculations that show that this is possible, I might be more inclined to believe it, but right now I just don't buy it. Of course, I'm making that statement from a position of almost total ignorance about the nuts and bolts of the current theory of evolution -- maybe somebody has done the math, or has an equally convincing explanation, and I just don't know it.

That said, I don't think you need to go as far as invoking the existence of an Intelligent Designer. I think that we just don't really understand evolution well-enough yet, and that as we gain further understanding of the natural forces that act to shape biological systems, we'll get to a more satisfactory answer than "Trial and error" to the question "How did all this get here ?".

[At one point, I was actually interested enough in this question to consider trying to "do the math" myself, for my PhD thesis, but I realized that there are times when discretion is the better part of valor: starting my scientific career in something as contentious as evolution just didn't seem like a smart idea, especially if I want to graduate in a reasonable amount of time].

Resistance is futile

... we finally crumbled and bought a TV. We didn't bring our old one with us from Seattle because it was too bulky, a little iffy already and probably wouldn't have survived the cross-country move in a truck with no suspension. We initially figured we didn't really want/need to replace it because we don't watch very much TV, but after a couple of months of having to listen to presidential debates on the radio, getting all our news off the Internet and having to watch movies on my laptop screen, we decided that it was time to just bite the bullet and spring for one. So now I'm sitting here watching the Nature channel [showing the usual "Nature red in tooth and claw" docudrama about wild animals trying to survive a harsh environment and each other] and, I must say, quite enjoying it. So much for holding out against the evil forces promoting mindless entertainment ...

Saturday, October 16, 2004

Evolution is an evil, evil lie

Thanks to my friend Lori for pointing me at this site about a Creation Science Fair. I don't know whether it's a spoof or not; I'm torn between thinking that nobody could possibly be that simple-minded and fearing that yes, indeed, there are people who think this way.

In any case, my favorite is

1st Place: "Using Prayer To Microevolve Latent Antibiotic Resistance In Bacteria"

Eileen Hyde and Lynda Morgan (grades 10 & 11) did a project showing how the power of prayer can unlock the latent genes in bacteria, allowing them to microevolve antibiotic resistance. Escherichia coli bacteria cultured in agar filled petri dishes were subjected to the antibiotics tetracycline and chlorotetracycline. The bacteria cultures were divided into two groups, one group (A) received prayer while the other (B) didn't. The prayer was as follows: "Dear Lord, please allow the bacteria in Group A to unlock the antibiotic-resistant genes that You saw fit to give them at the time of Creation. Amen." The process was repeated for five generations, with the prayer being given at the start of each generation. In the end, Group A was significantly more resistant than Group B to both antibiotics.

The bit I don't get, though, is: doesn't this experiment contradict their actual faith, which is based on denying the existence of evolution ?

Tuesday, October 12, 2004

Challenging the gods

Christopher Reeve, aka Superman, died yesterday, after spending the last 9 years paralyzed from the neck down due to a riding accident. He died of complications from a pressure sore.

That's a shitty way for Superman to die. Matter of fact, it was a pretty shitty deal that Superman was paralyzed by being thrown from a horse, not by fighting a super-villain, reversing the rotation of the earth or all the other cool stuff he did. And there won't be a Return of Superman. (Other random thought: "Kill Bill v2" has an interesting little snippet on what made Superman different from all the other superheroes].

Another thing I find pretty screwed-up, beyond just the fact that nobody should have Parkinson's, is Muhammad Ali's condition. The idea that somebody who was once one of the most fearsomely physically coordinated people in the world now has to submit to the indignities of Parkinson's disease killing off his motor functions just seems wrong, as if the universe is trying to make a point.

Looked at through the lens of Greek mythology, it's almost as if Christopher Reeve and Muhammad Ali were intended to be warnings by the jealous gods of Olympus against hubris etc -- come too close to having god-like powers and you get taken down a peg. (Yes, I know Christopher Reeve wasn't actually Superman). In mythology, the Greek gods are portrayed as being pretty human in their motivations, basically what you'd get if you took a random bunch of people and gave them immense powers -- chances are pretty good that you'd end up with a few a$$holes with immense powers, always a bad idea.

Ok, enough rambling about the symbolism associated with the lives and deaths of public figures.

Albino squirrel sighting

While talking a walk around Jamaica Pond yesterday, Christina and I were treated to the the sight of an albino squirrel -- full-on white fur and pink eyes. While they're not quite as cool as white tigers (which, btw, actually aren't albinos), they do have a few advantages:

1. you can see them in their natural habitat
2. you're much less likely to get mauled by one when you encounter them in the wild
3. they're more active than big cats, who tend not to do much other than sleep and eat, at least in zoos
4. you can feed them peanut butter and bread, which is much less expensive than the tons of meat required to keep a tiger sated.

These little critters are apparently somewhat of a local celebrity -- google "albino squirrel jamaica" and you'll get quite a few hits. Here are some pictures of them, off the first link that came up.

Just another little JP discovery that improves my already high opinion of our neighborhood [which Christina gets all the credit for picking].

Friday, October 08, 2004

No more life of leisure for Christina

After some frustrating setbacks, Christina has landed what seems like a pretty sweet job, namely being an assistant to Professor Carl Thompson, a Materials Science prof at MIT. It's sweet for a few reasons, in no particular order:

1. She doesn't have to bring work home with her, so she can start evening photography school in January
2. He appears to be a really nice guy; having a nice boss is very, very important.
3. She gets benefits like dental insurance which will hopefully plug the gaps in the sucky student medical insurance I have.
4. She can now support my crack cocaine habit and I won't have to keep mugging old ladies.
5. Our worlds are a bit more merged -- we'll be able to talk about what went on at work/school today and the other person will have a lot of context for understanding it because we're in similar environments.

