Research

I recently submitted a series of fellowship and award applications to help fund my work over the next year. The past summer was very productive (we got a paper accepted over the winter!) and I’m now working on some new ideas.

I was captivated by a recent preprint from Prof. Allyson Sgro’s research group on short-term memory in stochastic molecular circuits, which sent me on a kick back into developmental biology. Sgro’s work is an excellent introduction to the idea of biological noise and its effects on population-level heterogeneity as well as the cascading effects it can cause on lineages of individual cells. The code included in the paper is quite elegant; I ended up modifying some of it for my own simulations.

I dug up my copy of Turing, and also started tracing back citations on the early thinking on developmental biology. Unfortunately, there’s a lot of eugenecists there; fortunately, Turing remains evergreen.

Since my class schedule has shifted from last semester, I’m finally able to attend all of the seminars that I want: biochemistry, chemical biology, and even a few organic chemistry seminars! I’m trying to ask a lot of questions and pick up names in the field. All of the visiting speakers are so COOL.

Experiments are going well. Data is flowing. The lab has become my native environment. I think I spend more time there than at home.

Classes

Every semester I say to myself: “I think this will be a little easier than last semester.” This is a lie. I keep finding new and interesting courses to take that are just beyond my qualifications.

• Stochastic Dynamical Systems and Data-Driven Modeling. The most difficult math course I’ve taken to date. Most of my background is solidly theory: I can tell you a solution exists to a differential equation, but I can’t write it down. Now I can write it down, and I also know what a Schur complement is. This course is a great deal of fun, and it may also be the hardest I’ve ever worked in a class.
• Modern Algebra. Oh boy group theory! This one has been lots of fun.
• Biological Interactions. An extended journal club. I enjoy the unique structure of the course and the emphasis on reading papers. Most of the learning happens in small group discussions, where we try to come up with experiments to extend the ideas laid out in the literature or connect the things that we’ve learned across studies.
• Biochemistry II. Information transfer and the central dogma. Our professor has placed a limit on the number of questions my friends and I can ask per class. I choose to see this as a compliment.
• Machine Learning Techniques for Chemistry. This has been a great deal of fun for me, since it grounds some of the abstract algorithms in chemical applications. A gentle introduction to coding, scikit-learn, and the ideas behind different model architectures. I have a couple of ideas for this final project…
• Synthetic Biology Seminar. This has been excellent training to get me to read papers outside of my domain and ask questions.

Computer

Oh boy did I do some stuff with my computer. I’ve been leaning very heavily on uv to make some scripts to share with the rest of my lab, as well as manage all of the virtual environments. It handles this so beautifully that I don’t now how I spent so many years without it.

Also trying to pick up a better understanding of numpy and pytorch.

Reading

My favorite fiction from the past couple of months has been Ursula K. Le Guin’s The Left Hand of Darkness, which was an excellent study in cultural assumptions of gender. Every time I read her work my only regret is not having read it sooner. I also greatly enjoyed Mickey7—hoping to watch the movie at some point.

More recently, I started trying to fulfill the spirit of my liberal arts education by learning more economics and history. My eclectic choices have previously allowed me to skate by without taking such courses, but after reading Thomas Piketty’s Capital in the Twenty-First Century and starting on Sven Beckert’s Capitalism: A Global History, I find myself drawn in by these things. I think turning to history is also my way of trying to understand everything happening right now (hence The Dual State).