Ontological effect: Stages of evolution. Levels of part-whole complexity  in evolving organisms, described in the previous section are the ontological cause of another reproductive global regularity, namely, stages of evolution. It is a regularity that shows up over longer periods of time than the first, because it is a series of stages, each of which is the gradual change of organisms of some kind in the direction of their natural perfection (and the natural perfection of the ecology they help make up).

At each stage, some kind of organism starts off simple, uniform and weak and gradually becomes increasingly complex, diverse, and powerful. But evolution does not stop when they attain the natural perfection for organisms of their kind, if it is possible for those organisms (or important structures within them) to become, in turn, multiple structural causes bundled together in an organism with a higher level of organization that goes through reproductive cycles as a whole. If such a radical random variation is possible, it will eventually be tried out, and such higher-level organisms will also impose natural selection on themselves by their own reproduction. That will start another long stage of gradual evolution, because the part-whole complexity in their structures would make it possible to try out and accumulate a very wide range of traits.

Since one stage leads to another, the overall course of evolution is a ratchet-like series of stages of gradual change, each punctuated by a more radical, revolutionary change that begins a new stage of gradual change by trying out organisms with a higher level of part-whole complexity. The way that higher levels depend on the prior evolution of lower levels means that such evolutionary stages can occur only in a certain order, from simpler to more complex, working its way up the levels of organization. That gives evolution an overall direction that could well lead up to beings like us and, perhaps, beyond.

Reproductive causation can explain, therefore, punctuated equilibria and the enormous variety of organisms. Though reproductive causation implies that the gradual evolution at each stage leads to an evolutionary equilibrium, it also explains why such equilibria are punctuated. The punctuations occur when the natural perfection of organisms on one level of part-whole complexity makes it possible for random variations to try out organisms with a higher level of part-whole complexity (either higher levels of primary structures or higher levels of important structures set up by them, such as in the nervous system). And since their higher level of organization enables them to try out a wide range of new traits as random variations that can be accumulated and fit together harmoniously for controlling the conditions that affect their reproduction, a new stage of gradual evolution would begin, leading to another evolutionary equilibrium.

Moreover, if new stages of evolution can be explained by the higher levels of part-whole complexity in evolving organisms mentioned above, reproductive causation can also explain the variety and complexity of existing organisms. In addition to the many varieties of organisms that come to exist at each stage as they divide up the various sources of free energy and become more diverse, it implies that there are differences among organisms that come from their level of part-whole complexity, with each level initiating a radiation of kinds filling all the available ecological niches.

Since this explanation of evolution follows from our ontological foundation, however, its implications about evolution are ontologically necessary truths. They hold in any spatiomaterial world like ours (that is, where matter has a nature that explains ontologically the basic laws of physics and the universe has a large scale structure with planetary systems). Reproductive global regularities are among those necessary truths, including revolutionary episodes in evolution and the evolutionary stages they involve. The ontological cause of revolutionary evolution has been described: each new stage is the evolution of organisms with a higher level of part-whole complexity. But in order to prove that this more complex aspect of the basic reproductive global regularity is a necessary truth, the ontological cause must be shown to entail the effect. That is, it must be shown that each new stage is inevitable, given the previous stage. That is what is done in each of the ten following sections. But the arguments will all be of the same kind. In each case, the inevitability of the next stage of evolution is proved by showing that the relevant higher level of part-whole complexity is both possible and functional.

Possibility of higher level of part-whole complexity.  In order to show that a stage of evolution is inevitable, it must be shown that it is possible for organisms with a higher level of part-whole complexity to go through reproductive cycles as a random variation on the organisms that have already evolved. What is possible depends on what already exists, which, except for the first stage of evolution, includes whatever is provided by the natural perfection of organisms and ecology at the previous stage. Thus, the first task at each stage is to show how the outcome of the previous stage of gradual evolution makes possible the radical variation that bundles the lower level organisms together as a higher level organism. It must do so in a way that explains how the higher level structure can coordinate the behavior of the lower level organisms to generate both essential kinds of structural effects, reproduction and non-reproductive work, in one cycle after another. It is not always obvious how that is possible, especially at the first two three stages of evolution and in the case of the evolution of spiritual animals.

Function of higher level of part-whole complexity. Another stage of evolution would not follow, however, even if organisms with the higher level of part-whole complexity can be "tried out" in this sense, unless the higher level enables the organisms to control new conditions that affect reproduction. In order to evolve by reproductive causation, they must be able to control conditions that are beyond the reach of organisms at the lower level of part-whole complexity, or else they will not be able to compete with existing organisms. Indeed, there must be an entire range of powers that they alone can evolve in order for them to go through a stage of gradual evolution and become naturally perfect of their kind. The source of the increased power may be obvious in the earliest and latest stages, but it is less obvious in the case of the levels of neurological organization which fall in the middle.

