3. Eukaryotic stage: the nucleus. We have seen how the first two stages of evolution are caused by the first two levels of part-whole complexity in the organisms going through reproductive cycles, RNA molecules and those based on a single (looped) strand of DNA. And we have seen why those stages are inevitable. We identified the third stage of evolution when we were considering the levels of part-whole complexity in organisms on earth that might serve as ontological causes of evolutionary stage (in Change: Global: Revolutionary: Cause), because there are cells that are far more complex than prokaryotes, namely, eukaryotes, or cells with a “true nucleus.” They exists as independent organisms, but since they are basically the kind of cells that make up multicellular organisms on the fourth level of biological organization, they are an essential stage in the evolution of animals like us. In this case, however, it is not so obvious that the eukaryotic stage is caused by a higher level of biological organization.

Eukaryotes do not have the kind of structure we might expect on the model of the previous stage. Prokaryotic cells are not merely bundled together as parts of a larger structure, like RNA-level genes contained side by side in a DNA molecule — or for that matter, like cells in a multicellular organism. We have seen how it is plausible, nevertheless, to hold that eukaryotic cells have prokaryote-like parts. But the eukaryotic-level structure of which they are parts is so obviously functional that explaining its origin is problematic. It does not seem possible that the eukaryotic cell could have originated as a radical random variation on prokaryotic cells, and thus, the third stage does not seem inevitable.

Inevitability of eukaryotes. In order to derive another stage of evolution, given our ontological explanation of stages as a reproductive global regularity, we must show that a higher level of part-whole complexity in evolving structures is not only functional (in the sense of affording greater power to control relevant conditions), but also possible (in the sense that it can be tried out as a random variation on the organism that have been evolving at the current stage). In this case, the functional structure of eukaryotes makes it easy to see that they are more powerful than prokaryotes and can evolve an entire range of new powers that are out of reach for prokaryotes. But that same structure makes it difficult to see how they would ever be tried out as a random variation on prokaryotes even toward the end of their gradual evolution in the direction of natural perfection.

There is, however, an explanation of their origin that shows the eukaryotic stage to be inevitable. It has to do with how the higher level of organization that starts a new stage of evolution is not just bundling lower level organisms together, but also a way of coordinating the behavior those many lower level organisms. That is clearly what the nucleus of the eukaryotic cell is doing, and as we shall see, that function explains its origin. But before taking up the question about its possibility, let us be clear about the way in which organisms at the eukaryotic level of biological organization are inherently more powerful.

Greater power of eukaryotes. What distinguishes eukaryotes from prokaryotes is their nucleus, after which they are named. The nucleus is one indication of its higher level of biological organization, and by comparing the nucleus with the prokaryotic biological behavior guidance system, we can see how it is a new kind of biological behavior guidance system that makes eukaryotes far more powerful than prokaryotes.

Prokaryotic Cells. In the prokaryote, as we have seen, the biological behavior guidance system is a loop of DNA that is attached to the side of the cell wall that coordinates the behavior of RNA-level parts.

The cell’s behavior is generated ultimately by the synthesis of proteins, and behavior guidance is a structural global regularity caused ontologically by the structure of the prokaryote as a whole. Certain kinds of genes are selected for expression at any moment because of how the interaction of certain proteins with the DNA loop promotes the transcription of mRNA from certain segments of DNA, represses transcription from others, or de-represses transcription. When mRNA are translated into proteins (with the help of ribosomes), proteins interact with other molecules within the cell, and thus, the cell as a whole behaves. Behavior can depend on the situation, because the proteins triggering the expression of certain genes can be “messenger molecules” which are present only when certain conditions hold.

The same structural cause is responsible for the whole cycle of reproduction. The selection of certain segments of DNA for expression as proteins leads to the growth of the cell (including the acquisition of energy and parts, the construction of new cell wall and other non-reproductive work), and the selection of other segments of DNA reproduces the cell as a whole. After preparing the protein molecules required, the loop of DNA is replicated, the cell is divided, and one copy is enclosed in each new cell.

Thus, the prokaryote is lead through its cycle of reproduction by a simple, ratchet-like process that exposes certain segments of DNA and covers up others in lockstep with proteins that signal the success of each kind of behavior in the sequence, including growth and reproduction, at a minimum.

Eukaryotic Cells. The most obvious difference between eukaryotes and prokaryotes is the presences of a nucleus within the eukaryotic cell. The nucleus is one indication of the eukaryotes higher level of biological organization, as we have seen, it contains multiple chromosomes, each of which is roughly equivalent to one (or more) of the prokaryote’s loops of DNA. Each chromosome is also a DNA molecule containing many genes, but it is not a loop, it is much longer, and it is “complexed” with proteins.

