Working Content> Thermodynamics and Statistical Physics
Prerequisites:
From our previous readings about the distribution of energy, we have learned that in a thermal environment, with many molecules, there is a continuing boiling and buzzing of energy: it is continually being exchanged through the interaction of molecules from one degree of freedom to another. In a situation where energy is not (on the average) distributed equally to each degree of freedom, there is a tendency for the energy to redistribute itself so that there is (on the average) an equal amount of energy in each place where it can be put. This last situation is thermodynamic equilibrium. The second law of thermodynamics tells us that, as a whole, the distribution of energy in the universe tends to flow towards equilibrium. (See The 2nd Law of Thermodynamics: A Probabilistic Law and the example linked to that page.)
What's the implication of this idea for biological systems? Living systems are all about staying away from equilibrium: maintaining temperature differences between us and the environment, maintaining a higher pH in one part of our body and a lower in another, maintaining a separation between the environment inside our cells and outside. Equilibrium is death, disintegration, and decay.
If biology is about avoiding equilibrium, what does the spontaneous tendency of the universe to move towards equilibrium have to do with biology? Of course biological systems don't live outside of the physical universe. They are made up of physical elements that obey the laws of physics. Living organisms maintain their non-equilibrium states by coupling their activities to the non-equilibrium condition of the surrounding physical environment: the continuous flow of energy from the sun, to the earth, through both living and non-living bodies, and finally off the planet to the surrounding space. Our being imbedded in this energy flow provides opportunities: opportunities to capture bits of this energy flow on its way to becoming more uniform, and to slow it down at bit, extracting some temporary organization and structure by degrading other parts of the energy.
To continue to live, grow, reproduce, and evolve, biological systems have been shaped by natural selection to exist and function within this physical universe. They make their livings (create their metabolisms) by working with these physical laws. It is only by understanding the physical laws of spontaneity -- what energy tends to do -- that we can understand how life functions to obtain usable energy and information (organized structure) from this powerful stream of energy in which we are imbedded.
What a detailed understanding of the laws of thermodynamics show us (especially the second law), is that what is spontaneous and leads to higher total disorder may lead to local order; a critical necessity for life. The separation of oil and water looks like a process that creates order spontaneously, but a detailed analysis of the distribution of energy and entropy shows that this process is in fact favored by the second law. A similar process is responsible for the formation of cell membranes.
We often say as a shorthand, that the second law of thermodynamics tells us that systems tend to get more disordered. This is misleading. The second law of thermodynamics is a quantitative statement, not a hand-waving one about disorder. It tells us that the entropy of an isolated system always increases. But biological systems are not isolated: they exist in an open environment. The entropy of a biological system can decrease as long as the entropy of the rest of the universe increases by more. For example, a system goes from a disordered protein or a disassembled ribosome, and become an ordered structure without any obvious energy input. However, the surrounding water molecules acquire much higher entropy because they are no longer constrained to interact with the hydrophobic residues of certain amino acids. Water molecules have fewer degrees of potential motion whenever they are located in close proximity to hydrophobic surfaces, and protein folding results in complete freedom of motion for the water molecules so that they can now interact with other water molecules, plus the charged and polar surfaces.
To understand what can happen we will find it useful to create quantities that tell us not only what happens to the entropy of the system we are considering, but what must also be happening to the entropy of the rest of the universe, since that, not only the entropy of our system, tells us whether a process can be spontaneous or not. This careful quantitative consideration of the functioning of the second law leads us to consider the concept of free energy: quantities that combine the information about energy and entropy in a way that lets us see from internal considerations, whether a process can be spontaneous or not.
Follow-ons:
Joe Redish and Todd Cooke 2/3/16