The True Origin of Species

The True Origin of Species

The Great Loom of Life

by

John Kuti

Smashwords Edition

* * * * *

Published on Smashwords by:

John Kuti

The True Origin of Species: The Great Loom of Life

Copyright 2012 by John Kuti

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Contents

Why and How Life Comes to Exist

Darwin Was Wrong

All Life Is Bilateral

More Darwinian Errors

Irreducible Complexity

Darwin’s Big Error of Omission

The Fractal Nature of Life

The Bilateral Reality of Life

The Bilateral Subjective Architecture of Life

The Loom of Life

The Nine Rungs in the Ladder of Bilateral Subjective Complexity

The First Rung in the Ladder of Bilateral Subjective Complexity Action / reaction Communicative Responses

The Second Rung in the Ladder of Bilateral Subjective Complexity Communal Integration

The Third Rung in the Ladder of Bilateral Subjective Complexity Symbiosis

The Fourth Rung in the Ladder of Bilateral Subjective Complexity Spontaneous / Instinctive Response

The Fifth Rung in the Ladder of Bilateral Subjective Complexity Nurturance / competitiveness

The Sixth Rung in the Ladder of Bilateral Subjective Complexity Conscious / unconscious Pleasure / fear

The Seventh Rung in the Ladder of Bilateral Subjective Complexity Conscious / unconscious Emotion

The Eighth Rung in the Ladder of Bilateral Subjective Complexity Reciprocal Giving / getting

The Ninth Rung in the Ladder of Bilateral Subjective Complexity Inductive / deductive Reasoning

The Evolution of Bilateral Subjective Complexity

The Purpose and Meaning of Life

Chapter 1: The Theory of Bilateral Subjective Adaptation

Competitive Fitness and Cooperative Fitness

Subjective Response and the Nash Equilibrium

Adaptive Today—Maladaptive Tomorrow

The Story of Life

The Subjective Foundation of Life

Plants, Animals and Subjective Experience

How Evolution Really Works

Epigenetics: How Your Ancestors Changed Your Genes

Jumping GenesSymbiogenesis

Virogenesis

The Rate of Evolutionary Change

The Shifting Course of Evolution

Too Much Junk

The War Over Natural Selection: Dawkins V Gould

More Problems with Darwin’s Theory of Natural Selection

Evolutionary Change and Sexual Selection

The Bell Curve of Individual Variation Individual Preference, Variability and Sexual Selection

Approach Distance

Genomic Plasticity The New Chords of Life

The True Origin of Species Form Follows Subjective Function

Speciation and the Balance Within Shared interest / self-interest

Speciation Triggers Punctuated Nash Equilibriums

Speciation

Old Assumptions, New Conclusions

Chapter 2: The Nine Rungs in the Ladder of Bilateral Subjective Complexity

The Subjective Structure of Life The Genetics of Behaviour

The Economics of Behaviour

The Economic Tao of Life

Concerning Cooperation

Evolution and Subjective Response

Life’s Perfect Metaphor Songs in the Keys of Life

The Genome and Subjective Response

The Bilateral Subjective Response of ‘Me / Us’

The Bilateral Subjective Response of ‘Us / Them’

The Nine Rungs in the Ladder of Bilateral Subjective Complexity

The First Rung in the Ladder of Bilateral Subjective Complexity Action / reaction Communicative Response

The Second Rung in the Ladder of Bilateral Subjective Complexity Communal Affiliation

The Third Rung in the Ladder of Bilateral Subjective Complexity Symbiosis

The Fourth Rung in the Ladder of Bilateral Subjective Complexity Spontaneous / Instinctive Responses

The Fifth Rung in the Ladder of Bilateral Subjective Complexity Nurturance / Competitiveness

The Sixth Rung in the Ladder of Bilateral Subjective Complexity Conscious Pleasure and Fear

The Seventh Rung in the Ladder of Bilateral Subjective Complexity Conscious Emotion

The Eighth Rung in the Ladder of Bilateral Subjective Complexity Reciprocity

Chapter 3 Human Evolution

Early Relatives and the Path to Modern Humanity A Short List of Our Ancestors

From Prey Animal to Hunter

Neotony and Human Complexity

The Origin of Modern Human Behaviour

Becoming Human

The Androgynous Human Brain

Sexual Identity / Gender Identification

Sex and Love Among the Hominim

The Nuclear Family

Love and the Human Unconscious

Modern Humans: Inductive / deductive Reasoning The Ninth Rung in the Ladder of Subjective Complexity

