2.3.1 Human Perceptions

Humans want the world to be an ordered, logical place. They want the universe to exist for a reason, and they want a reason to exist in it. The philosopher Kant argued that because there was no justice in this world but justice must exist, there must be a future state, in which all the injustice of present life will be redressed. Yet the world that science, but especially evolution has revealed contains no purpose, intent, progress or justice. It exists, but for no apparent reason. Early evolutionists, even Darwin, thought that evolution resulted in progress towards complex life or that from lower forms of life higher ones evolved. This view is that although evolution arises from blind competition between individuals, it results in large-scale progress.

But now even that concession is under attack. Studies in sexual or host-parasite competition have shown that rivalry is the only end. The large antlers on a stag or the gaudy tail on the peacock might make individuals fit as sexual rivals, but this does not make a species fitter as a population. This is called the Red Queen effect. It means that rivalry is the sole dynamic of evolution. Any progress, if it occurs, is accidental. There is even a theory of how human intelligence evolved by the Red Queen effect. During evolution humans were in intense sexual competition. So, brains evolved to be ever larger in a runaway effect by allowing individuals to become "witty and engaging" sexual partners and that way procure more offspring. (Any comment would be superfluous other than to remark that if we cannot produce a better theory of how our brains evolved than the Red Queen effect, that is probably how they did evolve!)

Yet, in one sense the Red Queen effect is exactly how evolution works. Under stable conditions, fitness is a struggle for very slight advantage. If a father's gene can effect a slight transfer of extra resources from the mother to the womb, that is fit behavior and the gene will spread. Yet, it is only within a limit. Fathers are fit if their genetic offspring flourish at the expense of a mother not genetically related, ahead of a rival's offspring in a different womb. But fathers will loose fitness if their daughters suffer as mothers, depending again on relative success of male to female progeny within a species. Or if a male sperm can kill sperm of a rival that too is fit behavior, and will spread within some limit. As with host-parasite interaction there are hundreds of examples of slight fitness advantage first swinging one way, then another. Regardless of how we think humans behave in natural populations organisms, or even genes, cheat up to a limit where a counter-veiling effect reigns them in again. They cheat at "what they can get way with". Even in computers there can be a program for healthy 80 character long individuals. Then suddenly 45-character long parasites evolve by exploiting parts of the healthy 80-character host, damaging their fitness. Then 75-character parasite resistant hosts evolve and the effect swings the other way. It is an endless cycle. All the rivers run into the sea, but the sea is not full. It takes all the running you can do just to keep in the same place. This Sisyphean labor of change without progress is fascinating, well documented, and intensely studied. So much, that what the majority of us think of as "evolution" is now largely dismissed, or supposed not to exist outside of an indefatigable human longing for some type of progress in a world without meaning.

Yet, what is evolution in a generic sense? What is the human longing to see?

Cynically, evolution has become a term that we accuse somebody of not understanding the meaning of, when they ask us a question about it that we cannot answer! For example, in the universe light elements form by nuclear burning in stars, where elements like hydrogen and helium fuse giving off heat, which causes further fusion. Except the process of fusion burning only continues up to element 26, iron. Beyond iron, fusion is an energy-absorbing (not releasing) process, so it occurs against a loss (not a gain) of energy. It takes a special event in the history of the universe, a supernova, to produce energy absorbing fusion. Yet, supernovas can only occur after Type I Stars (of light elements) first evolve in the universe, and burn to completion. Even this process can only continue until element 94, Plutonium. Beyond that heavier elements can only be created by intelligent beings, composed themselves of highly evolved Type II material, on stable Type II planetary systems. The issue though, is not if we should call this cycle evolution, or misunderstand that evolution should only apply to living not innate things, or not apply to humans. The issue is that until we have explained about supernovas or Type I and Type II stars we have not explained how heavy elements come to exist in the universe. Or, until we have explained conditions under which intelligent life can evolve we have not explained how elements beyond 94 come to exist, or why it takes 15 billion years for such elements to first appear.

