Biophysics Seminar Series

This semester, in addition to Junior Lab, I am leading a one-credit biophysics seminar.  There are two biophysics graduate students enrolled.  Peter Relich is a 2nd year biophysics student, working in the Keith Lidke lab on (I think) super-resolution microscopy and hyperspectral imaging of live cells (in collaboration with the Diane Lidke lab).  Godwin Amo-Kwao is finishing his maters thesis in Physics, working on quantum mechanical calculations of amino acids to be used as a basis set for the charge-transfer (CT) force field for molecular dynamics in the Susan Atlas lab.  He is also beginning as a Ph.D. student in UNM's Nanoscience and Microsystems (NSMS) program.

So far, the course has been a lot of fun.  I like the small group as we can easily have discussions with everyone participating.  Our general plan for the course is to learn some biophysics while also learning about open science and modern tools that researchers can use in their research.  A mindmap of our initial thoughts is here: http://www.mindmeister.com/106137967/2011-phyc-500

We want to carry out the course as openly as possible, but we don't have a great way of doing that.  Especially since our meetings are face to face and we are not setup for video recording or anything like that.  But when we do have a chance to contribute openly, we are going to.  For example, when we read PLoS papers, we intend to rate them and leave comments, either as a group or individually.

For this week, we read two classic papers by Gilbert Lewis about the effects of heavy water (D2O) on living organisms.  These papers are:

• 1. Lewis, G. N. (1933). The biochemistry of water containing hydrogen isotope. Journal of the American Chemical Society, 55(8), 3503–3504. American Chemical Society. doi:10.1021/ja01335a509
• 2. Lewis, G. N. (1934). THE BIOLOGY OF HEAVY WATER. Science (New York, N.Y.), 79(2042), 151-153. doi:10.1126/science.79.2042.151

Both are easy read, fascinating, and in my opinion ground-breaking at the time.  We had a good time discussing the papers.  Much of the time we spent doing google searches for deuterium-depleted water, and wondering at the prevalence of companies selling deuterium-depleted water (DDW) as a cure for cancer and other health benefits.  I was really surprised that one company recommends that everyone should drink only DDW for two months out of every year!  Obviously there should be some fundamental research supporting this extreme recommendation.  In my own lab, we've begun DDW studies on  tobacco seeds, for the first time (that I know of) carrying out the research that Lewis proposed in the 1934 Science paper.  Our work is open notebook science and can be viewed on Anthony Salvagno's blog.  Certainly, basic research such as this is required to support any future therapies based on DDW.

In order to contribute a little bit publicly from our discussion, we used PaperCritic to leave feedback on the articles.  These entries are:

• Lewis 1934 Science paper: http://www.papercritic.com/mendeley-pub/0a6493d0-6d02-11df-afb8-0026b95d30b2
• Lewis 1933 JACS paper: http://www.papercritic.com/mendeley-pub/241ddab0-6d03-11df-936c-0026b95e484c

PaperCritic plugs into Mendeley, but has some significant bugs still.  For example, I cannot figure out how to edit the reviews after we submitted them.  So, on the second review linked above, I could not give credit to Peter and Godwin.

For next week, we are reading two items, to learn more about fascinating Archaea:

• Wikipedia article on Archaea. I am encouraging me and the two students to improve the article if we see opportunities.
• Iddo Friedberg's recent fascinating blog entry, "Why are there no (or almost no) disease-causing Archaea?"  We plan to leave a comment on his blog after our discussion.