Monday, November 29, 2004

Almost there ... stay on target ... stay on target ...

[The geeks among you will recognize where the title comes from. If you don't recognize it, frankly, you're not missing much =)]
Two more weeks until the end of the semester. In an attempt to limit the amount of pain that professors can inflict, MIT has the rule that courses that have final exams aren't allowed to have homework that's due during the last week of classes. The idea is to give students at least a week to prepare for finals. So, of course, some professors follow the letter but not the spirit of the law by assigning not one, but two sets of homework to be handed in the last-but-one week of class [ie this week]. It just continues to make me wonder whether the educational philosophy of the Institute has more to it than a bedrock of pain, suffering and bloodshed. Interestingly enough, I've found that the people who share my issues with the way MIT conducts business tend to be other people who've been out in the real world and have some work experience. I think us old fogies realize that unless you're at NASA trying to figure out how to get Apollo 13 back to earth before the oxygen runs out, there's generally no reason to do as much engineering in as short a time as is doled out here. I don't think people who come here straight out of undergrad realize that, so they just take their beating with not much more than a whimper.

So, in two weeks I get to sit back and think about what actually happened in the last 3.5 months =)

Tuesday, November 23, 2004

Mostly odds, and some ends

First off, a bit of alternative therapy: go to the Washington Post's "Day in Photos" for November 17 and look at the second picture in the gallery. Can somebody explain to me how riding on a dog that's dressed in a bear suit is supposed to help children with nightmares ? Are the kids having nightmares that they won't ever ride on a dog in a bear suit and this helps them get over it ?

Second, when is a panel a panel ? On today's News Hour, a reference was made to a "2-man panel" investigating something or other. Personally, I don't think 2 men can make up a panel; that's just two dudes looking into something. You need at least 4 people to be able to have a self-respecting panel that can get up in the morning, look in the mirror and say "I'm going to do some seeerious paneling today" to its reflection with a straight face.

Third, I think the dog in this picture ran afoul of Mr.Smith, from the Matrix, and lost his mouth ...

Tuesday, November 16, 2004

The worlds needs Terry Tate

One of the things that Christina and I have noticed a lot more now that we don't use the safe cocoon of our own car to get places is how insanely clued-out kids are. About 90% of them have absolutely zero manners and are just annoying as hell, especially when you're confined in a subway car with them -- yelling, throwing stuff, running around and being generally obnoxious. Maybe I'm getting old before my time, complaining about "the youth of today" and how the world is going to hell in a handbasket, but given the slice of kids that I've been exposed to, it is going to hell in a handbasket.

Anyways, instead of just bitching about it I've started to actually call kids on their sh!t. Doing so has just confirmed my impression that there's a serious lack of upbringing. Case in point: a teenage boy and girl got on the subway today and started eating candy and just blithely dropping the wrappers on the floor, like it was the most natural thing in the world to do. After they did it a couple of times, I leaned over and asked what they were thinking. The first response was utter shock that somebody would actually call them to task for acting stupid -- they asked me whether I was serious. Once they established that I was, they reacted by giving the usual flippant answers that people give when they're embarrassed. While they didn't pick up the stuff they'd dropped [something I asked them to do], at least they didn't drop any more stuff on the floor. Minor victory.

Sometimes, it sure would be nice to be able to go "Terry Tate, Manners Linebacker" on people ...

A bit too much school on the brain

Last night I had a dream that was a lot like one of those comedies where a series of small misfortunes line up just right to cause one big fiasco: I'd started working in a new lab and had spent a week doing a bunch of experiments, ending up with a test tube that contained a few drops of precious solution. Somehow, in a moment of inattention, the contents of the test tube spilled onto a plate that I was eating dinner on, but I thought "Ah, no big deal, I'll just pour it back into the tube" and put the plate off to the side. Somebody else, thinking I was done with it, put his salad leaves right onto the bit of the plate that my solution was on, so I started yelling at him.

At this point, the professor whose lab it was asked what was going on and I went through the internal debate of whether to just let it go or try to explain what had happened. Of course, I chose the wrong option: I tried to explain how I'd spilled my stuff onto the plate, but that it wasn't a big deal until this other fellow put his salad into it etc. While I was talking the professor didn't say anything, he just looked at me with an expression that said "What kind of idiot are you ?" which in turn made me even more nervous so I just kept babbling and trying to explain, which of course made it worse.

