The neo-Darwinian account of the evolution of life rests on two key pillars, each of which is deeply woven into our worldview: random mutation and natural selection. Randomness is the opposite of purposiveness, and a necessary adjunct to a world of standard, generic building blocks. Natural selection is the projection onto biology of the ambient anxiety and competitiveness of our culture. These associations ensure that neo-Darwinism will be orthodoxy in the Age of Separation.
But what exactly do random mutation and natural selection act on? What is the biological self that suffers mutation and that competes for survival against other selves? A coherent answer to this question is crucial to the coherency of the entire neo-Darwinian paradigm. If we find instead yet another projection of our culturally-constructed conception of self, then the entire edifice of neo-Darwinism is a projection as well.
The standard answer is that the subject of natural selection is the gene, biology's version of the discrete and separate self. Through their manipulations of the environment (via the organisms they "code for", command and control), genes enact the struggle for survival that drives evolution. By necessity, their primary relationship to each other is competitive: they are here because over the eons they out-survived and out-replicated all their competitors. Genes have no desire to evolve, but sometimes they mutate by chance into new genes that are even better at survival and replication. In this way, without any intention, purpose, or program, the genes evolve. The only direction to evolution is toward genes that are better and better at surviving and replicating. To the extent that the word "purpose" has any meaning at all, this is the genes' sole purpose. As for the organisms—such as you and I—that the genes code for, these are merely the instruments by which genes survive and reproduce. Insulated like the Cartesian soul from the environment, the interests of the genes are only coincidentally aligned with the interests of the organism. The struggles, desires, and adaptations of the organism do not affect the genes, nor do the needs of other organisms. The relationship between genes and environment is one-way: the genes alter the environment through the organisms they program, but the only effect the environment has on the genes is either to prevent them from being passed on, or to randomly alter them through mutation. The gene is the master, the organism the servant, the environment a reservoir of resources and a source of threats.
In parallel, we see humankind as the master, technology as the servant, and the environment again as a reservoir of resources and a source of threats. On the individual level, economics and other transactional models of human behavior utilize a structurally equivalent scheme. Life is about me, what I can get, and how I can get it.
The integrity of the neo-Darwinian world view depends on all of the elements described above. Remove one, and the whole fabric unravels. Along with it goes a whole constellation of intuitions about the nature of the self and the way of the world.
Today, indeed, the entire fabric of neo-Darwinism is unraveling, contributing to and impelled by the unraveling of the larger paradigms of world and self that embed it. We could start with any of neo-Darwinism's frayed threads and it will lead us to all of the others. So let us start with the core of the biological definition of self, the genes.
Contrary to prevailing dogma, the genes are not in fact the command and control center for the cell, nor do they stand in isolation from the non-random (and hence in some sense purposeful) effects of the environment. In his 1990 paper, "Metaphors and the Role of Genes and Development," the eminent biologist N.H. Nijhout argues that two central metaphors of biology, that "genes 'control' development, and the genes embody 'programs' for development," are highly misleading. He writes, "The simplest and also the only strictly correct view of the function of genes, is that they supply cells, and ultimately organisms, [and ultimately the environment?] with chemical materials." And, "When a gene product is needed, a signal from its environment, not an emergent property of the gene itself, activates expression of that gene." If the gene is the biological self, it has few of the attributes of Cartesian selfhood. These are projections. The gene is not the control center, not the brain of the cell. In fact, enucleated cells can survive for months without any impairment of their ability to move, digest food, excrete wastes, exchange gases, communicate with other cells, and otherwise respond to their environment—all without genes. Only when their protein parts begin to wear out do these cells' functions begin to deteriorate.
Applying the gene metaphorically as an analog to the self, we exist to contribute our gifts to the larger wholes of which we are part. Something in our environment calls upon us (activates expression of the gene), and we provide our unique gift that in turn activates the contribution of another. It is not about maximizing self-interest at all!
