The Genetic Plenum

A major flaw of complexity theory as an account of life’s origin is that it never works in a test tube. Critics of Stuart Kauffman point to the failure in the laboratory to create anything like the expanding, evolving autocatalytic sets he describes; invariably, instead, we end up with uninteresting tarry gunk sitting on the bottom of the flask at chemical equilibrium. Computer simulations of evolution, where various mutating organisms compete for memory or some other resource, similarly fail to generate genuinely new genes. Artificial life programs like Avida and Tierra appear to simplify and prune genomes rather than generating novel ones. Interesting variations on the original creatures emerge, but not to my knowledge truly new organisms at a higher level of complexity.[41] The only exceptions I could find are systems like Ray’s Tierra when length is specifically rewarded in the program environment, and Dawkins’ simulations where fitness is defined by proximity to a predetermined form. Ironically, such systems model Intelligent Design, not the undirected evolution Dawkins and Ray believe in.

Yet leaps in complexity do happen, not only in nature but in human civilization. In direct analogy to Lamarckian adaptive mutation, technological development is not a random search of the entire possibility space of new inventions, that are then selected according to fitness; rather, an awareness of purpose, a goal, an intention guides trial-and-error and narrows the search space. Scientists believe that such intentionality is only the province of human beings, not genes, not ecosystems, and not the planet as a whole. Creationists believe the same thing, except they ascribe intentionality as well to a supernatural intelligence. No one says that because human society is so complex, interdependent, and tightly coupled, it could never have evolved but must have been created this way!

The chicken-and-egg problem of irreducible complexity that plagues selfish gene biogenesis repeats itself on all levels of evolution. Generally speaking, a single mutation in an existing gene cannot produce a new gene with a different function. If two genes differ by only a single base pair, then a single point mutation could convert one into another. Usually, however, these two genes will be regarded merely as variants of the same gene, and will have an identical function unless the mutation is at some critical spot that renders the second gene non-functional. The same goes for other basic alterations, such as the deletion or repetition of an existing sequence. To get a gene with an entirely new function usually requires many, many alterations, a concatenation of several unlikely steps—a series of just the right mutations happening either all at once, or one after another. Unlikelihood multiplies into impossibility. If I guess the next card you draw from the deck, you’d be impressed but not amazed. If I guessed ten in a row, you’d suspect a trick because that would happen only about once every fifty quadrillion trials.

Well, maybe it isn’t so unlikely given billions of years for evolution to happen, right? Wrong. To give you some idea of the numbers involved, in 1997 a gene for an anti-freezing protein was discovered in an Antarctic fish that is extremely similar to another gene in the same fish that codes for a pancreatic enzyme—an entirely different function.[42] The two genes are so similar that indeed, a mere handful of mutations (a deletion, a duplication, a frameshift, an insertion of a short intron, and the amplification of a formerly non-coding spacer sequence) can take us from one to the other. However, if we assume that these mutations were totally random, the number of possible genes that can be made from the original by those steps is literally astronomical—one in 10exp370, according to one author.[43] And remember, these two genes are extremely similar: for most genes the number of steps to convert one to another is much greater.

The neo-Darwinist solution to the problem is to postulate that each of the intermediate genes has some kind of function that benefits the organism’s survival, allowing a gradual evolution from a warm-water fish to an antarctic fish. In general, though, getting halfway to a new gene won’t give you half of its new function. It’s usually all or nothing—or less than nothing, as intermediates might be useless for both the old and the new functions. The authors of the antifreeze paper were aware of this problem, and in a remarkable (though certainly unwitting) appeal to teleology wrote, “The selection of an appropriate permutation of three codons. . . was likely shaped by the structural specificity required for antifreeze ice interaction to take place.”[44] In other words, they realize it couldn’t have happened purely by chance, nor is it plausible that each intermediate conferred a survival advantage.

The problem is actually even worse than that. In most cases, a new gene with a new and genuinely useful function is only useful in the presence of a number of other new genes that must be expressed at the same time. For example, whatever mutation gives a giraffe a long neck would be fatal in the absence of some other gene to give it a special nasal structure and blood vessel network to cool the brain, and another to create the vascular adaptations that regulate blood flow to the brain when the giraffe lowers its head to drink water.[45]

The Intelligent Design proponent Michael Behe gives similar examples in his book Darwin’s Black Box. Most striking is the example of the synthesis of AMP, which is essential to all life. Behe describes thirteen steps of AMP synthesis requiring twelve separate enzymes, each of which is basically useless without the other eleven. Even if one of the requisite genes emerged through random mutation, in the absence of an adaptive advantage, why would it remain in the gene pool instead of any of trillions of other, equally likely mutations? A parallel situation pertains to blood coagulation, which requires numerous proteins and other substances that are highly specific to their tasks and useless outside of them. Both exemplify what Behe calls “irreducible complexity,” of which Darwin wrote, “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 break down.”[46]

