Biological stages of evolution. The basic series of levels of part-whole complexity in evolving organisms is the series of levels of biological organization, and we will use it to follow the course of evolution up to multicellular organisms. We will then take up, in order, the series of stages caused by the levels of neurological organization, including both the stages of animal evolution and the stages of spiritual evolution.

1. Molecular stage: RNA as a proto-organism. One of the biggest puzzles about evolution is how it began. Darwin did not try to explain it, speaking as if God has created the simplest organisms from which all the other species descended, and there is still no agreement on this issue. Indeed, it is sometimes called one of the great puzzles that natural science has yet to solve. But ontological philosophy affords a simple explanation of its beginning.

The beginning of evolution. What would solve this puzzle is a way of showing how the beginning of evolution is inevitable. Given that reproductive global regularities are ontologically necessary, that could be done by showing that, before biological evolution began, there is a region in which the ontological cause of gradual evolution exists, that is, in which there are complex material structures going through reproductive cycles.

Since the ontological cause of gradual evolution involves a kind of material structure that uses free energy to do work, the region in which they exist must be one in which there is a thermo­dynamic flow of matter (that is, a flow from potential energy through kinetic energy and photons to evenly distributed heat, according to the tendencies to kinetic energy and randomness). Such a region of increasing entropy is provided, as suggested at the end of Material global regularities, by the structure of planetary systems.

Stars involve fusion reactions, a form of the tendency of potential energy to become kinetic energy (and radiation), and thus, they supply free energy. And the surfaces of planets that intercept its radiation are a region within the thermodynamic flow where material structures could be using free energy to do work. Photons interact with molecules on the surfaces of planets, and that can produce molecules with energy-rich structures that supply, in turn, the free energy (as chemical potential energy) to drive many other kinds of interactions among molecules. Much of the energy eventually becomes kinetic energy, and the tendency to randomness distributes it evenly among objects on the micro level as heat (or bound energy) which cannot be used to do work. The planet tends, however, to have a certain temperature range, because it radiates low energy photons back out into the cold emptiness of space.

Since the right kind of region exists in planetary systems, all that is required for evolution to begin are organisms going through reproductive cycles. That may not seem possible before biological evolution begins. The surface of such a planet is composed only of naturally occurring molecules (that is, the kinds of material structures that come to exist naturally as a result of the tendency of potential energy to become kinetic). But even the simplest forms of life, such as bacteria and other prokaryotes, have a structure that is far too complex and functional to have occurred originally as a accident in the motion and interaction of molecules on the surface of a planet.

Organisms are nevertheless possible on the surface of such a planet, because what we mean by “organisms” is a complex material structure of the kind that can go through reproductive cycles and that can be surprisingly simple.

Organisms are complex material structures because they are bundles of structural causes with various structural effects. And to say that they can go through reproductive cycles is to say that these material structures can reproduce themselves as well as generate those structural effects as non-reproductive work. If they actually go through reproductive cycles, it is, as we have seen, ontologically necessary that such “reproducing organisms” will evolve toward maximum holistic power for organisms of their kind.

The ontological cause of gradual evolution we are seeking, therefore, could be as simple as a single molecule going through reproductive cycles. It would have to a rather complex molecule, but if it is possible, such a molecular level organism might be called a “proto-organism.”

The inevitability of evolution beginning. Given that there are regions where free energy is continuously supplied to molecules, what makes it ontologically necessary that such proto-organisms exist in a spatiomaterial world like ours is that the specific nature of matter makes matter is capable of forming itself into molecules of sufficient complexity (through the tendency of potential energy to become kinetic). We know that it is possible for molecules with complex enough geometrical structures to be proto-organisms, for we can conceive how a certain kind of molecule would be such an ontological cause.

Of course, knowing the molecular processes involved in life on earth makes it easier to think of this possibility. But it is clear that molecules are the simplest kinds of material structures that could possibly be the original bundles of structural causes going through reproductive cycles, because the natures of nucleons and electrons make only a few structures possible in atoms. 