All in all, goodness.

Some more musings about the educational philosophy of The Institute

Getting an education at MIT has often been compared to trying to drink out of a firehose ie you get way more information than you can actually absorb. I'm starting to wonder whether that's really a good thing; it seems like the main benefit of it is that you can later on say "Yes, we talked about that in class and I had to do some homework on it". However, the unspoken end of that sentence is "... but I really don't remember a damn thing about it anymore because I understood it just well enough to be able to do the homework that week and then promptly forgot about it because we were assaulted with more new material." In other words, the understanding seems fleeting and shallow -- I feel like if I had to go back in a month and redo one of my earlier problem sets, I'd have a hard time because we've covered so much other material in the meantime that the material we covered early on didn't have time to sink in and really take hold.

There are, of course, multiple possible explanations:

- I'm the only person who feels this way and all my classmates have fully internalized the material we've covered and have no trouble remembering and using any of it. Based on conversations I've had with people, that seems unlikely.
- At the end of the semester, we'll all realize that the material actually did take pretty deep hold because all the problem sets build on each other and keep reinforcing material from earlier in the semester. Possible, we'll see.
- Part of the point of deluging us with material is to train us to deal with an overwhelming amount of data and be able to pick out the bits we need to solve a particular problem. Again, a distinct possibility, but that seems a bit asinine.
- It's training for dealing with the high-pressure situations and stress that generally comes with jobs in science and technology. Been there, done that -- Microsoft is a pretty good training ground in that respect.
- The null hypothesis: there isn't really an educational point to it, it's just being done to uphold MIT's reputation as an excellent engineering school, part of which means making people work really hard. I don't really believe that, but like a good scientist-in-training I have to list all the possibilities I can think of.

... back to trying to drink from that hose without getting my teeth knocked out ...

Accidental electric chair treatment for E.coli

Part of the lab work I'm doing right now involves building up a piece of DNA and then getting it into a cell. The method for getting it into a cell is called electroporation and basically involves putting the cells and DNA into a tube and then applying a high voltage electric pulse to the tube. The electric pulse opens up some pores in the cell and the DNA then slithers right in. You then have to give the cells lots of nutrients so they can recover from the shocking [haha] treatment they've been subjected to, and in general they recover pretty well.

That's the theory, at least. In reality, what sometimes happens is that the electric pulse fries the cells, in which case the machinery that you use for this produces quite an impressive spark. And then you have to go back and basically start from scratch -- you have to prepare DNA that contains the bits of DNA you want to glue together, cut it apart, extract the bits you want, glue them back together and then you're ready to try again. Depending on where the DNA came from to begin with, that could easily be a couple of weeks worth of work, quite a high price to pay for a millisecond of electric pulse gone wrong.

So, yesterday, I saw The Spark ie I fried the cells I was working with. Rather annoying, but it's not as bad as it could have been -- I only fried a quarter of the cells I've been working with and it's not like I really have a lot riding on this series of experiments, since I'm just doing them to get some experience with lab work. As a result, I'm not really bent out of shape about it. That said, I'm sure it'll happen a few more times over the next few years and I won't be so blase about it ...

Friday, October 01, 2004

When experiments go wrong ...

... they can have unfortunate consequences, like the one above, after I tried to get some DNA to do some experiments. For some reason, the fellow in the white shirt really didn't want to have a big needle stuck into him ...

I've actually started doing some experimental work, which is basically going to consist of trying to glue some pieces of DNA together. My impressions so far:

- you work with really, really, really small amounts of material. For one of the mixtures I had to prepare, I had to prepare 0.5 microliters of solution. To give you an idea of how little that is, take the contents of a soda can and divide that into about 300 equal parts. Take one of those parts and divide it into 1000 parts. Now take one of those parts and split it into two. That's about 0.5 microliters. The amazing thing was that I didn't actually need any fancy machinery to do this -- there are entirely mechanical, manual pipettes that you can use to measure out something that small.
- A lot of the experimental procedures work simply because of the sheer immense numbers of molecules involved ie even though the chances of two molecules reacting the right way are pretty small, if you have enough molecules, the right reaction will happen often enough that you can actually get something useful done. To give a concrete example: the work I'm doing basically involves taking 2 pieces of DNA, mixing them together with molecules that cut the DNA strands at very specific spots and then trying to glue matching pieces back together simply by mixing them together in a test tube with other molecules that act like glue. There are lots of ways this can go wrong: the DNA has to get cut in the right places, the glue molecule and the two bits of DNA to glue together have to be in the same place at the same time for long enough that the reaction can happen, the right bits of DNA have to be next to each other to get glued together etc but somehow it works often enough to be useful.
- There's lots of room for automation. As cool as pipetting is the first few times, by the time you're halfway through the 10-step procedure for the first stage in your 10+ step process, for the first solution of the 10 solutions you're making, you're pretty tired of it.
- Temperature and timing are really important. All the incubation rooms and fridges are set at very precise temperatures - 37 degrees celsius, 4 degrees celsius etc, and kept at that temperature by lots of expensive machinery. Letting a reaction go on for a bit too long or too short can totally screw up your experiment and then you face a bunch of trial and error trying to figure out what went wrong.

All in all, though, I'm enjoying it so far. Let's hope it stays that way.