The Bilateral Human Brain

The Evolutionary Origin of Language

Human Language

Language and Self-awareness The True Sixth Sense

Our Big Brains

The Origin and Nature of Inductive / deductive Reasoning

Rationality and Personal Identity

Human Reciprocity and Morality

Deferred Gratification

Language and Perception

Reciprocity, Attraction, Desire, and Love

Monogamy and Adultery

Bilateral Psychological Paired Traits and Human Personality

Hunter / Gatherer Clans Male Practical Competency - Female Social Mastery

Personal / cultural Narrative

The Origin of Religion and Divine Narrative

Religion and Reciprocity

The Metaphorical Mind of Modern Man Reading, Writing, Numbers, Private Property and Money

Human Civilization

Money and Its Narratives

Civilization and the Human Psyche: Civilization and Gender

Since the Enlightenment The Modern Psyche

Self-esteem and Civilization

Unanswerable Questions

Why and How Life Comes to Exist:

Almost every modern scientist believes that Darwin’s theory of natural selection is correct. Although there are countless exceptions to the way natural selection is said to work, there has been no credible scientific alternative offered to it in the last 150 years.

It is undeniable that natural selection exists. How it works and if it is the mechanism for the creation of new species is something else again. To challenge the accepted explanation for how natural selection works requires a new and better theory to first identify and demonstrate how all the work on evolutionary theory could have preserved fundamental errors for a century and a half and then propose a better explanation for the countless observations that have been made on evolutionary change.

This book will propose an alternate theory for evolutionary adaptation and the origin of species. The Theory of Bilateral Subjective Adaptation answers most of the exceptions to Darwinian theory and offers a more comprehensive explanation for the way evolution works. It will propose that genetic adaptation is a process in which competitive and cooperative advantage are two inseparable and indivisible aspects of life that serve the bilateral shared interest / self -interest of all living creatures in every ecosystem. Shared interest / self-interest exists in the way space and time exist as the bilateral, inseparable, indivisible reality of space / time, the one inseparable from and co-dependent on the other.

Cooperative and competitive advantage exists because of the dynamic balance within shared interest / self-interest expressed in life through the subjective responses of cooperative and competitive behaviour, and it is the balance within competitive and cooperative behaviour within and among species that defines every ecosystem on the planet. Cooperative and competitive behaviour weaves together the warp and weft of shared interest / self interest in what is the great loom of life that produces the infinite tapestry of living ecosystems.

The Theory of Bilateral Subjective Adaptation will show how evolution is primarily controlled by changes in the subjective response and behaviour of living creatures and will identify nine distinct quantum leaps in subjective response that are the rungs in the ladder of bilateral subjective complexity that are the foundation of life’s infinite variation in form. The theory proposes to identify the underlying subjective structure in the ladder of life’s ascending complexity that has until now been hidden in plain sight.

The Theory of Bilateral Subjective Adaptation will also propose that new species are created by the awareness of external reality and the attendant plasticity of the DNA molecule network in living creatures responding to times of great stress or opportunity within the ecosystem of individual creatures. We propose that the network of DNA molecules that create every protein through which any life form responds to external environmental cues and internal metabolic needs, as well as past conditioning and learning, has within that network the ability to genetically reorganize itself to create fundamental new irreducibly complex forms and even new species. We will show that, like the brain, the network of DNA molecules in a living creature has a demonstrated plasticity to reorganize itself when its organism is fundamentally compromised or stressed. Like the brain, the network of DNA molecules in living creatures has within its own plasticity the ability to create irreducibly complex new processes, structures, organs that respond to new ecological opportunity or extreme stress often atavistically reaching back even millions of years to resurrect earlier genetic forms.

For the first time in evolutionary theory, we will propose an explanation for the undeniable rapidity and multiplicity in the appearance of new species that Darwin’s theory of natural selection through slow, progressive adaptive change has been unable to explain. Natural selection will be shown to have a limited role in genetic adaptation and virtually no role at all in the origin of species. The giant, silent elephant in the room of evolutionary theory is the fact that there is literally no evidence for slow adaptive change creating even one new species. There is considerable evidence that some other rapid form of genetic reorganization is responsible for new genetic forms and functions.

