Molecular Machines

I just finished reading Life’s Ratchet: How Molecular Machines Extract Order From Chaos by Peter M Hoffmann, a professor of physics and material science at Wayne State University. While the book purports to explain the mystery of life by examining molecular machines, it does well on the latter but not the former. Hoffmann’s prose is relatively easy to follow and he has uses simple and clear everyday examples to illustrate his main points. In some cases I feel the examples are a bit simplistic, and obscures the more complex and interesting questions. However the book overall does well in giving the non-biologist a good idea of how interesting and complex the molecular machines in our body can be.

The punchline of the book is that Life is based on both Chance and Necessity, a play on Monod’s famous book of the same name. The chance comes from statistical mechanics and thermal fluctuations at the molecular level. The necessity comes from physical law, the physics of chemical interactions at the molecular level. The book does well when the author focuses on describing phenomena at the nanoscale. It gets shaky or simplistic when he slides from physics into metaphysics. A philosopher of science might cringe at some of the metaphysical pronouncements made. Since I’ve started to think about my classes next semester, and in particular how our core curriculum revision will incorporate "scientific inquiry" into our introductory classes, my warning sensor alerts me when I see scientists slide into metaphysical claims.

I almost stopped reading the book after the first couple of chapters but I’m glad I persevered through Chapter 4. Right at the end of the chapter titled “On a Very Small Scale”, there is a section on how magnitudes of energies of a rather wide range of physical processes and interactions converge at the nanoscale and coincide with thermal energy at room or body temperature. I had never thought about this before (and I really should have as a physical chemist). Hoffmann's book led me to a superb 2006 article by Rob Phillips and Steve Quake titled “The Biological Frontier of Physics”. I’ve reproduced the key figure here, but the article can be found at Physics Today. (I highly recommend it!) Hoffmann discusses the examples used by Phillips and Quake, and in my opinion owes much of his book to their work, but in addition he adds a detailed description of myosin “walking” and does a nice job tying this to the Ratchet of his book.

In any case, learning about the interesting convergence of energies at the nanoscale was sufficient motivation for me to read through Hoffmann’s entire book. In all fairness, he does temper the strongly reductionist slant in the early parts of the book with the need to understand emergence, and how both approaches are two sides of the same coin. As scientists who study complex systems, we need to use both approaches, and Hoffmann acknowledges that we are indeed far from the “mystery of mysteries” that is Life. Hoffmann does not go as far as others who have delved into how exactly the second law of thermodynamics and statistical mechanics might work to support systems that maintain themselves away from equilibrium (one definition of life). But perhaps that is neither his intention nor his audience.

I’m not sure how I will use the idea of convergent energies at the nanoscale in my own research projects, but summer is approaching, and I’m looking forward to pondering this issue. But first I need to get through Finals this coming week!