26 March 2013

Catalyzing landscape genomics.

Earlier this month, I participated in a catalysis meeting at NESCent on landscape genomics. There is a common theme for each catalysis meeting. Sometimes that uniting principle is a historic area of research with multitudes of literature that could benefit from synthesis and identification of uniting principles. Sometimes the theme is an emerging area of science for which new questions are being elucidated. The landscape genomics catalysis meeting was interesting in that it addressed several major themes in evolutionary biology (population genetics, signatures of selection, comparative genomics) and was looking for ways to unite them theoretically and statistically into predictive methods. I was initially curious why the organizers chose to invite me, but quickly came realize how aligned the themes of the meeting are with my own research interests. Here are a few impressions from the time I spent sharing my thoughts with other scientists.

First, catalysis meetings are an interesting conglomeration of scientists. The goal of such meetings are to throw 25-30 scientists from different research foci and at various stages in their careers into a room together.  No one person was an expert on landscape genomics. There were experts in landscape ecology, comparative genomics and statistics, and we worked together to devise common projects and goals. The beautiful part of synthesis is that contributions from various participants are required to achieve the goals of the meeting. There are many people contributing, and everyone learns something. As a recent article from NESCentians points out, this is a fertile ground for incubating new collaborations, projects, and ideas.

Second, an aggregate of such brains allows new insight into how science works. Well, that's certainly a vague statement. At this meeting in particular, several of us were struck by the differences in how genomics and ecology view data. The former tends to throw out data left and right, paring down sequences and levels of variation so the remaining data can be described more easily. Ecologists, on the other hand, attempt to describe the overall variation in a given system, and try to model the nature of that variation. I personally believe genomicists have a great deal yet to learn from ecologists in this respect.

All in all, I believe this meeting was particularly fruitful. Sometimes tempers and egos flare at these meetings, to the point that I'm urged to start chanting "Fight, fight, fight!" and hope for fisticuffs. As exciting as it is to see other scientists so passionate about their research, I was pleased that members of this meeting were more focused on bridging gaps between disparate disciplines. There are a number of incipient projects jumpstarted from it, including one manuscript I volunteered to lead.

Synthesis FTW!

05 March 2013

How Dance Dance Revolution helps me relate to my students.

Before I met him, my boyfriend Matt spent a lot of time honing his technique at Dance Dance Revolution (DDR). Even after taking time off from practice, he still receives favorable scores while playing at expert level. More importantly, he very much enjoys playing and incorporates it into his rotation of cardiovascular exercise options (playing several songs at a challenging level really does get the heart rate going).

I'm always game to learn new things, especially games (see what I did there?), so I allowed him to drag me out to the arcade a few months back to gain some personal experience with DDR. A few songs convinced me that it might offer a way to blow off steam after sitting at my computer all day. Thankfully, Matt also possesses a home system for use with PS2, so I can play to my heart's content without waiting for other people or having to purchase tokens for an arcade machine.

The best part of playing DDR at home is having a smaller audience watching my sad, clumsy attempts to achieve passing scores on even simple songs. My coordination is suffering from such a narrow focus on mental rather than physical skills. That alone is frustrating. What's truly infuriating at times is having to switch the skill level back to beginner after watching Matt play his turn, and then still feeling like a drunken newborn giraffe as I attempt to translate arrows and music from the game to movement of my feet.

It's easy to fall into a trap of believing that, because one excels at some (or even many) things, all other activities of interest will be as easy to partake. I rely on intuition and a natural knack for understanding and interpreting broad patterns, which makes evolutionary biology a good fit for my brain. DDR, however, does not come without effort to my feet. In fact, it takes a great deal of effort.

Next time a student comes to my office hours to ask about a homework assignment, I'm going to remember my flailing attempts to play DDR. I'm going to answer that student's questions patiently, and explain concepts as many times and in as many ways necessary for them to understand. I've been studying phylogenetics for a decade now, and perhaps I take my knowledge for granted. My students need a little help, and I'm happy to be there to assist as they take their first steps toward understanding.

01 March 2013

Teaching phylogenetics part 2: asking questions.

I wrote a few days back about introducing phylogenetics to an intro bio class. I've been thinking a lot about the lab module I wrote. There were two sections to my lab: the first was a paperclip phylogeny exercise I modified from University of Virginia. In my version, students constructed their own data matrices for morphological paperclips. They then manipulated a random tree entered in Mesquite to look for more parsimonious trees. While they were switching branches around, one student asked, "Aren't there computer programs that do this for us?" I replied, "Yes, but you're not here to learn how to punch a button to make a tree. You're learning how changing a tree topology alters trait mapping and overall tree length." He was quiet for a moment and then said, "That's a good answer."

I believe in telling students what they are supposed to accomplish in lab. In this case, they were expected to learn something about 1) phylogenetic reconstruction methods, and 2) inferring patterns of trait evolution based on a phylogeny. This leads to the second part of my lab: I exposed my students to a new lab format that is simultaneously frustrating and rewarding: the minijournal. The basic premise is that the only materials students receive for the lab is a handout modeled after published scientific journal articles. Just like professional scientists, students must read the article, develop questions based on the "future research" section of the discussion, and conduct their own experiments using methods provided in the article. I learned about this format for inquiry-based laboratory exercises from colleagues at University of Missouri while in graduate school, and was happy to have a chance to expose ~450 students (divided into over 20 lab sections) to the exercise.

Overall, the response for the lab has been better than I expected. Students were thinking deeply about issues involved in phylogenetics, while at the same time, getting their feet wet with developing interesting questions about evolution. Hopefully I'll get permission from the department to post my modified lab exercises so other folks can test them out.