The extreme difficulty in using gradual, random genetic mutation to account for the complex, tightly coordinated systems of biology, added to the fossil evidence for sudden evolutionary jumps, is slowly eroding support for the conventional neo-Darwinian synthesis. A new paradigm is emerging to replace it, one which subverts many of our cultural assumptions about the nature of life. Part of this paradigm shift relies on the adaptive mutations described earlier. However, irreducible complexity poses difficulties even for adaptive mutation, because not one but many genes for complex interdependent processes must all appear at the same time. Alternatively, they can appear at different times, but then they must somehow be preserved in the genome without help from conventional selective mechanisms (because they have no beneficial expression). Either way, some coordinating influence is necessary to guide each adaptive mutation toward an outcome that meshes with all the others, whether this force is supernatural (Behe), an environmental purpose (Lamark/Buhner/Lipton), or the observer effect of the system’s own evolutionary future (McFadden).

Perhaps the difficulty again rests upon our assumptions about the nature of self. Adaptive mutation, even when triggered by environmental “purposes”, still preserves the gene as a unit of selfhood, albeit an evolving unit. But there is more. While adaptive mutation is certainly part of the story, perhaps the sheer complexity of the cooperative systems described in the last two sections demands an account of evolution that builds cooperation in to its fundamental mechanisms—a cooperative account of evolution to complement the cooperative nature of life.

According to Lynn Margulis, cooperation (i.e. symbiosis) is not only essential to the survival of all life on earth, it is also the driving force of evolution. Her theory of serial endosymbiogenesis explains the evolution of the modern eukaryotic cell as the progressive incorporation of simpler organisms. In her view, genuine novelty in evolution comes through the merging of simpler organisms, and not through the random mutation of DNA. Organisms—including higher organisms—evolve through the incorporation of external DNA. This has been well-documented for half a century in the case of bacteria, which have been closely studied to determine how they achieve resistance to antibiotics. While occasionally a point mutation will confer resistance, for example through the alteration of some surface protein, normally bacteria import resistance-encoding genes from other bacteria via viruses, conjugation, and other means. And it’s not just resistance. Recent studies have demonstrated that the genes for photosynthesis are also transferred horizontally among bacteria.[47][48] This phenomenon, named horizontal gene transfer (HGT), was observed in plants as long ago as the 1940s in Barbara McClintock’s pioneering studies of corn. More recently, evidence has mounted that HGT is also common in multicellular animals, even in humans. The following press release describing bacterial photosynthesis might therefore be generalized to all evolution:

The analysis revealed clear evidence that photosynthesis did not evolve through a linear path of steady change and growing complexity but through a merging of evolutionary lines that brought together independently evolving chemical systems — the swapping of blocks of genetic material among bacterial species known as horizontal gene transfer.[49]

A major piece of evidence for HGT in nature is the presence in unrelated organisms of similar DNA sequences that, based on molecular clock evidence, cannot be explained through common ancestry. While viruses are probably the main vector of gene transfer, there is also laboratory evidence for direct bacterial transmission of DNA into mammalian cells.[50] Other possible vectors include, in the words of one researcher, “External parasites, infectious agents, intracellular parasites and symbionts (especially those in the germline), DNA viruses, RNA viruses, retroviruses, even hitchhiking in other transposable elements.”[51]

The primary vectors of HGT, whether viruses or other parasites, are not merely germs or invaders but carriers of genetic information from organism to organism and species to species. In one study, researchers found that DNA from T. cruzi, a protozoan which causes Chagas disease in humans, had been incorporated into the nuclear DNA of laboratory rabbits and passed onto their offspring, thus having entered the germline.[52] Some scientists have even put forth evidence that the incorporation of viral DNA initiated the speciation event in which human beings and chimpanzees diverged six million years ago.[53]

These are not controversial findings by fringe scientists, but are reported in prestigious mainstream journals, as a cursory examination of this section’s footnotes will confirm. It is becoming increasingly apparent that eukaryotic genomes, including humans’, are riddled, perhaps even dominated, by the remains of viral DNA incorporated into the germline millions of years ago.[54][55] As Lynn Margulis puts it, “We are our viruses.”