The problem of explaining a sequence by which heavy elements first appear in the universe applies to life. The Solar System stabilized from Type II material four billion years ago and elements with greater than 94 protons have come into existence since. Only between these events new structures, materials and processes of life had to evolve for the first time. We can say this was due to the Red Queen effect, except the point of this effect is that it applies to very small changes in genetic distance of one or two genes or alleles, first one way then the other. Only while it is disputed, evolution of totally new materials and body plans requires accumulation of huge genetic distances, by consistently pushing small changes in one direction only. We accept that the cause of variation is natural selection, just as we accept that all heavy elements form by fusion of light ones. The issue is not the process, but that at some stage in the history of life selection will push species very far in one direction, while at other times, selection acts to retain species oscillating around an existing genetic mean. These different effects also produce an appearance of 'explosions' of new species diversity in the fossil record, intertwined with periods of stability and retention to existing forms. So, we want to know what is causing the same processes of mutation or selection to produce different effects at different times in the history of life. Saying that we only want to know this because we are confusing the term 'evolution' with the term 'progress' does not answer our inquiry, or explain why large-scale changes in the structure of life occur.

But are the effects driving large-scale change different? It takes a special event to produce heavy elements, but only because energy is absorbed for heavy element fusion, but released in light fusion. This is a measurable difference. Only most reasons offered why large-scale changes are different from small ones are philosophical, but not measurable. So, are there any measurable differences?

It is disputed, but if crucial measurements were taken they would show differences. For example, adaptation by the Red Queen effect will not register a change in metabolic rate, or any "leap" of thermodynamic complexity over life at lower levels. Yet complex organisms have higher metabolic rates than simple ones, and exist at a higher level of order, further from thermodynamic equilibrium than simpler organisms that they evolved from. Complex organisms also tend to have more cell types, and more genes as expressed DNA. (Total DNA can only poorly correlate complexity, as most DNA is unexpressed.)

Another controversial measurement is of total genome fitness, or how much DNA inherited from an ancestor is exactly copied into descendants as life becomes more complex. The only crude approximation of this is for sexual reproduction, which shows that fitness falls for complex, sexually reproducing types. Yet logically, if ancestors were simple, and descendants diverged a large distance from the ancestor to into greater complexity, less of the exact ancestor DNA will be copied each generation than if the species had stayed simple. Over the history of life types like cyanobacteria have not altered much so they were already fit as ancestral designs. But more recent, complex types must keep modifying their genomes to survive, so less of ancestral DNA is exactly copied. This leads to a startling hypothesis that complex types evolved against a loss of genome fitness. This implies that humans, who diverged furthest from ancestral types like cyanobacteria, or even primate ancestors, also lost the greatest genome fitness from the ancestors to get there. (So much for human or any evolution being progress, it might be that the fittest organisms are those that evolved first and diverged least from type over time!) So, while in orthodox theory it is a mystery why fitness would fall for sexual reproduction, in a new model we will use in this book genome fitness always falls as life becomes more complex. Although this assertion seems strange, appropriate measurements should eventually prove it true.

Is there a name for the type of evolution in which genome fitness might fall over a long lineage, or in which a whole lineage of types is pushed a very great distance in one genetic direction?

Steven Gould has called evolution in one direction orthoselection, but this term does not explain much. Today, adaptive change within a species, or non-progressive iterations like a Red Queen effect are often termed microevolution, while larger, supra-species level change is called macroevolution. Only these terms should not impute that separate forces act on different scales. Forces of mutation, adaptation and selection act the same. But the same forces either stabilize or disturb the fitness limits within which a population can alter. Plus we must not confuse the scale of large disturbances to the ecosystem against a scale of genetic distance. The radiation of mammals 65 myrs ago was a large-scale ecological event, but the large change in genetic distance was in the prior 140 myrs when mammals evolved from reptiles.

We also must distinguish if changes in an evolving system result from inherent dynamics or outside effects. Astronomical, climate, or geological disturbances cause step changes, but not because of mechanisms inherent to how life evolves. Opening a land bridge will cause step changes to land-based life on affected continents, but will only have a spill effect on life in the oceans. Yet, as in computer models step disturbances can arise due to dynamics internal to the system, such as evolution of viruses, or fortuitous gene combinations that allow individuals to leap a step distance for a nominal cost of change. Another internal effect is population size against dispersal. As explained, math and computer models consider that populations of any size equally respond to change without a dispersal factor. But in homogenous environments like the air, ocean, or large land tracts dispersal will slow rate of fixation of new traits. This will have a stepped effect on rates of evolution, because small populations will evolve fast until they mature, then slow down the rate of evolution as they disperse as matured types. This also affects how the fossil record appears, as there is less chance of finding fossils from small, rapidly evolving population than from a large, dispersed, slowly evolving one.

