Life's Ratchet - How Molecular Machines Extract Order from Chaos

Peter M. Hoffman, 2012

Nature's machines are not hindered by thermal noise; they exploit it. "Life's Ratchet" is literally a thermal version of Maxwell's demon; not magically reducing entropy by separating molecules, but using stored chemical energy plus ambient thermal energy to stretch that chemical energy as far as it can go. Evolution leads to molecules that thrive in their noisy, wet, chaotic natural environment, not rigid machines that operate with small-scale predictability and precision.

Nature does not use Drexler rod logic. If rod logic is possible (and it might not be), it must be constructed in a nearly perfect environment with perfect tools that were also constructed in that environment. Creating those environments, and pushing back the boundaries of everyday molecular chaos, will be energetically expensive, because a lot of entropy must be pumped out. And if entropy creeps back in (say, a cosmic ray scrambles some molecules), the defects must be detected rapidly (before the damage propagates), measured, modelled, and a specific repair strategy formulated and implemented. Organic molecular systems are more fault tolerant.

I arrogantly assume that we will someday learn to do better than nature; we will also build molecular systems that are fault tolerant, and designed for measurability and repair as systems. But we are far, far from that, and so far nature has us beat in every dimension - size, speed, and energy efficiency. It is true that our finished artifacts move electrons where nature moves atoms, and this seems energy efficient. However, at the atomic scale, free electrons are noisy and non-localizable.

Eric Drexler figured out that atoms are the smallest quantum objects we can reliably control at the atomic scale. I think of his rod logic as an easily understood gedanken model, not an engineering specification. Over billions of years of evolution, nature has done far better than rod logic, though admittedly for nature's "purposes", not ours. Nature has developed a set of alphabet blocks so clever that you can shake them randomly in a box, and they settle out to spell messages - though not "intellectual" messages.

Life's ratchets are the mechanisms that nature uses to combine randomness and energy to produce functional results. Page 195 of the hardback first edition, "ATP Synthase and the Amazing Spinning Baton" in the chapter "Twist and Route", describes how nature uses tiny motors to use glucose energy to convert ADP to ATP with at least 88% efficiency (page 197, describing the 1997 work of Hiroyuki Noji and co-workers at the Tokyo Institute of Technology). If our mitochondria merely "burned" glucose, the efficiency would be far lower, and involve temperature excursions that would tear apart molecular machines.

This has far reaching consequences for the evolution of computation. We can hypothesize reversable computers that are very energy efficient, but their actual construction (and repair!) may be incompatible with their operation - like changing a piston while an engine is running, the kind of thing nature does all the time. Nature's methods may teach us the best possible ways to build and maintain computing machinery. We will probably build machines that are fragile, incomplete in isolation, and evolutionarily unstable, because we can build larger cooperative systems that nature cannot. We can exploit dry, cold, chemotoxic environments, like vacuum and microgravity, which will give us access to far more material, energy, and heat sink. But we will will do this by understanding and translating nature's molecular inventions, not by trying to impose our deductive reasoning on a physical world that works differently than our crude gears-and-wires Victorian imaginations. To build this new world, we must work far outside our physiological and psychological comfort zones. Technology seems to be evolving fast, but that is only because we are so utterly ignorant of how far there is to go.

Hoffman's book is an eye opener, giving us a glimpse of a molecular world far different than our everyday experience, evolved for nanoscale success, not macroscale explainability. The dauntingly difficult discoveries ahead of us will require billions of discoverers working with vast amounts of computation. Server sky can help educate and connect those discoverers, and provide them with enough computation to do the job.