While complexity theory has some serious flaws as an explanation of life's origins, many of its features strongly correspond to a newly emerging understanding of life and evolution. Recent discoveries in ecology and genetics confirm two of the basic implications of complexity theory: (1) That life is at its basis cooperative, and (2) that there is no absolute integrity of biological self.
These new discoveries imply a different mode of understanding that subverts neo-Darwinism at its very foundation, calling into question the primacy of natural selection and random mutation as agents of evolution. While competition certainly may exist among members of an ecosystem or an autocatalytic set, each also depends on the others to survive. Each has its niche, its essential role and function, that the others would destroy at their own peril. There is no discrete replicating unit, and therefore nothing on which Darwinian laws can operate until much later, when semi-autonomous offbuddings of the set gain enough independence to compete as discrete individuals. But let me emphasize the modifier "semi", because no life form is ever fully independent of the rest of nature.
When we look at contemporary living systems, we find a situation similar to that of the autocatalytic set. Of course there is competition, but its primacy as the determining factor in behavior and evolution is exaggerated. We tend to find what we look for, and now that the cultural blinders of separation are beginning to fall away, scientists are discovering more and more the overriding importance of cooperation in biology. The extent of these cooperative relationships call into question the very coherency of the concept of an individual organism, threatening, as Kauffman's sets do, to deprive neo-Darwinism of the very subject of natural selection.
Let's look at some examples of cooperation in nature, starting with our own cells. Each of our cells are inhabited by mitochondria, which have their own DNA. These bits of protoplasm are parts of our selves (and of all other animals) that are not "coded for" by our nuclear DNA. In a sense they are separate organisms—in fact most scientists now accept Lynn Margulis' theory that mitochondria were originally aerobic bacteria that merged with other cells. Yet without them we'd be dead, for they provide at least 90% of our energy. Even on the cellular level, we are cooperative beings.
On the coast of Brittany there is a flatworm, Convoluta roscoffensis, that has no functioning mouth or digestive tract. Instead, its transparent body hosts trillions of green algae who provide the worm energy through photosynthesis. In that protected environment, generations of algae live and die. They even process the worm's metabolic wastes! Another worm, a roundworm that lives near undersea vents, also has no digestive tract but harbors bacteria in a special organ called a trophosome. The bacteria produce energy from hydrogen sulfide gas collected by the worm. What kind of bacteria? No one has named them, because they are impossible to culture in a lab. They can only survive in the worm. Bacteria and worm are each wholly dependent on the other.
I have already mentioned the dependency of ruminant animals on bacteria to digest cellulose. Recently, evidence has accumulated that humans too require a complex intestinal ecology to thrive. Hundreds of species of yeasts, bacteria, and other organisms inhabit the healthy human gut in numbers far exceeding our own cells. They produce K and B vitamins, protect us from colonization by pathogenic bacteria and fungi, assist digestion, and interact with the immune system in ways that are not fully understood. There is even evidence that human beings are meant to host certain species of "parasitic" intestinal worms, which have been used to successfully treat hundreds of cases of ulcerative colitis and Crohn's Disease. Not just our intestines, but all of our mucosa, skin, and even eyelashes are host to bacteria, yeasts, and microscopic insects that are not competitors drawing down our resources, but partners in health. Since we are partly or even wholly dependent upon them, no less than we are on our heart and liver, by what right do we exclude them from the definition of self?
Stephen Buhner gives many amazing examples of cooperation in nature in his beautiful book, The Lost Language of Plants.
In Central America and Africa certain species of Acacia, a large shrub or small tree, is covered with thorns, some of which are hollow and house ants. Much like coevolutionary bacteria, Pseudomyrmex ants recognize new shrubs as coevolutionary partners and colonize them. The trees produce special nectar along the stems for the ants to eat. Like the compounds released from plant roots, this nectar contains a rich mix of fats (lipids), proteins, sugars, and other compounds necessary for the ants to remain healthy. The ants remove vegetation from around the base of the plant, remove leaves of other plants that shade the tree, kill any vines that try to grow up the tree, and attack any herbivore that tries to eat the plant.
Which is the organism, the tree itself, or tree plus ants? Most plants could not survive without mycorrhizal fungi on their rootlets, which in turn depend on sugars provided by the plant. A similar relationship exists between legumes and nitrogen-fixing bacteria, except not only the organisms involved but the entire plant community depends on the fixing of nitrogen. This is typical. Cooperation in nature extends far beyond mutual dependency between plant and pollinator, flatworm and algae. More often, the dependencies are not one-on-one but highly distributed: thousands of species in mutually dependent partnership. Just as a mammal cannot survive without a heart or lungs, which justifies including these organs as part of "self", so also are these plants, insects, fungi and so forth unable to survive without their symbiotic community. Remove one element, and the whole system might collapse. Life does not thrive in sterile isolation.
