The Theory of Phylogenic Evolution
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PHYLO.PDF(Caution: I hope you did not find this looking for information on four-chamber hearts in dinosaurs, because the example used here, saying they could not evolve them, now seems incorrect. I will rewrite this part shortly. The example of feathers only evolving once is correct.)
(Note: This theory is to prove how saturation works, plus it touches on systematics and logic. You might skip ahead to
5.0 The "Smart Gene" Hypothesis. But if you are interested in human evolution, you should read this.)
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4.0 The Theory of Phylogenic Evolution
Crucial to any theory of evolution is clarifying exactly what is asserted to have evolved. There can never be a theory of pterosaurs evolving into birds, because they never did, and never could have. The taxonomic reason is that the common ancestor of birds and pterosaurs split into separate lines before pterosaurs flew or birds evolved. But this raises a question that although they were separate lines, why did pterosaurs not evolve feathers?
Yet once creatures with feathers took to the air, the novelty "feathers" offered such advantages for long-range flight that it soon dominated the niche. So once bird types stabilized no creature already a bird would face the need to evolve into something that was not a bird. And no creature, which was not already a bird, could ever afford the time or fitness cost of evolving feathers, to compete with creatures that were fully evolved birds.
We will term attributes that distinguish birds from pterosaurs or mammals from reptiles the phylogeny of a group. So, a phylogeny is the attributes that all members of one or many species share by direct, unbroken descent from the last common ancestor.
Taxonomically, some biologists treat birds as the same class as dinosaurs. But for a phylogeny an attribute only must be distinguishing, and of unbroken descent from the nearest common ancestor. So, "feathers" is a distinguishing phylogeny of birds. The nearest common ancestor of all birds had feathers, plus each and every descendent of that ancestor has feathers in an unbroken line of descent. Also, no other creature on Earth, which is not a descendent of the ancestral bird has (bona fide) feathers, or ever could.
We will call a phylogeny an exclusive set of unique attributes, shared in unbroken descent from the last common ancestor.
So, by restricting a phylogeny to exclusive sets of attributes we can make a phylogeny as broad as we like, or project it as far back in the history of life as we like. We only must be careful that the descent is always unbroken. If two species of anteater both have quills, but the nearest common ancestor did not have quills, those quills are not a shared phylogeny. So, phylogenies must be monophyletic by tautology. A correct phylogeny can no more be polyphyletic than a circle can be square. (There are disputes about this. Here we define a phylogeny logically first, then examine any case where the logic is broken to discover why.)
However, just as we can define phylogenies as unique, exclusive sets, so we can define species as unique, inclusive sets. Now humans and chimps have a shared (rather important) phylogeny, such as stereoscopic vision or opposed thumb. Yet humans and chimps form distinct species. If we include in the set of humans all attributes unique to humans, then we exclude from that set all chimps, because no chimps possess attributes (large brain, upright stance, etc.) inclusive of all human attributes. The distinction becomes crucial once we accept that traits form two broad categories.
Because all life consists of easy and hard to change attributes, these are present in every organism. Not a single cell or virus that existed or could exist, does not contain a "mix" of attributes, some easy and some hard to change.
But this ubiquitous presence of easy and hard to change attributes complicates evolution, because the easy-to-change, homoplastic traits, like moves in a game of chess, are infinitely variable. There are physical limits, we can call nodes, to any length, shape, size or sequence, but this does not restrict variation.
So, when we define a species as an inclusive set of attributes we include in that set (and in all species) traits that can vary indefinitely and continuously without progress towards completion. We also restrict species to millions of unique sets that have existed throughout life. From this we can only observe, taxonomically, that one species has "evolved" into another. Some evolutionists dispute that we can even make that distinction, in terms of continuous, incremental change.
Yet, once we restrict our observations to exclusive sets forming phylogenies, we can exclude the easy-to-change, continuously variable, homoplastic traits. It is contentious that we can do this, but it does offer a unique perspective on not just how species, but how their underlying phylogenies also evolve.