But let’s not limit ourselves to the uncontroversial. Perhaps the integration of exogenous DNA into the human genome is on-going and purposive. The great epidemics of agricultural civilization may have contributed important genes bearing adaptive utility for humans living in dense populations and carrying out civilized lifestyles. In particular, non-lethal viral diseases like measles, mumps, and chicken pox, which were pandemic until the era of vaccines, might comprise an important alternative transmission system for genetic material. Perhaps they are our symbionts, having adapted with us into a mutually beneficial relationship. If so, eliminating them could be dangerous. The precise consequences are hard to predict, but perhaps it has something to do with the alarming rise in autoimmune diseases and allergies over the past thirty years.

Orthodox genetics maintains, because of the slowness of evolution, that we are essentially the same species as our Stone Age ancestors 20,000 years ago. But if viral DNA is regularly incorporated into the germline, it is conceivable that the diseases of civilization are an agent of speciation, triggered by the population concentrations that come only with agriculture. Could it be that humanity is undergoing speciation right now? And if, as Bruce Lipton argues, our emotions, thoughts, and beliefs can modify our DNA, could speciation even be a matter of choice? Do we have the opportunity to literally become what we choose to be? I realize I have entered the realm of speculation, but even so, the metaphoric significance of this possibility are profound. We are not trapped into what we are by our biology. We can acquire new biology in the course of a lifetime. Neither are we trapped by our other inheritances. We are free to create ourselves.

On the level of the organism, HGT offers a model of evolution that does not primarily depend on random mutation, but rather on the integration of already existing external DNA. It offers a solution to many of the problems related to irreducible complexity, because it does not rely on the simultaneous occurrence of many highly unlikely mutations at just the right time. The necessary genes need only be imported, even sequestered in non-expressed form until needed. The ubiquity of HGT also suggests a new way of relating to other life forms such as bacteria and viruses (a matter I will explore in Chapter Seven) as well as a new model of progress outside the biological realm.

Horizontal gene transfer removes the biological underpinnings of the ideology of the discrete and separate self. It suggests a new self, a new identity that might be described as “interbeingness”. This is a much more intimate relationship than mere interdependency among life forms. Thanks to HGT, we are all incorporated into each others’ being. As we shall see in the next chapter, the spiritual and metaphorical implications for human technology, medicine, and economics are profound.

Horizontal gene transfer does not solve the problem of the origin of novelty on the genetic level, because those genes had to come from somewhere. If HGT is primary, it implies that many genes existed millions of years before they were ever expressed. Indeed, single-celled choanoflagellates have been found with genes for proteins previously thought to exist only in multicellular animals, and with no known function in the choanoflagellates.[56] Another, more general mystery is the appearance of homeotic genes (which coordinate embryological development) long before the genes for the structures of the features they coordinate. For example, genes that coordinate the development in embryos of the eye are older than the genes for the proteins that make up the eye. Brig Klyce sums it up quite nicely: “It is difficult for neo-Darwinism to explain the appearance of embryological coordinating genes before the appearance of the embryological steps they coordinate. It’s like saying that the blueprints for automobile manufacturing plants were on hand before the invention of automobiles.”[57] In both the above cases, there is nothing on which Darwinian natural selection could operate, no reason for the genes to persist. What survival advantage could they confer when they have no function?

That genes persist in the genome despite having no beneficial expressed function flatly contradicts Darwinian evolution: what would select such genes over trillions of useless variants? Oddly, ultraconserved elements—strings of 200 or more DNA base pairs—have been discovered that are identical across the genomes of rats, mice, humans, dogs, and fish, but which do not code for any protein and do not exhibit any regulatory function. Indeed, when these sequences are removed from mouse genes, the mice appear to be normal in every respect.[58] What selective mechanism, then, could preserve these sequences, virtually mutation-free (far below the “background” mutation rate), for hundreds of millions of years? Why are they so important if they don’t affect survival and reproduction? Clearly, other selective mechanisms are at work. The purpose of life is not, as Darwinism implies, to survive.[59]

Brig Klyce speculates that such genes are actually “high-level software capable of recognizing, installing, assembling and activating horizontally acquired genetic programs.”[60] As such they are agents of evolutionary purpose serving needs transcending individual organisms and their genes.

Klyce is an advocate of Panspermia, the theory pioneered by Fred Hoyle and Chandra Wickerhamsinghe that says that life on earth was seeded with biological material from outer space. Aside from the mysterious origin of genetic novelty, there are indeed indications of an extraterrestrial origin for life, such as the discovery of complex organic molecules on meteorites, and spectroscopic analysis of interstellar dust consistent with the presence of bacterial spores. Of course, on the cosmological scale Panspermia is not a satisfactory explanation for the origin of life either, since it just pushes the question back in time to before the earth was formed. If life didn’t start on earth, it had to have started somewhere. . . right? Very quickly (only three or four earth lifespans) we run up against the Big Bang, generating the same combinatorial plausibility problems as before. That is why Panspermia advocates usually subscribe to alternative cosmological models such as the steady-state universe. Life in that case never began; it has always been here, a property of the universe.