Buhner gives a striking example of a community of life in his description of the ironwood tree of the Sonoran desert:
Smaller plants begin to appear. Continually shaded from the desert sun, cooled by transpired water, and watered daily by hydraulic lift, some 65 species of plants will come to grow under ironwood. . . Thirty-one of these will grow nowhere else. This emerging plant community connects to the mycelial network and plant chemistries flow throughout the network. Wherever plant roots touch, they can share their chemistries directly. All the plants exude volatile aromatics. Some aromatics call in pollinators, others fall in a continual rain over the plant community and to the Earth below. The soil takes them up; the companion plants under the ironwood breathe them in. The smaller community plants cover the ground, keeping the soil moisture high. They all release their own unique mixtures of phytochemicals that blend together with ironwood's in maintaining the microclimate and soil community under the tree.
As leaves, bark, and limbs age, they fall to the Earth, forming a layer of decaying matter. Over the centuries, the tree and its community build up a mound of detritus around its trunk and under its canopy, in effect becoming an island or archipelago of life and richness amid the desert—a facilitative nucleus of life. Scores of insects, birds, and animals come to the archipelago. They pollinate, spread seeds, build nests from archipelago plants, dig burrows, mate, aerate the soil, use plant chemistries in their growth, as their medicine, as their food, and contribute, over the years, tons of their own "night soil." Ironwood increases the abundance of life by 88 percent and species richness by 64 percent in any area in which it grows. Plants such as the endangered saguaro cactus can rarely germinate outside the kind of zone that trees such as ironwood create. Ironwood, and similar trees, literally create the ecosystems in which they and other beings live.
The ironwood communities are unusual only in their relative isolation. In other ecosystems, the same kind of relationships exist among keystone species, the nurse plants which help them get established, and subordinate plants which regulate the flow of life and energy through the community. Of course, the community as a whole, which also includes insects, bacteria, birds, mammals, and fungi, does exercise limitations on the proliferation of each member, and in the establishment and maintenance of these, competition surely comes into play. But it is a mistake to try to understand the functioning of the whole community in those terms. Instead of seeing competition as primary and symbiosis somehow arising out of it, it might be more illuminating to see competition as one of several ways by which resource flow is optimized within a living community.
Understanding of human communities is crippled in a similar way, by insisting on viewing all reciprocity in terms of competitive economics. Some anthropologists have tried to do just this by analyzing trade between individuals or tribes in terms of net caloric gain or net time gain. However, this kind of analysis is motivated by the implicit assumption that calories or time are scarce commodities (an uneven trade would be no cause for concern for people without a concept of time scarcity or food scarcity), and therefore harks back to the assumption that primitive life was a struggle for survival. Orthodox biology holds an identical assumption, and like anthropology, cannot fully apprehend systems in which competition is not primary. Something is always missing.
Of course, none of the communities of life described above are autonomous. All organisms and microsystems depend on the health of the ecosystem in which they live, and each ecosystem depends on other, distant ecosystems. And all higher life forms depend on the bacteria which maintain a life-supporting atmosphere. While life on earth can sustain the loss of some species, each species depends on the whole. None can exist in isolation on a bare and lifeless planet. We may thus also consider the only viable unit of life to be the entirety of all life, along with inorganic processes relating to the water cycle and carbon cycle. The conception of the organism as an autocatalytic set is misleading, because no organism is fully autocatalytic. Like the human depending on essential amino acids, etc., all life forms depend on the rest of life for their long-term survival. The only autocatalytic set is the entire planet. If that.
These examples of flatworms and mycorhizza are not anomalies, not some odd curiosity of nature. They are ubiquitous. Cooperation is everywhere. Life depends on it. Only the cultural blinders of Darwinian survival-of-the-fittest, the dog-eat-dog world, prevent us from seeing it. We live in a cooperative biological world, a living entity which we call Gaia.
Some might quibble with the characterization of earth as a living organism, but it does possess many features of one, most notably homeostatic regulation of temperature, gases, salinity, and other variables. Each species contributes some way to the metabolism and homeostasis of the planet. Coral creates lagoons that help remove salt from the ocean, which would otherwise double in salinity in just 60 million years. Photosynthesizing algae and rainforests produce the oxygen that sustains animal life, while other mechanisms prevent oxygen levels from going too high and sparking devastating planet-wide forest fires. Bacteria accelerate rock weathering to bring carbon out of the atmosphere, while marine animals eventually turn that carbon into shells ultimately sequestered on the ocean floor. And something, some combination of organic and inorganic processes, has kept earth's surface temperature stable as the sun's apparent brightness has increased by 30 or 40 percent over three billion years. Gaia maintains homeostasis, responds to external stimuli, and grows, if not in size at least in complexity. The only attribute of a living being that Gaia does not possess is, we are told, the ability to reproduce.
