Biophysics Seminar: Archaea

This week, we held our biophysics seminar early because I have to fly out to Santa Cruz on Wednesday to meet some potential open science collaborators--something I'm really excited about and will hopefully have good news to report on my other blog next week.  The two students in the course, Peter Relich and Godwin Amo-Kwao are excellent students and opted to hold the class early instead of postponing until next week.  I was really glad they chose to do so--it showed that they care about the class and are learning from our meetings.

We had decided last week to use this meeting to learn about Archaea by reading two items:

• Wikipedia article on Archaea. 
• Iddo Friedberg's recent fascinating blog entry, "Why are there no (or almost no) disease-causing Archaea?"  

I spent about 3 hours myself re-reading these articles and venturing off to learn more about topics brought up in the articles.  I also read most of the article that Iddo was responding to: "The proportional lack of archaeal pathogens: Do viruses/phages hold the key?" Since hearing about Archaea ten or fifteen years ago, I've always found them fascinating, but never have learned much about them.  After just 3 hours of reading and our hour of discussion, I still don't know much, but am still in love with them.

I figured we'd have plenty to explore since none of the three of us knew very much coming in, and I was right.  I enjoy the format of our course--the students brought up what they found most interesting, and we'd Google & Wikipedia on the projector to find out more about what we were talking about.  Similar to what I'd do on my own "wasting time" learning about subjects not directly relevant to my research, but in this case, with an extra excuse that it counts as teaching :)

We also have an ongoing goal of making contributions publicly from our class, but it remains a challenge, since we don't have video recording and most of what we do is talk and browse articles online.  I've encouraged the students to individually leave comments on Iddo's blog, but at the time we couldn't find the commenting feature enabled.  So, for now, I'll just list a few fun things I learned and / or knowledge I was able to share with the students:

• I didn't know before today that Archaea use as their primary membrane component a kind of lipid different from that used in Bacteria and Eukaryotes.  They use glycerol-ether lipids instead of glycerol-ester lipids.  This may make their membranes more resistant to extreme pH and temperatures, according to the wikipedia entry.
• I learned that Archaea live in many parts of the human body, such as the gut.  Much of what is known about Archaea is about these methanogens, which are useful in industry for sewage treatment, biogas production and other purposes.  This is interesting to me for at least two reasons.  First, because I still hold the misconception that Archaea exist primarily in extreme environments.  This is what I first learned a decade or so ago, but it seems they exist everywhere and maybe most of them are not in extreme environments (though they certainly live there too--like hot springs, deep sea vents, highly salty water, etc.).  Second, it's interesting that Archaea thrive in our body but as Iddo and the research article talk about, we don't know of any pathogenic Archaea.
• Peter pointed out in our discussion that the articles have good hypotheses for non-existence of pathogenic Archaea, but he's not thoroughly convinced.  Even though I know very little, I agree with him.  We wondered whether a place to look for pathogenic Archaea may be in more "extreme" or unusual human populations.  There wasn't any detailed reasoning for wondering this, aside from the fact that there are some amazing extremophiles in the Archaea domain.  If there are pathogenic Archaea, would they be more likely in more extreme environments?  For example, in Ramsar, Iran, where the natural background radiation is 200 times higher than the global average?  Like I said, there's no sound reasoning for wondering this, but it lead to fun discussion.
• While thinking about environments and extremophiles, a question came up:  Currently, which domain of life has ventured farthest from Earth?  Archaea was our guess since they seem to be the extremest extremophiles.  We did a Google search for "archaea on the moon" and I was really surprised that there are zero hits.  We realize there is no atmosphere on the moon, but how preposterous is it that some Archaea from astronaut's boots were trampled into the soil and aren't yet dead?  "Archaea on the moon" should get at least one Google hit, right?  Well, more realistic is probably the possibility of Archaea on Mars.  As Peter pointed out, they seem to live everywhere, and we've possibly already contaminated Mars with the rover.  Since we can't culture the putative Archaea here on Earth, it will probably be tough to know where they came from if we do discover them on Mars. Like I pointed out above, our discussion group doesn't know much about the subject, but from what we know, it seems possible.
• Our discussion was entertaining and educational.  It led us to discuss some topics more likely to come up in our own biophysics research such as RNA polymerase, DNA polymerase, and DNA damage repair.  We went about 20 minutes overtime and I could have gone on for hours.