We will propose that the DNA molecule itself is responsible for the unconscious / conscious responses of living creatures, working together much like the neurons in the brain respond to unconscious / conscious perceptions to create a representation of reality through which an individual creature can interact with its environment and most importantly with other living creatures. We will propose that the network of DNA molecules that creates all life processes has the same kind of representational awareness of external reality as the brain as it creates the proteins that allow the unconscious / conscious behaviour and physiological response of every individual creature. It is the awareness arising from this network of DNA molecules that resides in every living cell of an individual creature that creates the unconscious / conscious representation of reality that allows subjective behaviour and instinctive response. This means that it is the network of DNA molecules within the cells of living creatures that is the ‘intelligent designer’ that is responsible for the creation of irreducibly complex new structures and living forms and every new species that has ever come into this world.

The idea of genomic awareness and plasticity is one of the most revolutionary ideas in the history of science. It is far more revolutionary than the idea that a network of neurons in the brain is responsible for creating representations of reality from sensory information, or the very recent new idea that the brain is able to reorganize its own form and function because of its own plasticity. It is also far more revolutionary than the idea that a series of ones and zeros can make a visual representation of reality in super high-definition or create a computer that can beat two Jeopardy champions in the associative retrieval of conceptual information. These recent revolutionary ideas were almost universally rejected in science until they were shown to be demonstrably true.

We will give examples of how genetic awareness of external reality has been demonstrated in a number of different species. We will give examples of how genomic awareness is able to perceive external reality and create a fundamental reorganization of its genes through its own innate plasticity. This genomic awareness of external reality and most especially the subjective responses of individual life forms to the balance within shared interest / self-interest within their ecosystem is the mechanism for the genetic reorganization that produces new species at times of extreme stress or opportunity.

Darwin Was Wrong

Darwin’s most fundamental error about how natural selection works was in stating that it was based on hereditary competitive advantage. There is no living system, no ecosystem, no society in which pure competitive advantage is the natural reality. Every living system, every ecosystem, every society dynamically balances the shared interest and self-interest of all living creatures within it. Darwin was only partly right about how natural selection creates variation within species, and completely wrong about how new species are created. And this fundamental error about competitive advantage has had enormous negative consequences to the understanding of nature and even human society since it was first proposed.

Darwinian competitive advantage has been used to justify the most monstrous social ideas and programs as well as pure unadulterated selfishness and greed. Fascism and capitalism have ironically each embraced Darwin. Social and economic theories have also used the idea of Darwinian competitive advantage as the scientific basis for the worst and least sustainable view of living systems. From eugenics to Wall Street greed, Darwin’s explanation of natural selection has been used to explain life in a way that is just demonstrably wrong, and The Theory of Bilateral Subjective Adaptation will attempt to explain why that is so and offer a better alternative that is in fact true to the nature of all living systems.

Shared interest / self-interest as the true bilateral economic foundation of life describes the world and living systems as the balance within the cooperating and competing interests of individuals and groups, and it is the bilateral reality of subjective response that reflects the true interrelationships and interconnections of all members of any ecosystem or social group; the one interdependent with the many, the many dependent on the predictable response of every one. Simply put, it means that getting and giving, competition and cooperation, strength and weakness, shared interest and self-interest get their very meaning from each other and are in fact bilateral in their very nature because life from the very beginning is based on bilateral subjective response.

This truer perspective on the natural world and the economic reality of life is also the only foundation upon which human society can endure because it has been the foundation of life since the first living creatures appeared on the earth balancing co-operative and competitive subjective responses.

The stark truth may be that human civilization will not survive if it continues to believe the half-truth of Darwin’s version of natural selection. This book will try to make that clear.

Darwin’s theory of natural selection says that evolution favors any genetically determined trait, whether behavioural, structural, physiological, or psychological that leads to greater numbers of offspring who pass those traits to the next generation. Darwin’s theory also says that such adaptive fitness evolving through natural selection is based on laissez-faire competition of individuals within and among species, in Hobbes famous characterization, ‘a battle of all against all’. This economic model for pure self interest in the competitive division of limited resources is universally accepted among scientists as the explanation of how natural selection and all evolutionary change work.