The microbiologist Bruce Lipton offers a conceptual model of the cell that makes the role of the genes clear. The brain of the cell, he says, is not the nucleus but actually the cell membrane, which senses the extracellular environment via its receptor proteins and then, via effector proteins, translates this data into instructions for the interior of the cell—including the DNA—to carry out. This, he observes, is on a schematic level exactly what a brain does. The genes cannot turn themselves on and off; it is the cell membrane with its chemical messengers that does that. The nucleus and ribosomes are merely the manufacturing facility and not headquarters, the hard disk and not the CPU. It is in fact the cell membrane, the mediator for the environment, from whence the instructions actually originate. So in contrast to a lordly self manipulating an external not-self from its headquarters, we have a two-way interaction in which environment defines self just as much as self molds environment, blurring the distinction between the two. No longer does biology lend itself as a metaphoric model for some Cartesian "seat of the soul", a center of awareness and free will looking out upon a mechanistic world of dead matter.
Further eroding the self/other distinction is the fact that not only does the environment turn DNA on and off, it can even change DNA in a non-random way. Cells and organisms—and through them, other life forms and the environment as a whole—can modify their own DNA to produce necessary traits. What's more, these modifications can affect germline cells, so that the associated acquired traits can be inherited.
Hold on. Haven't I just asserted Lamarckism, the thoroughly discredited theory of inheritance of acquired characteristics proposed by Jean Baptiste Lamarck in 1806? Lamarckism, of whose founder George Bernard Shaw wrote in 1921, "poor Lamarck was swept aside as a crude and exploded guesser hardly worthy to be named as [Darwin's] erroneous forerunner"? Despite 200 years of unremitting ridicule, Lamarck's basic idea is receiving increasing vindication. Much more than the mere mechanism of evolution is at stake, because Lamarck's theory was not so simplistic as the usual derided example of "each generation of giraffes stretched their necks to reach higher leaves, and the longer necks were passed on to the next generation." The crux of his thinking is laid out in the following:
It is not the shape either of the body or its parts which gives rise to the habits of animals and their mode of life; but that it is, on the contrary, the habits, mode of life and all the other influences of the environment which have in the course of time built up the shape of the body and of the parts of animals. With new shapes, new faculties have been acquired, and little by little nature has succeeded in fashioning animals as we actually see them.
Of course, we must interpret Lamarck's theory through our knowledge of the genetic basis of inheritance and morphology. To make the theory work, the acquired characteristics must arise from changes in the genes that can be passed on. Lamarckism in its modern form simply states that these changes can be acquired in the course of a lifetime through purposeful adaptation; neo-Darwinism, on the other hand, says they arise only from random mutation. Thus the experiment that purported to disprove Lamarckism once and for all is not really a test of Lamarckism at all. Weismann's experiment with mice, in which he cut off the tails of each generation and found that the next generation always was born with tails of normal length, demolishes at best a reduced and distorted caricature of Lamarckism.