Evolution is often depicted as an arms race, with plants developing ever more sophisticated chemical defenses against predation, while the insects that feed on them try to adapt to those defenses or face starvation. While examples of this do occur in nature, as between cheetah and gazelle, it is actually an unusual situation that we take as typical only because that's what we look for. Far more typical is the relationship between the Douglas fir and the spruce budworm. During periods of very light infestation the tree produces no response, but when budworm numbers begin to grow the trees alter their terpene releases in a way that interferes with budworm feeding and reproduction. The trees don't try to eliminate the budworm and other pests and take over the earth, but merely help maintain budworm populations at the right level. Many other plants do the same thing, tolerating moderate foraging but responding aggressively to severe infestation. Others possess compounds that are toxic only in large quantities, such as phytoestrogens that interfere with grazers' reproduction if eaten to excess.
With few exceptions, modern human beings are the only living beings that think it is a good idea to completely eliminate the competition. Nature is not a merciless struggle to survive, but a vast network of checks and balances that ensures each species occupies its proper place. Indeed, the extinction of any species usually has negative consequences that spread throughout the ecosystem, often to the detriment of even its former prey. Are the deer better off when they are finally free from the tyranny of the wolves? Only if you think starvation, bark stripping, and the degradation of the entire forest ecology are an improvement.
The study of ecology leads toward a view of nature as a vast gift-giving network, rather than a competitive, accumulative network. In his classic work, The Gift, Lewis Hyde observes that in primitive cultures it was in the essence of a gift that it had to be passed on or consumed—many cultures actually used the word "eaten". Gifts were not accumulated. Similarly, each species, each organism, has something to give to its environment, through which resources flow freely. Even in the case of predation, locutions like, "The deer gave itself to the wolf" reveal an unconscious insight, that underneath the very real life-and-death struggle there is a fateful and intimate connection between predator and prey.
Just as hunter-gatherers did not accumulate possessions, animals and plants don't try to make the world theirs by taking over ecosystems and wiping out other species. (Opportunistic weeds may "take over" an area for a time, but soon give way to more complex ecosystems. Their rapid initial takeover might be a gift to the community as well, for example by stabilizing denuded soil and preventing erosion.) In a gift-based world, the needs of the rest of the community define a purpose to life. Instead of a struggle to survive, life is an aspiration toward excellence in the role presented to each organism, or each person.
It was only with the advent of agriculture that human beings began to think in terms of eliminating the competition: weeds, wolves, and insect pests. What of the deer problem? We will cull the herd and manage deer populations. What of the diseases that afflict monocultures? We will manage them with chemicals. The project of eliminating the competition coincides with the ambition to order and manage nature, culminating in the total mastery of nature that is the fulfillment of the Technological Program. Or as a Scientific American cover once put it, "Managing Planet Earth."
Today, as the convergence of crises renders life increasingly unmanageable, we are realizing the bankruptcy of this ambition. We need only to look to nature to see the false premises on which it is based. Projecting our own alienation, competitiveness, and survival anxiety onto biology, we have seen life as a Steinerian war of all against all, but nature, like primitive society, is not like that. Yes there is competition and there are times of anxiety, hunger, and life-and-death struggle, but these are merely a few of the strands of existence, not its warp and woof. The entirety of life, Gaia, makes room for each species until its time has passed. We live, as Lynn Margulis puts it, on a symbiotic planet.
All of this suggests a very different way of relating to nature, which is another way of saying that it suggests a different mode of technology. Technology, ever directed at the management, subjugation, and supercession of nature, will be turned toward fulfillment of our proper role and function within nature. I will share the outlines of such a mode of technology in the next chapter, fleshing out a vision of the future that holds for humanity a beautiful destiny, an ascent which nonetheless explicitly rejects today's longstanding consumptive, linear view of "progress". Perhaps a better word for this ascent is "fulfillment".
 Wickelgren, I. Immunotherapy: Can Worms Tame the Immune System? Science vol. 305, 2004, pp. 170-171.
[38 Buhner, Stephen Harrod, The Lost Language of Plants, Chelsea Green, 2002. p. 163
 Just for fun, I shall note here that some renegade geologists think the planet does grow, and cite this as an alternative explanation for continental drift.
 Buhner, p. 160