The fundamental problem with Darwin’s theory is that it ignores the fact that all creatures live in ecosystems in which there is both competitive and cooperative behaviour that fundamentally affects the survival of creatures within that ecosystem. Seeing evolution simply as a matter of the heritable competitive advantage of individuals in any particular species ignores how any evolutionary change to one particular species affects all the others and vice versa. Creatures live in a dynamic equilibrium in which the balance within shared interest / self-interest expressed through co-operative and competitive behaviour is fundamental to survival. Since the beginning of life, all creatures evolve in ecosystems in which they balance traits that serve their autonomous self-interest and traits that serve their communal shared interest within and even among species. The balance within autonomy and community, competitiveness and cooperation in the expression of self-interest / shared interest defines the bilateral subjective nature of life. It is true of bacteria. It is true of human beings. It is the fundamental truth behind the evolution of life.

Darwin himself recognized that cooperative behaviour is a fundamental part of nature offering creatures recognizable survival advantages. What he and every other evolutionist since has failed to recognize is that shared interest expressed through cooperative behaviour also offers a fundamental adaptive advantage through which creatures in any ecosystem exist and evolve. Self-interest is not shared interest, but the two are inextricably linked in every ecosystem and in every evolutionary adaptation as the bilateral expression of the nature of life itself. Life is simply the warp and weft of shared interest / self-interest, the many intertwined threads of living species creating the dynamic fabric of life that has grown in complexity and intricacy of design over the last four billion years.

All Life Is Bilateral

A Theory of Bilateral Subjective Adaptation sounds complicated, a lot more so than Darwin’s theory of natural selection that says evolution is the result of small heritable changes over time that give creatures a competitive reproductive advantage.

It is slightly more complicated, but not difficult to understand. In evolutionary terms, bilateral simply means that there are two complementarily different sides working together to make one integrated whole organism. There is a gene in vertebrate animals called the hox gene that creates the adaptations in form that allow complex creatures to have a left and right side, a top and a bottom, a front and back and these bilateral features in form are in fact inseparable, the one meaningless without the other. The right and left limbs, the right and left brain, two eyes, two ears, two nostrils are examples of the bilateral form of many aspects of complex creatures that work together to create a unified, integrated representation of particular perceptual aspects of reality.

Bilateral subjective adaptation is the idea that the subjective responses of all living creatures also have two sides that are inextricably linked in the same way. For every action there is a reaction in nature because that is why and how creatures communicate, and all communication between living creatures requires a bilateral subjective response. Approach means nothing unless there are subjective responses for avoidance. Prey responses mean nothing unless there are predators that prey animals can detect; predatory responses mean nothing unless there are prey behaviours predators can perceive. Every ecosystem is created through the bilateral subjective action / reaction responses of the creatures within it. Bilateral subjective complexity is the idea that this interconnected reality through which creatures detect / perceive, communicate and respond to other creatures has created a ladder of subjective complexity on which all living creatures adapt and evolve. Approach / avoidance, conscious / unconscious instincts, pleasure / fear emotions, even traits for subjective response such as risk-taking / caution, and even the most complicated human personality traits such as optimism / pessimism, extroversion / introversion and even abstract ideas like good / evil exist as inextricably linked bilateral subjective realities like the independently functioning right and left side of the brain communicate to create one single perception of experience.

The most fundamental aspects of bilateral subjective adaptation is that it is based not on heritable competitive advantage that serves the self-interest of individual creatures but rather the balance within shared interest / self-interest between and among creatures expressed as traits for co-operative and competitive behaviour that defines the true bilateral nature of life. It is the feedback mechanism of bilateral subjective response that is the process through which cooperative and competitive traits become integrated within the dynamic equilibrium of every ecosystem.

The Theory of Bilateral Subjective Adaptation proposes that it is the inextricable, dynamic balance within traits that give creatures co-operative advantages and traits that give creatures competitive advantages that define evolutionary success. It is the dynamic balance within cooperative shared interest and competitive self-interest that creates the foundation of evolutionary change and complexity. Darwin was wrong in seeing life as a rigid zero sum pie in which more resources for one individual or species must come from the resources of other individuals and species. He ignored the economic fact that the success or failure of one species can be fundamentally important to the success or failure of many others. Life and evolution is far more about growing the pie of resources through cooperation than the way it is divided through competition. Life and evolution is a lot more complex than the simple advantage of heritable traits over time that is Darwin’s definition of natural selection.