Phylogenic evolution is the evolution of exclusive sets. In a way all evolution is phylogenic, because the tiniest divergence of offspring from parent produces an exclusive attribute. But sensibly, phylogenic evolution is evolution of new novelties that have not existed previously or elsewhere.
And while most of evolution is change without progress phylogenic evolution is irreversible. This is disputatious because if life on Earth were wiped out and started over vertebra life or four-limbs might evolve again in new circumstances. But;
The reason some traits evolve irreversibly while other traits oscillate without progress is a consequence of fitness. Any trait that evolves irreversibly is a complex accumulation. Complex accumulations do not result in complex organs, but simpler organs that evolved for complex reasons.
For eyes, increased vision however slight yields an immediate fitness advantage, one not necessary to coordinate with other improvements. (Unless a creature lives in total blackness, in which case it is fitter to atrophy the eye quickly, and improve something else.) But the fittest way to improve a heart is to make the organ bigger or beat faster. Extending the ventricle divide makes a similar size heart more efficient, but it requires complex pluming, respiration, digestion and endothermic regulation to turn efficiency into a fitness advantage. These further improvements (unlike say, just making the heart slightly bigger) require thousands of generations to coordinate and perfect. So of the millions of early species that might have benefited from a more efficient heart, only one, or a narrow range, bore the evolutionary cost of evolving one. Then it was a tiny creature, shunted off in the nocturnal "peripheral" niche of dark and cold, outside of the evolutionary mainstream for nearly 100 myrs that made that effort. Yet once the four-chamber heart design had matured, no creature without the new design could afford the fitness effort to itself evolve a four-chamber heart, especially facing competition from creatures with the new design.
The four-chamber heart then, was a complex accumulation. Its evolution took a concentrated, focused effort. (Although there was no teleological direction of this effort, apart from fitness.) Significantly then, the four-chamber heart, once it had matured, radiated within many types. Yet once a trait radiates into many types it becomes homologous, and by another of our definitions, harder to change. (It is not hard-to-change because it is homologous by definition. It was a hard-to-evolve trait, and that is why it radiated into a new homology.) Only complex accumulation, maturity, radiation, and homology are characteristics of all phylogenic evolution. At first, this is only an assertion of logic, which needs to be checked empirically (factually) against how evolution occurs. But research should confirm that;
This might seem true by definition (a tautology), but there can be exceptions. Body segmentation seems a basic homology but it evolved twice, so we need to check why it did not fit the pattern. Plus other complex accumulations might have matured but did not radiate. Yet, the primary pattern is that traits that end up radiating as homologies are going to be hard-to-evolve, which is why they only evolved once.
Defining phylogenies this way evolution is a single natural process but two analytical ones. We think of evolution of species as a natural process. But it is a human description of nature, analyzed as how whole individuals within a population evolve, including how both the easy and hard to evolve traits within individuals evolve. So;
Yet these are not different processes of evolution. They are the same natural processes analyzed by a different set of rules. This is a logical model that we use to examine the natural process. There will be exceptions, so where the model is broken (body segmentation evolving twice, say) we need to examine why the exception occurred.
Using these different analytical models of evolution (species and phylogenic) to examine the one natural process, we notice a crucial difference between them. Unlike species evolution, which never saturates, phylogenic evolution always saturates at some point. So, let us examine how this happens.
The new theory of evolution was devised initially to explain human evolution. There are many ways to explain this, but usually they require an effect called saturation. Only this effect has never been explained. There was saturation triggering human evolution, that human ancestors were evolved for forest life. But by the Pliocene Age the forests were shrinking, and had become saturated with the existing primate population. This forced a migration of individuals out onto the plains, which forced further adaptation, and so on.
Only if human ancestors adapted to life on the plains, they did not minimally adapt the way baboons did. Human ancestors adapted not as primate 'plain-dwellers' but evolved fully into humans. We can claim it was "for the good of the species" to become humans, but as explained (see theory of complex accumulations) large divergence from an ancestral type requires evolution against a loss of fitness. And genetically (by chromosomes) humans diverged furthest of all from great ape type. Plus other human adaptations such as the large brain (see Theory of Options) indicate that humans must have lost a lot of fitness to become 'humans'. Also, monophyletic evolution among a narrow group usually ends in a radiation once the evolving type matures. Human evolution was monophyletic (there are disputes about this) plus once the type did mature, it radiated in a huge variety to every continent on earth. But other patterns of this type resulted in radiation of many species as a class, order or family. Humans remained the one species, genetically little removed from great apes, while all the other indications are of evolution of a whole new order or family.
