Statistical mechanics in biology and biocomputation
So you know about molecular biophysics and want to think about cells. How should you get started? Let’s take the first few steps.
We’ll start with some concepts that should be familiar: coordinates and equilibrium vs. nonequilibrium behavior. We can frame our discussion by comparing something familiar, a protein, to a cell.
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I don’t about you but I grew up on equilibrium statistical mechanics. The beauty of a partition function, an ensemble, the ability to understand thermodynamic principles from microscopic rules. I love that stuff.
But what if we want to understand biology? Is a partition function really the most important object? This Fall, I’m going to lecture on biophysics for an assortment of biology and biomedical engineering students for just a few weeks; and for the first time in my teaching career, I’m planning to omit a partition-function based description of molecular behavior. I’m just not convinced it’s important enough for an abbreviated set of lectures.
“Proteins don’t know biology” is one of those things I’m overly fond of saying. Fortunately, it’s true, and it gives quantitative folks a foot in the door of the magical world of biology. And it’s not only proteins that are ignorant of their role in the life of a cell, the same goes for DNA, RNA, lipids, etc. None of these molecules knows anything. They can only follow physical laws.
Is this just a physicist’s arrogance along the lines of, “Chemistry is just a bunch of special cases, uninteresting consequences of quantum mechanics”? I hope not. To the contrary, you should try to see that cells employ basic physics, but of a different type than what we learned (most of us, anyway) in our physical sciences curricula. This cell biophysics is fascinating, not highly mathematical, and offers a way of understanding numerous phenomena in the cell, which are all ‘special cases’ … but special cases of what?
You’re a quantitative person and you want to learn biology. My friend, you are in a difficult situation. If you really want to learn how biology works in a big-picture sense, as opposed to cutting yourself a very narrow slice of the great biological pie, then you have a challenging road ahead of you. Fortunately, many have walked it before you, and I want to give you some advice based on my own experiences. I should say at the outset that my own learning has focused mostly on the cell-biology part of the pie – not physiology, zoology, ecology, … and so my comments here refer to learning cell biology.
The scary thing is that I have been at this for almost 20 years (very part-time admittedly) and I would never dare to call myself a cell biologist. But I think it’s fair to say that by now I have a decent sense of what I know and what I don’t know. I will never be able to draw out the Krebs cycle, but I have a qualitative sense of its purpose and importance, as well as of general principles of cycles and catalyzed reactions in biochemistry. Not that impressive, I know, but I’m proud of it anyway.