Traits for self-interest are predominantly expressed through changes in form. Traits for shared interest are predominantly expressed through changes in subjective response. We will show that there are nine distinct rungs in the ladder of subjective complexity upon which all adaptations in form ultimately rest. Simply put, traits for shared interest and cooperative behaviour are dominant over traits for self-interest that control changes in the form creatures take as they adapt to ecological change. Every creature from bacteria to human beings must establish and maintain a balance within shared interest / self-interest to find a place within a living ecosystem, unlike standard Darwinian theory that has no accepted definition for something as fundamental as adaptation.

In this book evolutionary adaptation is defined as the process through which creatures within and among species in any ecosystem balance and maintain shared interest / self-interest through cooperative and competitive traits that offers an improved margin of reproductive success to one or many species within that ecosystem.

In the conclusion to his book, The Master and his Emissary, on the bilateral nature of the human brain, Dr. Iain McGilchrist put it most succinctly, I believe our brains not only dictate the shape of the experience we have of the world, but are likely themselves to reflect, in their structure and functioning, the nature of the universe in which they have come about.

The bilateral nature of the universe may yet be established; the bilateral nature of life is what we propose to show.

More Darwinian Errors

Darwin’s theory of natural selection also contains a number of fundamental errors as well as many inadequate definitions of basic terms, some of which exist because it has not recognized adaptations expressed through changes in subjective response.

As we have said, Darwin’s first error was that natural selection is based solely upon the competition between individuals and species for the division of limited resources in any ecosystem. His idea of natural selection is based on the Malthusian theory of population growth that says that populations will increase until resources necessary for reproduction are exhausted.

There are countless examples of how species control population growth that have nothing to do with available resources. These include changes in fertility, alterations in the proportion of males to females as well as the sexual orientation of males. Loons, a species that has been on the earth for 60 million years, will stop breeding on lakes that have too much human activity, even though those lakes are established territories with all the resources necessary for raising offspring. Such a subjective response to stress and human intrusion often overrides fertility in many species, regardless of available resources. The only experiment that ever directly tested Malthusian population theory allowed an expanding population of mice all the necessary resources in food and space that they needed. The population grew exponentially for two years but then, for no discernible reason, collapsed completely until not a single mouse was left alive. With unlimited food supplies and expanding space to preserve population density, some subjective trigger altered the behaviour of these mice so that they lost all interest in food and sex, dooming the entire population. The only scientific test of the theory that is the foundation of Darwinian natural selection completely failed to prove its hypothesis. Although there are examples of creatures introduced onto islands eating themselves into extinction, these examples do not recognize that space is a resource as necessary and important as food to some creatures. Further studies may show that some creatures actually do reproduce as long as there are available resources, yet it is likely that social animals for whom subjective response is so complex and necessary are likely to need more than just safety and resources to achieve continuing reproductive success.

The other obvious challenge to Malthus’ idea that the population of a species will expand as long as there are available resources is in the life span of creatures in zoos. Most species in zoos live only a third to one half as long as the same creatures in the wild, this despite excellent diet, veterinary care and a complete lack of predators. Clearly the survival challenges of life in the wild are more than made up by some particular advantage having nothing to do with resources, health or danger. Clearly there is some necessary subjective response that comes from life in the wild that is crucial to the life span and the attendant reproductive success of many species.

Life is about more than the division of resources and the competitive advantage one individual has over another that offers it some better chance at reproductive success. The division of resources in any ecosystem is clearly a lot more complicated than the Darwinian battle of all against all.

A better model for the division of limited resources among creatures in any ecosystem was put forward by the economist John Nash in his Nobel Prize winning description for the division of limited resources called the Nash equilibrium. A Nash equilibrium is the balance between self-interest and shared interest expressed through competitive and cooperative behaviour by which individuals identify and accept a particular share of limited resources. In a Nash equilibrium, self-interest and shared interest are inextricably linked through subjective behaviour which controls the way creatures respond to each other. Life exists in a dynamic balance between traits that express shared-interest / self-interest in all living creatures and the ecosystems in which they live. And each Nash equilibrium depends on the ability of species to be consciously and or unconsciously aware of each other and to respond to other individuals of their own kind, as well as to other species that affect their lifecycle. This subjective awareness combined with the ability to communicate with others defines the nature of subjective response and makes it central to behavioural and even physical adaptation. Without subjective awareness and the ability to communicate with others, cooperation is impossible. Without subjective awareness and the ability to communicate with others, competition is also impossible. Competition between individuals is in fact impossible without the foundation of cooperative behaviour that is absolutely necessary for life itself to exist. And both cooperation and competition depend entirely upon the nature of the subjective responses of every individual in every species.

