Monday, November 30, 2015

What I Learned from Becoming A "Biologist"

Not what I do all day.
For those of you wondering what I'm doing this year, I'm a biologist now. By this I mean I now work in a Systems Biology group next to people who wear lab coats*. One time my officemate dressed me up in a lab coat. (See photo on left.) While I will follow up soon with a technical post, this post is about what I'm learning from being in an environment where I am not expected to be an expert.

In between my finishing my PhD in Computer Science and starting an Assistant Professor position, I negotiated a gap year. I had originally planned to spend the year visiting colleagues in Europe, but my PhD advisor convinced me to consider switching something other than my continent. "What about those applications of programming languages to biology you're always talking about?" he asked. For years, I had been fascinated with the emerging field of executable biology, where people use programs to model biological systems operationally (as opposed to denotationally using systems of equations). Now I finally had the chance to see what work I could contribute to the area.

So here I am, a member of the Fontana Lab. I had found Walter Fontana by asking a colleague for a list of all biologists in the world interested in executable biology. Prepared to relocate myself across the world for the love of science, I ended up moving my office less than six miles---but to a completely new environment. My former colleagues got excited about making it easier to prove software correct and build software that runs fast. My new colleagues are primarily interested in understanding biological mechanisms that underlie diseases such as cancer. While the work in understanding these biological mechanisms often looks like work in building better software--especially for me--the words my new colleagues use and the ways they approach problems are markedly different.

Here are some life facts that I forgot during my PhD that I am learning again:
  1. There is no shame in asking naive questions. When I first started working in the Fontana Lab, I was telling some molecular biologist friends about the goals of the lab. They asked a few questions and quickly reached the limits of my knowledge. "Maybe you should talk to us again once you've read Wikipedia," they teased. Given where I started, I have no pretensions. I show up to meetings and am not embarrassed to ask about anything from the premise of the work to the meaning of specific symbols. My questions occasionally lead to interesting discussions, thus motivating me to continue asking questions. This is a refreshing change from the end of my PhD, when I felt that there were many questions too embarrassing to ask as a supposed expert. I am no longer afraid!
  2. Nomenclature matters. My first few weeks, I furiously wrote down all words that were said in meetings, thinking to myself "OHMYGOD WILL IT BE LIKE THIS ALL YEAR" and then looking up all the words on Wikipedia for hours. One time I made a sample program for a biologist and he told me he had no clue what was going on. (The biologists out there might find this amusing: I called MEK a "site," Serine a "protein," and S222 a "kinase.") With his help, I renamed the data types with the correct identifiers and then the program made perfect sense. The other day, I was telling a couple of former groupmates about my current work when one of them said, "How do you know all of these words?" In Computer Science, I had been against using technical words when simpler ones were sufficient for explaining the concepts at hand. With biology, I have been forced to use technical words because there is simply too much complexity. From being forced to use nomenclature, I have learned that nomenclature 1) is efficient for communication, 2) builds trust by showing people you are one of them, and 3) is intimidating to people who don't know it. I now accept--and even embrace--the importance of nomenclature.
  3. Learning new things is energizing! When I started learning about the biological modelling space, I realized how easy it is to learn new things if I know nothing about a field. This is in contrast to the end of my PhD, when, saturated in the knowledge of my field, it felt very hard to learn anything that would rock my world. Now I'm excited to learn about even parts of my field that I didn't previously think interested me, for instance hybrid systems and stochastic model checking. It is so reinvigorating to learn at such a fast pace that I'm going to make a policy to continually learn new things. In fact, this learning experience has also motivated me to start learning French again. (I'm also in the middle of a French immersion experience due to how many French collaborators I now have.)
In short, this biological immersion experience provides quite a nice reset. Understanding the biological world is helping me feel more empowered to work within Computer Science as well as outside of it. I look forward to seeing what the remainder of the year will bring!

* Fear not: this is only for the year! I am not planning to abandon security and privacy. I describe my future research agenda here.

4 comments:

ashwani pandey said...

You have been learning great things, and your post, as always, inspires me to continue my studies in computer science with full interest, and just be in awe of the breadth and depth of this field.

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