The other internal factor usually overlooked is that some traits will be easier-to-alter than others. This is not considered in current math or computer models, which treat all changes as equally likely. But in reality some changes extract less cost than others do. This will restrain individuals to seek quick, low cost fitness-rich enhancements like improving shape, length or sharpness of an attribute. Eventually these types of changes will saturate for a given level of complexity, and individuals will be forced to adapt more costly changes that increase complexity to survive. Again, individuals in a large population in a homogenous environment will not be able to adapt via high cost changes. But as homogenous environments saturate, small populations will become isolated in "peripheral" niches such as the dark, cold, or less penetrated environments, where high cost, directional adaptations over a long time are possible.

To distinguish it from macroevolution, which includes all large changes, we will refer to the process by which populations acquire a directional increase in complexity as phylogenic evolution. We define a phylogeny as the attributes that any organisms share in common, by direct, unbroken descent to the last common ancestor. Large brain, upright stance, and hairless body is the phylogeny of humans. Opposed thumb and stereoscopic vision is part of human phylogeny, but one that humans share with apes. An important phylogeny in the history of life exclusive to primates is connection of the tactile nerve endings in the hand directly with the brain. Yet, primates are mammals, sharing a phylogeny of body fur, four-chamber heart, milk to suckle young with other mammals, but not with reptiles, fish, birds, or any other creature. Birds, mammals and reptiles are all tetrapods, sharing a phylogeny of four limbs, heart, and lungs. Fish are not tetrapods, but still share a phylogeny of vertebrae, brain, and respiratory and circulatory systems. Further back are deeper phylogenies. All plants and animals have eukaryotic cells, which are a major phylogeny of life. Eukaryotic cells share features of life such as cell wall, DNA and RNA, with prokaryotic cells, which evolved first. Prokaryotic cells form two types, made from slightly different cell materials. Plus there exist viruses, which are not living cells, but share the phylogeny of RNA, and some DNA and other materials of life. So, by making a phylogeny the exclusive attributes of any individual, we can make a phylogeny as broad as we like or stretch as far back in the history of life as we like.

Only for phylogenies, sharing of attributes must be by unbroken descent, back to the nearest common ancestor. Birds have wings, but so do pterosaurs. Yet the nearest common ancestor of birds and pterosaurs did not have wings, so while wings are separate phylogenies of birds and pterosaurs, they are not a shared phylogeny like vertebrae, hatched young or a two-chamber heart. So, evolution is replete with convergent or analogous evolution. Sharks and porpoises share a common analogous appearance, but one is a fish, which existed for 350 myrs, the other is a mammal, which adapted to sea life only in the last 50-60 myrs. Sharks and porpoises do share a phylogeny, but dating back to the common ancestor of fish and reptiles, 400 myrs ago. Because they are shared back to the nearest common ancestor, phylogenies represent homologous evolution, or underlying structures that relate species by descent, rather than the modern appearance of species. Although it need not happen, for life on Earth all phylogenies relate to deeper ones, because life on Earth evolved from a single ancient phylogeny or a single dominant phylogeny that displaced all the rest.

We can use the concept of a phylogeny to examine what is truly new in evolution, against mere Red Queen effects. Now in one sense each species has a unique phylogeny, so the slightest alteration in a species, even a Red Queen effect, is phylogenic evolution. But unlike for species we can make a phylogeny as broad or deep as we like, effectively stripping away all the analogous, convergent, and easily variable traits of species, to see if anything new evolved. In the period from 200 to 65 myrs ago there were huge changes in the appearance of life. But if we examined the phylogenies of dinosaurs or fish as an order over that period, not that much had changed. Yet for mammals, at that time a tiny, almost insignificant creature several important new phylogenies had evolved, such as body fur, four-chamber heart, endothermic regulation, improved dentition, live birth and so on. Only we could not from an arbitrary yardstick say this made mammals 'fitter' as a type. As contested, if we measure 'fitness' as amount of exact copy of genome each generation, mammals are likely less fit than the reptile ancestors they evolved from. (They evolved at a fitness cost.) But mammals had a higher metabolic rate, more varied cell types, more intelligence, and could adapt, penetrate new ranges, and evolve faster than any previous large animal type. Now we can call these changes in mammals progress, macroevolution, "production of higher animals" (Darwin) or anything we like. Here we call it phylogenic evolution. The importance is not what we call it, but that we can correctly explain how and why these new novelties and technologies evolved at all.