That is, the parts of each chromosome are held together by a scaffold, and they can be drawn together in a tight, condensed form in order to be pulled around during reproduction. Normally, the strand is periodically wrapped around small proteins, like beads on a string, preventing transcription into mRNA.

Because the eukaryote has multiple chromosomes, it needs a nucleus to coordinate the expression of genes on different chromosomes at once. Since that it to coordinate the behavior of the lower level organisms bundled together in this higher level organism, the nucleus serves as its biological behavior guidance system. The nucleus selects and generates both essential kinds of behavior: growth (including various kinds of non-reproductive work) and reproduction (the construction of another object like itself).

The eukaryotes behavior is also generated ultimately by the synthesis of proteins. During periods of growth, the nucleus receives input from other parts of the cell (and the situation outside the cell) by messenger molecules transported into it. An interaction between those proteins and the chromosomes exposes certain segments of DNA on various chromosomes for transcription into mRNA, thereby selecting a kind of behavior for each situation. Behavior is generated as mRNA flows outward from the nucleus to the outer cell, where it is used to synthesize proteins (with the help of ribosomes). The flow of molecules is channeled throughout the cytoplasm by complex plasma membranes (the endoplasmic reticulum), and as protein machines interact in the outer cell, they generate the behavior of the cell as a whole.

Reproduction is an enormously complex process in which the chromosomes are replicated, the nucleus is dismantled, centrosomes form a spindle that divides the chromosomes, two new nucleuses are constructed, one for each copy, and the cell as a whole divides.

Though the behavior of the eukaryotic cell, like any machine, ultimately depends on its whole structure, its structure as a whole is such that its behavior is guided by only part of it, the nucleus, its behavior guidance system.

With the ability to express genes on multiple chromosomes at the same time, eukaryotes are able to coordinate the behavior of many prokaryote-level organisms, and thus, they are able to control conditions that are out of reach for solitary prokaryotes. That is, the source of greater power, as for all levels of biological organization, is the higher level of part-whole complexity itself. Size is a source of power in a world of space and matter.

Possibility of eukaryotes. In order to prove the inevitability of a new stage of gradual evolution, according to our ontological explanation of evolution, it is necessary to show both its possibility as well as its inherently greater power. Though the greater power is obvious, its possibility is problematic. It is not easy to see how its higher level of part-whole complexity could be tried out as a variation that somehow occur during the previous stage at the lower level approached maximum holistic power for organisms of their kind. The way that lower level organisms are bundled together in the eukaryotic cell is so highly organized and functional that it could not possibly have begun as just a random variation that happened to occur one day in the motion and interaction of prokaryotes and other molecules. Such an accident would be as incredible as supposing that life itself began as a random variation in molecules moving and interacting at random on the surface of a planet.

On the other hand, there is good reason to believe that prokaryotes played an important role in the evolution of eukaryotes, because there is another indication, besides a nucleus with its multiple chromosomes, of the eukaryote’s higher level of biological organization. It is the presence of mitochondria (in animals) or mitochondria and chloroplasts (in plants) in the cytoplasm outside the nucleus. These organelles are like organisms at the prokaryotic level of biological organization, because they contain their own DNA and reproduce themselves in the cytoplasm. Indeed, it is widely assumed that they are descendents of prokaryotes that existed about the time eukaryotes evolved. But their role in eukaryote evolution is unclear, because of the functional way that these lower level organisms are “bundled together” in the higher level organism. Though the behavior of these organelles is also coordinated by the nucleus, they are combined in the cytoplasm with a rich variety of other organelles that are constructed from molecules (and torn down) as part of the eukaryotic level behavior generated by the nucleus. What is needed is an explanation of the origin of those other structures in the eukaryote.

Received explanations of the origin of eukaryotes. Current speculation about the origin of eukaryotes is not very helpful in showing the inevitability of eukaryotes.

For example, it is not likely that one kind of prokaryote enslaved others, because prokaryotes are so equal in their abilities. And it does not explain the origin of the nucleus in any case, for it is very unlike a prokaryote.

Others suggest that the nucleus was originally an entirely different form of life that enslaved prokaryotes to exploit them for energy. But in order to explain the origin of the nucleus, there must have been a second origin of life entirely independent of prokaryotes. And if it needs prokaryotes as a source of energy, it does not explain where the nucleus obtained the energy that enabled it to enslave the prokaryotes -- or why it would bother, if it already had a source of energy. In any case, there is no trace of any such independent kind of living objects.