The explanation of why saturation occurred or why humans radiated as a species requires not just a new theory of human evolution. It needs a new theory of virtually all evolution, in which processes of fitness, selection and reproduction are the same, but the circumstances under which these processes act will vary. In the "old" theory evolution is serial, acting only in time. One species evolves, then another evolves from the first. But "species" is just a human definition. It is a "view" of evolution, which reveals some aspects of the process but hides others. Species reveal how populations evolve because species compose of individuals who form populations. But how species as a category evolve depends on which attributes evolved in earlier species.
Ancestral species of humans are extinct, they do not existing in "living" time. But the ancestral phylogenies are not extinct. (Some are. Just as there were species dead ends, there were phylogenic dead ends. If a six-limbed vertebrate ever existed, its phylogeny is extinct. In human evolution there were many branching designs that did not make it.)
However, if phylogenies exist in layers even though all phylogenies evolve in time, their final structure is not just dependent on time. This is contentious. One argument of evolution is "given sufficient time" any combination is possible, but this is not correct. Among highly adaptable phylogenies new species can evolve in 104 generations, which is not a long time. But the structure of existing phylogenies will determine what can evolve and when and how. So, for some changes we do not even require much time.
The reason is that while adaptations of any existing phylogeny brings immediate fitness gains, evolving new phylogenies extracts fitness costs. So once a phylogeny (as defined here) is perfected no competitor can afford the fitness penalty of re-evolving that phylogeny in rivalry. This will give a stepped effect to evolution, because organisms will always try to adapt existing phylogenies first, rather than incur the fitness penalty of evolving new phylogenies.
(Caution: This next example about four-chamber hearts needs more research
. Scientists have now discovered a dinosaur with a four-chamber heart, so some of this needs rewriting!)Again, an example is the four-chamber heart. For its size, a four-chamber heart is more efficient than a two-chamber one, and extending the ventricle to fully isolate two chambers into four seems a simple adaptation. But no creature other than a mammal ever did, or could evolve again a four-chamber heart.
So if a reptile, with a two-chamber heart, competes in a niche against a mammal, with a four-chamber one, the reptile will stick to reptile moves, and the mammal to mammal ones. Only the reptile will have to make smart moves to win head-to-head against a mammal. If a reptile can evolve a slightly bigger heart, so can a mammal. But the mammal heart will still be more efficient, plus other indications are that the mammals can evolve faster. (Mammals do not evolve faster because their genes mutate faster, but they alter behavior faster, so they adapt behavior "first". Plus even if mammals do not mutate genes faster, there is a good chance that they redistribute allele frequencies or alter traits faster.) No other creature on Earth could evolve a four-chamber heart in the time a mammal could adapt another part of its phylogeny, to beat the other creature in a race for adaptation. (Competition will be more between members of the same species, in competition for fitness against another species, etc.)
The result of phylogenies being structured around pre-existing complexity, rather than passage of time, is that phylogenies saturate. The issue is again fitness, existing phylogenic structure, high variability among modern types, and the evolutionary costs to altering a proven attribute against fierce competition. We have seen how fitness will prevent a rival to mammals evolving a four-chamber heart, but why could not mammals evolve a six-chamber heart? (This example makes the point, but I am looking for a better one.) Even if a six-chamber heart were more efficient, it still must evolve, and there are so many simpler, faster, and more fitness effective ways to evolve and to compete. (To compete, why worry about the heart at all? Why not just evolve a bigger brain?) There is an example of this. Continental drift split mammals into separate evolutionary paths as marsupials. (They also split off monotremes. This is where disputes start about mammalian evolution being polyphyletic, etc.) But following the split 'northern' mammals underwent phylogenic evolution into placentals. But if recent migration brings the two types together again, the more advanced placentals usually displace the marsupials. Yet, marsupials can never evolve in rivalry the novelties of placentals. The placenta was a complex accumulation, which once it evolved the first time cannot evolve again. So along separate paths, marsupial and placental mammals reach phylogenic saturation of their possibilities. Or perhaps, placentals reached mature saturation of the phylogenic possibilities of large animal life on Earth. Marsupials never reached theoretical saturation, but they reached practical saturation in a crowded world, against more advanced rivals who evolved further.
