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For a 2,500-year-old religion, Buddhism seems remarkably compatible with our scientifically oriented culture, which may explain its surging popularity here in America. Over the last 15 years, the number of Buddhist centers in the United States has more than doubled, to well over 1,000. As many as 4 million Americans now practice Buddhism, surpassing the total of Episcopalians. Of these Buddhists, half have post-graduate degrees, according to one survey. Recently, convergences between science and Buddhism have been explored in a slew of books—including Zen and the Brain and The Psychology of Awakening—and scholarly meetings. Next fall Harvard will host a colloquium titled “Investigating the Mind,” where leading cognitive scientists will swap theories with the Dalai Lama. Just the other week the New York Times hailed the “rapprochement between modern science and ancient [Buddhist] wisdom.”

Four years ago, I joined a Buddhist meditation class and began talking to (and reading books by) intellectuals sympathetic to Buddhism. Eventually, and regretfully, I concluded that Buddhism is not much more rational than the Catholicism I lapsed from in my youth; Buddhism’s moral and metaphysical worldview cannot easily be reconciled with science—or, more generally, with modern humanistic values.

For many, a chief selling point of Buddhism is its supposed de-emphasis of supernatural notions such as immortal souls and God. Buddhism “rejects the theological impulse,” the philosopher Owen Flanagan declares approvingly in The Problem of the Soul. Actually, Buddhism is functionally theistic, even if it avoids the “G” word. Like its parent religion Hinduism, Buddhism espouses reincarnation, which holds that after death our souls are re-instantiated in new bodies, and karma, the law of moral cause and effect. Together, these tenets imply the existence of some cosmic judge who, like Santa Claus, tallies up our naughtiness and niceness before rewarding us with rebirth as a cockroach or as a saintly lama.

Western Buddhists usually downplay these supernatural elements, insisting that Buddhism isn’t so much a religion as a practical method for achieving happiness. They depict Buddha as a pragmatist who eschewed metaphysical speculation and focused on reducing human suffering. As the Buddhist scholar Robert Thurman put it, Buddhism is an “inner science,” an empirical discipline for fulfilling our minds’ potential. The ultimate goal is the state of preternatural bliss, wisdom, and moral grace sometimes called enlightenment—Buddhism’s version of heaven, except that you don’t have to die to get there.

The major vehicle for achieving enlightenment is meditation, touted by both Buddhists and alternative-medicine gurus as a potent way to calm and comprehend our minds. The trouble is, decades of research have shown meditation’s effects to be highly unreliable, as James Austin, a neurologist and Zen Buddhist, points out in Zen and Brain. Yes, it can reduce stress, but, as it turns out, no more so than simply sitting still does. Meditation can even exacerbate depression, anxiety, and other negative emotions in certain people.

The insights imputed to meditation are questionable, too. Meditation, the brain researcher Francisco Varela told me before he died in 2001, confirms the Buddhist doctrine of anatta, which holds that the self is an illusion. Varela contended that anatta has also been corroborated by cognitive science, which has discovered that our perception of our minds as discrete, unified entities is an illusion foisted upon us by our clever brains. In fact, all that cognitive science has revealed is that the mind is an emergent phenomenon, which is difficult to explain or predict in terms of its parts; few scientists would equate the property of emergence with nonexistence, as anatta does.

Much more dubious is Buddhism’s claim that perceiving yourself as in some sense unreal will make you happier and more compassionate. Ideally, as the British psychologist and Zen practitioner Susan Blackmore writes in The Meme Machine, when you embrace your essential selflessness, “guilt, shame, embarrassment, self-doubt, and fear of failure ebb away and you become, contrary to expectation, a better neighbor.” But most people are distressed by sensations of unreality, which are quite common and can be induced by drugs, fatigue, trauma, and mental illness as well as by meditation.

Even if you achieve a blissful acceptance of the illusory nature of your self, this perspective may not transform you into a saintly bodhisattva, brimming with love and compassion for all other creatures. Far from it—and this is where the distance between certain humanistic values and Buddhism becomes most apparent. To someone who sees himself and others as unreal, human suffering and death may appear laughably trivial. This may explain why some Buddhist masters have behaved more like nihilists than saints. Chogyam Trungpa, who helped introduce Tibetan Buddhism to the United States in the 1970s, was a promiscuous drunk and bully, and he died of alcohol-related illness in 1987. Zen lore celebrates the sadistic or masochistic behavior of sages such as Bodhidharma, who is said to have sat in meditation for so long that his legs became gangrenous.

What’s worse, Buddhism holds that enlightenment makes you morally infallible—like the pope, but more so. Even the otherwise sensible James Austin perpetuates this insidious notion. ” ‘Wrong’ actions won’t arise,” he writes, “when a brain continues truly to express the self-nature intrinsic to its [transcendent] experiences.” Buddhists infected with this belief can easily excuse their teachers’ abusive acts as hallmarks of a “crazy wisdom” that the unenlightened cannot fathom.

But what troubles me most about Buddhism is its implication that detachment from ordinary life is the surest route to salvation. Buddha’s first step toward enlightenment was his abandonment of his wife and child, and Buddhism (like Catholicism) still exalts male monasticism as the epitome of spirituality. It seems legitimate to ask whether a path that turns away from aspects of life as essential as sexuality and parenthood is truly spiritual. From this perspective, the very concept of enlightenment begins to look anti-spiritual: It suggests that life is a problem that can be solved, a cul-de-sac that can be, and should be, escaped.

Some Western Buddhists have argued that principles such as reincarnation, anatta, and enlightenment are not essential to Buddhism. In Buddhism Without Beliefs and The Faith To Doubt, the British teacher Stephen Batchelor eloquently describes his practice as a method for confronting—rather than transcending—the often painful mystery of life. But Batchelor seems to have arrived at what he calls an “agnostic” perspective in spite of his Buddhist training—not because of it. When I asked him why he didn’t just call himself an agnostic, Batchelor shrugged and said he sometimes wondered himself.

All religions, including Buddhism, stem from our narcissistic wish to believe that the universe was created for our benefit, as a stage for our spiritual quests. In contrast, science tells us that we are incidental, accidental. Far from being the raison d’être of the universe, we appeared through sheer happenstance, and we could vanish in the same way. This is not a comforting viewpoint, but science, unlike religion, seeks truth regardless of how it makes us feel. Buddhism raises radical questions about our inner and outer reality, but it is finally not radical enough to accommodate science’s disturbing perspective. The remaining question is whether any form of spirituality can.