We define subjective response as the ability of creatures to detect / perceive, communicate and respond to other living creatures in order to establish and maintain a balance within shared-interest / self-interest expressed through competitive and cooperative behaviour. It is this ability to detect / perceive, communicate and respond to others that allow both competitive and cooperative advantage to exist in evolution. It is this ability of creatures for subjective response that is the foundation of life because the economic reality of life: its cost and benefit, its risk and reward, the basic purpose of supply and demand cannot exist without it.

Darwin’s theory ignores the question of why natural selection, even in bacteria, the most primitive and basic of life forms on the planet, would have selected for the many proteins which they use to communicate with other bacteria and for which they have countless receptors on their cell walls, if life is all about mindless competitive advantage. These proteins and receptors are in fact the basis of all cellular communication, complexity and subjective response in all living creatures great and small. Why would individual creatures mindlessly competing against one another to serve their own individual self-interest need to have evolved such complex means of communication? How would the communication necessary for cooperative traits expressing shared interest ever evolve? The only logical answer is that communication is necessary to maintain the balance within self-interest / shared interest expressed through traits for competitive and cooperative behaviour.

Darwin was also wrong in believing that natural selection created adaptive changes in species by favoring and preserving traits that offered the possibility of greater reproductive success, and eliminating those traits that were maladaptive to reproductive success. If standard Darwinian theory is correct, there are far too many maladaptive traits that limit reproductive success such as homosexuality, asexuality, maternal infanticide, depression, fatal genetic disease in immature offspring, and even human suicide. Such traits should have been eliminated through natural selection because they are so completely maladaptive to reproductive success.

We propose that rather than preserving adaptive traits and eliminating maladaptive ones, evolutionary adaptation is the process by which a bell curve of heritable traits is maintained in order to give creatures the widest range of individual variation through adaptive options. It is simply because environments can change rapidly and radically that it makes much better economic sense for natural selection to preserve the widest range of options for adaptive success rather than favoring and eliminating positive and negative traits for a particular ecosystem at a particular time. An adaptive trait in one period of time may be maladaptive in another and vice versa, and the most recent body of experimental evidence clearly indicates that natural selection often favors opposite traits in different years.

Within individual families, evolution clearly selects traits for particular adaptive fitness, but in breeding populations, the best option is to preserve the broadest bell curve of heritable traits that give adaptive fitness its widest range of options for the species.

Darwinian theory is also wrong in believing that evolution is a slow process solely based on random genetic mutations that offer individuals some reproductively adaptive advantage. The standard unit for evolutionary change called the darwin is in fact a change of one percent in one million years. But recent experiments have shown that evolution in some species can be extremely rapid, sometimes 60,000 darwins per year, which means that there must be some mechanism for genetic change that is much more rapid than random genetic mutation allows. We will show how form follows function, and the primary function of life is to allow creatures to detect / perceive, communicate and respond to other living creatures in order to establish and maintain a balance within the shared interest / self-interest of creatures in any ecosystem. The nature of subjective response is to serve as the foundation of most adaptations in form. If this is true, it is the genes that code for subjective experience in living creatures that predominantly control the form that creatures will take as they adapt to particular ecosystems, and this process can be very rapid or slow depending on how creatures are able to perceive the nature of their ecosystem, its prevalent stress and opportunity. Virtually all of the recent evolutionary research has confirmed that evolutionary change often happens with stunning speed and rapidity.

Another fundamental error in Darwinian theory is the belief that the behaviour of individuals can have no genetic influence on offspring. The new science of epigenetics has shown that in some species both diet in mothers and their nurturing behaviour with their offspring can actually turn genes on and off, and these genetic changes may persist for generations. There are also many experiments that show how genetic expression of particular proteins is influenced by environmental conditions. In some creatures, females transform themselves into males because of the sudden loss of the dominant male. Saltwater Stickleback fish have the ability to completely transform their bodies in one generation when moved to a freshwater environment. Epigenetic research and many new experiments in evolutionary genetics are proving that the genome has an incredible plasticity and responsiveness based on as yet undiscovered processes.

It has recently been discovered that there is more to genetic processes than the standard model in which DNA produces RNA which then create the proteins out of which all living things are formed. DNA also produces micro-RNA that create no proteins and yet are instrumental in the timing and quantity in which proteins are combined to form living tissue. The process through which changes in micro-RNA change the recipe of life is as yet little understood.

