I’m back from a long hiatus!

It turns out applying and interviewing to faculty jobs and then starting one is a busy time. I’ve just begun my junior sabbatical leave, so now have a bit of bandwidth to write again. It was always my hope to write and do my day job at the same time.

That was a silly, silly idea.

But, I’m hopeful now that I’ve figured things out at work, I will be able to keep this up even once sabbatical is done.

As a fair warning, instead of having different spaces for different things, just about everything is going here. Research paper discussions, science education, personal stuff like trips and fitness, etc…

I will do my best to not embarrass myself and I will also use tags so you can find the content you want.

FYI, most personal/fitness stuff, and anything pre-2017 will be password-protected. If you know me, and want in on these posts, I am happy to send you the password.

At some point I’ll also make a meta-post of with links to all my writing from other sites, news outlets, etc. (i.e. the stuff that had an editor and I sometimes was paid for.)

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Protein Folding

I’m currently in the process of going through a monstrous stack of periodicals I’ve accumulated, including the magazine Physics Today, which comes with my APS membership.

This article by Ashley Smart is simply a research summary on experiments on proteins.

But Smart evoked a lot of thoughts about proteins. We need them to be folded correctly to work, but how are they folded? How is this the minimum energy state.

Smart’s description of various denatured (unfolded) proteins reminded me a lot of the language used in the glass/jamming community. A fried egg consists of proteins denatured by heat. A similar transition happens for
“glassy” systems: raise the temperature and the material will flow.

Mechanical stress can cause also cause the protein in egg white to denature, resulting in a foamy, stiff, meringue. In jammed systems, like mayonnaise, mechanical stress (i.e. using a butter knife) causes the material to unjam (i.e. deform and spread on the sandwich).

The third variable discussed in the jamming community is volume fraction, which I won’t delve into here. The third variable for the egg example is acidity, mixing egg whites with lime juice will also cause the proteins to denature. Completely different, can’t win ’em all.

What also drew me into this simple piece was the description of the experiments. (Smart does a commendable job of trying to explain the math in words.) There are two processes that contribute to the overall signal the researchers measure, only one of which relates to protein folding. But if you change the temperature, each process responds on a vastly different timescale.Taking measurements at the right frequency and using a trick of derivatives, they can isolate the process of interest. An experiment like this would be a great lab in a biophysics class.

Good Science Explaining =/= Good Science Writing

“The general public is pretty intimidated by science since it sounds like homework. It’s not fun. The biggest reason science isn’t accessible is that it’s boring. Not inherently boring, but people want stories. We’re a storytelling species. This is a book about a family, losing a mother, scientists doing research. There are characters. It takes work to read science, but when there’s a story you don’t care. It’s like taking medicine with something that tastes good. Storytelling shows people why it’s relevant to them—everyone out there has benefited from the research done with HeLa cells.”

This is the mantra I repeat to myself when I’m teaching, and have been working on getting better at this in technical and popular science writing as well. The good explanation is not good enough to excite the reader to read, unless the reader already so deep down the rabbit hole of the discipline he or she can appreciate it.