Kauffman was an early faculty member in residence at the Santa Fe Institute, which is well known for its contributions to complexity theory, chaos theory, and information theory. His strong views on the need to augment natural selection have been controversial among systems biologists, but Kauffman said that himself at the outset about his work. He called it a "heretical possibility."

The origin of life, rather than having been vastly improbable, is instead an expected collective property of complex systems of catalytic polymers and the molecules on which they act. Life, in a deep sense, crystallized as a collective self-reproducing metabolism in a space of possible organic reactions. If this is true, then the routes to life are many and its origin is profound yet simple.

This view is indeed heretical. Most students of the origin of life hold that life must be based on the self-templating character of RNA or RNA-like molecules. Because of such self-templating, any RNA molecule would specify its base pair complement; hence a "nude gene" might reproduce itself. After that, according to most thinkers, these simplest replicating molecules built up around themselves the complex set of RNA, DNA, and protein molecules which constituted a self-reproducing system coordinating a metabolic flow and capable of evolving.

Chapter 7 unfolds this new view, which is based on the discovery of an expected phase transition from a collection of polymers which do not reproduce themselves to a slightly more complex collection of polymers which do jointly catalyze their own reproduction. In this theory of the origin of life, it is not necessary that any molecule reproduce itself. Rather, a collection of molecules has the property that the last step in the formation of each molecule is catalyzed by some molecule in the system. The phase transition occurs when some critical complexity level of molecular diversity is surpassed. At that critical level, the ratio of reactions among the polymers to the number of polymers in the system passes a critical value, and a connected web of catalyzed reactions linking the polymers arises and spans the molecular species in the system. This web constitutes the crystallization of catalytic closure such that the system of polymers becomes collectively self-reproducing.

While heretical, this new body of theory is robust in the sense that the conclusions hold for a wide variety of assumptions about prebiotic chemistry, about the kinds of polymers involved, and about the capacities of those polymers to catalyze reactions transforming either themselves or other, very similar polymers. It is also robust in leading to a fundamental new conclusion: Molecular systems, in principle, can both reproduce and evolve without having a genome in the familiar sense of a template-replicating molecular species. It is no small conclusion that heritable variation, and hence adaptive evolution, can occur in a self-reproducing molecular system lacking a genome. Since Darwin's theory of evolution, Mendel's discovery of the "atoms" of heredity, and Weismann 's theory of the germ plasm, biologists have argued that evolution requires a genome. False, I claim.

Also, this new body of theory is fully testable. If correct, sufficiently complex systems of RNA or protein polymers should be collectively autocatalytic.

In Chapter 8 these new concepts are extended to the crystallization of a connected metabolism. I strongly suspect that, rather than having formed piecemeal, a connected metabolism, like a self-reproducing set of catalytic polymers, emerged spontaneously as a phase transition when a sufficient number of potentially catalytic polymers were mixed with a sufficiently complex set of organic molecules. In this condition, a critical ratio of number of catalyzed reactions to number of molecular species present is surpassed, and a connected web of catalyzed transformations arises. Life began whole and integrated, not disconnected and disorganized,

(The Origins of Order, 1993, p.285)

Kauffman's ideas about autocatalytic systems are shared by Terrence Deacon.

Kauffman thought that he might even discover "laws" of self-organization. In his 1995 book, At Home in the Universe, he identified the discovery of such laws as showing that human life followed directly from these pre-existing laws, which would replace the arbitrary and purposeless system of Darwinian natural selection. Humans (and even paradise?) would be implicit in those additional laws.

Random variation, selection sifting. Here is the core, the root. Here lies the brooding sense of accident, of historical contingency, of design by elimination. At least physics, cold in its calculus, implied a deep order, an inevitability. Biology has come to seem a science of the accidental, the ad hoc, and we just one of the fruits of this ad hocery. Were the tape played over, we like to say, the forms of organisms would surely differ dramatically. We humans, a trumped-up, tricked-out, horn-blowing, self-important presence on the globe, need never have occurred. So much for our pretensions; we are lucky to have our hour. So much, too, for paradise.

Where, then, does this order come from, this teeming life I see from my window: urgent spider making her living with her pre-nylon web, coyote crafty across the ridgetop, muddy Rio Grande aswarm with nosee- ems (an invisible insect peculiar to early evenings)? Since Darwin, we turn to a single, singular force, Natural Selection, which we might as well capitalize as though it were the new deity. Random variation, selection-sifting. Without it, we reason, there would be nothing but incoherent disorder.