Lynn Margulis, a professor botany at the University of Massachusetts at Amherst, has proposed other possibilities, in which eukaryotes began as prokaryotes in which chloroplasts and mitochondria were invaders that were transformed into slaves. But like the predator hypothesis, it does not explain where the nucleus came from or how such an energy-consuming mechanism could evolve without prokaryotes to perform its energy functions.

Metabolic clue to the origin of eukaryotes. The clue that points the way to an explanation of their origin is, however, the energy function of chloroplasts and mitochondria in eukaryotes, at least, when we assume that stages of biological evolution are caused ontologically by organisms at one stage becoming organized as multiple parts of higher level organisms that go through reproductive cycles as a whole. That suggests that the eukaryotic structure was tried out, not on the model of enslavement or warfare, but on the model of cooperation. It could have been a result of change at the ecological level in the direction of maximum holistic power and a form of group level natural selection, as in the case of RNA evolution.

The function of the prokaryote-like organelles in eukaryotes is to acquire and process energy. Chloroplasts are organelles that trap the energy of photons in energy-rich molecules, and mitochondria are organelles that use oxygen to dismantle energy-rich molecules all the way down to water and carbon dioxide. Though they lack rigid cell walls, these organelles appear to be descendants of prokaryotes because they contain their own DNA and reproduce by binary fission in the cytoplasm of the eukaryotic cell. (Since chloroplasts contain chlorophyll a and b, whereas blue-green algae have only chlorophyll a, chloroplasts probably derive from the ancestors of Prochlorphyta, a recently discovered kind of prokaryote that contains both chlorophyll a and b.)

These organelles are the basis for classifying single-celled eukaryotes, or “protists,” into three basically different groups. Plant-like, animal-like, and fungus-like – are simply the three ways of exploiting the three prokaryotic methods of acquiring and processing energy.

Plant-like protists, which contain both kinds of organelles, are autotrophs, because (with chloroplasts to absorb energy from the sun and store it in energy-rich molecules and with mitochondria using “respiration” to turn those energy-rich molecules into free energy that can be used by molecular processes in the cell) they need only simple inorganic molecules, which are available everywhere, to complete their cycles of reproduction.

Animal-like protists, which contain only mitochondria, are heterotrophs, because they obtain energy-rich molecules from the environment to fuel behavior by incorporating other living objects as parts of themselves.

Heterotrophs that lack both kinds of prokaryote-like organelle are fungus-like protists, such as yeast, which use fermentation, the first way that prokaryotes found to process energy, to fuel behavior. (Fermentation releases only a fraction of the energy that respiration could extract from the energy-rich molecules, and thus, they are much less active than animal-like protists.)

What the ontological explanation of stages of evolution suggests is that the energy function of chloroplasts and mitochondria were coordinated in some way long before eukaryotes evolved, so that the nucleus was tried out as a variation on the natural perfection of certain ecologies of prokaryotes.

What I will describe here is speculative, and it is probably  mistaken in some details. But such errors are not crippling in this case, because it still shows that it was possible for the evolution of prokaryotes to lead to a variation that made the eukaryotic level of biological organization inevitable. It is something like a “second origin of life,” but it is just as inevitable as the first origin of life.

There may be simpler ways in which the eukaryote level structure could be tried out by random variations, but they would also show the inevitability of the third stage. And as long as there are no such possibilities, this one can serve as a model for discovering the details about how it did happen.

The origin of eukaryotes. Traces of prokaryotes apparently date back about 3.5 billion years, within a billion years after the formation of the Earth. But since there are no traces of eukaryotes until about 1.4 billion years ago, prokaryotes probably had been evolving for about two billion years before eukaryotes showed up. Eukaryotic cells and multicellular organisms both evolved well before the Cambrian era, some 0.6 or 0.7 billion years ago, when the detailed fossil record begins. Empirical evidence leaves us in the dark, therefore, about how eukaryotes originated. But with the help of what we know ontologically about evolution, it is possible to see how it is would have been inevitable that eukaryotes evolved.

Aquatic balloons. Eukaryotes must have evolved after prokaryotes had discovered all three basic energy strategies and filled all the ecological niches that were possible for them in the habitable space near the surface of Earth. Fossils that date back 1.4 billion years suggest that the first eukaryotes were plant-like protists that floated near the surface of the ocean. This suggest that eukaryotes evolved when photosynthesizing prokaryotes happened on the trick of constructing a plasma membrane to contain them, thereby floating themselves together near the surface. The molecules making up plasma membranes form themselves into spheres in water that are relatively impermeable to larger molecules.

