...so anyway, let me remind you what I’ve been trying to show: non-equilibrium thermodynamics teaches us that the emergence of life required at least three critical conditions be met on the early earth. First was a source of concentrated chemical potential energy. The ultimate energy source for all life processes today is, of course, the sun. There’s mounting evidence, however, that the energy sources for the emergence of life were geothermal vents at the bottom of the ocean. Whatever future investigations ultimately decide, it remains the fact that the emergence of life is physically inconceivable apart from some energetic source. Equally necessary is a sink to receive heat dissipated from irreversible, entropy-producing chemical processes. This is the role of water in biochemistry, and the role of outer space for the earth as a whole. Given source-sink conditions, energy flow becomes a physical necessity. Whenever you see large numbers of particles moving spontaneously in concert, such as in the flow of water downhill, you can be certain that energy dissipation is the cause.
The third condition required for the emergence of life is the molecular complexity required to create chemical cycles capable of turning energy flow into organization. Again, if it is possible to increase the heterogeneity of matter in a system, this will always be entropically favorable to some extent because it well increase the number of accessible microstates and thus increase entropy. So for a closed system containing a set of molecules capable of undergoing chemical transformations and subject to persistent energy flux from a source to a sink, it is physically necessary that the diversity of molecules increases up to at least the formation of the first chemical cycles.
Once the first chemical cycle or cycles formed on the early earth, the prebiosphere moved from its abiotic phase to what might be called its proto-biotic phase. Chemical cycles driven by free energy gradients are already the fundamental components of living organizations, but by themselves they still lack the capacity for reproduction that is fundamental to life and necessary for biological evolution. Reproduction is accomplished through genetic information. The task now is to see how chemical cycles, of themselves, give rise to function-assessing contexts which can select and store information which exists only in the network of chemical relationships, in and by virtue of the whole organization itself, rather than its molecular parts. The central example of such information is the genetic code. One common misconception is that DNA or RNA are “self-replicating” molecules. This is misleading shorthand, promoted by the interpretation of evolution as a competition amongst genes. Genes have the capacity to be copied by proteins which in turn are reproduced through the sequences encoded by the genes. Rather than view this circularity as a problem to be resolved by appeals to a world in which naked RNA molecules competed to see which could copy itself the fastest, the thermodynamic view suggests that this circularity was an essential and necessary feature of life from its beginning. The genetic code exists because of the chemical relationships that exist throughout the entire organism. It exists because of every molecule that is involved in the replication process and it does not act for the perpetuation of any one of them in particular, the genes included.
So, mostly because I can't figure out yet how to encode these ideas mathematically, I’m going to try and illustrate the logic of biochemistry with a story about some of the games chemicals play and about frustration. The details are grossly oversimplified and the physics is romanticized but those are essential components for any good myth, the emergence of life included...
First off, molecules aren’t alive, and like everything that isn’t alive they naturally evolve towards equilibrium with their surroundings, which is their, static, deterministic way of minimizing their energy/maximizing their entropy. For an individual molecule stuck inside a membrane with a bunch of other molecules, this can be difficult, and existence is a constant search for more stable ways to fold up and get into the lowest energy state possible. Except some proteins aren’t very stable by themselves in water and so they wrap onto some RNA as a way of reducing their free energy. But there's these free floating nucleotides that have this weird chemical handle with three phosphate ions attached to it, which we call ATP, and one of them comes along and it puts a phosphate ion on this protein attached to the RNA. The phosphate ion has a very high chemical potential in water, and pretty much every molecule that gets a phosphate stuck onto it just can’t wait to get it off, the ATP included. But the energy in this phosphate ion commits the protein-RNA structure to a cycle of steps, the end result of which is the creation of a strand of RNA complementary to whatever RNA that protein is attached to, and which the molecules perform exclusively as a way of trying to get back to their most stable conformation. Except that there’s more ATP coming!
You see, there is a tightly knit group of proteins just across the way that are busy making more ATP like crazy. Why are they busy making ATP? Because there is chemical potential energy in the form of food coming in to the cell, being pumped in by this totally annoying protein in the membrane that is only stabilizing itself by binding food molecules outside the cell and then just spitting them back out on the inside of the membrane for the rest of the molecules to deal with. Okay so this group of proteins grabs the food, and the food has got high potential energy and they hate that, so they rip it apart and use the energy to make more ATP...it isn’t their fault though, that’s the only way they know how to dissipate that chemical potential. They too, are simply acting to try and get themselves into the most low-energy structure they can, but the food keeps coming, so they keep making ATP, and the ATP keeps ending up over at the protein latched on to the RNA, and raising its energy, so the protein copies yet another nucleotide of the RNA to which its attached.
Eventually, the nucleotide sequence being copied by the protein breaks off, either because its now long enough to be stable on its own or because the protein encounters a kink in the RNA strand that repels it, so the nucleotide strand the protein just made floats off and finds its way to a ribosome which... is stabilized by the binding of the RNA the protein copied! So the ribosome grabs the RNA in order to lower its energy, but then there’s another RNA that has this amino acid attached to it that it really will do anything to get rid of because the bond just has too much energy, and this RNA can also stabilize itself by attaching to the ribosome so it hops right on, bringing the amino acid with it which destabilizes the whole thing again, and now more of that high energy ATP shows up, and now the ribosome is really in a (high-energy) state, and the only way for the ribosome to relax is to do something that seals the fate of all the unfortunate molecules trapped inside the membrane with it: it uses the nucleotide sequence to make more of those goddamn proteins making the ATP which keeps raising the cell’s energy level so that nothing can settle down like it’s trying to!...do you see? Now they’re going to have to do the whole bothersome thing over again. It’s a chemical catastrophe one moment, the next its doing everything in its power to struggle for survival.
Reproduction is essential to life, but in my estimation it is a symptom of this wholeness: the functional closure of a set of material transformations which begin to act in concert because they are orchestrated by relationships which exist among the parts because of the whole. It is tempting, but maybe indulgent, to believe that the universe itself is also a similar kind of closed process in which parts exist through the whole, and that life is not a radical discontinuity in the fabric of nature, but simply a local instance of a pattern being repeated again and again at every scale, nature self-organizing as a means of making the possible actual and in the process occasionally “pinching off” a new, self-referential totality, dumbfounded by and exulting in its sudden and inexplicable freedom. Obviously that’s not a scientific claim, but it’s a personally palliative image.
At any rate we do not know the details of the earliest chemical organizations, and we may never. Whatever forms of chemical organization existed before the definitive establishment of the genetic code have been erased by the more sophisticated life which succeeded it. The logic of living organizations, however, is still there for all to see, and the physical conditions which made some form of organization necessary on the early earth are understood. So while we may never know precisely how life got started, why life exists has been clear for some time. I have tried here to lay out in non-technical terms the basis for our understanding of natural self-organization because the scientific consensus on these issues concerns, in the most intimate way, the sense in which we belong in nature.