If acquired characteristics may be inherited, the door is open for this inheritance to reflect purpose, both of the organism and the environment. Shaw interprets Lamarck along these lines: "How did he come by his long neck? Lamarck would have said, by wanting to get at the tender leaves high up on the tree, and trying until he succeeded in wishing the necessary length of neck into existence." Evolution happens, in other words, through wanting, through intention. Shaw goes on to write:
Another answer was also possible: namely, that some prehistoric stockbreeder, wishing to produce a natural curiosity, selected the longest-necked animals he could find, and bred from them until at last an animal with an abnormally long neck was evolved by intentional selection, just as the race-horse or the fantail pigeon has been evolved. Both these explanations, you will observe, involve consciousness, will, design, purpose, either on the part of the animal itself or on the part of a superior intelligence controlling its destiny. Darwin pointed out—and this and no more was Darwin's famous discovery—that a third explanation, involving neither will nor purpose nor design either in the animal or anyone else, was on the cards. If your neck is too short to reach your food, you die. That may be the simple explanation of the fact that all the surviving animals that feed on foliage have necks or trunks long enough to reach it. So bang goes your belief that the necks must have been designed to reach the food. But Lamarck did not believe that the necks were so designed in the beginning: he believed that the long necks were evolved by wanting and trying. Not necessarily, said Darwin. . . suppose the average height of the foliage-eating animals is four feet, and that they increase in numbers until a time comes when all the trees are eaten away to within four feet of the ground. Then the animals who happen to be an inch or two short of the average will die of starvation. All the animals who happen to be an inch or so above the average will be better fed and stronger than the others. . . And this, mark you, without the intervention of any stockbreeder, human or divine, and without will, purpose, design, or even consciousness beyond the blind will to satisfy hunger. It is true that this blind will, being in effect a will to live, gives away the whole case; but still, as compared to the open-eyed intelligent wanting and trying of Lamarck, the Darwinian process may be described as a chapter of accidents. As such, it seems simple, because you do not at first realize all that it involves. But when its whole significance dawns on you, your heart sinks into a heap of sand within you. There is a hideous fatalism about it, a ghastly and damnable reduction of beauty and intelligence, of strength and purpose, of honor and aspiration. . . To call this Natural Selection is a blasphemy, possible to many for whom Nature is nothing but a casual aggregation of inert and dead matter.
Ironically enough, it is now neo-Lamarckism that offers a "third explanation" besides intelligent design and random chance: "consciousness, will, design, purpose" can guide evolution even without an external designer or purposer. And just to make the full extent of the heresy plain, let me emphasize that it is not just organisms or cells that modify their own DNA—the blurring of self/other goes further than that. The extra-somatic environment also participates in the modification of genes, so that they serve the purposes not only of the organism but of the community, the ecosystem, and the planet. . . maybe even of the cosmos.
In other words, it is not just that the giraffe wants to reach the higher leaves, or that protohumans wanted hands that could grasp tools. An empty niche in the environment exerts an evolutionary pull. An unfolding pattern draws creatures to occupy the necessary roles. That is to say, the world wanted it too! Speaking metaphorically, our gifts and potentials are called forth by life's opportunities and by the world's needs. They are not independently preexistent, to be imposed by force upon an unconscious universe. Evolution, whether of the soul or of the species, unfolds in coordination with the evolution of all. "Lamarkism" stands as a term of disparagement because its doctrine is inescapably teleological.
That heritable change is more than a haphazard triage of randomly generated possibilities is problematic to our culture's program of control, for it undermines the ideology that leaves us the "lords and possessors of nature." While in Darwin's scheme the ultimate purpose of life is to survive, Lamarck's admits to a higher sort of purpose associated with will or intention. And if nature's forms and systems express a purpose, then we must doubt our absolute suzerainty over nature; we must doubt the assumption that we can engineer nature endlessly with impunity, especially when we do so in ignorance of its purposes. In a blind, purposeless universe we are at perfect liberty to do our will, for there is no natural order on which we might infringe, no destiny to interfere in, no destiny at all, in fact, except that which we create. But if there is a purpose inherent in the way of the world, then the whole bent of science must change from understanding for control's sake, to understanding for the sake of according more closely to nature's purpose. Asking of ourselves, "What are we for?" we will seek out our proper role and function on the planet and in the universe. This transition, which I believe will inevitably flow from the new scientific paradigms described herein, represents our abdication from the pretense to lordship over nature, to become nature's humble student.
Observing nature through our cultural lenses of separation, competition, and survival anxiety, we have long been blind to the fact that nature doesn't always work that way. Nonetheless, evidence for the non-randomness of genetic change is mounting. It is now widely accepted that rates of genetic mutation increase when organisms are under stress, presumably to increase the likelihood that a mutation will arise that is better adapted to the stressor. Reflecting consensus, a recent article in Nature opines, "It makes sense for stress responses to cause mutations; it may be a 'selected' feature that increases genetic variation, thus increasing 'evolvability' under stress when organisms are suboptimally adapted to their environments. Most of the mutations would be harmful or neutral, but rare adaptive mutations would also occur." Recent research implies that this "stress" can be the quite common occurrence of running low on food, implying that accelerated mutation is an ordinary feature of bacterial life. Even though such mutations are thought to still be random, stress-induced mutagenesis is immensely problematic to standard selfish gene theory. The unit of selection is supposed to be the gene, not the organism! Genetic characteristics, such as mutability, that benefit the organism in a way that does not promote the gene's replication in future generations would be selected against.