I shall argue in this book that this ldea is wrong. For, as we shall see, the emerging sciences of complexity begin to suggest that the order is not all accidental, that vast veins of spontaneous order lie at hand. Laws of complexity spontaneously generate much of the order of the natural world. It is only then that selection comes into play, further molding and refining. Such veins of spontaneous order have not been entirely unknown, yet they are just beginning to emerge as powerful new clues to the origins and evolution of life. We have all known that simple physical systems exhibit spontaneous order: an oil droplet in water forms a sphere; snowflakes exhibit their evanescent sixfold symmetry. What is new is that the range of spontaneous order is enormously greater than we have supposed. Profound order is being discovered in large, complex, and apparently random systems. I believe that this emergent order underlies not only the origin of life itself, but much of the order seen in organisms today. So, too, do many of my colleagues, who are starting to find overlapping evidence of such emergent order in all different kinds of complex systems.

The existence of spontaneous order is a stunning challenge to our settled ideas in biology since Darwin. Most biologists have believed for over a century that selection is the sole source of order in biology, that selection alone is the "tinkerer" that crafts the forms. But if the forms selection chooses among were generated by laws of complexity, then selection has always had a handmaiden. It is not, after all, the sole source of order, and organisms are not just tinkered-together contraptions, but expressions of deeper natural laws. If all this is true, what a revision of the Darwinian worldview will lie before us! Not we the accidental, but we the expected.

(At Home in the Universe, 1995, pp.7-8)

We need a place for our spirituality, and a Creator God is one such place. I hold that it is we who have invented God, to serve as our most powerful symbol. It is our choice how wisely to use our own symbol to orient our lives and our civilizations. I believe we can reinvent the sacred. We can invent a global ethic, in a shared space, safe to all of us, with one view of God as the natural creativity in the universe.

(Reinventing the Sacred, 2008, p.xiii)

Like many emergentists, Kauffman attacks the reductionist views epitomized by the great physicist Steven Weinberg's two famous dicta:

"The explanatory arrows always point downward" to physics, and "The more we comprehend the universe, the more pointless it seems." In brief, reductionism is the view that society is to be explained in terms of people, people in terms of organs, organs by cells, cells by biochemistry, biochemistry by chemistry, and chemistry by physics. To put it even more crudely, it is the view that in the end, all of reality is nothing but whatever is "down there" at the current base of physics: quarks or the famous strings of string theory, plus the interactions among these entities. Physics is held to be the basic science in terms of which all other sciences will ultimately be understood. As Weinberg puts it, all explanations of higher-level entities point down to physics. And in physics there are only happenings, only facts.

(Reinventing the Sacred, 2008, pp.10-11)

What does Kauffman put in place of reductionism, which he calls the "Galilean ideal?" Beyond the complexity and self-organization of complex adaptive auto-catalytic systems of his earlier work, he adds a "partially lawless" element that he sees in a non-standard interpretation of quantum mechanics called decoherence. His explanation of mind and consciousness depends on his idea of a "poised state"

must conscious mind be classical, rather than quantum or a mixture of quantum and classical? Could consciousness be a very special poised state between quantum coherence and decoherence to classicity by which "immaterial, nonobjective" mind "acts" on matter? Most physicists say this is impossible. As I will show in the next chapter, recent theories and experiments suggest otherwise.

I am hardly the first person to assert that consciousness may be related to quantum phenomena. In 1989, the physicist Roger Penrose, in The Emperor's New Mind, proposed that consciousness is related to quantum gravity, the still missing union of general relativity and quantum mechanics. Here I will take a different tack and suggest that consciousness is associated with a poised state between quantum "coherent" behavior and what is called "decoherence" of quantum possibilities to "classical" actual events. I will propose that this is how the immaterial—not objectively real—mind has consequences for the actual classical physical world. I warn you that this hypothesis is highly controversial—the most scientifically improbable thing I say in this book. Yet as we will see, there appear to be grounds to investigate it seriously...

(Reinventing the Sacred, 2008, pp.196-197)

I will make use of decoherence to classical behavior as the means by which a quantum coherent conscious mind of pure possibilities can have actual classical consequences in the physical world. This will be how mind has consequences for matter. Note that I do not say "how mind acts on matter," because I am proposing that the consequences in the classical world of the quantum mind are due to decoherence, which is not itself causal in any normal classical sense. Thus I will circumvent the worry about how the immaterial mind has causal effects on matter by asserting that the quantum coherent mind decoheres to have consequences for the classical world, but does not act causally on the material world. As we will see, this appears to circumvent the very old problem of mental causation and provide a possible, if still scientifically unlikely, solution to how the mind "acts" on matter...