The plasma membrane is made of phospholipid molecules (simple sugars with a pair of long hydrocarbon tails on one side and an organic molecule attached to phosphate on the other). When phospholipids are lined up side by side, like matches, forming a two-dimensional sheet, there are weak bonds among them (Van der Waals forces, which come from synchronizing the electric forces exerted within each molecule), but since such bonds hold on all four sides of each tail, they are strong enough to preserve the configuration. Furthermore, the phosphate ends of the molecules have residual electric charges that attract water molecules (which also carry such residual charges), whereas the lipid ends of the molecule lacks any residual electric charge and thus do not attract water molecules. In a watery medium, as a result, water molecules tend to gather on the hydrophilic sides of the sheets that they form, thereby pushing the hydrophobic sides of the sheets together and forming a membrane of two layers. When enough phospholipids are present in the water, these bi-layered membranes naturally form themselves into the surface of a sphere, for that is their configuration of least energy: The membrane close holes that are made in it, giving up energy as bonds form among their hydrocarbon tails. The molecules can move past one another rather freely in the plane of the membrane, and thus, it is actually a two-dimensional liquid. But in order to preserve the integrity of the cell, their configuration as a closed surface in space must continue over the whole cycle of reproduction.

The proteins needed to construct plasma membranes had already evolved, since they are used to line the rigid walls of prokaryotic cells. But with rigid walls, prokaryotes are denser than water and normally sink to the bottom. They could inhabit only limited regions near the shores of the ocean. But prokaryotes would be able to float nearer the surface where they could absorb energy more easily, if they exported the proteins for managing their plasma membranes and used them to construct a large membrane. By including molecules of the right kinds within the membrane, the whole would be less dense than water, and it would open up a new habitat from which they could acquire energy to complete their cycles of reproduction.

Aquatic balloons would be, therefore, a result of the gradual evolution in the direction of natural perfection for ecologies of prokaryotes. The energy they needed was scarce near the bottom on the water, and since prokaryotes whose random variations contributed in some way to this joint control of that relevant condition would more likely be the right location to benefit from it, it would be a group-level natural selection of colonies of prokaryotes by the greater reproductive success.

The group level selection of entire ecologies also occurred, as we have seen, in the evolution of RNA. Combinations of RNA in favorable local regions were selected when storms or other disturbances came, because there would be more RNA molecules of their kinds to populate the new favorable locations. But group level selection occurs in prokaryotes because of how they cooperate in the construction of aquatic balloons in order to tap a new source of free energy.

At first, these aquatic balloons may simply have crashed when their residents had divided too many times and they grew too large. Then, new membranes would have to be constructed, and the scale of the task would require the cooperation of many prokaryotes. But this would have been possible only if their efforts were coordinated in a natural way, for example, by the rise of the sun and the increase in temperature.

Before long, however, some groups would have happened on the trick of dividing their membrane, instead of constructing a new one each morning, and could thereby stay afloat. Again, the scale of the task would require the cooperation of the many prokaryotes in each aquatic balloon, and the problem of coordination could be solved only by a regular, natural change, such as sunset and the fall in temperature. The reproductive cycles of these aquatic balloons were probably entrained, therefore, with the cycle of night and day. Once again, the circadian cycle was the mold for a reproductive cycle that only later evolved its own behavior guidance system.

Aquatic balloons would be, therefore, complex material structures with both kinds of behavior required to go through reproductive cycles, making them subject to reproductive causation. The aquatic balloons would multiply to fill the space in which reproductive cycles of this kind could be completed at all, and the resulting scarcity would impose natural selection on them. Though this would be group level natural selection relative to the prokaryotes involved, aquatic balloons would be organisms on the third level of biological organization, and as variations on the combinations of prokaryotes that made them better able to manage their membrane and coordinate their behavior completed reproductive cycles while others failed, they would become increasingly powerful in their new ecological niche. But they would not be living organisms on that biological level until they evolved a biological behavior guidance system  of their own.

The nucleus. The nucleus would evolve as an improved means of coordinating their behavior. Instead of exporting the proteins from member prokaryotes, prokaryotes could have exported copies of the segments of their DNA, or genes, for handling the plasma membrane and housed them in a special membrane-enclosed chamber inside the outer membrane. It would be transformed by the gradual evolution of aquatic balloon into a nucleus that would serve as its biological behavior guidance system.

