The Gradual Evolution of RNA. We assume, therefore, that RNA molecules were the original proto-organisms. But the original RNA molecules must have been simple, with only a few varieties, and barely able to go through reproductive cycles at all. Reproductive causation would, however, make them more complex, more diverse and better able to control the conditions affecting their reproduction. The major accomplishment of this first stage of gradual evolution is a much more efficient and reliable way synthesizing protein molecule, which helps make the second stage possible. But at this first stage, when the proto-organisms are so simple, there is a way that reproductive causation works on them at two levels of part-whole complexity.

Natural selection at the individual level. At the level of individual RNA molecules, reproductive causation leads us to expect that every new power to control relevant conditions would evolve as it becomes possible, that is, as random variations on extant RNA synthesize proteins happen to control some new condition that affects reproduction or controls some old condition better.

Those RNA molecules whose proteins controlled some relevant condition, such as supplying nucleotides for reproduction, would be more likely to reproduce, because they would be more likely to be located where RNA were benefiting from them. There would be random variations on them, because RNA reproduction is far from perfect. Kinds of nucleotides would be substituted, new nucleotides would be added, and whole RNA could be spliced together. Such random variations on existing RNA would sometimes alter the kind of amino acid used at some point in the protein or add new amino acids, and if these slightly different proteins or slightly more complex proteins were any better able to control the relevant condition, the RNA molecule producing them would be located where it was somewhat more likely to benefit from them and, thus, would be more likely to succeed in reproduction.

Since the triplets of nucleotides are the structural causes bundled together as a proto-organism, the relevant condition that is controlled by the work each does is determining which amino acid is appended in the growing peptide chain at some point. Different triplets of nucleotides in the RNA would control different relevant conditions by determining amino acids at other points in the protein being synthesized. Thus, reproductive causation would make these proto-organisms gradually more powerful over their whole reproductive cycles by altering the bundle of structural causes — shaping each structural cause to be as effective as possible in determining some amino acid, adding new structural causes when the amino acid they add makes the chain more power, and fitting those structural causes together harmoniously as parts of a single RNA — so that the RNA molecule eventually has maximum power over the whole cycle. But maximum holistic power for an RNA molecule is just whatever power comes from the kind of protein it produces existing in the neighborhood.

Even if evolution began with a single variety of RNA whose protein did some useful work, evolutionary change would not stop at making its protein as powerful as possible, because some random variations on existing RNA would synthesize proteins that controlled other relevant conditions. If the first kind of protein supplied nucleotides for RNA synthesis, there are surely random variations on its RNA template whose slightly different protein molecules would supply other kinds of nucleotides, or supply the same kinds of nucleotides in from other sources. Again, random variations on existing RNA that happened to control some new condition affecting RNA reproduction would be more likely to succeed in reproducing, because their location in the region would make the more likely to benefit. Thus, from the original RNA molecule(s) would evolve a variety of RNA molecules serving as templates for proteins with different functions, and each would become maximally powerful in serving its function.

Natural selection at the group level. The increasing diversity of RNA molecules would make their combination in local regions an ecology, and the most spectacular accomplishments of the first stage of evolution, such as a more efficient and reliable process of synthesizing proteins, would come from the increasing power of the ecology as a whole.

Natural selection would not be very selective at first. Though RNA whose proteins controlled some relevant conditions would be more likely to reproduce because they would be in the right location to benefit from the protein, other nearby RNA would also tend to benefit. But once there were enough different kinds of RNA whose proteins making different contributions to the reproduction of them all, change in the direction of maximum holistic power at the ecological level would be accelerated by a weak form of reproductive causation at the level of local ecologies.

Different local ecologies would be like different higher level organisms trying out different combinations of RNA. Each local region would contain various kinds of RNA, synthesizing various kinds of proteins, and they would all be driven through cycles of reproduction by the cycle of night and day side by side in the water. The varieties of RNA would be like the many structural causes “bundled together” like a higher level organism, for the proteins synthesized by all of them would tend to jointly control conditions in their local region that affected the reproduction of them all. And such ecologies of RNA molecules would also be able to reproduce as a whole, like higher level organisms, because when storms or other major disturbances scattered molecules to new local regions, and RNA that wound up in favorable circumstances where they could have both structural effects would start new colonies. Colonies with the right combinations of varieties of RNA would generate proteins of different kinds whose joint control of conditions affecting the reproductive of them all would make their populations of RNA grow faster. Thus, when the next storm came along, the more powerful combinations of RNA molecules would tend to populate the favorable locations when more normal conditions resumed. Random variations in bundling RNA together would be introduced by the reproduction of such “higher level organisms,” because the varieties of RNA that would wind up together in any given local region would be a mixture of varieties of RNA from several local regions. Since there are only so many favorable locations for such colonies of RNA to be set up, their reproduction would eventually make free energy scarce, and a natural selection would be made by the greater reproductive success of some whole colonies.

The relative lack of selectivity about natural selection at the level of individual RNA molecules would, therefore, make possible a powerful form of group selection, which would make the combination of different varieties of RNA in each region as powerful as possible as a whole in controlling all the conditions that affect RNA reproduction generally. Since random variations at the level of these higher level “ecological organisms” are made possible by how they are made up of RNA molecules as parts, there are three ways in which random variations may make them more powerful as a whole.

The first kind of change that occurs at the higher level of part-whole complexity (the local regions where RNA exists side-by-side in space) is the gradual change in each variety of RNA that shapes its protein to perform its function as effectively as possible. This is the gradual change described at the outset of this description of the gradual evolution of RNA, which itself involves three kinds of change because each RNA molecules is a bundle of structural causes, with each triplet of nucleotide determining the amino acid for some location in its protein molecule. Random variations on the RNA molecule that synthesizes it would try out variations on the protein, and the more effective varieties would tend to be the ones that succeed in reproducing, because they would be located in the local region where the condition was controlled and so there would be more of them to be scattered to new regions when a storm or other disturbance occurred.