Given the nature of the ontological cause of gradual evolution, all that is necessary is that a molecule have multiple parts, each of which is the structural cause of both essential kinds of work, one by which it reproduces itself and one by which it helps construct another molecule — assuming that it actually goes through reproductive cycles in which it normally does both. It is possible for a macromolecule to have both kinds of structural effects, because it is a long chain of simpler molecules of a few kinds and there is a simple way that segments of such a molecule could do such basically different kinds of work.

Assume that matter is capable of enough complexity that the simpler molecules that are linked as parts of a macromolecule can form weak bonds (such as the hydrogen bond) with other simple molecules. And assume that when they attract the other simple molecules, the other simple molecules become linked to one another as a second macromolecule (with strong chemical bonds). There could then be parts of such a macromolecule that are capable of doing both essential kinds of work.

The macromolecule could reproduce itself when each simple molecule in the chain did such work on molecules of its own kind. And it could do non-reproductive work when short segments of such simple molecules in the chain did such work on molecules of a basically different kind, for that would be to construct another kind of macromolecule, whose structural effects would be the work it does. (See accompanying diagram of proto-organism as a bundle of structural causes each with two kinds of essential structural effects.)

Proto-organisms of this kind can be said to have a higher level of part-whole complexity than ordinary molecules, because they must have parts that are capable of doing both kinds of work. Those parts are the structural causes that are bundled together as a complex material structure that goes through reproductive cycles as a whole, and as depicted in the diagram, each structural cause is composed of three of the simple molecules that make up the proto-organism.

That puts proto-organisms on a rather high level of what has been called the “ladder of nature.” Even if we count all subatomic particles as being on the first rung, that puts atoms on the second rung, and since ordinary molecules are a third rung, proto-organisms would be a fourth rung. But it would be higher, if we took into account the levels of part-whole complexity among the parts of atoms, for setting aside the electrons, the nucleus of an atom may be composed of many nucleon, and each nucleon is composed of three quarks. These lowest rungs on the ladder of nature are relevant here, for as we shall see, each of the levels of biological organization above the original proto-organisms is another level of part-whole complexity and, thus, another rung on the ladder.

If any macromolecules that can serve as proto-organisms occur naturally on the surfaces of suitable planets,, there are probably at least several kinds of them, because it is a world in which matter has a nature that enables atoms to constitute molecules that are sufficiently complex and stable. Now, we know that it is ontologically necessary that, if proto-organisms were to go through reproductive cycles regularly for a long period of time, they would change gradually in the direction of maximum holistic power for proto-organisms of their kind. But that final condition could also be satisfied on planets that are not only in orbit around a star, but also rotating on their own axes.

The circadian cycle on the surface on the planet involves a regular change in the supply of free energy, and that is a way that at least some kinds of proto-organisms would be driven through reproductive cycles. Any kinds of proto-organisms that tended to do one kind of work during the day (when free energy was more abundant) and the other kind of work during the night (when less free energy was available) would go through reproductive cycles indefinitely. Hence, they would inevitably evolve.

Which kind of proto-organism would be responsible for the subsequent evolution on the planet (and thus, perhaps, how far evolution can go) would depend on which kind of macromolecule is most susceptible to this influence of the cycle of night and day and which kind had non-reproductive work that was most capable of controlling relevant conditions. We know which kind it is from what has actually evolved on earth. But what we know from the ontology alone is that there is a way in which it could be inevitable throughout the universe that macromolecules evolve in the direction of maximum holistic power for proto-organisms of their kind. It depends only on the large scale structure of the universe and the nature of matter, and since we know that those conditions are satisfied in our spatiomaterial world, we know there is a way that the beginning of evolution could be inevitable.

Thus, I shall take it to be an ontologically necessary truth that in a spatiomaterial world like ours it is inevitable that evolution by reproductive causation begin. It is not a logical consequence of spatiomaterialism itself, because it also depends on the specific nature of matter and structure of the universe. (We have assumed, for example, that matter is capable of such complexity that other naturally occurring macromolecules could serve as possible proto-organisms). But a conditionally necessary truth is sufficient for my present purpose, since I am merely outlining the ontological argument that could eventually show that the beginning of evolution is inevitable on earth. However, we must now consider how likely it is that the actual world satisfies those further conditions.

