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.


Dad can affect baby’s health

I saw this blog post referencing an article I wrote for the Raleigh News & Observer.

 I really just wanted to make 3 comments on it:

1) The blog post really goes where I never ever expected it to go, which is why I had to share it.

2) The author uses my first name. It appears only women are prone to this infantilizing treatment. Yay.

3) It would have been really cool to have made this one research paper part of a longer story explaining epigenetics. I think a good percentage of newspaper readers (sadly not 100…) get genetics, and epigenetics would blow many of their socks off. If they are above a certain age (not very old!) they certainly wouldn’t have learned it in high school and perhaps not even in college.

Writing the Great American….Textbook or Nonfiction book

I am extremely excited about the possibility of one day writing a book, so this post struck a chord, especially since it’s specific to academics.

 I’m saddened by the “wait for tenure” advice because that seems so far away right now. At the same time, I certainly wasn’t expecting to have the patience and experience to take on anything that involved yet, or even in the next 10 years.

 I suppose it’s good to know I’m on the right track: I’m writing articles and starting to write book reviews now, and hopefully will be ready do a longer feature in a year or so.

It’s daunting how many things are going to happen in the next ten-ish years, but reassuring that they are happening at a pace I can handle: The real job, the real place to live, the seeds of a book, perhaps the seeds of a family(!), and (hopefully) tenure.

So when am I going to take my backpacking tour and get my mohawk? I don’t want to ever call myself a grownup, even though I have mostly acted like one since I was 7.

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.