What is the big picture of the evolution life on Earth? A global view that takes into account chemistry and thermodynamics is provided by R. J. P. Williams and J. J. R. Frausto da Silva in their book The Chemistry of Evolution, subtitled The Development of our Ecosystem. It’s not an easy book to read; sometimes dense, sometimes opaque, sometimes repetitive, and difficult to wrap your mind around. Systems thinking is difficult, and those seemingly circular parts are a grasp at something potentially profound. Or it could be rubbish masquerading as erudition.
Why did I read this book? Origin-of-life research has mainly focused on organic compounds composed of the elements C, H, O, N, S, P. When inorganic elements are mentioned (~15 of the metals utilized in extant life), these are usually in very specific contexts without considering their co-evolution with the organic compounds. I’m also about to teach a special topics class titled “Metals in Biochemistry” and I want my students to appreciate the big picture view before they get into the weeds of specific enzymes, co-enzymes or signal/transport factors. I estimate it took me ~24 hours to read through the eleven chapters, one chapter per day.
Here’s the big picture, partly in my own words, and partly quoted from the concluding chapter of the book.
Thermodynamics rules. You can try to ignore it, but you won’t get very far. Most scientists have some familiarity with equilibrium thermodynamics, the type that applies to isolated systems. The second law of thermodynamics states that the system inevitably moves towards equilibrium by maximizing entropy production. But living organisms are open systems; energy (and materials) flow through the system building biomass, excreting waste, and engaging in the properties of staying alive. On Earth, the main source of energy comes from the sun, and in particular its high-energy (or high-frequency) photons. Living organisms degrade this into low-energy (high-entropy) “heat”. The analog of the second law in non-equilibrium thermodynamics, according to Williams and Frausto da Silva, is this:
“… in an open system the absorption of effective energy of high frequency sets in motion flow and that this flow adjusts materials aiming as far as possible to generate thermal low-frequency energy as it moves towards an optimal cyclic material steady state. This final cyclic steady state is one which retains a fixed amount of energy in the flow of material while generating optimum energy output and degradation. It thereby generates a randomisation more rapidly than would otherwise have been the case… The rule is in accord with the second law… but relates to kinetic, not equilibrium thermodynamic, factors.”
Here’s my visual aid comparing the two. In an isolated system, the high-energy (and therefore less stable) compound A converts into the lower energy (and more stable) compound B, which can continue this process turning into C and finally into D (the most stable of the lot). As this conversion takes place, (chemical) energy is dissipated from the compounds into “heat” which cannot be recovered. In the beginning, the reaction proceeds from left to right, but over time the reverse reactions also take place until at some point equilibrium is reached. The rates of the forward reactions equal the rates of their reverse reactions. All the arrows are the same size as shown in the upper representation. There is no longer net dissipated heat. You’ve reached thermodynamic death.
Contrast this with a system that receives energy from an external source. As long as that energy is provided, the long-term fate of the system is to organize itself in a cycle so that no material is wasted. The reaction rates of the clockwise cycle continue to be larger than those of the anti-clockwise cycle, as indicated by the different sized arrows in the lower representation of a tiny cycle. The energy flowing into the system continues to be dissipated as heat in accordance with the second law. In reality, each of the reaction steps is likely to generate some “waste” molecules and therefore the entirety of the chemical materials is not truly cyclic. However, that waste could be incorporated into another cycle, and so on, until everything is recycled (no waste!). Cycles coupled to other cycles, cycles within cycles. This is the ideal climax of an ecosystem, assuming no change to the energy source.
What sorts of chemical reactions are driven by the external energy source? In life, redox reactions. Essentially “there is reductive synthesis in life and oxidised chemical waste… and there was the possibility that the waste would have just accumulated and would have diminished the capacity or even poisoned the living system. For example, all carbon could have finished as trapped wasted coal, while oxygen could have built up as a poisonous gas.” Anaerobic organisms today essentially try to avoid oxidative environments. Without the evolution of aerobes, the “system is unstable and doomed to die”. This is also true “if individual organisms lived forever [with] no return of elements to starting material, no cycle, and any evolution would be frustrated.” Life on Earth is evolving to reach the ideal climax, following the thermodynamic imperative. It hasn’t reached that point. Nor will it do so anytime soon, and our sun will die out some day.
The authors use the example of light as an example of chemical and biological adaptation. (Ultraviolet light is still damaging to surface organisms today.) The overall sequence is that a new environmental factor that initially acts as a poison leads to protective adaptation and subsequently to adaptive use. Here are their six steps.
· new environment (light) -> damage to proteins
· protein damage requires new protein production
· new protein production involves local loss of DNA protection [as it necessarily becomes exposed to be transcribed]
· loss of local DNA production -> localised random mutation
· localised random mutations -> proteins protective against light
· further mutation of local region -> proteins making use of light
Thus, seemingly random variation at the smaller time-scale local level is, in the big picture, driven by a longer time-scale process that is governed by chemical thermodynamics. But humans might be upsetting the natural process on Earth that has occurred for 4.5 billion years. We are making use of much more than the twenty elements in the periodic table utilised by extant life. We have created wondrous new materials from concrete to computers. We have generated new waste rapidly that cannot be recycled in a short period of time. We are driving changes in the environment much faster than ever before. (And yes, the environment is always changing.) We’ve created tools to modify entire ecosystems exponentially more rapid than nature without humans could ever do. Ecosystem evolution has taken a different turn in the Age of Man.
A final word about the book. If you’re curious about why extant life uses just 15-20 elements, you’ll get a reasonable explanation by the authors. It has to do with availability both physically and chemically. Other questions which you might have pondered: Why are Na, K, Cl ions involved in nerve cells? Why is Mg2+ involved in ATP activity while Ca2+ is a widespread signaling ion? Why were Zn2+ and Cu2+ incorporated later in proteins? Why do they do play such different roles in biochemistry? Why are they found in superoxide dismutase of eukaryotes while prokaryotes use iron and manganese? What is the effect of different metals used in porphyrins? Why are there iron-recovery subsystems? Why is selenium used in life, but not arsenic? All these and more are discussed, if you’re willing to plow through the book. It was a slog, but I’m glad I did, and I now have a broader picture of the interplay between metals and organic compounds in biochemistry. Gotta go write up my syllabus!
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