Jumping genes or transposons are bits of DNA that move freely about the genome and they either travel to a new spot or paste copies of themselves into random stretches of DNA, often with extremely negative consequences. University of Michigan geneticist Fred Gage and his colleagues found that a transposon called LINE-1 readily moves around in the brains of mice, suggesting that the same gene may do likewise in humans. Their reshuffling seems to take place starting before birth and continuing throughout life in places like the short-term memory center. According to Gage, not only do humans have a much higher proportion of transposons in their genomes than other animals but the LINE-1 seems predisposed to alter genes for brain function… If transposons do spawn variety in mental architecture, that can help explain the differences in identical twins, says Gage. Even though they are clones, they have their own personalities."

This is clear evidence of the incredible plasticity of the DNA molecule and strongly suggests that there must be a communication network among DNA molecules that allows for rapid reconfiguration. The creation of a new species may be dependent on particular individuals within particular existing species that are capable of fundamental genetic reorganization at times a great stress. Humans and chimpanzees are a good example. Chimpanzees have 47 chromosomes. Two of those chromosomes joined together to create the 46 chromosomes in the human genome, a genome with a plasticity that created as many as 20 different proto-human species while chimpanzees evolved into only one new form, the bonobo. Clearly genomes of some closely related species have widely different expressions of genetic plasticity. This may also be true of individuals within species from which new founder genes may create new species.

Other experiments have also shown that there are yet undiscovered genetic processes that allow rapid transformation in form completely outside the range of natural selection that may in fact be responsible for the fundamental genetic changes that create new species. We propose that these processes are based on the genomes ability to perceive external reality and then use its own plasticity to reorganize itself in fundamental new ways to respond to external stress or opportunity.

In September of 2012, 30 papers in the journals Nature and Genome Research and Genome Biology established that the 80% of the genome that was once thought to be junk DNA was active and needed, and included a vast system of switches that control which genes are used in cells and when they are used.

These discoveries are considered a revolutionary new view of the genome that will change the way science understands genetics. The discovery of these countless new switches gives the idea of genetic awareness and plasticity a means for creating irreducibly complex new adaptations and new species because it establishes that the genome is an interconnected network of switches that creates the homeostatic infrastructure expressed within living organisms.

Darwin’s most obvious error is actually found in the title of his most famous book, Origin of Species. In the last 150 years in which the genomes of some creatures like fruit flies have been altered in every possible way, not one new species has ever been created. The fossil history of life over the last 6 million years is contained in many different undisturbed sedimentary layers of rock, yet there is no evidence of any new species being formed through slow progressive change. In most of the fossil record, creatures appear and disappear in an evolutionary blink of the eye, and even those creatures that are seen as transitional species arrive suddenly in the fossil record after long periods of genetic stability. Stephen Jay Gould called this process punctuated equilibrium, yet there is no genetic explanation for such rapid change contained in such clear evidence found in the fossil record.

We will propose an alternative theory for how new creatures come into existence because of genomic awareness and plasticity responding to changes to the Nash equilibrium of ecosystems that trigger extreme reorganization of the genome in particularly adaptive species. These quantum leaps of extreme genetic changes come from outside the bell curve of heritable traits that define the extremes of variation in individual species, often atavistically reaching back to earlier genetic potentialities in other earlier species. Human beings have many more traits in common with Orang-utans than Chimpanzees who are genetically far closer to us, even though they appeared on the planet as a species millions of years before the common ancestor of chimps and humans. In his book The Red Ape, Jeffrey H Schwartz identifies 23 traits we share with Orang-tans and only 6 with Chimpanzees. Human nature may be closer to Orang-utans than Chimps because those were the traits genomic plasticity found most useful to proto-humans.

Darwin himself was on the brink of understanding the power of the genome to reach back to earlier forms and solutions. Stephen Jay Gould in his article Hen’s Teeth and Horses Toes discusses atavism, the ability of the genome to produce variations in individuals that have been lost in a species for millions of years. One example he gives is Julius Caesar’s horse, a horse that was born with five toes instead of the hoof that’s been a part of equine anatomy for the last several million years. Gould quotes Darwin on the subject of atavism and how it exemplifies the incredible complexity and potentialities in the genome whose existence he intuited, but which would remain undiscovered for the next hundred years.