Proteins from the prokaryote’s DNA-based regulatory mechanism for selecting which segments of DNA to transcribe as mRNA could be adapted to handle strands of DNA in the nucleus. In order to synthesize proteins from these strands of DNA, however, genes for transcribing mRNA, ribosomes, and tRNA would also have to be donated to the nucleus by the prokaryotes -- as well genes for proteins that assist in replicating DNA. Since genes for proteins that divide the outer membrane would already have evolved, only minor modifications would have been required to manage a nuclear membrane as well as the outer membrane and to control the division of both so that each half of the outer membrane received one half of the divided nucleus. At first, the nucleus just assisted in managing the outer membrane, because the reproductive cycle was imposed by the cycle of night and day. But once the nucleus evolved mechanisms that enabled it to lead the whole through its cycle of reproduction, eventually even telling prokaryotic members when to divide, it would be a behavior guidance system that works on a new level of natural organization. Thus, reproductive causation once again free a new form of life from its natural mold.

Mitochondria and chloroplasts have a slightly different genetic code (that is, triplets of nucleotides determine slightly different amino acids in protein synthesis), and that might be expected on this explanation of the origin of the nucleus. Since the nucleus is a new kind of biological behavior guidance system which evolves from the cooperation of prokaryotes, it would not be surprising if rather fundamental changes occurred in the process.

Though chromosomes are on roughly the same level of natural organization as prokaryotes, it is not surprising they are much more complex than the prokaryote's loops of DNA. We should expect the nucleus to involve a complex process of molecular interactions for handling chromosomes, if the nucleus evolved from the cycle of night and day driving the cooperation of many prokaryotes through reproductive cycles. Since the nucleus was not responsible for leading the whole organism through its cycles of reproduction at first, it could start off simple and slowly acquire the complex machinery that would eventually enable it to take charge. The molecular machinery built into the cytoplasm and nucleus could be come quite elaborate, as during reproduction, when the nucleus closes up the chromosomes (in condensed form), connects them to other special molecules (and later disconnect them), moves them around in the cell, opens them up again so that its structure may flow from certain segments to protein synthesis, and much more.

Indeed, the new mechanisms of reproduction in the nucleus would be the foundation for much greater power, because the nucleus could use the condensation of chromosomes to help control which segments are exposed for transcription into mRNA during period of growth by opening up only certain parts of them. In any case, once the nucleus had taken over the function of a behavior guidance system, eukaryotes would be capable of a scale and variety of behavior that greatly exceeds prokaryotes or anything that multi-prokaryotic organisms could do. It would enable eukaryotes to establish cycles of reproduction in a much wider variety of ecological niches than prokaryotes.

This origin of the nucleus might also explain another peculiar difference between prokaryotes and eukaryotes. In eukaryotes, proteins are often synthesized from genes that are split up in several pieces of DNA separated by apparently meaningless stretches of DNA called "introns." The RNA transcribed from these meaningless segments are cut out and the meaningful segments pieced together before the mRNA are translated into proteins. This may be a new mechanism for controlling the synthesis of proteins, perhaps for synchronizing the synthesis of several different proteins.

Second origin of life. Unlike the enslavement model, this explanation of the origin of eukaryotes depends only on prokaryotes and kinds of behavior that are within their range. Living eukaryotic cells evolve from them in much the same way as living prokaryotes evolved from RNA molecules.

The key is how natural perfection at the ecological level becomes a form of group level natural selection because of how certain ecologies of prokaryotes happen on a way of taping a new source of free energy, controlling what is the most important condition affecting reproduction. The photosynthesizing prokaryotes that became chloroplasts in eukaryotic cells must have been involved in aquatic balloons from the beginning. The bacteria that became mitochondria in eukaryotes were probably also members of aquatic balloons from the outset, living in symbiosis with chloroplasts as part of the ecologies in which it happened. When they became organelles in the eukaryotes cytoplasm, both kinds of prokaryotes gave up their rigid cell walls in favor of plasma membranes.

However, if mitochondria were not members of the colony from the beginning, their presence in eukaryotic cells is not problematic, because evolving the ability to invade aquatic balloons later on to feed on the abundant supply of energy-rich molecules would have enslaved them in order to dismantle energy-rich molecules produced by chloroplasts into energy-rich molecules of a more usable kind.

The explanation of the origin of eukaryotes does, however, involves a "second origin of life" in a sense, because, once again, the cycle of reproduction was originally imposed by the cycle of night and day.

What made the origin of life inevitable was the cycle of night and day, for it drove RNA proto-organisms through reproductive cycles long enough to evolve, by way of DNA, into prokaryotes.

