In Consilience, his master project to unite the physical and biological sciences with the humanities and social sciences, Wilson speculated on the problems of consciousness and free will.

On Consciousness

Consciousness satisfies emotion by the physical actions it selects in the midst of turbulent sensation. It is the specialized part of the mind that creates and sorts scenarios, the means by which the future is guessed and courses of action chosen. Consciousness is not a remote command center but part of the system, intimately wired to all the neural and hormonal circuits regulating physiology. Consciousness acts and reacts to achieve a dynamic steady state. It perturbs the body in precise ways with each changing circumstance, as required for well-being and response to opportunity, and helps return it to the original condition when challenge and opportunity have been met.

(Consilience, p.113)

On Decision Making and Creativity

Ordinary words used to denote emotion and other processes of mental activity make only a crude fit to the models used by the brain scientists in their attempts at rigorous explanation. But the ordinary and conventional conceptions — what some philosophers call folk psychology — are necessary if we are to make better sense of thousands of years of literate history, and thereby join the cultures of the past with those of the future. To that end I offer the following neuroscience-accented definitions of several of the most important concepts of mental activity.

What we call meaning is the linkage among the neural networks created by the spreading excitation that enlarges imagery and engages emotion. The competitive selection among scenarios is what we call decision making. The outcome, in terms of the match of the winning scenario to instinctive or learned favorable states, sets the kind and intensity of subsequent emotion. The persistent form and intensity of emotions is called mood. The ability of the brain to generate novel scenarios and settle on the most effective among them is called creativity. The persistent production of scenarios lacking reality and survival value is called insanity.

(Consilience, p.115)

On Free Will

An old impasse nonetheless remains: If the mind is bound by the laws of physics, and if it can conceivably be read by calligraphy, how can there be free will? I do not mean free will in the trivial sense, the ability to choose one's thoughts and behavior free of the will of others and the rest of the world all around. I mean, instead, freedom from the constraints imposed by the physiochemical states of one's own body and mind. In the naturalistic view, free will in this deeper sense is the outcome of competition among the scenarios that compose the conscious mind. The dominant scenarios are those that rouse the emotion circuits and engage them to greatest effect during reverie. They energize and focus the mind as a whole and direct the body in particular courses of action. The self is the entity that seems to make such choices. But what is the self?

The self is not an ineffable being living apart within the brain. Rather, it is the key dramatic character of the scenarios. It must exist, and play on center stage, because the senses are located in the body and the body creates the mind to represent the governance of all conscious actions. The self and body are therefore inseparably fused: The self, despite the illusion of its independence created in the scenarios, cannot exist apart from the body, and the body cannot survive for long without the self. So close is this union that it is almost impossible to envision souls in heaven and hell without at least the fantastical equivalent of corporeal existence. Even Christ, we have been instructed, and Mary soon afterward, ascended to heaven in bodies — supernal in quality, but bodies nonetheless.

In our model of the mind" as the immaterial information stored in the brain, it can be separated from the body.

If the naturalistic view of mind is correct, as all the empirical evidence suggests, and if there is also such a thing as the soul, theology has a new Mystery to solve. The soul is immaterial, this Mystery goes, it exists apart from the mind, yet it cannot be separated from the body.

The self, an actor in a perpetually changing drama, lacks full command of its own actions. It does not make decisions solely by conscious, purely rational choice. Much of the computation in decision making is unconscious—strings dancing the puppet ego. Circuits and determining molecular processes exist outside conscious thought. They consolidate certain memories and delete others, bias connections and analogies, and reinforce the neurohormonal loops that regulate subsequent emotional response. Before the curtain is drawn and the play unfolds, the stage has already been partly set and much of the script written.

The hidden preparation of mental activity gives the illusion of free will. We make decisions for reasons we often sense only vaguely, and seldom if ever understand fully. Ignorance of this kind is conceived by the conscious mind as uncertainty to be resolved; hence freedom of choice is ensured. An omniscient mind with total commitment to pure reason and fixed goals would lack free will. Even the gods, who grant that freedom to men and show displeasure when they choose foolishly, avoid assuming such nightmarish power.

Free will as a side product of illusion would seem to be free will enough to drive human progress and offer happiness. Shall we leave it at that? No, we cannot. The philosophers won't let us. They will say: Suppose that with the aid of science we knew all the hidden processes in detail. Would it then be correct to claim that the mind of a particular individual is predictable, and therefore truly, fundamentally determined and lacking in free will? We must concede that much in principle, but only in the following, very peculiar sense. If within the interval of a microsecond the active networks composing the thought were known down to every neuron, molecule, and ion, their exact state in the next microsecond might be predicted. But to pursue this line of reasoning into the ordinary realm of conscious thought is futile in pragmatic terms, for this reason: If the operations of a brain are to be seized and mastered, they must also be altered.

Beyond deterministic chaos, there is indeterministic noise

In addition, the principles of mathematical chaos hold. The body and brain comprise noisy legions of cells, shifting microscopically in discordant patterns that unaided consciousness cannot even begin to imagine. The cells are bombarded every instant by outside stimuli unknowable by human intelligence in advance. Any one of the events can entrain a cascade of microscopic episodes leading to new neural patterns. The computer needed to track the consequences would have to be of stupendous proportions, with operations conceivably far more complex than those of the thinking brain itself. Furthermore, scenarios of the mind are all but infinite in detail, their content evolving in accordance with the unique history and physiology of the individual. How are we to feed that into a computer?

So there can be no simple determinism of human thought, at least not in obedience to causation in the way physical laws describe the motion of bodies and the atomic assembly of molecules. Because the individual mind cannot be fully known and predicted, the self can go on passionately believing in its own free will. And that is a fortunate circumstance. Confidence in free will is biologically adaptive. Without it the mind, imprisoned by fatalism, would slow and deteriorate. Thus in organismic time and space, in every operational sense that applies to the knowable self, the mind does have free will.

(Consilience, p.118-20)