Only what happens to placentals, the most advanced mammals, is that they split into still more advanced sub-phylogenies. (Again, placental evolution was monophyletic. One species perfected the placenta, then it radiated. If diverse species separately evolved the placenta that is polyphyletic, which needs explaining!) Once a phylogeny starts to sub-branch, it is hard to claim that a new phylogeny in one branch is more advanced than another one. (We can claim that placentals are a phylogenic advance over marsupials. But until we know the branching sequence it is problematic that dolphins are a more advanced phylogeny than rodents or bats.) However, over all the sub-phylogenies of placentals, one order seems to have evolved further than the others, to a point of what we might call general saturation. And evolution beyond a condition of general saturation can have far reaching consequences, for life on Earth and in the universe.
4.4 General Saturation
The problem with any theory of evolution (including this one) is that we cannot tell from an initial condition what the final state will be.
If anything, the opposite often happens. It is 'weaker' initial designs that might be pushed into a peripheral niche, where they eventually accumulate advanced phylogenies in parallel evolution with rival branches.
Again, primate ancestors, a weaker initial design were confined to the more "peripheral" niche of forests, while stronger carnivores roamed the plains. (Later we will see the reverse. A 'weaker' and less fit relative pushed out of the forests and onto the plains evolves into us!) But life in the forests brought special demands. Not only did a wide diversity of species evolve, the primate phylogeny itself evolved. Litter sizes went down, paws evolved into hands, limbs and backbones become more flexible, brains become larger, behavior became more complex and more social.
Only with these further changes creatures themselves increase ability to adapt faster.
But flexibility causes saturation. If primates can already adapt fastest of all species to climate and vegetation changes, the phylogenies of other species who cannot adapt as fast as primates are saturated (for like competition).
So once we come to primate phylogeny, which branches into Great Ape phylogeny, we reach general saturation for large animal life on Earth. Once a species has hands, versatile limbs, large brain, varied diet, social behavior, opposed thumb, stereoscopic vision, crude tools, not much more can be squeezed from evolution of large animals as new novelties. Or at least, there is nothing that can evolve as fast as behaviors or other simple changes can be adapted.
Another factor causing saturation has to do with the brain. Now the theory is complex. (See separate essay in the Theory of Options on Brain, Mind and Consciousness.) But roughly, early neurology evolved for specific functions, we can call reflex. Then there evolved circuits for simple learned behavior, such as imprinting, which we see mostly in birds. (Birds evolved in a separate line to mammals. Most likely imprint learning exists in all vertebrates, but is overshadowed in mammals by more advanced leaning.) But finally in mammals, we have increased numbers of pure learning circuits. This is contentious, but "learning circuits" start to move evolution outside of DNA. That is, DNA can express the basic design of a "learning circuit", and multiply the number of circuits in a brain, but DNA does not have to design each learning circuit each generation by selection. So we end up with an effect similar to the microchip in technology.
If anything, as with human evolution, evolutionary costs become morphological, such as how a large brain can egress the womb, rather than any penalty to increasing neural bulk.
Only every species is still locked into its own fitness trajectory.
But somewhere in the vast interacting system of life, the cost of evolving new novelties must be measured against what it would cost an ape to evolve a bigger brain. Very crudely, in the Age of Reptiles one can calculate the evolutionary costs to a large animal adapting its phylogeny to flight. Until birds have evolved feathers, pterosaurs can evolve wings at the least cost from a given starting point. Yet once feathers evolve, these are so efficient that long-range flight becomes saturated for all other tetrapods. Mammals can still adapt short-range flight as bats, but this option saturates too once the bat phylogeny matures. And this leaves one other option for flight among advanced mammals, and that is to build an airplane! Only remarkably, this optional way to adapt flight turns out to be very fast. Only five million years of evolution from human ancestors to airplanes, and only 150,000 years after evolution of the first humans.
