Reflecting on my first experience with research.

I often tell undergraduates about the importance of conducting research projects in their senior year if they intend to pursue graduate studies in science. There are two main reasons for this. The first is that the labs that they have experienced up to that point in undergraduate courses, though useful for introducing specific concepts, are a poor reflection of what real science is like. As such, it is important for them to experience original lab work, rather than simply following a pre-defined, “cook book” protocol with an expected result. Novel studies have no pre-defined sequence, no a priori expectation of the outcome, and in many cases no established methods in place for generating data. The second is that there are some important lessons that they need to learn about research, perhaps most importantly that whatever they try to do in the lab will not work the first time. The sooner they hit that wall — and get around it — the better. Nature does not give up her secrets easily, I sometimes say.

My first experience with original research came during my fourth year at McMaster University (Hamilton, Canada), though the story actually begins the year before. In the late 1990s, McMaster offered a course on “environmental physiology” which explored the various ways that animals had become adapted to different extreme environments and lifestyles. For example, how insects can survive in deserts or how deep diving mammals conserve oxygen. I was very interested in organism biology and wanted to take this course, but it was a senior course and was only offered in alternate years. This meant taking it in my 3rd year without the prerequisites, which the instructors agreed to let me (and my roommate) do, as long as we took the prerequisities after the fact.

There were fewer than 10 people in the class (several of whom were graduate students) as it had a reputation for being very intense, with long labs on Friday evenings. Because of the small class size, we came to know the professors rather well, and I naturally asked them to supervise my undergraduate thesis project the following year. Specifically, I worked with Dr. Chris Wood, who is a very well regarded fish physiologist. Most of the work in his lab at the time had to so with metal toxicity, waste excretion, and so on, but one area struck me as particularly interesting — it turned out that an earlier study had suggested that fish who grew the most rapidly did not swim well. Being interested in evolution and organism biology, the notion of a trade-off between growth and swimming seemed like a very interesting issue to explore. I proposed a project that would look at this possible trade-off between growth and swimming, but also would include a component of feeding competition and social hierarchy (Who gets the most food? Who grows fastest? Do dominant fish swim worse than subordinate fish?).

There were, of course, numerous obstacles to overcome. How could I identify individual fish? How could I measure dominance rank and feeding? How should swimming performance be assessed? What size of fish should be used? And so on. After much trial and error, I settled on a system for identifying fish using a coded system of ink dots on the skin which were made using an injector that was once used to inject anaesthetic into the gums of dental patients. Lesson 1: Be prepared to be creative in terms of what counts as a scientific apparatus. (Dr. Wood once published a study conducted in Kenya which described the fish as being kept in “amber Tusker chambers” — Tusker being the local beer).

Figure from my undergraduate thesis indicating the identification
method I developed. Pretty decent for Windows Paint, if I may say so myself.

Growth rate was relatively straightforward in principle: weigh and measure the lengths of the fish at regular intervals. Fortunately, someone else in the lab had constructed a “fish measuring tube”, which was a transparent plastic half-cylinder with a ruler under it, on a slant with drain holes at the bottom. Worked a treat.

Some dude weighing a fish.

Swimming performance was assessed using a huge swim tunnel that had been built years before, but which was modified so I could reach in and get the fish to keep swimming once they had become stuck against the grating at the end of the swim section. I measured both maximum sustainable velocity (called Ucrit) as well as burst swimming.

Diagram from my thesis showing the swim tunnel apparatus.

The actual swim tunnel, which we knew as “Big Bertha”.

The quantification of feeding rates of individual fish (and by extension, their dominance rank) probably represented the most unusual component of the study. These were assessed by feeding the fish opaque glass beads mixed into the food and x-raying them so the beads in their stomachs could be counted. Mc