What made the evolution of eukaryotes inevitable was also the cycle of night and day, for it drove groups of prokaryotes, whose reproductive cycles were independent of the circadian cycle, through cycles in which a higher level organism, the aquatic balloon, was reproduced.

Furthermore, in both cases, what evolved was a higher level organism.

What evolved in one case was the DNA molecule, its regulatory mechanism, a cell and, finally, the first biological behavior guidance system able to go through reproductive cycles independent of the circadian cycle.

What evolved in the other case was the aquatic balloon, the nucleus with chromosomes, and, finally, the second biological behavior guidance system that was able to go through reproductive cycles independent of the circadian cycle.

This shows that the origin of eukaryotes was inevitable, for the only way that eukaryotic cells could fail to evolve in this way in a spatiomaterial world like ours is if there is some simpler way in which the structure of eukaryotic cells could be tried out as a variation that occurs during the gradual evolution of prokaryotes. If not, it would eventually occur as described here on any planet where life can get started at all, and thus, the eukaryotic stage of biological evolution will occur throughout the universe.

Gradual evolution. The evolution of the nucleus was the beginning of a new stage of gradual evolution in which eukaryotes change gradually in the direction of natural perfection for organisms of their kind. Ironically, the main accomplishment of that stage was the evolution of a way of incorporating the evolution of lower level structures within the eukaryotic cell. That innovation was sexual reproduction, which increased the power of reproductive causation and accelerated the pace of evolutionary change.

We have already encountered other increases in the speed of evolutionary change in tracing the overall course of evolution.

The natural selection of colonies of RNA for their combinations of kinds of RNA molecules was relatively weak at the first stage of evolution, because it depended on them having greater populations and, thus, being more likely to populate new colonies after a storm or other disturbance. But functional combinations of RNA level organisms could be naturally selected more reliably when they became genes included as segments of DNA molecules, because as DNA molecules, the combinations were more stable, and they could be tried out in a wider variety of locations.

Natural selection of RNA and DNA within colonies of molecules in favorable locations during the first and second stages was relatively weak, because the greater success of more functional RNA or DNA molecules came from being located in the colony where the proteins they synthesized had their effects. But natural selection of DNA molecules became more discriminating when they were enclosed in cells, because the fate of each DNA depended mainly on the non-reproductive structural effects that its own segments generated (rather than on the proteins synthesized by other DNA in the region).

In yet another way, even the evolution of the first biological behavior guidance system accelerated the pace of evolution, because the ability of prokaryotes to go through reproductive cycles more quickly than the circadian cycle meant that there were many more occasions for organisms to be selected by their success in reproducing.

Similar problems arose in the evolution of eukaryotes. The evolution of aquatic balloons enabled colonies of prokaryotes to focus natural selection on the combinations of prokaryotes and made them responsible for their own non-reproductive structural effects, and the evolution of the nucleus enabled aquatic balloons to go through reproductive cycles fast than the circadian cycle. But the increasing power of the eukaryote as a whole entailed a similar weakness about natural selection in eukaryotes, because the kinds of RNA-level and prokaryote-level organisms combined in the nucleus could be selected only by the natural selection of the eukaryote as a whole.

This limitation was less severe in the early in the evolution of eukaryotes, when aquatic balloons regularly disintegrated and had to be reconstructed by the prokaryotes in the region, because that meant that different combinations of prokaryotes were continually being tried out. Aquatic balloon with more functional combinations of prokaryotes would supply more members to be involved in constructing the new aquatic balloon the next day, but the mixing of prokaryotes meant that the evolution of prokaryotes with new powers in some aquatic balloons would soon be found in other aquatic balloons.

But as combinations of prokaryotes became powerful enough to maintain their aquatic balloon through many cycles of night and day, and as they came to reproduce by dividing their aquatic balloon and nucleus into two eukaryotic cells, the combinations could only be selected only by the reproductive success of entire eukaryotes. They evolved in the same way as prokaryotes, even though they were much more complex than prokaryotes and had many more random variations to try out.

Prokaryotes evolve by branchings and extinctions, so that a favorable random variation begins a whole new lineage. That lineage may exist alongside the other kinds or replace them, but other lineages cannot acquire the favorable mutation, unless their own random variations happen to try out a similar trait. This was enough for the evolution of prokaryotes, but eukaryotes were on a higher level of biological organization, and this compounding of complexity meant that reproductive causation would take much longer to approach natural perfection. And the more complex eukaryotes became, the longer gradual evolution would take.

