I've been creating a new course on biomechanics, which I'm teaching for the first time this semester. It's been a rough start, but today was incredible!
My (ambitious) goals are to use biomechanics as a means for students to gain hands-on and practical experience with real research methods, real data, and real analyses. At the same time, I want them to learn about local resources, for example, that we have pistol shrimp, an animal that basically explodes water to catch prey, right here on the coast. Most lab exercises are developed around replicating or adding to current datasets from the literature and I've spent considerable time trying to organize this. On Day 1, I was pumped to start this class!
However, our first few classes covered basic concepts (math) and it has been really difficult to get the students interested and excited. When we talked about distance, velocity, acceleration, force, work, and power, I wanted to give them an opportunity to measure at least one of these things for themselves. I made a handout with select frames from a video of a guppy feeding on plankton and thought I was clever to suggest they overlay a piece of paper to mark the eye across successive frames. Then they used a ruler to calculate the change in distance across frames, velocity (more technically, speed), and acceleration. But this didn't work well because the guppy didn't move much and I only gave them 5 frames. This made it hard to take measurements and hard to see a pattern. I had the feeling they could care less about velocity and acceleration after that. So I tried my next trick - I brought in a pistol shrimp that day since we discussed shrimp fight clubs and basic biology, a podcast interview with Sheila Patek, the day before. That also flopped because I couldn't get the shrimp to snap for us...
This week we were talking about scaling and the role of body size. I planned to use Monday to introduce them to the idea of scaling and work with some data from the recent Labonte et al. 2016 PNAS paper on scaling of adhesive pads in animals. Again, I thought I was clever because I found this Data Nugget resource by Travis Hagey, providing lab activities to go along with this paper. However, his exercises are geared toward K-12 students and I wanted to push my students a little further. I wanted them to think about plotting the data themselves, calculating and plotting the expected isometric line, and relating this back to the paper.
This also didn't work because I didn't actually do the math ahead of time and I managed to lecture myself into a circle, confusing myself and the students. By this time, it was the middle of day 3 and I was still feeling like the students were second-guessing the chance they took on this new course. So we moved ahead to the next activity - learning morphometric analysis by measuring scaling of traits with body size using preserved fish from our ichthyology teaching collection. We had 5 types of local fishes: menhaden, croaker, redear sunfish, filefish, and mullet. These had good variation in body size, allowing the students to see for themselves how traits change with size. We spent the rest of the day taking photos of our fish.
What's that in the second picture? Are they...smiling!? They were clearly getting more out of this than anything else we did so far.
They did a great job taking photos! Here are some examples:
I couldn't sleep last night thinking about how I can help make the lab go better today. In a mix of last minute preparations and despair, I downloaded their photos and began working with them in ImageJ to remind myself how to use some of the tools and think about what we should do next. In the process, I found a quick-start manual and had the idea to create a worksheet that would serve as their own guide for later use in the course. We would use this to learn how to use ImageJ, discuss what measures we wanted to take, analyze the photos and maybe even have time for some stats. I feverishly made a worksheet this morning before rushing off to 3 meetings, that turned into 4, and heading off to start class.
Then, today was different.
After some initial difficulty getting ImageJ to install on so many different versions of operating systems, they were off and running! They were helping each other and commenting on how cool it was that ImageJ can do so many things. The last part of the worksheet included brainstorming what variables we should measure on our fish, and how. We used a shared google doc so everyone could contribute and then narrowed our list to 6 traits. Then we used a shared google sheet to assign images and record data. This is when they really started getting into it.
One student decided we needed a reference so we would all quantify measurements the same, and drew one on the board for us. Two other students were competing over who would get to analyze a photo. Students who finished the fish they were assigned then helped the remaining students finish. When all the fish were measured, I pointed out that they officially collected their first dataset, and they cheered. It. was. magical.
Then it was time for some lecture. What are stats for? What kind of tests would we run? How would we know if we saw allometry? We were quickly running out of time so we did some quick figures to look at our distributions, found some questionable data that we double checked, log-transformed our first two variables, and did a regression. Negative allometry. Ok, but what about each species? Good question...5 regressions later, we found out that body height was positively allometric with standard length in redear sunfish (bigger fish are taller than we would predict), and nearly isometric in the rest (equal changes in height and length), with the exception of croaker where there was no relationship. We then determined that croaker didn't have a big enough size range to see a relationship.
Our conclusion: As a whole, body height is negatively allometric but it's probably because of the croaker. Otherwise, most species are close to isometric. This raised some eyebrows and nodded some heads. It made sense now. After class, one student asked where he can get JMP so he can play with more of the data outside of class (I'm not sure but I can ask). I was curious too, and opened it back up when I got back to my office. To my surprise, someone was still in there and had color coded the rows to make it easier to read!
This is their data and they are proud of it. Today was a breakthrough, for me and the students. It's going to be a fun semester!
If you're curious, here is what the rest of their data look like. Pectoral fin distance was a measure of vertical position of the pectoral fin; Dorsal ridge angle was a measure of the slope of the body at the transition from the dorsal fin to the caudal fin.
Next week, we're getting crabby...
