Drawing Space II (2)

I am out of my math element here. I’m in the BU bioinformatics REU, and the lab I was placed in is a biochemistry group.  My desk is literally in the middle of a chem wet lab, which is somewhat of an inconvenience as I like to take off my shoes and drink coffee when I program or do math. But, of course, that’s against lab safety rules! :P

I like the work that I’m doing, which is primarily writing scripts for a protein sequence clustering analysis program. I don’t understand enough biology or chemistry to tell you what type of proteins I’m putting through my programs or why we’re clustering them in these ways: to me they’re just numbers. I like it better that way, and see my programs as puzzles in which I need to trick the computer into outputting the groups of numbers that I want.

Being in the chem lab is kind of cool, if somewhat uncomfortable. The grad students around me are doing things with chemicals that I will never do and are far outside my range of knowledge. I’ve learned what a glovebox is, and have been able to see and appreciate the way chem experiments are very time, location, and temperature sensitive.

On Friday I took a break and walked across the street to the Mathematics + Computer Science building. Whenever I am working for a long time, I tend to take short mental breaks where I just sort of wander the halls and stare at the posters.

Outside my chem lab, I see symposium advertisements for “21st Century Genetics: Genes at Work” and research posters on “Reductive Activation and Catalytic Insights in Bacterial c Peroxidases.” In the math department, I saw their posters for SIAM and BSM, as well as a course descriptions list that I fully understand. It was very comforting. Home-y.

I think I’m going through a culture shock and homesickness of sorts up here in the chem department!

Bio_Info REU Day 1


Monday I found myself in a conference room on the tenth floor of the Life Sciences building, listening to my post-doc advisor explain his most recent project. Hundreds of issues of Nature and Science covered the bookshelves, and a wall of windows overlooked the Charles, Harvard, MIT, and the “infamous CITGO sign.”


10th Floor LSEB

My post-doc said something that I was acutely aware was meant to be a joke. The biology reference went over my head, but I pretended to laugh anyway to ease the awkward.

I took notes while he was talking to me, but most of them consisted of things I was too embarrassed to ask about:

  • What does SSN stand for?
    sequence similarity network, not social security number
  • What’s the workflow?
    the order in which you run big programs? sort of?
  • What does “PI” stand for?
    principle investigator, aka the head of the lab. not 3.14159

I only have a NYS 10th-grade knowledge of biology. Yet this is the second time I’ve decided for some reason to join a bioinformatics research group.

For both projects, the first day has been the same: someone with a PhD in a biology-related field explains to me what they are working on while I try to keep my brain from exploding. It always makes me wonder why I’m doing what I’m doing.

Last fall, on the first day I met the Hungarian neuroscientists, for example, I spent the entire 2-hour research meeting thinking they were studying this phenomenon called SHARK wave ripples instead of SHARP wave ripples. I thought that was cute, and totally saw the resemblance between the SWR pattern and a shark fin in the ocean:

Drawing Space II (1)

(to be fair, their Hungarian accent was really thick)
These kinds of experiences make me worry that I don’t belong here, that I’m not going to be able to help with the project, that I will be annoyingly slow– IMPOSTOR syndrome.
I try to remember that this is an REU and the point of it is for me to learn. I’ve already been handed a textbook and five papers to read through! That should be a start!