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.

Open Notebook Science @ UNM Physics, Round 3 -- If you have technology for us to try, let us know

2009 fall semester has started at UNM and I'm teaching Junior Lab (Physics 307L) for my 3rd and "final" time^*. I've described in an earlier post the open science aspects of this modern physics undergraduate lab course. In a nutshell, it's a typical modern physics lab course with an important twist in that we operate completely using open notebook science (ONS). I still believe (but don't have proof) that these students are at an excellent stage in their careers to learn skills and habits in ONS. We've been through about a week of the course, and already I can see that we again have a great batch of talented students! I wish I could fast forward a decade to see what they're going to be achieving in the future. Right now, though, you can see their mug shots on our course people page on OpenWetWare.

The thing that inspired me to dust off this blog is the realization that even though we've already started the semester, there's no reason we can't continue trying new things throughout the semester. So, if you're aware of new (or old) technology that you think would be good for ONS, I think we have several students who would be interested in testing it out in a real ONS atmosphere. If you do, please post a message here, or on the friendfeed thread. As noted earlier, OpenWetWare is the foundation for our ONS. But we've started to include other tools as well, many of them integrated into OWW thanks to Bill Flanagan's hard work. One big change this year is that I think students are likely to use Google Docs as a way of recording spreadsheet data. Tables in WikiMedia are just too annoying. And now, Google Docs are easily embedded in OWW pages. You can see an example of an embedded spreadsheet in Tom Mahony and Ryan Long's open notebook.

There's another thing that I'm excited about that may make ONS much easier for us. Currently, the standard method for uploading photos or other documents to OWW is inconvenient. It can take a good minute to snap a photo of your experimental setup and then go through a convoluted process of emailing it to yourself, saving, uploading to OWW. I think we're close to a good solution that leverages Evernote's nice application for mobile phones. I recently discovered that you can easily make public notebooks in Evernote, and that these public notebooks have a nice RSS feed. Tom Mahony noticed that there is a MediaWiki widget for embedding an RSS feed in a page. He even implemented a test public evernote feed in his OWW notebook (see this page). So, now we're to this point:

1. Snap photo with mobile phone, using Evernote application. (Actually can be any kind of note, photo, voice note, etc.)
2. Photo is stored by default in your public notebook (or you move it over manually).
3. RSS feed embedded in OWW shows new content.

Only step #1 requires user involvement. But the problem is that currently the image is not actually displayed or uploaded in OWW, and there isn't a good way to selectively show only relevant parts of the feed. But it seems to me those are very solvable steps. I think this will be a very nice feature, because over the past couple years, I've seen all my students struggle with barriers to getting information into their electronic notebook. So, any steps that are removed are a big deal.


^* The tradition in the department dictates that I must demonstrate teaching diversity in order to obtain tenure. There is also the belief that instructors become bored and their teaching stale after 3 semesters of teaching a course. I think these are fairly common beliefs in physics departments around the country, and it means that next fall I'll have to teach a new course. I find this policy de-motivating and inefficient, and will do my best to help the policy evolve over the next many years.

Get 'em while they're young: Open Science for Junior Physics Lab

I've been wanting to write about an open science teaching experiment I've been doing at U. New Mexico that I think has been really successful. I've been thinking about presenting at a local teaching conference on campus (and I should still do that), and other venues, but I think blogging about it here will be an effective way of letting others know about it.

What it is in a nutshell

The course is Junior Lab (modern physics lab course) at the U. New Mexico. We run the course as close to "open science" as we can, with a course wiki on OpenWetWare as the foundation. The students post everything on the wiki: their primary lab notebooks on the wiki, analysis notes, Matlab code and Excel sheets, formal report rough drafts, and final drafts. Further, all of my instructor feedback is also posted on their work, in the margins. The only written things we don't put on the wiki are letter grades and a few confidential emails. (We also have no mechanism for putting video or audio conversations on the wiki...though that's an interesting and scary idea that just occurred to me.)

Does it work?

I say emphatically: YES! I have just finished teaching the course for the second time and I have been very pleased both times. I've also only received positive feedback about the open science style of the course--including many unsolicited emails from students saying the wiki was very helpful for them. Unfortunately, I only have anectdotal evidence...next fall I want to implement some kind of pre- and post-testing for assessment, as I talked about in yesterday's blog.