So, why did they evolve?

Here, we really ask two questions.

1. We want to know why life evolves or increases in complexity at all, to which we can give vague answers.
2. We want to know, assuming that life tries to increase complexity, the patterns and mechanisms it follows. We can offer better answers to this, though they are not the answers of orthodox theory.

As to why life evolves at all, it is difficult to narrow this to a single "cause" such as natural selection. Explaining why the universe exists is a legitimate inquiry of theoretical physics, but beyond this science can only measure how the universe behaves and try to explain it. Yet, measurements of how or why complexity increases too are vague, but it has roughly to do with energy and information in the universe. In the early universe part of the huge energy of creation is converted into enduring structures of matter. But for innate matter this process can only proceed up to a complexity level of amino acids or other building blocks of life. Beyond this, complex forms of order have to self-replicate, or 'live' to maintain themselves in the face of what we call Second Order dissipation. There is some confusion over what this means, but very roughly life requires that energy pass from cold objects into hotter ones, which is not its normal direction. Significantly then, early life evolved near heat sources where energy was plentiful, and only needed to overcome a shallow Second Law gradient. But early life could not move away from energy-rich heat sources because it would encounter too much Second Law cost to maintain. Except once life evolves DNA it acquires means to lower the cost of evolving new forms by accumulating the information of how to build-up complexity over time. It took over two billion years or 60-70% of time since life evolved and 15% of time since the universe began for life more complex than single-celled organisms to emerge. There are many reasons, but broadly we say that the universe 'wants' energy to condense into complex structures. But it is hugely difficult to maintain structure in the face of Second Law dissipation, or far from thermodynamic equilibrium. The universe tries to evolve complexity, but only at an energy-information cost it can afford.

Now we come to the second question, of which pattern of build-up of complexity does life follow?

Well, we know from the fossil record that the pattern of change is mostly stepped. There are many theories to explain this, but mostly they use a 'dam-burst' mechanism. (The rain falls and the river rises steadily, but when the dam bursts there is a step upset in equilibrium.) The theory of phylogenic evolution is that there is one more dam against steady progress; a form of fitness barrier. All change comes at a fitness cost, but some changes are easier to enact than others. New phylogenies evolve from hard-to-enact changes, but at any point since life emerged there is always at least one existing phylogeny that can be adaptively exploited. The early thermophilic phylogeny eats sulfur, directly converting heat to energy. This can still allow many types, but it limits life to the heat and sulfur sources. Cyanobacteria were a new phylogeny, which could move away from the heat sources by converting sunlight to energy, releasing oxygen. This too allowed many types. But as the oxygen built up, a new phylogeny evolved, which could directly convert oxygen as a rich, versatile energy source. This too allowed more types at this next level, and so on, all the way up the much-dreaded scale of life. Only at each step on the way there was a pause. Each new phylogeny allowed a fresh radiation of types adaptable around the basic design. There is a cost to evolving major new phylogenies, so organisms will not pay that cost when they can more simply adapt an existing phylogeny by quick, fitness rich changes. Most of life, as evolved in time and as exists today, is simple phylogenies such as bacteria, existing at a low fitness cost to evolve.

But if organisms prefer to adapt existing phylogenies than evolve totally new ones, what "forces" some of them to make a new, large, high cost change? Why do major new phylogenies evolve at all?

Well, we know why the last major large-animal phylogeny evolved on Earth. Great apes, primarily, are forest dwellers. That is what they evolved to be for over 55 myrs. They can adapt to other life, but only at a cost to change. Yet over the last few million years, when the forests shrank, one branch of great apes was forced out from the forests, from the life it was comfortable with, and evolved for, and onto the plains. Because of our prejudices, we see man's ancestral move out of the forests as a 'winning' move, a move that led to us! And in terms of our modern options, we would rather be humans than apes. We were also fruitful as a species, and now we are foolishly destroying the forests that were our ancestral homes and killing the primates who are our ancestral cousins. But we paid other costs to evolve that only seem worth the sacrifice to modern humans. If our ancestors could have avoided the costs and stayed in the forests they would have. Species refine and adapt through intraspecific competition between individuals, which applies all the time. But evolution of significant new phylogenies is not an end product of intraspecific competition alone. If a species alters far from what it was, it is only because a force external to the species has pushed it far in one direction.

