February 2013 – Boundaries in Biophysics

Nature Turning Point’s interview with Carl Boettiger

CSGF alumnus Carl Boettiger is featured in a recent edition of Nature: Turning Point. Much of the interview focuses on Carl’s open research notebook, a bold experiment in sharing research as it is being done, before it’s actually “research product.” Kudos.

“Were you afraid of getting scooped?

That concern is there, but I haven’t experienced any scoops. I think it is an overrated fear, especially when compared with the risk of being unknown in your field. My notebook has helped me to extend my reach in ecology and computing. People were aware of me before I had published — which led, for example, to invitations to review papers. If anything, I was reluctant to put things up in case they contained mistakes. Every mistake that I made during my PhD is in there. But if I am trying to resolve an error, I can easily show others all the work I have done and the steps I have taken, and ask them for advice.”

Hot off the presses: my new review article on electrostatic models for proteins

My second article in the open-access journal Computational Science and Discovery has been published.

The article, a rather sizable review of implicit-solvent models for proteins and other molecules, is here; the odd title is a punning nod to one of my favorite bands, Rancid (see here for the reference).

I had always wanted to write a different kind of review article, one which provides more philosophy and an integrated view of progress; the process of writing this one revealed just how hard that is. For one thing, many reviews are written to meet deadlines. Academics tend to be fairly busy types (“If it weren’t for the last minute,” quipped one mentor, “I wouldn’t have any minutes at all.”) so that many reviews end up being annotated bibliographies: “The group of X has been looking at Y [1, 2], which is new.”

My thanks to the numerous individuals who slogged their way through early drafts to provide really helpful comments and suggestions (among others: Geoff Oxberry, Matt Knepley, Ahmed Ismail, Christopher Rinderspacher, and Matt Reuter). I am especially indebted to Nathan Baker and Dirk Gillespie for encouraging me to get my thoughts together for a review article. Your comments and criticisms are welcome as well!

Onward.

Talk about your two cultures!

Georgia Tech’s Prof. Lipton has posted an amazing story that you’ll enjoy.

It’s about Frank Ryan, the NFL quarterback with a PhD in math, who was a professor at Case Western Reserve University while he was still a star in the NFL.

Prof. Lipton notes that today no NFL team would sign a player with such a significant outside commitment, and of course he’s right. On the flip side: how do faculty hiring committees and promotion committees view outside activity?

Also, beyond the epic awesomeness, Prof. Lipton makes an interesting point about his former teacher’s approach to teaching mathematics.

Thanks to Matt Knepley for the link.

P.S. Yes, I know these aren’t the two cultures C. P. Snow discussed. That’s the joke.

Lanczos and Einstein’s correspondence

Lanczos once wrote to Einstein about his work on iterative methods,

“The reason I am interested very much in dealing with methods of approximation is not the practical applicability of the solution but rather the fact that a very ‘economical’ solution is possible only if it is very ‘adequate’ too. To get a solution in a few steps means nearly always that one has found a method which is consistent with the intrinsic nature of the problem.”

Einstein replied,

“Your remark concerning the significance of the adapted approximation methods is very enlightening, and I am convinced that it represents not merely a practical method but also is a promising mathematical viewpoint.”

[Via C. Brezinski , L. Wuytack, “Numerical Analysis in the 20th Century,” the Introduction to the volume “Numerical Analysis: Historical Developments in the 20th century” (eds. Brezinski and Wuytack, North-Holland, 2001)]