The cornerstone of my theory is that the conscious mind is a persistently poised quantum coherent-decoherent system, forever propagating quantum coherent behavior, yet forever also decohering to classical behavior. I describe the requirements for this theory in more detail below. Here, mind—consciousness, res cogitans—is identical with quantum coherent immaterial possibilities, or with partially coherent quantum behavior, yet via decoherence, the quantum coherent mind has consequences that approach classical behavior so very closely that mind can have consequences that create actual physical events by the emergence of classicity. Thus, res cogitans has consequences for res extensa! Immaterial mind has consequences for matter.

More, in the poised quantum coherent-decoherent biomolecular system I will posit, quantum coherent, or partially coherent, possibilities themselves continue to propagate, but remain acausal. This will become mental processes begetting mental processes.

Information philosophy agrees that mind is immaterial, but it is also "objectively real"

Some physicists will object to my use of the word immaterial with reject to quantum phenomenon. They would want to say instead, "not objectively real," like a rock. I am happy to accept this language, and will use immaterial to mean "not objectively real."

(Reinventing the Sacred, 2008, pp.208-209)

In a recent paper on arXiv, Kauffman speculated about solutions to the problem of free will, the mind-body problem, and suggested a new interpretation of quantum mechanics. He calls the "causal closure" of classical physics (basically reduction ) the source of the idea that we are machines and our minds are epiphenomenal. He proposes a new dualism of ontologically real actuals (he uses Descartes' term res extensa) and ontologically real possibles (he calls res potentia, which could come from Aristotle or Werner Heisenberg). The Schrödinger equation describes the evolution of these possibilities, allowing the calculation of quantum probabilities..

He puzzles over nonlocality. And he presents his "poised realm," which hovers reversibly between quantum coherent and "classical" worlds. He then proposes a "quantum mind" in which decoherence produces an "acausal loss of phase information from the open quantum system to the universe." This has "acausal consequences for the classical 'meat' of the brain," he says.

Kauffman suggests that he can "decircularize" the "Strong Free Will Theorem of John Conway and Simon Kochen. He first states the two-part standard argument against free will. If the mind is determined, "classical physics holds we have no free will at all."

If we try to use quantum indeterminism to achieve an ontologically free will, it is merely random...So a random quantum event occurs in my brain,...but I am not “responsible”, the quantum event was random. So even if measurement is real, and ontologically indeterminate, so underlies a “free will”, that will cannot be responsible.

(arXiv,pp.10-11)

Kauffman proposes "a broad new formulation of quantum mechanics in terms a new triad: Actuals, Possibles and Mind - conscious observation acausally mediating measurement, and doing. Here new actuals create new possibles which are available via mind to be measured to create new actuals to create new "adjacent possibles" in a persistent becoming of the universe.

I want us to consider a totally new view of quantum mechanics and reality, consisting of ontologically real actuals that obey the law of the excluded middle, ontologically real possibles that do not obey the law of the excluded middle in quantum behavior before measurement, and mind measuring and responsible free willed. In this view, measurement creates new actuals that acausally and outside of space and inside time consistent with Special Relativity, can instantaneously and acausally alter what is now possible, hence account for instantaneous changes in wave functions upon measurement and non-locality.

If new "actuals" are created acausally by quantum mind "measurements," the outcomes are statistical, that is random. We need the randomness to create the alternative possibilities in the "first stage" from which the choice/selection is adequately determined in the "second stage" of two-stage models of free will.

In turn new possibles are available for mind to measure and do, creating new actuals, in a persistent cycle of quantum enigma free willed and conscious becoming in a radically participatory universe with a non-epiphenomenal “cosmic” consciousness and doings wherever measurements happen.

(arXiv,pp.17-18)

Kauffman's res potentiae replace René Descartes' res cogitans, the thinking thing or < href="/mind/">mind, in the great mind-body problem.

In our two-stage model of free will, the mind creates alternative possibilities for thoughts and actions in the first stage. The decision process in the second stage evaluates these possibilities and adequately determines one of them to become actual.

We agree with Kauffman that "possibles" exist, but are hesitant to describe them as "real" in the same sense that material objects are "real." The fact that some possibles are created randomly does not make our decisions themselves random, as Kauffman fears.