RNA as the original proto-organism on earth. Knowing how the beginning of evolution could be ontologically necessary, we know what to look for to discover whether it was inevitable that evolution begin on earth. We know that evolution did occur on earth, and thus, if it did begin with molecules of some kind serving as proto-organisms going through reproductive cycles, we can identify the specific kind of macromolecule in the molecular structure of the organisms on earth. Not surprisingly, it turns out to be RNA molecules. If we now see how RNA would play the role required by the foregoing ontological argument, we will learn something new about the nature of RNA.

Despair about explaining how RNA can evolve has, however, led some to look in entirely different directions to explain the origin of evolution. For example, some think it must lie in larger configurations of molecules, such as coacervate droplets, or micro spheres made of protein molecules, that naturally form in water. Others look favorably on even more extreme solutions, such as panspermia, the belief that the structure required for life is spread throughout the universe in the form of seeds, which grow on young planets.

RNA molecules are made up of some four different kinds of simpler molecules, nucleotides, linked together in long chains (by a sugar and phosphate backbone). What makes such macromolecules a likely candidate is that they reproduce their own structures when supplied with nucleotides, albeit inefficiently. (Each nucleotide exerts weak forces by which it attracts a complementary nucleotide so that the latter becomes attached to the new chain, and thus, after two rounds of reproduction, there is another RNA molecule of the same kind as the original.) But RNA molecules could be bundles of structural causes that also do non-reproductive work, because short segments of adjacent nucleotides could work together under different circumstances to attract simple molecules of another kind so that the latter also became attached to one another in long chains. (That is, different triplets of nucleotides could determine different kinds of amino acids in protein synthesis.) If RNA molecules are the bundles of structural causes that were doing both kinds of work, the synthesis of another macromolecule like themselves and the synthesis of a different kind of macromolecule, they could be the proto-organisms that were going through cycles of reproduction at the beginning.

If this is what RNA molecules were doing, they would not only be proto-organisms, but since they are composed of structural causes that are responsible for both kinds of products (reproducing themselves and determining a kind of amino acid), they would also be able to try out random variations on traits that are heritable by their offspring. Thus, if RNA molecules were to go through cycles in which they normally did both kinds of work, they would inevitably evolve.

Reproduction would cause their population to grow, and population growth would eventually make resources scarce. (The chemical processes by which molecules have effects like these depend on their having a supply of energy-rich molecules, and whatever the ultimate source of energy-rich molecules on the surface of a planet, the supply will be finite in any region during any finite period of time.) Thus, RNA molecules would eventually have to compete for resources to do the work involved in completing a reproductive cycle. Only the fittest would succeed in the end.

The range of variations would be large, for if the structural causes bundled together in these proto-organisms is each composed of three nucleotides from four different kinds, there are potentially as many as sixty-four different kinds of simpler molecules (amino acids) that could be linked together in the secondary macromolecule (the protein molecule). Thus, if the varieties of secondary macromolecules they could produce were potentially useful in controlling conditions that affect their reproduction, they would inevitably evolve greater power.

The primitive non-reproductive structural effect of RNA.  This is how the beginning of evolution could have been inevitable. I say “could have been,” because biologists do not know that RNA were able at the beginning to generate the second kind of macromolecule and they must have done non-reproductive work of some kind in order to evolve. What is known is that RNA molecules produce such secondary macromolecules in all extant life forms. RNA guides the synthesis of protein molecules, or chains composed of twenty or so different kinds of amino acids (attached to one another by peptide bonds). And in life forms on earth, proteins are the molecular machines responsible for doing virtually all the work of controlling relevant conditions. But RNA molecules generate this kind of secondary product only in the presence of a very complex structure, called a ribosome, which is composed of many different kinds of complex proteins and other RNA molecules, and no such complex molecular machine could possibly have existed naturally at the beginning of evolution (that is, as a simple product of the tendency of potential energy to become kinetic energy).