That was when I woke up and had one of those "Oh, thank God, it's just a dream !" moments.

Moral of the story: I'm definitely ready for Christmas break =)

The Republican everybody could agree on ...

... namely Colin Powell, is resigning. Bummer. I don't know much about Condoleeza Rice, his expected replacement, other than that she looks scary a lot of times and is scary smart. Check out this great bit of satire, though: Condoleez Rice as Gollum. [Just about anybody could be portrayed as Gollum and get a few laughs, I think ...].

Monday, November 15, 2004

Ils sont incroyable(s ?), les Incroyables

Christina and I went to see "The Incredibles", Disney's new animated movie about superheroes. Outstandingly funny movie, with a fair bit of social commentary woven in. The scene at the end where the baby goes nuts is worth at least half the price of admission. My favorite line belongs to the Underminder: "I declare war on peace and happiness". [G, there's even a French supervillain in it ;-)]

Friday, November 12, 2004

Definitely not in Kansas anymore

It's snowing. In Seattle, we were lucky [so to speak] if we got any snow before Christmas and here it's already snowing two weeks before Thanksgiving. Good thing Christina just finished knitting me a nice warm sweater [Yes, she knows how to do that too. A woman of many talents =)].

And, of course, I saw somebody walking around in a T-shirt and shorts today. I've ceased to be surprised.

Tuesday, November 09, 2004

Rotation over. Your score: 3 to 1.

I'm done with my rotation in Drew Endy's lab. So, what did I get done in my rotation ? I built three new Biobricks, namely:

- Part I6401: Yellow Fluorescent Protein (YFP) with an AAV degradation tag transcribed from the pTet promoter
- Part I6402: YFP with an AAV degradation tag transcribed from the Luxpl promoter.
- Part I13976: (Actually a duplicate of an existing part, but I didn't know that) YFP with an AAV degradation tag transcribed from the Lac promoter.

[Actually, I was supposed to build four Biobricks, but I fried the pieces for one of them ...]

What does all this gobbledygook mean ? It's actually quite simple once you hack your way through the random jargon forest that seems to be a core attribute of biology: YFP is a protein that basically glows yellow when you shine light on it; it's a pretty useful experimental thing to have because it means you can "paint" things that you're interested in with YFP and watch what they're doing by following the yellow dot, so to speak. Now, in a cell, proteins aren't only manufactured, they're also broken down, and the breakdown process is so important that the folks who discovered how it works won this year's Nobel Prize in Chemistry. The way the breakdown works is that each protein is basically tagged with an "expiration date" ie something that tells the cell how quickly to break it down; these labels are called "degradation tags". Different degradation tags lead to different rates of breakdown. The "AAV degradation tag" that is on my protein is a medium-strength tag meaning that the protein is broken down at an intermediate rate. And, finally, "promoters" are essentially on/off switches that determine whether a protein gets made or not; different promoters respond to different chemicals to turn them on or off.

So, in summary, I built three proteins that glow yellow, have a medium lifetime, and can be turned on and off by 3 different switches. Pretty simple, isn't it =) ? Currently, the folks in the lab are using a version of the protein that hangs around for a really long time, which makes some of their measurements problematic, so my medium-lifetime protein should come in handy. And even if nobody ends up using it, hey, I still had fun doing the work.

My main intentions during this rotation were to get some experience with lab work, do something that would be useful to the other folks in the lab, learn more about synthetic biology and get a feel for the lab's culture and the way they approach problems. I think I achieved all of those goals and have a strong suspicion that it's the lab I'll want to end up in long-term.
My next rotation is in Doug Lauffenburger's lab; I have no idea what I'm going to work on there but he has a pretty big lab with people working on a host of different things so I'm sure I'll be able to find something interesting.

Saturday, November 06, 2004

Operation "Shock and Awe" in the War Against Bacteria is over

... but it'll be a while before we land on an aircraft carrier and declare "Mission Accomplished". In other words, Christina doesn't have to go to the hospital every 6 hours to get pumped full of antibiotics anymore. Now we're sending in the ground troops to clear out any remaining bacterial insurgents, by having her take antibiotic tablets twice a day.

Friday, November 05, 2004

The nanoscale war rages on ...