To the linear mind, that life has always existed, beginningless, is a mind-blowing concept. (At least, it blows my own linear mind!) Unlike primitive people, who thought in terms of cycles and lived in a timeless world, the modern mind understands all things, including the universe, as having a beginning and an end, just as our way of life is based on the linear consumption of raw materials that end up, finally, as useless waste. It is surely no accident that standard cosmology posits precisely this model: the universe began in a state of low thermodynamic entropy and ends in “heat death” when all usable energy has been consumed. The Second Law of Thermodynamics, that entropy always increases, is the ultimate statement of the ideology of domestication: nature is bad, a force to be resisted. We establish a separate human realm, a realm of order, maintained only through constant and eternal effort against the forces of chaos. Can you feel the despair implicit in the Second Law? No more possible is it to overcome entropy, than to build a tower all the way to Heaven.

How different a universe it is that is continually created, in which new matter and new order is continually being born in perfect counterbalance to the entropic tendency toward death. It would be a living universe, a fecund universe, a universe consistent with the hunter-gatherer’s view of nature as endlessly provident. We don’t need to establish a separate human realm. We can instead turn to the extension of the natural realm. No longer need we strive to build a Tower to the sky, when we realize that the sky is all around us already. Order, creativity, birth are in nature, woven into mathematics and physics and biology. Instead of building toward an unattainable and ever-receding Heaven, we turn instead toward another kind of edifice designed for beauty instead of height.

If humankind is now shifting toward a way of life that no longer denies nature’s cycles, then perhaps the Big Bang will lose its intuitive appeal. (There are already cracks in the Big Bang facade, most notably in the work of astronomer Halton Arp and plasma physicist Hannes Alfven.)[61] Deep cosmological and philosophical issues are embedded in the debate over life’s origins and evolution: Is the universe finite or infinite? Created or eternal? Random or purposeful? Or could it be, perhaps, that even these dualities will ultimately collapse?

My problem with Panspermia is that just as Intelligent Design postulates a divine plan (i.e., from outside nature) for evolution, Panspermia explains away the miracle of genetic novelty by saying it arrived from outside the earth. Both agree that such an irreducibly complex phenomenon as life could not arise spontaneously. Both agree that the genes for each jump in evolution already existed, whether in outer space or from the mind of God. But following their logic, are we to believe also that the emergent complexity of human society, economy, culture, and the noosphere couldn’t have just happened either? As Ilya Prigogine observed in the 1960s, order and even organization—new structures—emerge spontaneously in any non-linear system. Why not life? Like the created universe of ID, Panspermia’s “steady state” universe is one which is not inherently creative, but in which creativity is an already-accomplished fact. That conflicts with my deepest spiritual intuitions. Is not life the very essence of creativity?

On the other hand, Panspermia has much in common with the complexity theory arising from Prigogine’s work. The universe, they both believe, is abundant with life. Like Stuart Kauffman’s theory, Panspermia implies that life is extremely likely, if not inevitable, on any planet within a fairly broad range of parameters. If the universe is replete with life, then the chances of its seeding earth are also very high. If on the other hand Stuart Kauffman is wrong, and life is an incredibly unlikely fluke, then the chances of its having originated somewhere else and found its way to earth are equally unlikely. Both theories agree that, one way or another, ours is a living universe.

In this statement lies the solution to the serious difficulties that complexity theory encounters in the lab. Just as order arises out of chaos, it is equally true that, as I wrote in the context of symbiosis, “Life does not thrive in sterile isolation.” It is in the nature of a controlled experiment that it must be a closed system—you cannot leave the beaker open and claimed to have created new life inside. Perhaps what is missing from laboratory and computer experiments aimed at creating life is a seed, a seminal power that originated at the beginning extraterrestrially. Perhaps, indeed, life cannot originate or persist in a closed system; that in addition to an input of energy it needs an input of information; that no one part of the universe can be alive unless the entirety is also alive. Just as we humans are neither discrete nor separate from the rest of life on earth, perhaps Gaia herself is a dependent, semi-autonomous off-budding of a living universe.

It is possible that both theories are true, that life on earth is of dual parentage: a female parent, the earth, and a male parent, the sky. Ours is a living universe. No less than a gene, an organism, or an ecosystem, perhaps Gaia herself is also dependent on an open, fluid interaction with the outside. By sealing the beaker in origin-of-life experiments, we create conditions that are fundamentally anti-life.