(Note: Great Ape is a family, not a species. The human species did not evolve from a modern ape species. There is a Great Ape phylogeny shared by gorillas, orangutans, chimps and humans, a slightly more advanced chimp-human phylogeny, and separate human and chimp phylogenies. All these phylogenies are very close to general saturation, and the human phylogeny is fully saturated.)
So as stated many times, any trait encoded in DNA is easy-to-evolve. Wings can evolve, and have many times. (If we include insects, most animals fly.) But traits are dynamically only easy-to-evolve if there is a fitness reason to evolve them, in selective rivalry to other means of adaptation. That is why we get saturation. Different organisms perfect phylogenies along various evolutionary paths. If a trait like a wing, eye or flipper is easy to evolve, it does so many times. But if a trait like limbs, feathers, amniotic egg or four-chamber heart evolved at a fitness cost, no modern creature can afford the fitness penalty to evolve that novelty again, facing the fiercer competition the new novelty brings. But as life evolves, phylogenies themselves become more versatile.
As species evolve so do phylogenies and what one phylogeny becomes already, another cannot be. When the trait in one phylogeny cannot evolve at the speed or minimal fitness cost of the trait in a rival, that phylogeny is in saturation. Theoretically the trait could evolve further, but not in a practical struggle for fitness against fierce competition. Finally, Great Ape evolution brings a state of general saturation for large animal life on Planet Earth. This means that all the major classes, orders, families and even the genus of large animals have been established. And nothing could evolve a significant new novelty to break this pattern, faster than a Great Ape could evolve into a human. (Unfortunately, this is now bringing tragedy. Humans have already destroyed many species such as the Mammoth, which could not adapt fast enough, and threaten many more. Humans have also deforested whole continents, and might bring on another major extinction.)
Yet, if the effect of saturation seems strange, there is a crude way to quantify it. Humans are morphologically, behaviorally and culturally very different from chimps. Yet the human genome is only 2-4% different from the chimp genome, and expressed genes are very similar. This means that while humans evolved fast and far from chimps, they only evolved a very short genetic 'distance' to get there. Again, this is a saturation effect. If for a 2% genetic distance a species can evolve from a chimp-like ancestor to a human, with all the adaptability humans have, how can another species afford the fitness penalty to evolve a much greater 'distance' for whatever adaptability gains that might bring? It is like with flight. For a 2% change over genetic distance a Great Ape can evolve into a creature that can build airplanes. So, another large creature (other than a bat or a bird that can already fly) cannot evolve that far or fast in modern times for any fitness advantage such a change could bring. And what applies as an example to flight applies to everything, even further human evolution. In millions of years hence we will not know how humans will evolve. But for present population, no new allele could sweep to fixation among such a huge, diverse population for whatever advantage it could bring, that could not be achieved faster culturally. (Humans could not evolve mental telepathy faster than they could build hand-phones. Or they could not evolve bigger brains faster than they can build computers.) As stated, tragically, many species in competition with humans now face extinction rather than further adaptation. Change can avoid extinction, but it can also bring fitness cost. And when the fitness cost of change exceeds the rate at which another species can change at less cost there is saturation. Large life on Planet Earth can no longer adapt at the rate and fitness cost at which humans can interfere with the ecology of the entire planet, so all large life on Planet Earth is now in phylogenic saturation.
But saturation means one more thing.
So, while saturation mainly affects phylogenies, species, individuals and traits, it also effects how genes will distribute and evolve throughout the gene pools of life. This is a major contention, which we call the "smart gene" hypothesis. It means that through homologous, phylogenic evolution, certain gene sets outlive the lives of individuals, species, or even orders or classes, to become widely distributed and highly conserved throughout all life.
Peripheral Niche Mechanism