What have been some good outcomes?

Good science. When I decided to teach this course on OWW (OpenWetWare), I purposefully didn't put much planning into it (my style of time management). I also decided to just give it a whirl and "be bold" figuring the worst that could happen would probably not be much worse than an average lab course. Thus, I didn't really imagine all of the wonderful things that would happen as we got started. I think the thing that I have enjoyed the best is seeing the students reading the lab notebook of other students to get hints for how to set it up, how to do the analysis, etc...and then citing and linking the help they got!. I was seeing this happen and just so delighted to see them practicing science the way it should be practiced. For some of them, this was natural, for others, I could tell they felt like they were cheating or something, because it seemed too easy. I just constantly reminded them that this was science and too keep looking at previous work and to keep citing.

Open science training. I don't have evidence for this, but I feel like these students will be much more likely to practice open science later in their careers. I suspect they'll be required by at least one future instructor or advisor to go back to paper and pen and "science 1.0" ... and having been through this course, I also suspect they will rebel and lead changes wherever they are.

Much better instructor / student communication. One of the principles from "The One Minute Manger" (a cheesy little book that is very much worth reading) is to give feedback as close to instantaneously as possible. After reading that book, I think it's pretty obvious that early feedback is much more valuable than delayed. But in traditionally run lab courses, where labs are handed in on paper, the feedback is necessarily delayed quite a bit. Having the course in public on the wiki allows me to leave feedback and "grade" any time I have internet access. My goal is to give the feedback very quickly, but to be honest, I didn't do so hot this semester. Maybe for the first half of the course, I was able to provide written feedback within one week, but attending the New Faculty Workshop in November completely derailed me and I wasn't happy with being two to four weeks behind sometimes. Fortunately, I think the feedback is much more important early on in the course. Even with my failures, I still think this was a very positive aspect of the course compared to the paper alternatives.

What have been some of the challenges?

It takes a lot of time. Having 14 students in the lab, I'd say I spent at least 10 hours / week (a lot more at certain times) providing written feedback (aka "grading"), plus the 6 hours in lab, and about 3 hours / week preparing low-quality lectures. (We have one hour of lecture on statistical data analysis and other science topics, see agenda here.) Adding up those numbers doesn't seem like a lot, so I maybe am estimating incorrectly. In any case, it feels like a lot of time, and for sure the way I teach it is not at all scalable to more students. I feel like the one-on-one interactions (both real and virtual) are a critical aspect of the course--the students are apprentices. This is in contrast to the other course I teach (Conceptual Physics for >100 non-scientists), where I also value the personal interactions with the students, but not as essentially as in this course.

Technical difficulties. OpenWetWare is a fantastic resource, and I am enormously grateful for everything the OWW founders and Bill Flanagan have provided to help with this course. It is a very solid foundation and pretty much has everything we need for this course to work very well and to be far superior to the traditional version of a lab course. That said, there are very many technical improvements that could add a lot of value. Some of these were brought up at the Lab Notebook brainstorming session we had in October 2007. For example, integrated spreadsheeting would be great (but time-intensive to implement). Also, some kind of "auto-save" is necessary...a few students throughout the semester lost data due to either glitches or being logged out, or even their own mistakes. As we all know, losing data is a crushing blow, so it needs to be kept very much to a minimum. Two good students lost this battle and resorted to paper and pencil followed by uploading later, which of course is not a desirable outcome. (One idea I have to solve this with MediaWiki is to just install a "Save and Keep Editing" button, which would essentially be a "preview" button that actually saves the entry in the data base in addition to keeping the editing window open.) There are all kinds of other things, but I think I'm getting into a broader discussion of electronic lab notebooks in general.

What do I want to do differently next year?
I'm very happy with the way the course has worked so far. Most of the ideas I have for changing things next year are not related to the open science aspects of the course (for example, improving or adding new experiments). I would love to hear about any ideas you have, so please post them on the comments here! Also, if you would like to emulate open science aspects of this course at your institution, I would be really happy to help you get started.