Several times so far I’ve taught a graduate course on biophysics. Last term I taught it again, but with a twist: it was a combined graduate and undergraduate course. There were two motivations for this. First, biophysics is unfamiliar enough to physics graduate students that upper-division undergraduates aren’t at any significant disadvantage. In fact, I’ve had a few undergraduates take the graduate course in the past, successfully. Second, the undergrad/graduate combination can boost enrollment numbers enough to offer the course every year, which is otherwise a bit of a struggle. We’re a medium-sized physics department (The University of Oregon) with about 30 faculty, about 15 graduate students per incoming class, and about 30 undergraduate majors graduating every year. (Yes, that last number is tiny.) I wrote a blog post last year as a trailer for this class; here’s a post-class recap.
The class had 9 students, 3 undergraduates and 6 gradate students — a healthy number. Notably, some of the grad students were from programs other than physics, as has been the case in the past as well: Bioengineering (new here at UO), the Optics Master’s program, and Chemistry. The variety of students is wonderful, adding fascinating perspectives and expertise. Nine is a healthy number, too, for enrollment accounting.
Some sort of differentiation of assignments between the undergraduate and graduate levels is required by the university, so I spared the undergraduates from having to do one or two of each week’s homework problems, and their final project tasks were smaller than the graduate students’.
The course as a whole was a success, as were past versions. I’ll briefly describe a few pieces of it, but the more general lesson, not confined to biophysics, is the one given above: that combined undergraduate / graduate courses can be useful for both students and departments. This isn’t news, of course, but I hadn’t thought much about it in the past.
Topics covered and not covered
The syllabus is here. The major flaw of the course is that it’s impossible to survey biological physics in one 10 week quarter. I’ve always thought that this should be at least a two-term (20 week) course — particle physics here gets three terms! — to do the subject justice and to serve students in physics and related fields.
The topics we cover in the course are:
- Introduction; Physics, statistics, and sight. What are the fundamental limits on vision, and how close does biology come to reaching them? (A brief look.)
- Components of biological systems. What are the components of biological systems? What are the length, time, and energy scales that we’ll care about? How can we organize a large list of “parts?”
- Probability and heredity (a quick look). We’ll review concepts in probability and statistics. We’ll discuss a classic example of how a quantitative understanding of probability revealed how inheritance and mutation are related.
- Random Walks. We can make sense of a remarkable array of biophysical processes, from the diffusion of molecules to the swimming strategies of bacteria to the conformations of biomolecules, by understanding the properties of random walks.
- Life at Low Reynolds Number. We’ll figure out why bacteria swim, and why they don’t swim like whales.
- Entropy, Energy, and Electrostatics. We’ll see how entropy governs electrostatics in water, the melting of DNA, phase transitions in membranes, and more.
- Mechanics in the Cell. We’ll look more at the mechanical properties of DNA, membranes, and other cellular components, and also learn how we can measure them.
- Circuits in the Cell. Cells sense their environment and perform computations using data they collect. How can cells build switches, memory elements, and oscillators? What physical principles govern these circuits?
- Cool things everyone should be aware of. We live in an age in which we can shine a laser at neurons in a live animal to stimulate it, paste genes into any organism we wish, and read the genetic information in a single cell. It would be tragic to be ignorant of these almost magical things, and they contain nice physics as well!
The Mechanics section is usually brief, but this time it was almost nonexstent — more a statement that one can characterize DNA and membrane mechanical properties than an exploration of how one does this. (I don’t know why, but our progress was a bit slower than usual this term.)
Dynamical systems are barely glimpsed in the “Circuits in the Cell” section, and these deserve many weeks, perhaps an entire term. I’ve daydreamed about restructuring the whole course around Phil Nelson’s excellent Physical Models of Living Systems book. Relatedly, population dynamics and evolution — popular among biophysicists, important, and fascinating — falls into this horribly neglected category.
The Cool Things section is always a lot of fun. Even 10 years ago, I was stunned at how few physicists — not just students, but faculty — were unaware of amazing advances like DNA sequencing and genome editing (CRISPR especially), feats that are as remarkable and significant as nuclear fission; I continue to be stunned. On the plus side, it’s exciting to watch students learn about the existence of these “cool things.” And, as I’ve written about extensively, they’re inherently biophysical, though they aren’t commonly thought of as such. We can read and write genomes because we take seriously the physical characteristics of DNA.
Course components
The class sessions consisted of lecture and discussions, into which I mixed a lot of contemporary research papers. I also included a bit of history, sometimes by asking students to guess when various insights were discovered or figured out.
There were weekly homework assignments that often included computational exercises, for example simulating bacterial motion and assessing algorithms to infer its parameters. Students found these quite challenging; perhaps they were too challenging, but the skills they helped develop were arguably the most general and transferrable of the course, and they often led to conclusions and discussions that were uniformly considered interesting.
Students also completed a final project, exploring some biophysical topic based on papers I suggested. The list and details about the assignment are here. It’s challenging to research a specific unfamiliar subject when the broader subject of biophysics is unfamiliar and the term is only 10 weeks long, but the students did a remarkably good job of this. The end-of-term presentations were lively and informative.
I enjoyed the class tremendously, and students seemed to as well. Class sessions were a lot of fun. I’m glad I was able to teach Introduction to Biological Physics last term. We’ll see what the future brings!
Today’s illustration
Smith Rock, again. I like it better than my last attempt.
— Raghuveer Parthasarathy. January 26, 2024
The Eighteenth Elephant 