For next week, we're going to read a couple papers about stochastic simulation--a more focused topic, and one definitely important for the research of all three of us. The papers are:

• Gillespie, D. T. (2007). Stochastic simulation of chemical kinetics. Annual review of physical chemistry, 58, 35-55. doi:10.1146/annurev.physchem.58.032806.104637
• Voter, A. F. (2005). Introduction to the Kinetic Monte Carlo Method. Radiation Effects.

I learned about these paper a few years ago when we began using stochastic simulation in our lab to study kinesin (see "A discrete-state model for kinesin-1 with neck linker tension").  I had been using stochastic simulation for years before that, as a very useful tool in the lab.  But I wasn't aware of the seminal work of Gillespie until I read an excellent paper on transcription out of the Kornberg lab, which pointed to Gillespie's 1977 paper: Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81(25), 2340-2361. doi:10.1021/j100540a008

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.

Junior Lab Brainstorming Exercise: Good science

Last year (August 2010) and this year (August 2011), I have led a brainstorming exercise in Junior Lab lecture. I believe Katie Richardson (aka Karma) may have had the idea for this exercise when she was TA last year. The exercise has two main goals:

• Learn something about what makes "good" science
• Get used to talking and contributing to class discussions

As you can see from the links to the brainstorming pages (above), these goals are clearly stated to the students, and they seem to embrace them.  The students quickly formed groups and there was a lot of discussion.  The students texted or emailed their brainstorming results to me, and I collected the data on the page.  Then there was about 10-15 minutes for students to volunteer to nominate items as most important.  The students also gave pitches in support of their favorite items.  Following this, there were two rounds of voting, with students voting for 0, 1, or 2 items each time.  In both years, "reproducibility" won the contest, something which makes me very optimistic about these early-career scientists!  Of course not all of them will continue on in science, but I would say an understanding of good science will be important for all of them, no matter what their career.

Here are the items that made the final round of voting for 2010 and 2011.  The first number is the votes from first round, the second is the second round:

• 2010
• Reproducibility 11, 15
• Objective / aware of biases -- so the work is actually useful 7, 9
• Creativity -- ask creative questions that are relevant and answer them in creative ways 6, 10
• 2011
• Verification by peers 4, 6
• Reproducibility (detailed procedures) 12, 15
• Objectivity, unbiased 5, 4

Week 4 Lecture, Law of Large Numbers, Intro to Central Limit Theorem and Related Terminology

Yesterday was the 4th week of Junior Lab, and the third lecture (no class Labor Day week).  We started discussing some of the fundamentals that underlie a lot of data analysis.  To do so, we started with a group exercise that involved flipping coins and recording the number of heads and tails.  One of the main goals of the group exercise was to get students involved and contributing to the discussion.  In my opinion, that goal was successful. Out of 16 students, I can recall at least six students who were actively contributing to the discussion for the whole hour. 

The other goal was to use the coin flip as a launching point to discuss probability distributions, probability functions, parent distributions, the law of large numbers, central limit theorem(s), independent measurements, random error, systematic error, etc.  I think this goal was achieved as well.  Below are two photos of the chalkboard, following our 30 or 40 minute discussion. 

Almost all of the words / equations on the left chalkboard were contributed by students.  To spur discussion, I collected the results of their coin flip trials, and then asked an open-ended question "what can we say about these data?  What should we do with them?"  Mean and standard deviation were suggested by Alex.  I used this to define Xi, Xbar as we will talk about them during this semester.  One group of students recorded ten heads in a row.  I pointed out that set of Xi and asked, "how come you were reluctant to report this?  Who cares that it was 10 heads in a row?"  This got students to mention things like "unlikely" and "probability" and even mentioning binomial distributions.  One student, I think Kirstin, described in words how the probability function for 10 coin flips would look, which led to the drawing in the right photo above.