2.3.3 Saturation, Concatenation, and Radiation

We will call forces that push some populations into strongly directional changes a concatenation. A concatenation is not a direct force, but evidence of underlying saturation pressures acting on an entire biota. It acts not at the prolific center of life, but on an outer periphery where a population might be "pushed" into an unusual behavioral or migratory pattern. If we see early ocean life being "pushed" onto land there is concatenation in the ocean. If eons later we see land adapted life being "pushed" back into the sea there is concatenation on land. Concatenation occurs when there are no fit moves left for weaker organisms, within the restraints of an existing phylogeny or range. The oceans are huge, but if life reproduces prolifically eventually the oceans will saturate with all types that can be optimally adapted to life in the sea. Then saturation will push life onto land. Only the first time it occurs there will be major alteration to existing phylogenies, which had been adapted only for life in the sea. This need to alter not only a habitat, but also a phylogeny to a mode of life not previously encountered will place huge directional pressures on organisms undertaking this move for the first time.

So if a bird species had migrated to an uninhabited island then radiated, like Darwin's finches did, concatenation causing this was small. If the finches had been forced to migrate because of mainland population pressure, that was evidence of a minor concatenation. But if they had just been blown off course there was almost none. If the finches were forced to change diet or breed with smaller clutches, that might have been minor loss of genome fitness. But it would require phylogenic pressure among the mainland biota that forced the birds to migrate, then stopped them radiating back to the mainland until they had altered type for evidence of a large concatenation. On the other hand, the phylogenic pressure that forced ancestral birds to evolve feathers was an episodic (once only) monophyletic accumulation. It began when among thousands of Jurassic species one small creature could no longer compete within the existing dinosaur niche and the limits of the dinosaur phylogeny. This creature was pushed by competition into a "peripheral" niche such as a colder climate, or cold on high mountaintops just to survive. Except if a creature is pushed out from a niche it was adapted to, into a less comfortable, harsh niche where it must alter to survive, it is already facing fitness loss, or extinction in its present state. So, the creature will accept any cost to survive. No organism measures fitness scientifically, but eking out existence, altering type or reducing litter size in harsh times eventually extracts a cost measurable in exact copy of genome DNA. (Humans alone behave the opposite to this. The more desperately poor they are, the more atrocious their conditions of life, the more a failing individual tries to pass on DNA through increased offspring.)

Moreover, when a lineage enters a niche where it must alter to survive it must keep changing. Fitness as genome DNA is measured as passing on exact copy of total DNA, but exact copy of the prior design will not be optimized for the new niche. An exact copy of dinosaur DNA was not optimized for the niche where birds were forced to evolve feathers to keep warm. A creature intermediate between a dinosaur and a bird will still not be an optimal design so its lineage will need to alter further to survive, which means it too must pass on altered rather than exact copy DNA. In any altering lineage the most recent descendant 'wants' to be the last in the lineage to alter genome. That way the most recent descendant can be the most fit, because it can copy its genome into a huge radiation. Only there might be thousands of intermediate steps between a bird and a dinosaur before the optimum design is found. While each step in the lineage is fit in isolation no one intermediate is stable and the type must go on altering, and altering its genome, until the full bird type evolves. Over such a period the lineage will be subject to "directional" selection. Evidence of directionality is that the type stays confined to a narrow line and cannot radiate as the fittest move. Except lack of radiation among prototype lines often continues for millions of generations, while large alteration to its genome accumulates.