Second, new varieties of RNA would be added to the colony when random variations on existing RNA happen to synthesize a protein that controls some new condition that affects their reproduction (or some old condition in a new way). Not only would it tend to be selected within the colony by its greater likelihood of being located where the protein’s benefit was provided, but it would eventually be added to the mix in other local regions. To take an extreme example, suppose that it alleviated some bottleneck in the process affecting them all. That would make all the RNA in the local region would be more successful in reproducing, and there would be more RNA from that colony to scatter to new local regions when the next storm came.

Third, the useful proteins that were being synthesized would also be shaped to work together as harmoniously and efficiently as possible with other proteins in local regions, because the reproduction of all the RNA molecules in the neighborhood is the joint result of the proteins synthesized by all the RNA. Thus, as different combinations of RNA molecules were tried out in different regions, those combinations that worked together most harmoniously and even assisted one another would tend to succeed, while less harmonious combinations would fail, because there would be more of them to scatter to new regions when storms or other disturbances occurred.

Reproductive causation was still weak, but since it was operating on the level of whole ecologies of RNA as well as on each variety of RNA within a local region, there would be an increase in the power of whole colonies of RNA to control conditions that affect the reproduction of them all. Although RNA molecules start off simple, weak and uniform, their stage of gradual evolution would eventually make them complex, powerful and diverse. Indeed, this would happen to whole colonies of RNA, because insofar as there is a range of different favorable locations for them, different combinations of RNA would evolve to tap the free energy available in all of them. The surface of a planet surely makes it possible for RNA molecules to go through reproductive cycles on a sufficiently large scale to try out all the random variations on existing RNA that are possible, and thus, each new relevant condition that could be controlled would be brought under control as it became possible.

More efficient and reliable protein synthesis. It is not necessary to trace the whole course of the gradual evolution of RNA, but it is worth mentioning what is probably its most significant contribution to subsequent evolution, namely, an efficient and reliable way of synthesizing protein molecules.

The original process by which RNA molecules synthesized the proteins that brought the first relevant conditions under control (such as supplying energy-rich parts for RNA replication) was probably weak and inefficient. The power to control relevant conditions of all kinds would have been greatly increased, therefore, by random variations whose proteins made the synthesis of proteins more reliable or powerful. There are many ways it could have been improved, including changes that expanded the kinds of amino acids that could be used. The first improvements may have been proteins that helped line up amino acids with the RNA and a substratum so that the protein chain was more likely to form. Such changes could have had far reaching effects, because it could give a function to previously useless proteins that were relatively abundant because they were so simple that they were continually being tried out, eventually selecting the RNA molecules that synthesized them. But the nature of the primitive means of protein synthesis is obscure, and the reason could be that major changes occurred its early evolution.

One indication that the original way of having a structural effect in addition to reproduction involved the synthesis of amino acids is that the successive bases, which are the information-carrying face of nucleotides, can be held together in chains by amino acids as well as by the phosphates used in RNA (and DNA). Such chains of amino acids are called "peptides," the chain that carries these bases are called PNA (rtaher than RNA or DNA). It means that amino acids interact with the molecules by which nucleotides determine which kind of amino acid to attach next in a way that could have occurred without the elaborate molecular machinery now used.

An example of a major evolutionary change would be the addition or deletion of the kinds of nucleic acids used. Protein synthesis may originally have involved only two or three nucleic acids and others were added as special proteins evolved that enabled them to use new kinds of amino acids in the proteins being synthesized. Or it may originally have used kinds of nucleic acids that interact more readily with amino acids and they subsequently dropped out when proteins evolved that enabled fewer nucleic acids to determine the amino acid to be added. It may even be possible that the original code used only two nucleic acids to identify which of the amino acids then being used were to be added, and later, assisted by new proteins, it was replaced by the three-nucleotide code found in existing living objects. But whatever the major changes were that occurred early in its evolution, they not only made it possible for RNA molecules to do their work more reliably and efficiently, but probably also increased the variety of amino acids used in constructing proteins from the few kinds that were probably involved at first to the twenty or so kinds of amino acids found in living objects.

Only 20 or so kinds of amino acids are used in synthesizing proteins, but they were selected from the enormous variety of amino acids that was availabe at the time. What singled these amino acids out was presumably that they provided enough variety for sequences of them to serve as all the kinds of molecular machines needed to handle other molecules. There is probably a geometrical aspect to the amino acids used that enables them to be combined in all the basic ways required to construct complex structural causes, and when it is explained, the currently intractable problem of predicing the conformations of proteins from their amino-acid sequence will have largely been solved.

Though the addition of new proteins to assist the process of protein synthesis would make such major changes possible, they would, at the same time, make the link between the nucleotides and amino acids more indirect. That would explain how the primitive way of synthesizing proteins evolved into its current, complex form. Even in the simplest forms of life on earth, protein synthesis depends on the interaction of RNA molecules with a complex machine composed of as many as fifty-five different protein molecules and three RNA molecules. "Ribosomes", as they are called, assemble themselves automatically in water because of their geometrical structures and how weak forces located on them bind them together. And they can consume only amino acids that have been attached as parts of tRNA molecules. But little is known about how ribosomes works, and when it is worked lut, there may well be empirical proof that original way in which RNA structural effects for doing non-reproductive work was a direct interaction between RNA and amino acids that linked them together in short chains.