More controversial by far is a concept sometimes called adaptive mutation that has cropped up intermittently in biology under various guises ever since the days of Jean-Baptiste Lamarck. Reintroduced in 1988 by John Cairns, it claims that mutations are not fully random but are somehow biased toward an adaptive purpose. Cairns disabled a gene in E. coli that produces an enzyme to digest lactose, then put the E. coli in a lactose-only medium. To his surprise, the disabled gene mutated back to the original enzyme-producing version—not in every bacteria, but at a higher rate than in a control culture where the bacteria had food sources other than lactose. While the consensus is that an overall elevated (but still random) stress-induced mutation rate can explain this finding, other research supports the idea that it may be truly adaptive. B.G. Hall found that a similar E. coli mutation happened to permit utilization of the sugar arbutin in the presence of starvation—but only when there was arbutin in the medium! The mutation happened at a much higher rate specifically when it was useful. Other research has found that increased mutation rates under stress are not evenly distributed across the genome, but are much higher in precisely those areas which may generate beneficial mutations. The controversy rages on today, with orthodox opinion maintaining that stress-induced hypermutability can fully explain adaptive mutation, and thus preserve Darwinism.
There are several reasons for the mainstream aversion to true adaptive mutation. Some commentators seem to feel it would entail "spooky foreknowledge" of what mutations would be useful. Personally, I am a fan of spooky foreknowledge, but in the case of adaptive mutation it is unnecessary. All that is needed is a way for the DNA to sense and internalize signals from the environment; in other words, a way for the environment to speak to the DNA, to alter it purposefully just as the DNA, mediated by the organism, alters the environment. Adaptive mutation implies a tight coupling between gene and environment that calls into question the very definition of the biological self. To say that the gene responds to the environment is a conceit; just as easily we could say that the environment molds the gene.
The precise mechanisms by which this happens are unknown and mostly unexplored due to the widespread belief that nature doesn't work that way. Nonetheless, there are several confirmed examples already, along with some interesting speculation. Mainstream biology has long accepted that reverse transcriptase allows RNA to rewrite DNA, and that antibodies in immune cells help to modify the DNA that produces them. More radical, but now also widely accepted, is the observation that epigenetic proteins, which envelope the DNA double helix, also carry heritable information that affects the way genes are expressed. What's more, these epigenetic proteins are also subject to heritable environmental modification. More radical still are proposals that invoke electromagnetic or other vibrational induction of genetic change. Finally, I must mention Johnjoe McFadden's very clever effort to bring "spooky foreknowledge" back into evolution through the Quantum Zeno Effect. His full argument is beyond the scope of the present chapter, but essentially he believes that genes take advantage of quantum superpositions of states to scan the search space of possible mutations, whose viability is confirmed by the observer effect of their own progeny.
Whatever the mechanism, evidence is mounting that the environment influences genes through mechanisms beyond mere natural selection. The evidence has been mounting, in fact, for a long time, as Charles Darwin, himself remarkable free of the dogma of Darwinism, acknowledged in 1888:
In my opinion, the greatest error which I have committed has been not allowing sufficient weight to the direct action of the environments, i.e. food, climate, etc., independently of natural selection. . . . When I wrote the "Origin," and for some years afterwards, I could find little good evidence of the direct action of the environment; now there is a large body of evidence. [emphasis mine]
If Darwin was aware of it in 1888, why do most biologists still ignore this "good evidence" today? Indeed, the evidence today is far greater. The institutional insistence on the primacy of the DNA as the "controller and program" for morphology and behavior, and on the randomness of its evolution that is driven solely by natural selection, derives not from the evidence, but from deeper cultural assumptions about who we are.