Mammal evolution provided classic evidence of a concatenation. From about 320 to 200 myrs ago, mammal-like reptiles evolved with minor radiation, but not in a peripheral niche or at a great fitness cost, which reflected a weak concatenation. But from 200 to 100 myrs ago, ancestral mammals became confined to the nocturnal or small animal niche. They then evolved in a narrow line while undergoing major phylogenic accumulation. This indicates a strong concatenation. A similar effect produced the evolution of birds. Or an earlier concatenation among marine life produced the evolution of amphibians, as one among amphibians had produced the evolution of reptiles. In each case a population was forced to adapt in a "peripheral" niche while its lineage evolved in a narrow line. The evolving line did not radiate from its peripheral range until it matured. Birds did not radiate until they evolved feathers, or mammals did not radiate until they accumulated their novel attributes. (Non-placental mammals did radiate slightly earlier and monotremes earlier than that.) In each case there was a cost to change as well, such as increase in metabolic rate or genome complexity, reduced litter size, new material or body plans, or a combination. The new model proposes that all major phylogenic change evolved during concatenations. Roughly

1. There was saturation among an existing phylogeny. This led to expulsion of organisms into a peripheral, under-exploited niche.
2. The exiled population then evolved in a narrow line against heavy fitness costs, altering radically from what it had been in the old niche, into a type that had not previously existed anywhere on Earth.
3. Finally, once the new type matured and the new technologies and body plans were perfected the type radiated into many new ranges, as a step change in the history of life.

In the new theory we will call any new environmental range a population is forced to adapt to by some external pressure a "peripheral" niche. The plains are a peripheral niche to forest dwellers. Loss of heat is peripheral to thermophilic life. The shoreline is peripheral to fish. Cold is peripheral to reptiles. An unpleasant or low quality diet might be a peripheral change in minor speciation. But the conceptual difficulty is not that such niches exist, but how and why individuals are forced into them. Large peripheral niches become supernovas of evolutionary change, from which species mostly emerge 'higher' up the scale of life than species that stayed in a comfortable niche. But because of our prejudices we confuse the term 'higher' with 'fitter'. Because we see mammals as 'higher' up a scale than reptiles, we assume that mammals 'climbed' or 'ascended' a metaphorical fitness slope to get there, as though motivated by a goal to become 'better'. But more likely mammals were pushed out from a comfortable niche by competitive pressure. They did not climb a fitness slope but slid down a fitness decline to become, strangely, more complex and versatile creatures. In comfortable, stable ranges already populated by fit, felicitously adapted organisms, no creature can afford to alter too much from already proven designs. But once creatures move into peripheral niches all bets are off. Individuals on a fitness decline still compete with each other to be fit relatively. But in a new niche novelty, change, and experimentation is more likely to be fit than marginally improving a design adapted for a niche past. There is evidence that in times of stress and change, some genes will force higher rates of mutation that might prove disruptive or fatal for competition in comfortable niches.

Still, apart from claiming that fitness declines in peripheral niches, populations being forced to evolve faster in marginal or changed conditions is already known. What is not known, or often overlooked, is that very large changes of this type can only occur a limited number of times in the history of life. There are two reasons. Migration from the middle to the edge of a forest, or slight change of climate or diet, is a common evolutionary event, which happens all the time. But in the history of life on any planet there are a limited number of totally new environmental ranges that must be penetrated for the very first time. Life begins at the thermophilic heat sources. Moving away from these means penetrating a new range for the first time. Moving from oceans onto land, or from warm to cold climates is also a one-time, major event the very first time it happens. These events will also require major, phylogenic changes to the structure of life the first time they occur. But once all the new ranges are penetrated the first time such radical alteration to phylogeny will never be required again. The ranges available on a planet are now saturated. Anywhere on a planet with a livable environment an organism wants to go, a phylogeny as biological novelty already exists to penetrate that range.

Only there is one other reason these large changes occurred only in the past, and will not happen again. Just as a change of climate or vegetation is an endless event in evolution, many adaptive features of organisms are endlessly or continuously variable. The length of a worm can be physically constrained to a theoretical maximum and minimum possible we can call a node. But the property "length" is infinitely and minutely variable within those constraints. Length, shape, color, texture, size, sharpness and behavior all have physical nodes placing constraints on variation. But within constraints, in multiple combinations of varying each possibility, the size, shape, color, texture and behavioral possibilities are endless. Because a species is an inclusive set of all traits distinguishing one group of individuals from another, a species includes all infinitely variable traits that cannot saturate. So adaptation of a species cannot itself saturate. Anything that a species is today there can exist some other appearance or behavior that it could evolve into. Only by the same definition phylogenies are an exclusive set of traits, stripping away exactly those traits that are highly and continuously variable, to reveal the core homologies around which life is structured. So if species as an inclusive set of traits never saturate, do phylogenies as an exclusive set invariably saturate?