The fertilized germ of one of the higher animals… is perhaps the most wonderful object in nature… On the doctrine of reversion (atavism)… the germ becomes a far more marvelous object, for, besides the visible changes which it undergoes, we must believe that it is crowded with invisible characters… separated by hundreds or even thousands of generations from the present time: and these characters, like those written on paper with invisible ink, lie ready to be evolved whenever the organization is disturbed by certain known or unknown condition. We believe this disturbance in the organization of the genome is in direct response to major disturbances to the Nash equilibrium of the environment to which a creature belongs. We believe this was Darwin’s glimpse of genetic awareness and plasticity.

The evolutionary potential and plasticity of the genome is just beginning to be understood, and is proving to be infinitely more complex than simple natural selection based on competitive adaptive fitness. And that genetic complexity and plasticity must be built on the foundation of subjective responses of creatures because life depends primarily on the balance within the shared interest / self interest of creatures in every ecosystem.

Irreducible Complexity

Perhaps the biggest challenge to the Darwinian model of natural selection is at the level of cellular and microbiological processes. Although microbiological research has established the detailed functions of many life processes such as blood clotting and immune system response, there is virtually nothing in the literature that even begins to offer an explanation for how such exceedingly complex life processes could have evolved in slow adaptive steps. At the cellular level, life processes are irreducibly complex in that the timing, order and structures of the proteins that achieve a particular physiological end are all absolutely dependent on one another for that life process to function at all. Like a common spring mousetrap, all the parts have to fit together and work in exactly the right order for it to work at all.

Michael J. Behe in his book Darwin’s Black Box makes an overwhelmingly persuasive case for the fact that all life processes are irreducibly complex. He points out that a bicycle can never evolve into a motorcycle by the slow and progressive improvement of the individual bicycle parts because there are no possible transitional steps between gears and pedals and an internal combustion engine. The irreducibly complex engine must fit into the bicycle frame and entirely replace the pedals and gears or neither the bicycle nor the new form of the motorcycle would work at all. There simply is no way for any one of the parts of a bicycle to slowly evolve into a gas engine that could power a motorcycle.

Like other life processes, even the various parts within a cell are irreducibly complex. There is no way for them to have evolved by slow, progressive adaptive change. They either work or they don’t. They either exist or they don’t. The way protein waste is disposed of by the lysosome is an irreducibly complex, multi-stepped intricate process, just like blood clotting and immune system response

Behe gives an excellent description of the structure of cilia and flagella, tiny structures some single celled creatures and bacteria use to propel themselves. He then goes on to describe the deeper problem. As biochemists have begun to examine apparently simple structures like cilia and flagella, they have discovered staggering complexity with dozens or even hundreds of precisely tailored parts. It is very likely that many of the parts we have not considered here are required for any cilium to function in a cell. As the number of required parts increases, the difficulty of gradually putting the system together skyrockets, and the likelihood of indirect scenarios plummet.…. Darwinian theory has given no explanation for the cilium or flagellum. The overwhelming complexity of the swimming systems push us to think that it may never give an explanation. As the number of systems that are resistant to gradualist explanations mount, the need for a new kind of explanation grows more apparent.

As Darwin himself said, If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous successive, slight modifications, my theory would absolutely breakdown.

On the larger scale, within 10 million years, whales evolved from a land mammal that looked much like a wolf. As the whale evolved, the pelvis of the land animal changed so that a tail that moved back and forth became a tail that moved up and down. There is simply no possible way for such a complete pelvic reorganization to occur through slow step-by-step adaptation. A functioning tail either goes back and forth or up-and-down. Only a complete and instantaneous change from one irreducibly complex pelvic form to another irreducibly complex pelvic form would allow such a transformation.

The irreducibly complex ear in mammals has been identified as having its genetic origin in the lower jawbone of a reptile. Stephen Jay Gould proposed that this is possible because a jawbone may also be sensitive to sound, and so, through natural selection, slowly be transformed into a mammalian ear. It strains credibility to imagine a jaw and an ear existing coincidentally until the jaw function was lost and the ear finally began to work, especially when you consider that mammals have lower jaws. Both are irreducibly complex systems and they either work or they don’t.

Virtually all life processes are just as irreducibly complex and there is simply no denying that in the course of evolution these countless irreducibly complex life processes within and among differentiated cells did come to exist. In Darwin’s Black Box, Behe makes the case that only some form of intelligent design could possibly create such irreducibly complex life processes. He