In order to show that all the stages are inevitable, however, it will not be enough to show that each stage is inevitable, given the natural perfection of organisms during the previous stage. It will also be necessary to identify certain major accomplishments of gradual change at each stage of evolution, because certain powers included in their natural perfection are what make it possible to try out the radical random variation that makes possible the next stage. That is how each stage contributes to overall course of evolution.

In the following sections, we shall derive the ten stages of evolution that lead up to rational beings like us. We shall see, in other words, how one stage of gradual evolution makes the next stage inevitable, staring with the beginning of evolution and tracing a series of stages that leads up to beings like us. The relevant levels of part-whole complexity in the structures of organisms have already been identified, and since each new stage is the evolution of the next higher level, we already know that they occur in a certain necessary sequence, if they occur at all. Thus, it remains to be shown that they do inevitably occur, and that will accomplished by showing that each is both possible and functional, given what is accomplished at the previous stage.

Though it is possible, in principle, for such a derivation to be formally compelling, what follows is only the outline of such an argument. Though the possibility and function of the level of organization that evolves at each stage will be shown, we shall not show what the natural perfection of organisms of each kind is by tracing the long course of gradual evolution. Instead, we shall use what has evolved on earth to tell what is naturally perfect (since it is ontologically necessary that gradual change in the direction of natural perfection occurs). And in some cases, the possibility of trying out the higher level of part-whole complexity will be only be shown to be probable. That is to leave the project of formulating this argument as a logical deduction until later, but it will identify the conclusions of those yet-to-be-constructed ontological arguments.

Though we shall follow out a series of stages that begin with biological evolution itself and lead up to beings like us, that is not to deny that there are other stages involved in the evolution of life on earth. Not much attention will be paid, for example, to the evolution of plants. And there may by other series of stages that branch off in other directions. But the one we shall trace is the most important one, because it leads to the organisms with the greatest power.

Natural perfection of life. The proof that evolution goes through a series of inevitable stages is proof that evolution by reproductive causation is change in the direction of natural perfection in a far grander sense that the natural perfection of organisms and ecology, which are the direction of gradual evolution at each stage. It is an additional form of natural perfection, which implies that each new stage has a function and is good in virtue of contributing the natural perfection of the whole of which it is part. I will call the increase in such levels the “natural perfection of life,” because each higher level of part-whole complexity in the natural perfection of organisms enables life generally to control a wider range of relevant conditions

Furthermore, if we recognize that evolution by reproductive causation is itself a kind of natural perfection because of how it makes the most of substances by using their endurance through time to bring about the natural perfection of organisms, the ecology and life itself, then each stage of gradual evolution (like each phase within each stage) also has a function and is good in virtue of making an essential contribution to the natural perfection of the whole of which it is part.

The natural perfection of life is a form of natural perfection of by our definition of doing the most with the least. In this case it does the most because it brings more and more conditions in the world under the control of living organisms (as structural causes), and it does it with the least, because the organisms with which it does so have the natural perfection of organisms and they are parts of an ecology that has the natural perfection of ecologies. This is not to say that life becomes absolutely perfect in this sense, but only that it is change in the direction it would have to go in order for life to be absolutely perfect in the sense of doing the most with the least. We will see in the chapters on What ought to exist what kind of perfection it leads to in the end.

It should be emphasized, however, that although higher level organisms would evolve only if they were more powerful in some way, that does not mean that organisms from lower levels must stop going through reproductive cycles on their own alongside the new organisms. The natural perfection of the ecology at later stages includes organisms from all previous stages, completing reproductive cycles side by side.

As we have seen, the varieties of organisms that come to exist during each stage tend to mirror the physical sources of free energy available in the region, and some sources are so limited that lower level organisms are more efficient in tapping them than higher level structures. They cannot easily be displaced by higher level organisms.

Moreover, though the advent of higher level organisms may displace lower level organisms from niches with larger sources of usable energy, they also provide new sources of usable energy for lower level structures to invade, for example, in their wastes, decaying bodies, or as diseases (such as viruses, bacterial infections, and eukaryotic parasites in multicellular organisms).

Thus, as higher level organisms of some kind are evolving toward natural perfection for organisms of their kind, there is also gradual evolution of organisms with all levels of part-whole complexity in the direction of the natural perfection of the ecology at that stage. Each species imposes natural selection on itself, and since organisms with different levels of part-whole complexity go though reproductive cycles side by side, they all become increasingly diverse and powerful, dividing up the free energy available among themselves to fuel their reproductive cycles. (As we shall see, the natural perfection of both the organisms and the ecology are usually involved in making the next stage possible.)