Now at the dawn of the twenty-first century, the notion that the brain is somehow involved in mental life and consciousness is one that even the most devout among us would be hard-pressed to question. As consciousness researcher Marilyn Schlitz put it on the PBS program Closer to Truth, “All we have to do is take a sledgehammer and bang somebody over the head to see a reduction in consciousness.” But the question of just what role the brain plays in mental and emotional life is another matter. And it is here that we enter the thorny territory.

In a recent New York Times column entitled “The Duel Between Body and Soul,” developmental psychologist Paul Bloom describes a conversation he had with his six-year-old son, Max, in which he asked him about the function of the brain: “[Max] said that it is very important and involved in a lot of thinking—but it is not the source of dreaming or feeling sad or loving his brother. Max said that's what he does, though he admitted that his brain might help him out.” Bloom, who clearly aligns himself with the neuroscientific perspective, goes on to explain that “studies from developmental psychology suggest that young children do not see their brain as the source of conscious experience and will. They see it instead as a tool we use for certain mental operations. It is a cognitive prosthesis, added to the soul to increase its computing power.” And, Bloom laments, “This understanding might not be so different from that of many adults.”

In my own case at least, Bloom has, I think, hit the nail on the head. For all of my studies in psychology, I must confess that my own idea about the relationship between the mind and the brain has remained something like that portrayed by the scarecrow in the Wizard of Oz. Despite his melancholy mantra, “If I only had a brain,” the straw-stuffed overalls still had plenty of personality and emotion and at least enough cognitive capacity to get through the day. Although you probably wouldn't ask him to sort out the dinner bill, there was clearly somebody home. Indeed, when I was cast in the role in an eighth-grade school play, I knew what I had to do. Just act a bit dopey and absent-minded. Probably to the play's benefit, I didn't consult with any neuroscientists about what it might actually be like to not have a brain. And while my ideas have no doubt matured somewhat over the years, if you were to ask me to describe my current thinking on this issue, I don't think I could do better than Bloom's description of the brain as a “cognitive prosthesis” for the soul.

In light of Bloom's analysis, it seems likely that I'm not alone. Which means we have a bit of a problem on our hands. Because, although in the case of children this belief could be attributable to a lack of learning, where adults are concerned, the issue seems to cut deeper. A lot deeper. Despite the insistence of neuroscientists that our brains are the sole source of our experience and behavior, there are very strong reasons why most of us don't want to believe that this is the case. For starters, for most of us with religious or spiritual inclinations, accepting such a premise would eradicate, in one fell swoop, one of our most basic convictions—the belief in an immaterial soul or (if we're Buddhists) “mind essence” that transcends the physical body. Even for those who do not count themselves among the faithful, the notion that we are entirely reducible to brain stuff still seems to take away something essential—our humanity, our dignity, our sense of meaning. In my own case, no matter how hard I try, I find it exceedingly hard to accept that I am just my brain. And it's not just because I've had mystical experiences that point to the existence of something beyond the material. There is something about the experience of consciousness itself, some kind of mystery inherent in the fact that we are conscious at all, that seems irreducible to the mere firing of our neurons. As convinced as the neuroscientists are of their case, I can't help feeling there must be more to the story.

And here, as they say, is the rub. Because if I take a step back from my own convictions, there is something about this picture that starts to look suspiciously familiar. After all, isn't this how religious people always feel when their ideas are being challenged by science? Is there any difference between what I'm experiencing and what the elders of the Church felt when Galileo attempted to oust the Earth (and thus human beings) from the center of God's universe? Could it be that far removed from how some Southern Baptists feel when the science teachers try to convince their children that God didn't create the world in six days? In all of my postmodern sophistication, those stories sound to me like an adolescent unwillingness to grow up. But can I be sure that I'm not guilty of the same thing?

I would, of course, like to think that the current situation is different—that, in attempting to penetrate the mysteries of the human soul, science has finally flown a bit too close to the sun. But given the trajectory of the science and religion debate over the past few hundred years, it would be hubris at this point not to take the claims of neuroscience seriously. As atheist apologist Keith Augustine put it in a recent essay on infidels.org:

Indeed, given the legacy of abandoned dogmas that the encounter with science has left in religion's wake, it would be more than a little naïve for us to think that as scientists begin to probe the mysteries of the brain, our sense of who we are would come out unscathed. We are clearly in a challenging predicament. And for all of my ambivalence on the science and religion debate, I have to admit that this round makes the others look easy—particularly for those of us with spiritual inclinations who also feel compelled, as a matter of integrity, to follow the truth wherever it leads. Are we willing to question our spiritual convictions deeply enough to grapple with what neuroscience has to say about the matter?

It was my own recognition of this predicament last spring that convinced me that if I was to avoid ending up on the side of ignorance, I would have to dive into the unknown waters of brain science and find out for myself what the fuss is all about. What does it actually mean to say that our brains are the sole source of our experience? What evidence is there to prove it? And assuming it was true, would that mean that all of our spirituality is a ruse? Could the brain in fact be the soul? Over the past year, my journey into this mind-bending world has taken me from the cutting-edge conference on “consciousness studies” to the offices of some of the leading thinkers in the field to the laboratories of a few pioneering scientists who, far from the mainstream, are working to usher in a new, more holistic paradigm that is as true to the spirit as it is to the data. In the course of this adventure, I have moved in and out of confusion more times than I care to count. And though I can't say that as of this writing I have entirely found my way to the other side, what I can say is that I have learned a lot about the miraculous and as-yet mysterious workings of a part of myself I had honestly never given much thought—my own brain.