Thus, the benefits of greater power that come with their higher level of biological organization and greater complexity tended to be lost because of the cost of slowing down the pace of gradual evolution.

Sexual reproduction. Eukaryotes solved this problem by happening on a way of accelerating the pace of gradual evolution. It was sexual reproduction, or the mixing of the structural causes bundled together in the complex material structure of eukaryotes as part of their process of reproducing.

The function for which this innovation was selected was accelerating the pace of gradual evolution. Those eukaryotes that tried it out were able to evolve faster, and thus, they were naturally selected because of their greater power.

The most obvious way of accelerating gradual evolution comes from how sexual reproduction makes it possible to combine favorable traits that evolve in different individuals. When random variations are functional in a eukaryotic cell, it does not start a new lineage by asexual reproduction, as in prokaryote evolution. Instead, sexual mixing as part of the process of reproduction makes it possible for favorable random variations that occur in different individuals in one generation to be combined in a single individual in a later generation. Thus, functional traits can be accumulated from different individuals in single individuals, combining their powers.

The sexual mixing also accelerated gradual evolution by focusing natural selection on the lower level organisms of which eukaryotes are parts. In effect, it internalized reproductive causation so that the lower level organisms of which eukaryotes are composed would gradually change in the direction of greater power in their ecological niche as parts of eukaryotes. At any point in the evolution of sexually reproducing eukaryotes, only the most powerful bundles of lower level organisms would exist, because they would be naturally selected. At that point, what makes some eukaryotes more powerful than others would depend only on differences in certain of their lower level structures, and since they would be the only parts that distinguish them after sexual reproduction, the natural selection of the whole eukaryote would turn on their contributions to the power of the eukaryote as a whole. Natural selection would be focused on different parts at different times in the gradual evolution of eukaryotes, because the powers that it is possible for them to evolve at that point would depend only on certain lower level parts and how they work together with what has already evolved to control relevant conditions. Thus, as natural selection shifted from one part of the eukaryotic structure to another, eukaryotes would become increasingly powerful.

The mechanism of sexual mixing means that natural selection can be focused on structural causes at both levels of biological organization below eukaryotes. The shuffling of chromosomes from different parents in the process of reproduction tries out different combinations of DNA level structural causes, and that was probably the original form of this mechanism, because the nucleus had evolved as a mechanism for handling whole chromosomes.

But eukaryotes also evolved a way of extending this effect to the RNA level structural causes of which prokaryotes are composed, that is genes. "Crossing over," as it is called, is a process in which segments of the paired chromosomes from different parent are recombined before being separated from one another and bestowed on different cells. Thus, sexual mixing affects the combinations of units of behavior that make up eukaryotic behavior at both lower levels of biological organization.

Furthermore, the shuffling of chromosomes (and crossing over between them) meant that a far wider range of random variations would be tried out by each generation.

Finally, when eukaryotes evolved the trait of carrying two copies of each chromosome (diploidy), it was possible to preserve genes that might turn out to be useful later or in different combinations with other genes.

The advantages of sexual reproduction are general and would have accelerated the evolution of prokaryotes as well as eukaryotes. But the rigid cell walls of prokaryotes made it difficult for sexual mixing of DNA to be a regular part of reproduction, whereas it was relatively easy for eukaryotes.  

In eukaryotes, the self-forming nature of plasma membranes made it relatively easy to mix parts of their DNA, because that enabled different eukaryotes to merge into a single cell. Moreover, from the beginning, in order to reproduce at all, the eukaryote had to replicate each chromosome in its nucleus, separate the copies, divide its nucleus, and bestow one copy of each chromosome on the nucleus of each half of its dividing outer cell (mitosis). Since it already had mechanisms for handling multiple chromosomes and putting them in the nuclear plasma membranes it constructed, the eukaryote could evolve a mechanism that would shuffle the chromosomes from different cells when they merged, separate chromosomes of the same kind from one another, and bestow a nucleus with one complete set on each half of the dividing cell. This second way of dividing of dividing the cell (meiosis) would account for the various patterns of sexual reproduction found in extant eukaryotes.

To be sure, bacteria, such as E. coli, have a process, called conjugation, which accomplishes much the same thing, although it is not part of reproduction. These prokaryotes construct a cytoplasmic bridge between them and exchange segments of DNA, called “plastids.”

But conjugation is not common in prokaryotes, and it may reflect the selection pressures of being confined to the digestive tracks of multicellular animals. Conjugation enables E. coli to share the mutations by which they can consume new kinds of energy-rich molecules, which stem from changes in the animal's diet. Not only were their non-conjugating cousins not selected, but neither could the animals that lacked conjugating E. coli survive when radical changes in diet were required.

