What constitutes an explanation?
Correspondent Eric Reitan makes a provocative point in an interview (ignore the first 5 minutes) and elsewhere, that the naturalistic world view has to explain away many realities (such as religious belief and ideas) in a way that does not do it credit. If we just took our inner experiences more seriously, (not assigning them to "the brain" and related scientific accounts, sometimes further derided as "scientistic"), they would be taken to point to realities as real as the much-vaunted "empirical" realities of modern scientific naturalism.
The most popular form of naturalism today extends a preferential bias to empirical experience. It begins with the assumption that only experience of this sort is veridical (that is, it assumes that only experience of this sort connects the subject to a reality “out there,” tracking it in such a way that one can learn about that reality through the kind of careful examination of the content of the experience that scientists engage in). It then constructs an account of reality on the basis of this kind of experience alone. And when other kinds of experience, were they to be treated as veridical, would require one to posit orders of reality transcending this “naturalistic” account, naturalism explains away these other experiences as epiphenomenal by-products of entities whose reality is endorsed by the naturalist metaphysics (e.g., the brain).Hence, for example, my immediate sense of my daughter’s intrinsic value is not treated as an experience of something real “out there.” Since there is nothing in the naturalistic account of reality that corresponds to “intrinsic value,” the experience I am having is explained away as nothing but an inner psychological phenomenon, a product of brain activity whose neural subroutines probably evolved because of their role in promoting reproductive fitness.
As Reitan says, naturalism has a working model (though partial) for how emotions like his regard for his daughter arise. They come from specific locations like the amygdala upon the perception of things we are highly attached to- attachment that arises from prior learning and memory. People have been known to assign such value to pet rocks or to blankets. The subjective feeling consists of brain activity, though we do not have an account of exactly how that relation works- what qualia or conscousness really "is", bridging the subjective / objective divide. But much of the circuitry is clear, and the study of oxytocin gives a compelling example of the chemical underpinning of social bonding, helping explain its mechanism and origin.
Is that an explanation? People with strokes and dementia lose this valuing connection to people they have known their whole lives. How can this connection and sense of value then be spoken of as real and "intrinsic", if it is actually ephemeral and mechanistic, however strongly felt? If it is a matter of computational data storage, just as the naturalistic account has it? Whether the naturalistic account is sufficient as an explanation of these emotions or not, it is certainly a necessary component. Even as advanced theists posit that god works "through" evolution, so must she work "through" the brain mechanisms to generate thoughts and emotions, leaving aside the question of whether the assumed external actuation makes any sense or is supported by any evidence.
Explanation is a process of creating a narrative of whatever it is that we wish to "understand", which is to say, creating an abstract model of a phenomenon that serves to simplify its workings and relations, hopefully to the extent that we can mentally project its activities backward and forward in time. That is the whole point of our big brains- to understand (or explain) social relations and other aspects of the world in order to bend them to our needs. To understand an episode of a TV show means that we have knowledge of the setting, the predicament, and the traits of the characters, such that we "get" why they conspire to defraud their friends, or whatever the plot developments happen to be.
Such understanding depends on accurate knowledge of all the components that make up the phenomenon- the causes and effects that surround it, which in turn make up a consistent model we can use to work with the phenomenon. That consistency is the hallmark of accurate models of reality versus other worlds of imagination and dream, since outer reality is both self-consistent and also is the object of our very extensive sensory capacities that give us a leg up in evaluating it (in contrast to our extremely poor internal senses). Thus the critical importance of empiricism when making explanations of "reality".
Do intuition and spritual feeling amount to other forms of "knowing", thus also to understanding and explanation? That is a tricky question. These ideas and feelings are certainly real subjectively. They exist. They are even "empirical experience". They may guide one to a correct model of reality. Our instincts and intuition can be incanny in their accuracy. Yet they can also lead us terribly astray. The sense of value you ascribe to another is a datum about you, but it is quite simply not a datum about the other. Rather it is a projection, which in our social world is all we have to rely on and is extremely important. But that projection is evanescent, and can turn (subjectively) into its opposite with tragic consequences, as dramas are only too ready to illustrate.
There is no way from the content of hunches, dreams, and visions alone to verify their correspondence with reality, even while they may be accompanied by the strongest possible "sense of truth". Intuition is a good bet in areas where it has been honed over evolutionary time- estimating how hard to throw a stone, guessing which plant might be edible, figuring whether to trust someone with your money. Science has shown time and again, however, that the farther a phenomenon from our common experience, the poorer intuition is in deeply understanding it.
Lightning is a simple example, where intuition leads directly to supernatural explanations, while the corrective of empirical science has substituted a more naturalistic one. Supernatural explanations have the virtue of extraordinary simplicity. For the cost of one mystical being or realm, all other mystifying phenomena can be swept under its rug. But they have little to do with reality or the consistency that is reality's hallmark, since they do not rely on detailed knowledge of the phenomena in question, nor on a system of logic in explaining it, other than the ad-hoc and jerry-rigged. Attempts to make such systems more "explanatory" end up with pantheons of gods and reams of myth, like those of ancient Greece, which in the end do more harm than good to the credibility of the enterprise, though they are highly entertaining.
But whyyyyy?
Like children driving a parent crazy, the last refuge of the theist is to say that for all that science tells us, it can not "explain" the really deep questions- why we exist and where our meaning lies. But these questions have been answered, (Darwin and all that ...), just not to the satisfaction of those who believe we have a purpose dictated by a higher being and communicated by way of maddeningly contradictory scriptures. Only if one imagines and assumes that we need a cosmic meaning does the question even arise. Far from being deep, these questions simply restate theism as an assumption rather than a hypothesis.
In the end, it seems cheap rhetoric to disparage detailed naturalistic explanations as "explaining away". If they are wrong, then impeach them on their merits and details. If they are right but not complete, then extend and deepen them. If their perspective is different from your own, then put up your own explanatory narrative to compete on the merits of clarification, unification, and predictive value (and empirical detail), keeping in mind the premises that you are importing and their plausibility. The only improvement to be made on a bad explanation is a better one, since explanations are by definition our mental narratives of all phenomena.
It is particularly wrong-headed to fault science on its explanations of human cognition, just when it is making so much progress. The impulse to tap "transcendent orders of reality" to account for our behavior and thoughts completely ignores the bounds of basic biology and physics, and takes the experience of consciousness as a fundamentally inexplicable and mystical datum, which it is not. Articles just in the last month have tackled the computation of social behavior and the nature of cognitive attention by way of long-range gamma wave coupling across the brain, each of which speak to our regard for our children, among other things. The extraordinary resistance of theists to regarding themselves as computational machines will lead them to grief as this last bastion of mysticism and human special-ness is breached by serious explanations.