Well factually, they do. There can be a two and four-chamber heart, but never a six chamber one for present life on Earth. RNA evolved into DNA (perhaps twice) but then saturated. There will be no more genetic codes. DNA might have first coded for a few amino acids, then 16, and now 20, but the progression has saturated, and there will be no further natural coding for amino acids beyond 20. All the major phyla, classes, orders or even families have evolved for life on Earth. All the major phylogenic possibilities are saturated.

We have already explained in the previous chapter why this is. All change comes at a cost, while large changes extract large costs, which few individuals can be prepared to pay. But change not only comes at a cost, it evolves new means to adapt at lesser cost once the new novelties have evolved. There is no need to re-evolve the DNA code every time an organism needs to vary slightly. Organisms with DNA can already adapt much faster than a new code could evolve. Today, reptiles could not evolve in competition with mammals novelties such as endothermic regulation or live birth. These novelties already allow mammals to adapt to change and competition at a much lesser cost than to evolve the novelties again from the start. Plus as we shall see in the next few chapters, evolution of life on Planet Earth has now entered into general saturation caused by the uniqueness and adaptability of primate phylogeny, but in particular by the great adaptability of human phylogeny.

Once we can accept that unlike for species, phylogenies will saturate, we can at last see why there will be very large, directional changes in evolution in the past that cannot occur today. The first, thermophilic organisms will begin evolving close to heat sources. The phylogeny that allows tissue to convert sulfur to reproductive energy will allow many variations, but eventually it will saturate. Through natural selection, from a given starting point which is set historically there will come another point where sulfur cannot be converted more efficiently than by present organisms. If the population is to keep expanding, if life is to evolve further, it must move away from the sulfur sources. Those best adapted to the old way, the 'fittest' of the early organisms will stay with the existing, primal niche. But other organisms will be pushed out peripheral niches, where to survive at all they must evolve new phylogenies, regardless of the fitness cost. This process will continue, relentlessly, remorselessly, until every niche is penetrated and every major phylogeny is saturated.

In a phylogenic sense then, life evolved from simple to complex through a progression of events that unfolded as episodic events in the history of life. Only in life, complexity does not replace simplicity, but it builds in layers on top of simpler forms. Life is not a ladder of complexity but a pyramid of it. Eukaryotic life, which is about 100 time more complex at its base than prokaryotic life, evolved later than prokaryotic life but it did not replace it. Prokaryotic life is possibly more extensive today as a base layer of life than when it first evolved. Also, like in computers, once complex life exists it allows viral and parasitic sub-life, which previously could not exist. Or in a temporal scale, mammals evolved from reptiles, they from amphibians, and amphibians evolved from fish. Only although there have been dramatic extinctions like that of the dinosaurs, modern fish, reptiles and amphibians live today, as do dinosaur descendants in birds. Or while large, complex life such as mammals is more adaptable than simpler large life like reptiles, simple life like bacteria, worms or insects enjoys greater survivability against extinction. So all of life evolves, but some at faster rates than others, while some life retains its initial simplicity, relative to complex forms which evolve later.

Human evolution too occurred as an episodic event when life on Earth evolved to a state of general saturation. Today, it has become incredibly political to insist that there is nothing special to human evolution. A "relatively minor phenomenon" as Steven Gould never tires of lecturing us. But politically correct perspectives in science are only useful if they aid further understanding. If there is nothing special about human emergence it also means that we have no way to explain it, except by wringing tired mileage from problematic theories like the Red Queen effect. Later we will show that if species form inclusive sets, and phylogenies are exclusive sets, then there will evolve at least one unique set with the qualities of both, once the system is driven into general saturation. We cannot prove that this would apply anywhere but on Earth, which is our only case, but we can provide a more balanced logical model of why complex life evolves.

Yet, in a strange way anything one says about phylogenies, species, human evolution, saturation, directionality or any other topic is almost academic. It is like trying to explain the workings of a company to an auditor, without showing him the accounting books. Complex life is incredibly fragile and hard to evolve, so it can only succeed at all if every change is carefully recorded as what the change was and how much it cost. Nature records the accounting books of life in the DNA code. So if phylogenic evolution occurs, its history too will be written in the DNA record.

What then, does the DNA record tell us about how life evolved?