School!

I’m back to taking a lot of classes about different things. I finally got in the paperwork to declare my double major in math and biochem (tacking on the math), so I can officially introduce myself as the most fun combination of fields. I’m taking a somewhat intimidating courseload right now, so I expect this semester will be more of a test than last year.

• Applied dynamical systems, chaos, and modeling. I can never remember the name of this class - I keep on calling it something either “chaos theory” or “dynamical systems” or “nonlinear dynamics.” Only a week in and this may be my favorite class this semester: phase portraits and linear stability analysis feel magical compared to the solution methods I learned last semester for systems of differential equations.

• Organic chemistry. I’ve been excited for this since before entering high school, since I’ll finally be able to understand a lot of the reactions that I see in biochemistry and chemical biology. Also, chemistry is just plain fun—it’s the science of matter! I got a taste of organic chemistry in high school, but it was only as a month-long primer.

• Electricity and magnetism. This feels like a continuation of the rather intense physics crash course that I received as part of my quantum mechanics class last fall. I have this distinct memory of blinking and then seeing some surface integrals appear on the board in QM, but now we’re actually using them. I’m thankful that I had a class on linear algebra before taking physics, since being able to think of things as vectors and using vector techniques has been super helpful in these first few assignments.

• Ecology, evolution, and genetics. We get to go to a prairie and survey things! One of the instructors handed me some plants (mountain mint and wild quinine) and told me to eat them (I did). I don’t think I would have been as excited for ecology if I hadn’t gotten a taste of it during my entomology class. Evolution will be a lot of fun too.

Cleaning out my literature bin

I have this bad habit of saving up lots and lots of papers that I never end up reading. I took a few weeks at the end of the summer to skim some of the best ones and discard the rest—I can always get them again later. I was pleasantly surprised by the zotero 7 update (Better BibTex is still blessedly functional in the beta), so reading papers electronically has been less of a chore.

A few favorites:

• Gao Y., Cournoyer J., De B., Wallace C., Ulanov A., La Frano M., Mehta A. Nature Communications 2024. From my mentor. The researchers engineer a cyanobacteria into a chloroplast-like endosymbiont, then introduce it into yeast. Super cool idea with a lot of neat applications in bioreactors, I think.

• Hinnen A., Hicks J., Fink G. Proceeds of the National Academy of Sciences 1978.. I started down this rabbit hole during the summer when I tried to figure out why we use salmon sperm DNA to transform yeast. I kept on tracing it further and further back. This is as far as I got, but I’m sure there’s even more.

• Mengiste, A. A.; McDonald, J. L.; Nguyen Tran, M. T.; Plank, A. V.; Wilson, R. H.; Butty, V. L.; Shoulders, M. D. ACS Synthetic Biology 2024. This one I found through trawling my selection of RSS feeds. It mentions some work done by the Neugebauer lab, which a friend of mine works in, and I found the design of the MutaT7 chimeras really cool.

I also set up a folder in my RSS reader for keeping track of scientific publications. I like this much more than emails or checking websites because I can do it on the bus when I would be reading a book or staring at my phone anyway. Not every paper is one that interests me, but every now and again I find some really neat stuff!

Incredibly responsible uses of time

Rest assured I was not simply productive this summer, I was also incredibly creative in finding productive-sounding ways to procrastinate on the important stuff. So in between troubleshooting this tricky python pipeline, I also learned enough lua to write configuration files for neovim and wezterm. I’m now using neovim as my default editor and do most of my coding in its text buffers.

Since I use different computers at work and at home (but still tinker with the work code at home), I learned how to set up some file paths in ways that are compatible across Windows and MacOS. That was a pain, but now I have some semblance of cross-OS compatibility to my code!

Reading

I’m currently working through Babel by R. F. Kuang. I’m loving the etymologies and footnotes, which could be compiled into a primer in their own right. Just as compelling as the first Poppy War novel, though I appreciate that thus far there has been less incredible violence.

I also read Moonbound by Robin Sloan. I loved this—Sloan’s writing feels like a cross between Terry Pratchett and Douglas Adams. I want to read more of this.

Watching

My roommate and I are watching Erased, only six years after one of my friends recommended it to me. The animation is gorgeous, and so far I’ve been really engaged with the story. The time travel plot feels much less contrived than I expected.

Listening

I discovered [Dirt Poor Robins][DPR] at the end of last semester and have been working through their discography for the past few months. Personal favorites include Babylon, Enchanté, and To the Heights. I appreciate that each album that they put out feels very different (though no less weird) from the one before.