The third in a series of biophysical questions (one, two). Finding food is an essential activity for any organism. We and many other animals interpret sights, sounds, and smells to make decisions about where to go or what to do to get things to eat. But what about a bacterium, a single-celled organism just a … Continue reading Can a brainless bacterium navigate? (What is biophysics? #3)
This past term (Fall 2021) I taught a course on image analysis. It was a new course — not just new for me but completely new, though it grew out of an informal image analysis class I’ve taught “off the books” before and have posted about. The class went well, though I severely underestimated how … Continue reading Image Analysis: Reflections on a New Course
Once again, my favorites of the books I read during the past year, plus some that weren’t favorites but worth noting nonetheless. (Previous posts: 2020, 2019, 2018, 2017, 2016, and 2015.) The Covid-19 pandemic continues, though halfway through 2021 we were at least allowed to browse the public library in person again, which the kids … Continue reading The Year in Books, 2021
The second in a series of biophysical questions. Proteins are molecules. As is the case for every molecule, the constituent atoms and inter-atomic bonds determine the overall shape. In general, a small or stiff molecule has a well-defined form. In contrast, long, chain-like molecules as found in plastics or the gel-formers of the last post … Continue reading What’s the shape of a protein? (What is biophysics? #2)
An introduction to the series: It’s easy to write that biophysics is the intersection of biology and physics, but this is a minimal and cryptic description. We could elaborate, and describe biophysics as the study of how living things use physical forces to shape themselves, how we can harness physical processes for technological ends, and … Continue reading How can you push DNA through Jello? (What is biophysics? #1)
A terrible question to ask in science is unfortunately quite common: Does something affect something else? It seems innocuous enough — after all, one might want to know whether exposure to sunlight affects one’s risk of skin cancer, or whether the location of the moons of Jupiter affects the stock market. The answer, however, is … Continue reading Pushed around by stars
Our microbial ecology journal club, in addition to being fun and educational, is a limitless source of data presentation examples both wonderful and terrible. Here’s a recent example that drives me up the wall. It’s from a study [1] on correlations between pre-term births and various chemicals that may or may not be associated with … Continue reading When Should You Make a Plot of p-values? Never.
About a recent paper from my lab: B. H. Schlomann and R. Parthasarathy, “Gut bacterial aggregates as living gels,” eLife, 10: e71105 (2021). DOI: 10.7554/eLife.71105. What do gut bacterial colonies look like? My group has been exploring this question for years, and ever since our first forays peering inside larval zebrafish it has been evident … Continue reading Living Gels
Before my memories grow even dimmer I should write down some thoughts about the class I taught Spring term: The Physics of Solar and Renewable Energies. Like its companion course, The Physics of Energy and the Environment, which I taught the quarter before and wrote about here, it’s a course for non-science-major undergraduates at the … Continue reading Course Recap: Physics of Solar and Renewable Energies, Spring 2021
When I graduated from the University of California at Berkeley in 1997, non-California-residents made up about 10% of the undergraduate population [1]; the fraction now is 25% [2]. Here at the University of Oregon (UO), also a public university, out-of-state undergraduates are 44% of the student body. Why have these numbers increased so much at … Continue reading Graphs about out-of-state college students and money
The Eighteenth Elephant 