Monday, February 8, 2010

Courses for this semester

This semester's coursework has two themes: "Let's Read And Discuss Primary Literature", and "Time To Stop Abstracting Away The Physical Nature Of Biology". Both of my required bioengineering core classes are about cells, molecules, and tissues from a mechanical engineer's perspective. All three of my electives are literature-discussion classes on various topics.

  • 20.310 Molecular, Cellular, and Tissue Biomechanics - think introductory mechanics, only all the examples are biological things instead of, you know, steel beams or something. Up till now, I've been accustomed to thinking of DNA as a string of digital (AGCT) information, or maybe as a helical molecule; now it's time to think of DNA as a charged elastic rod, or a randomly-walking polymer. How much force can a motor protein exert to pull a vesicle where it's going? What happens when you push and pull on the cytoskeleton? What's the effect of pressure on cells? How do bones reshape themselves in response to forces?

  • 20.330 Fields, Forces, and Flows in Biological Systems - fluids and E&M, only again all the examples are biological things. How do things like diffusion and electrophoresis work? How can you model the cell membrane as an RC circuit? What's the best shape / flow pattern for this sample chamber so that the most protein binds to the sensor on one side?

  • 20.385 Advanced Topics in Synthetic Biology - this is paired with a freshman design/seminar course, 20.20, which I took two years ago and which rocked my world so hard. It's a great introduction to synthetic biology. The frosh get to do design projects, and because it's surprisingly hard to do this when you've only had introductory biology, the upperclassmen mentor the frosh teams. And when we're not busy mentoring, we have synthetic biology journal club. I'll be presenting a couple of papers and I'm super pumped.

  • 7.25 Biological Regulatory Mechanisms - this just sounds fascinating. All the different ways gene expression or protein action can be controlled. Apart from being cool, this is also highly relevant for synthetic biology. Even apart from that, I'm excited about the lectures. This class involves picking apart the experimental logic of papers in a more rigorous way than I've ever had before, which I'm sure will be good for me as well as being fun. We're focusing on demonstrating results and excluding alternative explanations to an extent that seems to be missing in the modern age of "let's generate a zillion data points and then sift through them". Plus, it's a chance to pick the brains of some aged, sage professors. All in all, it really reminds me of ((my interpretation of) what Raffi said about) learning Talmud.

  • 7.346 RNAi: A Revolution in Biology and Therapeutics - yet another paper reading class. I know nothing at all about RNA interference, but it's extremely important both theoretically and (potentially) medically. I'm also interested in using it to make synthetic-biological parts that don't crosstalk as much as protein-based parts do; we'll see if that's feasible.

I plan to blog a lot more about the papers I read in these classes. It probably won't be a full Journal Club post for every paper because I'll be reading about 6-8 papers a week, but I'll at least try to summarize them. (This is partly for your benefit and partly for mine -- I expect that writing paper summaries for the blog will help me read and understand the papers better.) But I will do full Journal Club posts for the papers that I find most interesting, and definitely for the ones I present. I might also write about interesting things that happen in the other two classes.

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