The fight against the "wee animalcules" continues. Christina's hand is better but still not quite good enough, so she has to spend another night in the hospital. At least the food is good, she can leave the hospital in between her IV's and there's a German TV station on the MIT cable network that she can watch when she wants to look at and listen to "ze master race" ;-)

Thursday, November 04, 2004

Ah, the wonderful diversity of MIT

Today I saw a guy in shirtsleeves, in 40 degree weather, holding a pair of chopsticks in his hand like he was about to use them and singing to himself quite animatedly while walking down the street ... barefoot.

Sometimes I really wonder whether people do things like this just to feed the stereotype of the eccentric genius who is so lost in his/her mental world that simple things like putting on a pair of shoes are forgotten about. I mean, c'mon ...

Bobcat bites woman who thought it was house cat

A couple of days ago, one of our cats bit Christina, twice, and pretty deep each time. Why ? Let's just say that trying to take an indoor cat on a walk outside, in a harness, is a bad idea, especially when it's a skittish cat to begin with ... apparently he was ok until, oh horror of horrors, somebody walked by; after that, he turned into the Tazmanian Devil on a rope. I'm told it was quite an impressive sight and sound, involving unaided mid-air backflips, rolling on the ground and growling, until Christina tried to pick him up to calm him down, at which point he decided that it was a good idea to quite literally bite the hand that feeds him. Twice.

We weren't entirely sure what to do, so we did what anybody in our position would do: we googled "cat bite treatment" and, lo and behold, got about 110,000 hits in 0.33 seconds. Perusing a few of the links produced the obvious: wash the wounds, put some iodine on them, hope that it'll all go away and, if it doesn't, go see a doctor. We did all of those but, a little scared by the statistic that about 40% of all cat bites get infected, Christina went to the MIT Medical Center the next day and they gave her a prescription for an antibiotic and sent her on her way.

Today, the hand was looking even worse, so we went back to the Medical Center and happened to get a specialist in infectious diseases to look at it. He looked at it for about 10 seconds and said "Ok, you're going to need to get an antibiotic intravenously, every 6 hours, until this clears up, so you're going to have to spend the night in the hospital". Not exactly what we were expecting, but after a couple of "C'mon doc, you're kidding, right ?"-type questions, he laid it out pretty bluntly -- apparently cats have some bacteria on their teeth that tend to cause bone infection, so when they bite people in an area where bones are close to the surface [like the hand], there's a danger of developing bone infection and that's Very Bad, like losing-your-hand-type Bad. After that, we meekly asked things like "Can we at least go home and get her some clothes before she comes back ?"

So, Christina is spending the night in the hospital getting pumped full of antibiotics and I'm sitting here giving the cat the Evil Eye. He, of course, is totally unaware of this and is passed out on his back, fast asleep because, you know, he had such a rough day, what with all the sleeping and eating he did.

Here's hoping those antibiotics kick some bacterial ass ...

Wednesday, November 03, 2004

Back to the "United" States of America ?

I've heard/read some speculation that since Bush actually won the popular vote, not just the electoral college vote, Americans would become more unified because this time he actually has the people's mandate in all senses of the word.

If the heated debates I've heard today are any indication, that may not be the case. People who didn't like Bush really didn't like him, and now they're even more upset because there's four more years of Not-Very-Curious George. My favorite tidbit of overheard conversation was something I heard on the subway today:

Man 1: "Yeah, I voted for Bush"
Man 2 [friend of Man 1]: "Man, you're poor. How could you vote for Bush ? Are you retarded ?"

Then again, maybe it's just the backlash from all the disappointed voters and it'll ebb away over the next few days.

You can only have so much luck ...

... and it looks like Boston/Massachusetts used it all up in giving the Red Sox their World Series title. Maybe they should have held a bit back and given it to John Kerry who, short of a miracle, is not going to win the election.

*Sigh* 4 more years of the Dark Lord and his minions. Or, rather, the Dim Lord. On the positive side, at least that'll give us 4 more years of Bush-isms and provide comedians with lots of cannon fodder. Not exactly an equal trade but you gotta look for the silver lining, however slim it is.

Man, that's just a huge pile of dead kittens ...

Monday, November 01, 2004

A final reminder for those of you who get to vote tomorrow

Please, think of the kittens ...