Thursday, February 17, 2005

State of the academic union

3 weeks into the semester and the overall situation is ... manageable. I haven't been totally overwhelmed with work due to my 4 classes yet, but it's still early days. One class in particular may yet prove to be my undoing, more on that below.

Individual situation reports:

My cell biology class is great, primarily because the professor, Frank Solomon, is a really funny man. Among my favorite quotes are "[This molecule] is like happiness -- fleeting", "Here's a little shout-out to all the neurobiologists in the room" and "I haven't won a Nobel prize yet, but that's only because I'm tied for second in the department".

I like my molecular biology class -- it's neat to learn about all the "mechanistic" details of how DNA gets replicated, repaired etc. It's really reinforcing what an amazing machinery it is that keeps us all alive. My favorite analogy so far is this: DNA polymerase is the molecule that synthesizes [ie makes] DNA, by basically matching 4 different types of pegs with 4 different holes -- each peg only fits properly into one hole, and if you fit a peg into the wrong hole, you've messed up the DNA, a bad thing. Now, imagine that your DNA is a pipe that's 1 meter thick. Then, the DNA polymerase molecule in the bacterium E.coli is
- about the size of a FedEx truck
- moves at about 375 miles an hour
- puts around 1000 pegs into a hole each second
only makes a mistake [ie puts the peg into the wrong hole] once every 40 minutes

Now that's a mighty machine !

There was also a funny bit today when we were talking about a protein called "Dam methylase"; the professor kept saying "the Dam protein" and I, being juvenile, couldn't help snickering each time she said it. Didn't see anybody else laughing, though. Nothing funny about molecular biology, jawohl !

The "Fundamentals of Computational and Systems Biology" class is OK so far, not great and not bad. My favorite thing about it is that the assignments involve doing a bit of programming, in Python, so I get to do some programming and learn a new language, which is fun. The algorithms we're covering in the class are sort of interesting and good to know as a basis, but not something I can really get excited about.

"Functional Genomics" is the dragon that may yet rise up and slay me, because it relies heavily on statistics and probability, two things at which I've always sucked. Maybe that's because I never took a college-level class in it, but even in high school questions like "If you have 5 red balls, 4 black balls and 5 green balls in a bag and you reach in and take out 3 balls, what are the chances of getting 2 red balls and 1 green ball ?" always gave me an instant headache and the desire to go do some straightforward integration or differentiation.

In this case, the situation is made worse by the fact that one of the lecturers is, ahem, confusing, shall we say. He has a tendency to write formulas containing a bunch of symbols [each with at least one subscript or superscript] on the board, not really define what the symbols are, and then start messing around with the formula, adding a subscript here, putting a summation sign there, taking the log of all of it, while he's giving an explanation that I can't follow. The end result is that, as the German phrase goes, "Ich verstehe nur Bahnhof". The English translation of this is "The only thing I understand is 'train station'", which doesn't make any sense in English and, in an indirect, recursive kind of way, is exactly my point.

The saving grace is that his lecture notes are actually very good and the TA has been very responsive to my expressions of bewilderment, so I may make it through the class yet.

Ok, time to go flesh out an implementation of an Expectation Maximization algorithm which finds promoter motifs in DNA based on initial motif matrices and a given background distribution. [No, I'm actually not kidding. That's a question on my latest Functional Genomics problem set. Can you hear that train whistle ? I can ...]


Anonymous Bill Tozier said...

Regarding DNA polymerase: add to the list "In an effectively solid environment filled with other molecules." Viz: cytoplasm.

Go look at David Goodsell's drawings of the inside of a cell. I've always told everybody in your position (bossy ain't I?) to go and get Machinery of Life and photocopy a huge big blowup of Goodsell's image of bacterial cytoplasm, and stick it on the wall.

4:32 PM  

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