Holiday Science Read: How Nanobiology Battles Chaos

When science assaults our intuition, sometimes we respond with fascination, and at other times, when our favorite beliefs are on the line, with resistance. Can our mundane actions really change the climate of something so large as the Earth?
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The great physicist Richard Feynman put it best:

"Things on a very small scale behave like nothing that you have any direct experience about. They do not behave like waves, they do not behave like particles, they do not behave like clouds, or billiard balls, or weights on springs, or like anything that you have ever seen... Because atomic behavior is so unlike ordinary experience, it is very difficult to get used to, and it appears peculiar and mysterious to everyone."

The same could be said about things on a very large scale, and about extremes of time and temperature. We have no direct experience with galaxies, with microseconds or millions of years, or with what happens at thousands of degrees or near absolute zero temperature. Scientific concepts that deal with such extremes defy our medium-scale common sense.

When science assaults our intuition, sometimes we respond with fascination, and at other times, when our favorite beliefs are on the line, with resistance. Can our mundane actions really change the climate of something so large as the Earth? How could we possibly have descended from small, furry dinosaur prey? And if a tornado whipping through a junkyard can't spontaneously create a Boeing 747, can it really be true that complex, living, self-directing beings are formed out of molecules that merely follow the laws of physics and chemistry, without the guiding influence of vital spirits?

Nanoscale Weird Tales: Peter Hoffman's Life's Ratchet

That last question is the subject of Peter Hoffmann's fine book, Life's Ratchet: How Molecular Machines Extract Order from Chaos (Basic Books, 2012), an introduction to nanoscale biology that you should be buying as a holiday gift for your friends and relatives. The weird world of nanoscale biology operates in a constant "molecular storm" (i.e., the molecular battering of random thermal motion), where careful accounts are kept in the currency of "free energy." The science that explains how this world operates is statistical mechanics -- a field that may not sound as sexy as the Higgs Boson, genomics, or quantum computing, but it's one of the hottest scientific topics out there right now. Statistical mechanics is the science of how the macroscopic emerges from the microscopic, and it is the basis of our understanding of the nanoscale machines and systems that build life from molecules.

Hoffmann has written a fun, accessible introduction to crucial ideas that explain how a bunch of mindless, jiggling molecules can work together to run the sophisticated operations of our cells. Using examples from snowflakes to mayonnaise, Hoffmann explains Brownian ratchets, entropy, free energy, cooperativity, and the Second Law of Thermodynamics. He has a knack for metaphors: Our molecular motors are like a nanoscale Sisyphus who exploits Brownian motion to move his boulder up the mountain. Lipid molecules "are a kind of conjoined twin, with each part having different affinities. In a mixture of oil and water, lipids can satisfy each part of their split personality." Building our intuition with his metaphors, Hoffman explains how the complex and functional components of our cells arise spontaneously out of molecular chaos and blind physical forces.

Genetic Gripes

While this book is an outstanding read on biophysics, there are some misguided ideas about genetics. Since I used to work in a biophysics department, and I'm now employed in a genetics department, I'm acutely aware of how biophysicists tend to disregard genetics, viewing DNA as just one particularly lazy macromolecule among many. (Geneticists, in turn, often consider proteins a sideshow.) Hoffmann attacks what he characterizes as the DNA-centered view of life. He suggests that an excessive focus on DNA gives ammunition to creationists: "The whole idea of DNA containing information is, in my opinion, one of the main culprits in maintaining the myth of creationism and intelligent design." Why? Because the "DNA-centered view emphasizes chance over necessity," and because DNA, in the absence of protein machinery to read it, is meaningless: "I think the utter insufficiency of the information in DNA to specify an organism is one of the most powerful arguments for evolution."

What Hoffmann is missing here is the role of heritable information. Nobody doubts that the physical properties of individual proteins and their ionic environment are what cause molecular complexes to self-assemble and assume their functional shapes. And it is true that biologists tend to insufficiently appreciate the fact that physical laws give us, in biologist Stuart Kauffman's term, "order for free", order which does not need to be explicitly specified by DNA. But the most fundamental difference between self-assembling snowflakes and self-assembling living beings is that living beings inherit genetic information and snowflakes don't. In the absence of the stabilizing influence of genetic information, cells could not self-propagate, and life would peter out in the face of molecular chaos.

Gripes aside, Life's Ratchet is a valuable introduction to the non-intuitive, nanoscale world at the foundation of our biology. To quote Peter Hoffmann quoting the great biologist Ernst Mayr, one of the big questions we face is "how living, as a process, can be the product of molecules who themselves are not living." Much of the answer is coming into view, thanks to the ingenuity of biophysicists.

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