The challenge that adaptive mutation presents strikes at the heart of our culture's dualistic conception of world and self. Purpose, once the sole province of the conscious self of psychology (or at least the sentient self of biology), escapes the confines of individual actors—purposers—to become a property of the world as a whole. No longer do the genes necessarily act in their own self-interest, nor even, as we shall see, the selfish interest of the organism they are part of. Rather than being the source of purpose (which is only to survive), they are a means by which organism and environment enact purpose. And in that case, in what sense are the genes the kernel of biological selfhood? Yes, they carry heritable instructions for building bodies, but it is outside signals that activate them. Nor are these instructions inviolate; they are readily modified according to need. Wouldn't that-which-modifies-them be a more appropriate choice for selfhood? Our Cartesian intuitions tell us that ultimate authority must reside somewhere. But the invoker or modifier is not a discrete entity either: it is the cell, the organism, even the environment. The self is no longer so rigidly defined; therefore neither is self-interest. Who are we? The question has no definite answer. Different answers are expedient for different purposes, but none is complete. Natural selection depends for its primacy on a discrete self to act on, but we are now learning that the self of biology, the subject of natural selection, is not discrete but fluid, merging by degrees into the genetic plenum.
Direct evidence for adaptive mutation is still ambiguous. However, if natural selection on random mutations of replicating DNA is not the prime mover of evolution, then we must construct a coherent understanding of life, its origins, and its evolution that does not rely on competition among discrete genetic subjects. Fortunately, just such a story is emerging today and gradually infiltrating mainstream biology. It is a story in which cooperation just as much as competition defines relationships among living beings, in which symbiosis and merger across fluid genetic boundaries drive evolution, and in which purpose arises from both within the organism and without. No longer is biology a study of separate and competing selves, and no longer will that idea inform our intuitions about the way of the world.
 Nijhout, H.F., "Metaphors and the role of genes in development." BioEssays, vol.12 (1990) p.444-446.
 Lipton, Bruce. The Biology of Belief. Mountain of Love Productions, pre-publication draft, no page numbers.
 From the Preface to Shaw's play Back to Methuselah. It is worth reading the whole of the remarkable essay, which eloquently lays out many of the spiritual ramifications of the Darwinian paradigm.
 Larmarck, Jean Baptiste, Philosophie zoologique, ou exposition des conside'rations relatives a` l'histoire naturelle des animaux. (Zoological Philosophy. An Exposition with Regard to the Natural History of Animals), 1809. Translated by Hugh Elliot Macmillan, London 1914, Reprinted by University of Chicago Press, 1984
 Studies supporting this assertion are almost too numerous to mention. Many have been done with bacteria, for example Loewe, L., Textor, V., and Scherer, S., "High deleterious mutation rate in stationary phase of Escherichia coli." Science vol. 302 (2003), pp. 1558-1560
 Rosenberg, Susan M. and P.J. Hastings, "Genomes: Worming into Genetic Instability", Nature vol. 430, August 5, 2004, pp. 625 - 626
 Cairns, J., J. Overbaugh, and S. Miller, 1988 "The Origin of Mutants." Nature vol. 335, pp. 142-145
 B.G. Hall, "Activation of the bgl operon by adaptive mutation", Molecular Biology and Evolution. Jan. 15, 1998 pp. 1-5.
 Rosenberg, Susan. "Evolving Responsively: Adaptive Mutation" Nature Reviews Genetics , vol. 2, 2001, pp. 504 -515. This is a comprehensive review of the state of research on adaptive mutation.
 T. Beardsley, "Evolution Evolving," Scientific American, September 1997, pp. 15–18
 McFadden, Johnjoe, Quantum Evolution, Norton, 2001.
 Darwin, Charles, 1876 letter to Moritz Wagner, referenced in Obituary Notices of the Proceedings of the Royal Society, vol. 44, 1888.