The current need for ribosomes does not necessarily mean, however, that RNA was not the proto-organism with which evolution began, because RNA could have had a simpler and much less efficient way of catalyzing the synthesis of proteins under conditions that prevailed on the early planet.

When the RNA backbone was attached to a clay substratum, for example, certain triplets of its nucleotides may have been able to attract a few kinds of amino acids, thereby helping to attach them together in chains. Even a very inefficient way of synthesizing proteins involving only a few kinds of amino acids could have promoted the reproduction of the RNA molecules that synthesized them, for even very simple proteins could make a big difference in completing reproductive cycles. For example, simple proteins could help supply parts needed for reproduction (by preparing nucleotides). And some of the first powers to evolve would have been selected for making the synthesis of proteins more efficient, which would expand the range of possible non-reproductive structural effects. For example, one kind of simple protein might have helped attach RNA backbones to clay at an angle that promotes protein synthesis. Another might attach to RNA in a way that makes the synthesis start at a certain nucleotide, so that the triplet code was read the right way. At later points, new kinds of amino acids (or, perhaps, even the fourth kind of nucleic acid) may have been added to their repertoire, increasing the range of possible powers. Alternatively, other kinds of nucleotides or amino acids may have been going through a similar process, and they may have been left behind by the greater efficiency of the protein synthesis generated by those RNA molecules that are now parts of living organisms. In any case, with natural selection caused by their reproduction (that is, the scarcity due to their population growth), continual improvements like these on a primitive form of protein synthesis could explain where the ribosomes now found in all forms of life come from.

That is how evolution could have begun. That is, nothing known to biology shows that RNA did not have such a primitive way of generating secondary products. And if they did, not only the beginning, but also the course of evolution would be inevitable. As we shall see, such gradual change in the direction of natural perfection together with one episode of revolutionary evolution would explain the origin of life, and from there, it is clearer how it is inevitable that one stage follow another.

The original reproductive cycles of RNA. Assuming that RNA did have a primitive non-reproductive structural effect, it may still seem that evolution could not have begun this way in earth, because in order to evolve, RNA molecules would have to go through cycles continually in which they produced both kinds of molecules, and that hardly seems likely, given the complexity of the process of synthesizing either kind of molecule. The synthesis of either kind of molecule requires a series of steps in which one simpler molecule after another is attracted to the RNA molecule and attached to a growing chain. Thus, the fact that one and the same RNA must generate both kinds of molecules suggests that these two processes are likely to interfere with one another. That makes it seem that RNA could not go through reproductive cycles regularly enough over a long period of time for reproductive causation to have its inevitable effect.

The foregoing ontological explanation of the inevitability of the beginning of evolution, however, includes an explanation of why RNA molecules would have gone through reproductive cycles indefinitely. They were driven through reproductive cycles by the nature of the larger context in which evolution begins.

Earth is a planet, and as is widely assumed, life can evolve only on planets orbiting at the right distance from their stars for water to be liquid. Water provides a medium in which the kinds of chemical interactions on which both kinds of products depend are more likely to occur (if only because water stabilizes molecular structures by limiting the range of energies at which they interact). And radiation from the sun is a source of energy that fuels the chemical interactions that result in the energy-rich molecules used as resources by RNA molecules to generate their two products.

Thus, RNA could have been driven through reproductive cycles by the circadian cycle that occurs on planets that rotate on their own axis as they orbit their star. If RNA were disposed to produce one molecule during the energy conditions that prevailed during the day, and if they were disposed to produce the other kind of molecule during the energy conditions that prevailed at night, they would have gone through one cycle after another in which they generated both essential kinds of molecules (perhaps each of them several times during each cycle).

There is good reason to believe that RNA is susceptible to such an influence, assuming it can generate both kinds of products at all. Its reproduction requires only the free energy contained in the simpler molecules that it uses to construct another molecule like itself. (Nucleotides come with phosphate tails, and breaking them off supplies the energy needed to bond them together.) But the parts attached to one another in protein synthesis do not supply their own energy. They need other energy-rich molecules, which were probably most abundant during the day (such as ATP, or adenosine triphosphate). Thus, RNA could have been driven through cycles of reproduction by the cycle of night and day.