My memory is hazy at this point, but we started talking about how to test whether the coins were actually fair.  I asked what the measurements would look like if I asked them to measure the widths of the coins.  Students' intuition, not surprisingly was that most sets of observations we thought of would have a bell-shaped distribution.  I asked if anyone knew why this was, and there were many good intuitive explanations.  Alex, brought up the Central Limit Theorem, which delighted me.  At that point, I wrote down in words / symbols a version of the central limit theorem, and we ended class pretty much on that note.  I then showed them a Google spreadsheets example of the Central Limit Theorem in action for uniformly distributed random numbers from 0-1, see below.

Central Limit Theorem Spreadsheet


All in all, I think the class was successful, but I don't have any real measurement of that.  Many students were very engaged, and almost all of the terminology and principles were contributed by students as opposed to me.  I told them my goal for them is not to memorize any formulas or theorems, but rather to gain an understanding of them and an intuition so that when they encounter data analysis tasks in the future, they will know that there is an underlying theoretical framework that they can go read about and relearn.  I feel like the kind of discussions we had yesterday will likely achieve that goal for most of them.

Next week, we'll continue along these lines.  We'll look at their coin-flip data and approach the question, "how do we test whether the coins are fair coins?"  Or, we may do another group exercise that generates new measurements that we can look at.  Or, a third option is to use data that students generate during the lab sessions.  My gut is telling me to continue trying to do small group exercises at the beginning of class, since it does seem to be boosting student engagement quite a bit relative to prior years.  Thanks to TA Katie Richardson for suggesting I do the group exercises!

FriendFeed thread:

Ffff! Ffff! Dusting off my blogs maybe? Junior Lab for the 4th time!

I am a lousy blogger, but I am considering dusting them off this fall.  The main reason is because the research in our lab is heating up, and some students (Larry and Andy) are getting close to finishing their PhDs.  For the most part, I have found that short comments and conversations on FriendFeed are a better way for me to communicate with people, compared with blogs.  But I think blogging will be useful for describing our research results, as it will allow use of figures and better formatting.  And maybe it will help the students a bit in terms of publicity.  Soooooo, as a way of dusting off my blogs, I'm going to make a short little blog here on my teaching blog, just to get warmed up.

Junior Lab just finished it's second week.  (You can read about our Open Notebook Science Junior Lab course in prior blog.)  I'm excited that I get to teach it a 4th time, despite being told that this would not be possible last year.  This year, we have 19 students -- 3 more than the "maximum."  Since I interact with each student one-on-one, It's going to be a lot of work, but a lot of fun too.  I have an excellent TA, Katie Richardson, who already has provided good ideas for the course.  She suggested promoting interaction early on, so that lectures will be more likely to involve student questions.  So, the first "real" lecture was earlier this week, and we did a fun exercise, brainstorming on what is needed to carry out "good" science.  You can see our exercise on the OpenWetWare page.  I also posted this to the Science 2.0 room on friendfeed, and I'll embed the thread below if I can figure out how.  It was not a "good" scientific exercise, but I was still very happy that "reproducibility" (loosely-defined) emerged as the ingredient with the most votes.  This led naturally to discussion of how to keep a good primary lab notebook.  OK, hopefully more to come on my other blogs!
Related FriendFeed threads:

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.

Soap film interference: One of my favorite homework assignments for conceptual physics

This weekend I posted one of my favorite homework assignments for my conceptual physics students.  You can read the assignment on OpenWetWare.  There are a variety of questions and activities related to the thin film interference colors in soap bubbles, including an easy kitchen experiment using a coffee mug.  Based on experience, most of the students who submit answers (it's completely voluntary) will not upload photos or videos.  However, a few of them will, and I really enjoy seeing what they do and sharing it with everyone during lecture!

OK, I'll leave this blog entry short, as I also have to finish writing a quiz before the end of the night.  Oh and also get some writing done on a proposal before my international would-be collaborators wake up!