Saturday, March 5, 2016

Biology Midterm:What we learn from teaching

Note: This program first aired on March 5, 2016.

This semester has been a busy one, as I am teaching the freshman biology class for our Ocean Studies majors, and find myself relearning topics I haven’t thought about in a long time. This week we reached the midway point of the semester, and in the time honored tradition of academic institutions everywhere, we are having a midterm exam. I don’t give a lot of tests in my classes, but I do feel that it is prudent to stop every once in a while and take stock of where we’ve been and what we’ve learned. Just as the students review their notes and try to prioritize the content of the last seven weeks, so do I. I want to craft an exam that emphasizes the most important ideas and provides an opportunity for students to actually apply those ideas, rather than simply parrot them back at me.

In reviewing my notes from the first several weeks it became clear we had covered some serious ground. It took a few days to distill out the big ideas, but eventually they floated to the top. We started by thinking about the biggest idea you can in a biology class—what is life? How do we determine when something is alive or not? In many ways this is clear cut, things that are alive are made of cells, use energy, have genetic information, have a means of reproducing them selves and evolve over time. The longer you spend in biology though the more amazing and wonderous life gets, and I hope that my students will spend their careers parsing its beautiful nuances, rather than resting on these five broad criteria. A central tenant of modern biology is Cell Theory: all living things are made of cells and all cells arise from other cells. When you think of the implications of that in your own body, all of your cells, the trillions of cells in your body, came from one original cell, the fertilized egg in your mother’s womb. And all of us as leaves on the tree of life, came from one original cell, a mash up of phospholipids and primitive RNA in a hydrothermal vent or mud volcano nearly 4 billion years ago.

We are doing the cellular biology part of freshman biology this semester, trying to understand how those fundamental units of life work. To do that we cover the basic classes of biological molecules: proteins, nucleic acids, carbohydrates and lipids. Each of these classes plays a critical role in cell function, and therefore life. Proteins have the highest diversity, because they have over 20 different subunits (called amino acids) that can be arranged like beads on a string in a nearly infinite number of different combinations. Carbohydrates also have relatively high diversity, based not on having lots of different kinds of sub units—because carbohydrate subunits are very similar and there aren’t that many of them—instead carbohydrate subunits have many many different ways they can get hooked together. If proteins and carbohydrates were Lego sets, proteins would be a set with many different kinds of  small Lego blocks, carbohydrates would be a set with lots of blocks that were all the same, but each of which had several places it could be connected to another block.

We also looked at nucleic acids, which look a bit like proteins, but actually hold all of our genetic information, and at lipids, which make up the membranes of all of our cells and the specialized organelles within those cells. The cell is an amazing structure, functioning on a scale we can scarcely understand, even though we are made of cells. Gravity doesn’t really matter to a cell, the forces that dominate the cellular environment are electrochemical gradients, concentrations of various ions and molecules and electrons that push and pull substances to one side of a cell membrane or another. The pull is passive, it happens without any work involved. The push however, requires an energy source. To push a substance against a concentration gradient takes energy, just like pushing something heavy uphill. And what we find in cellular function is that, just like Sisyphus, our cells keep pushing things up hill, just to let them roll down again. In the Greek myth this was a punishment, but in cellular respiration it is a clever trick. Our cells use spontaneous reactions, reactions that result in a release of free energy, reactions that roll down hill on their own, to power non spontaneous, energy absorbing reactions, up hill reactions in a perfect system of energetic coupling.

We learned that at this level, biology is really chemistry. Life is just an organized system that fights entropy, the tendency of a system towards disorder in the absence of input of energy. Life organizes and inputs that energy, pushing the burden back up the hill, over and over and over again, forming the chemical bonds that would otherwise NOT form. I hope my students have been touched by this wonder. I know I certainly have.