An ontological argument for RNA’s primitive non-reproductive structural effect. The need to assume that RNA had a primitive way of synthesizing protein molecules is the weak link in this demonstration of the inevitability of the beginning of evolution on earth. It is possible that RNA has no such structural effect. Some accident may be responsible for evolution beginning on earth. Or there may be some other way in which it is inevitable. But the capacity of spatiomaterialism to explain other aspects of the world, including, as we shall see, the inevitability of the subsequent stages of evolution, will make it seem likely that many more aspects of the world are ontologically necessary than it now appears to us. And if we suspect that evolution must have had an inevitable beginning, we can take this explanation of how it would be inevitable in a spatiomaterial world to be a reason for believing that RNA does have a primitive way of doing non-reproductive work.

Given the enormous variety of molecules made possible by the nature of atoms and the bonds among them that are stable on suitable planets, there were probably several kinds of macromolecules that could have served as proto-organisms by virtue of being bundles of structural causes that could do both kinds of work, that is, produce molecules of both essential kinds (reproducing themselves and constructing a secondary molecule),. However, they could evolve greater power only if they were to go through reproductive cycles regularly, and whichever kind of proto-organism was driven through reproductive cycles by the cycle of night and day (or was more susceptible to that influence) would have led to all subsequent evolution. (And if there were several kinds, the one with the most powerful structural effects for controlling relevant conditions would have led to subsequent evolution.)

It is possible, therefore, to identify the original proto-organism, if this is how evolution began and has been caused on earth. That proto-organism would still be doing both kinds of work, reproductive and non-reproductive, in existing organisms, because they would be merely higher level of part-whole complexity in the coordination of such behavior. The simplest structures doing both kinds of work in living organisms are RNA molecules.

Thus, if we believe that the beginning of evolution must have been ontologically necessary, like so many other aspects of the world, we discover something that empirical biology does not recognize. RNA had a primitive way of synthesizing proteins at the very beginning, for unless it was able to do non-reproductive work of that kind, it could not have been the proto-organism with which evolution on earth began. Thus, we predict that RNA molecules will eventually be discovered to be a structural cause capable, in suitable, natural circumstances, of generating a structural global regularity in which amino acids are assembled as a protein molecule.

All that has been demonstrated, however, is that it is possible that this is how evolution began on earth and, thus, that it was inevitable. When I argue, therefore, that the course of evolution is inevitable, as I shall at each of the subsequent stages, it should be understood as an ontologically necessary truth that depends on RNA having a primitive way of synthesizing proteins as well as on the specific nature of matter and large scale structure of the actual world.

This ontological explanation of the inevitability of evolution by reproductive causation does not imply that evolution begins in every planetary system.

Unless the planetary system forms out of the debris of super nova explosions, they will not have the heavier atoms needed for many of the more complex molecules that are needed for there to be proto-organisms of this kind. (But since stars that explode as super novas are rather large, they form early after the Big Bang and have rather short life spans. Thus, there is likely to be a supply of heavy atoms where middle range stars like the sun form.)

It is also necessary that a large range of different kinds of molecules actually exist and interact in the various ways possible for them. That is not likely on the surfaces of some planets. Some are too hot (and supply too much energy) for such molecules to exist, and others are too cold (and do not supply enough energy).

Furthermore, it has long been recognized that the kind of planet on which conditions are most favorable for a wide variety of molecular interactions are those on which the temperature allows water to be liquid and there is enough water to provide a medium in which larger molecules can interact. (Water moderates the kinetic energy with which other molecules can interact and, thus, makes it more likely that they will not be destroyed by the ambient motion and interaction. Not only is water one of the simplest stable molecules, making it rather abundant, but the range of temperatures at which it is liquid is exceptionally wide.) Thus, we can be sure that at least one planet in many, if not most, planetary systems around stars like the sun include one that is favorable for such a wide variety of molecular interactions.

Nor is it easy to rule out the possibility of evolution occurring under substantially different conditions, such as orbits in systems with binary stars or planets with only water and no land. If evolution is possible in such situations, it might follow a somewhat different course.