Metaphorically, we have also replicated the controlled conditions of the laboratory in the modern “world under control.” Believing ourselves fundamentally separate from a mechanistic universe of inert matter, we have sought to insulate ourselves from its vagaries, to bring it under control through the Technological Program. That this program, too, is anti-life is becoming more and more apparent. The reduction of life—literal in our devastation of the ecology, figurative in the conversion of human life into money—is reaching its apogee. Fortunately, the new paradigms that this chapter has gathered from every corner of science invite us into a new way of relating to the universe that is not anti-life. What kind of society will emerge with the fall of the Newtonian World-machine? How will the human spirit blossom, when we no longer enforce the artificial boundaries of the discrete and separate self? What will human life look like, when we cease seeing it as a competition for survival in a objective universe devoid of purpose, sacredness, and meaning? The second Scientific Revolution that I have outlined is but part of a vaster sea-change in our own self-conception, a symptom as well as a cause for a new way of relating to the world. It marks a turning point, the end of the Age of Separation and the beginning of a new Age of Reunion.


[41] The lack of new, more complex organisms is hidden by the fact that complex and unforeseen patterns of behavior indeed arise among the seed creatures and their variants, which do indeed evolve, only not toward leaps in complexity. See Richard E. Lenski, Charles Ofria, Robert T. Pennock and Christoph Adami, “The evolutionary origin of complex features”, Nature, vol, 4238, May 2003, p 139-144 for some interesting examples.


[42] Liangbiao Chen, Arthur L. DeVries and Chi-Hing C. Cheng. “Evolution of antifreeze protein from a trypsinogen gene in Antarctic notothenioid fish” vol. 94, Proceedings of the National Academy of Sciences, USA, April 1997, p 3811-3816.


[43] Klyce, Brig, “The Origin of Antifreeze Protein Genes”,


[44] Thanks to Brig Klyce’s close reading of the paper for spotting this teleological phrase.


[45] Mckee, Jeffrey, The Riddled Chain, Rutgers University Press, 2000. p. 196.


[46] Charles Darwin, Origin of Species, p. 154, cited in Behe, Michael, Darwin’s Black Box, Free Press, 2006.


[47] Debbie Lindell et al., “Transfer of photosynthesis genes to and from Prochlorococcus viruses”, Proceedings of the National Academy of Sciences, USA, vol. 101, July 27, 2004, p 11013-11018.


[48] Jason Raymond et al., “Whole-Genome Analysis of Photosynthetic Prokaryotes”, Science, v 298, Nov 22 2002, p 1616-1620.


[49] “Photosynthesis Analysis Shows Work of Ancient Genetic Engineering,” Arizona State University, 21 Nov 2002.


[50] Grillot-Courvalin, Catherine, Sylvie Goussard, and Patrice Courvalin, “Bacteria as Gene Delivery Vectors for Mammalian Cells”, Horizontal Gene Transfer, ed. Michael Syvanen & Clarence Kado.


[51] Hartl, D.L., Lohe, A.R. And Lozovskaya, E.R., “Modern Thoughts on an Ancyent Marinere: Function, Evolution, Regulation.” Annual Review of Genetics, vol. 31, 1997, p. 337-358.


[52] Nature Reviews Genetics, vol. 5, 2004, p. 638-639


[53] Svitil, Kathy A. “Did Viruses Make Us Human?” Discover, Nov 2002.


[54] Hughes, Jennifer F. and John M. Coffin, “Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution”, Nature Genetics, vol. 29, Dec 2001, p 487-489, n. 4


[55] Herbert, Alan, “The four Rs of RNA-directed evolution” Nature Genetics, vol. 36, Jan 2004, p 19-25, n. 1


[56] Nicole King et al., “Evolution of Key Cell Signaling and Adhesion Protein Families Predates Animal Origins”, Science, v 301, July 18, 2003, p 361-363.


[57] Klyce, Brig, “Neo-Darwinism: The Current Paradigm”,


[58] Westphal, Sylvia Paga’n, “Life goes on without ‘vital’ DNA”, New Scientist, June 3, 2004


[59] For you sticklers out there, I understand that what Darwin implies is not “The purpose of life is to survive” but “The purpose of life is to survive long enough to pass on my genes and ensure their survival and further replication.” Don’t you think the first sentence has a better ring to it though? Anyway, the upshot is the same.




[61] See Arp, Halton, Seeing Red, Aperion, 1998, and Lerner, Eric, The Big Bang Never Happened, Vintage, 1992.