Life began about 3.5 billion years ago, less than a billion years after the formation of the planet, and eukaryotes evolved between one and two billion years ago. But the evolution of sexual mixing during reproduction would explain why evolution has taken less time to reach its present state than it took for prokaryotes to evolve into eukaryotes.

Species. Another dramatic effect of sexual reproduction on the nature of the ontological cause of evolutionary change was to advent of true species. The ability to mix genes sexually with one another makes eukaryotes members of a species that share a common gene pool. Since parts of their complex material structures from the lowest level of biological organization (the RNA level) are regularly mixed in constructing new organisms, there is a sense in which what is evolving is not the organisms, but the gene pool species. The gene pool is just all the genes in the particular organisms that are capable of sexual reproduction and, thus, make up the species.

This does not mean, however, that the gene is the “unit of selection,” as many contemporary Darwinists would have it. The unit of selection is determined by the ontological cause of gradual evolution, or the reproductive cycle, and that depends on the whole organism. The whole reproducing organism is what is naturally selected, because that is the complex material structure that does all the non-reproductive work, the structure that is reproduced, and the structure whose reproduction imposes natural selection on itself.

When the individual organisms are mixing their genes sexually, however, what makes some individuals more powerful than others at any point in their evolution usually comes down to a few genes that are responsible for the differences between their traits at that point. Natural selection is focused on those genes because they affect the reproductive success of the organisms. But that does not mean that the gene is the “unit of selection.” That is just an appearance, which is due to the way in which sexual reproduction makes reproductive causation more efficient. Though the sexual mixing of genes during reproduction has the effect of focusing natural selection on the genes, it is still the reproducing organisms that are being selected by their success in reproduction. And the frequency of genes in the gene pool is merely a useful way of describing the change taking place in the evolution of species by the natural selection of reproducing organisms

Indeed, in organisms that can reproduce only sexually, the unit of selection is not the individual organism, but a larger unit, the mating pair. The individual organism is not a complete bundle of the structural causes that is going through reproductive cycles; it not the material structure that is responsible for the reproductive cycle. Since only a pair of organisms can reproduce, each individual is just half of the material structure that is responsible for the whole cycle of reproduction. Each individual organism must seek its other half in order to be complete. What obscures the unit of selection is that the other half of the reproducing organism is not determined until mating actually occurs.

Even in organisms that can reproduce asexually, the mating pair is a unit of selection, because as long as they can reproduce sexually, that will involve a much more efficient form of natural selection and the mating pair will be the organism that is responsible for the reproductive cycles that constitute gradual evolution.

Eukaryotes drop sexual reproduction only when they occupy stable ecological niches in which they have already reached maximum holistic power for organisms of their kind. But if the environment were to change, closely related species that still reproduce sexually would adapt faster and replace them.

Furthermore, with the evolution of multicellular animals, the unit of selection is sometimes even more inclusive, because multicellular organization enables generations to live side by side.

In protists, or single-celled eukaryotes, sexual reproduction means death to the individual organism, because individual organisms must merge with one another in order to mix their genes in the process. But multicellular organisms do not need to die in order to reproduce. They can set aside special cells for that function, because multicellular organisms reproduce, as we shall see, from a fertilize egg cell. The multicellular organism can, therefore, live side by side with their offspring after reproducing.

Many kinds of animals take advantage of this fact to control more of the conditions affecting their reproduction, for example, by caring for their offspring. Thus, their offspring may go through periods when they are unable to fend for themselves before they take on the adult role of parents themselves. To the extent that a species comes to depend on this generational overlap, the reproducing organism may include not only the parents, but also their offspring, that is, the whole family. In that case, the unit of selection is the multi-generational entity, or “composite organism,” that includes, at least, periods during the cycle when two (or more) generations live side by side and do the non-reproductive work of controlling conditions that affect the reproduction of them all.

In addition to parental behavior that nurtures and protects offspring, the traits that may evolve because of this larger unit of selection include behavior in the offspring that contributes to the maximum holistic power of the composite reproducing organism, such as dispositions to follow parents and altruism toward other parts of their composite organism. This accounts, I would argue, for what is called "kin selection", which will be discussed later.

There are, as we shall see, even larger units of selection, if evolution is due to reproductive causation. But the cause is not the sexual nature of reproduction. It is group-level selection, and it may cause the evolution of composite organisms at the same time mating pairs and families are evolving by their natural selection.