When it comes to science, ours is a paradoxical era. On the one hand, prominent physicists proclaim that they are solving the riddle of reality and hence finally displacing religious myths of creation. That is the chest-thumping message of books such as The Grand Design by physicists Stephen Hawking and Leonard Mlodinow and A Universe from Nothing by Lawrence Krauss. A corollary of this triumphal view is that science will inevitably solve all other mysteries as well.

On the other hand, science's limits have never been more glaringly apparent. In their desperation for a "theory of everything"—which unifies quantum mechanics and relativity and explains the origin and structure of our cosmos—physicists have embraced pseudo-scientific speculation such as multi-universe theories and the anthropic principle (which says that the universe must be as we observe it to be because otherwise we wouldn't be here to observe it). Fields such as neuroscience, evolutionary psychology and behavioral genetics and complexity have fallen far short of their hype.

Some scholars, notably philosopher Thomas Nagel, are so unimpressed with science that they are challenging its fundamental assumptions. In his new book Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False, Nagel contends that current scientific theories and methods can't account for the emergence of life in general and one bipedal, big-brained species in particular. To solve these problems, Nagel asserts, science needs "a major conceptual revolution," as radical as those precipitated by heliocentrism, evolution and relativity.

Many pundits calling for such a revolution are peddling some sort of religious agenda, whether Christian or New Age. Nagel is an atheist, who cannot accept God as a final answer, and yet he echoes some theological critiques of science. "Physic-chemical reductionism," he writes, cannot tell us how matter became animate on Earth more than three billion years ago; nor can it account for the emergence in our ancestors of consciousness, reason and morality.

Evolutionary psychologists invoke natural selection to explain humanity's remarkable attributes, but only in a hand-wavy, retrospective fashion, according to Nagel. A genuine theory of everything, he suggests, should make sense of the extraordinary fact that the universe "is waking up and becoming aware of itself." In other words, the theory should show that life, mind, morality and reason were not only possible but even inevitable, latent in the cosmos from its explosive inception. Nagel admits he has no idea what form such a theory would take; his goal is to point out how far current science is from achieving it.

I share Nagel's view of science's inadequacies. Moreover, I'm a fan of his work, especially his famous essay "What Is It Like to Be a Bat?", a quirky take on the mind-body problem (which inspired my column "What Is it Like to Be a Cat?"). So I was a bit disappointed by the dry, abstract style of Mind and Cosmos. The book seems aimed primarily at philosophers and scientists—that is, professionals—rather than lay readers.

Nagel acknowledges that his attempt to envision a more expansive scientific paradigm is "far too unimaginative." He might have produced a more compelling work if he had ranged more widely in his survey of alternatives to materialist dogma. For example, complexity theorist Stuart Kauffman has postulated the existence of a new force that counteracts the universal drift toward disorder decreed by the second law of thermodynamics. Kauffman suspects that this anti-entropy force might account for the emergence and evolution of life. Nagel mentions Kauffman's theory of "self-organization" in a footnote but doesn't elaborate on it. (I critiqued the field of complexity research in a recent column.)

According to the physicist John Wheeler, quantum mechanics implies that our observations of reality influence its unfolding. We live in a "participatory universe," Wheeler proposed, in which mind is as fundamental as matter. Philosopher David Chalmers, Nagel's colleague at New York University, conjectures that "information," which emerges from certain physical configurations and processes and entails consciousness, is a fundamental component of reality, as much so as time, space, matter and energy.

I never took Chalmer's hypothesis seriously—in part because it implies that toaster ovens might be conscious—but I would have appreciated Nagel's take on it. (For a critique of the ideas of Wheeler and Chalmers, see my column "Why information can't be the basis of reality.")

Nagel touches briefly on free will, when he suggests that our moral and aesthetic choices cannot be reduced to physical processes, but I expected a deeper treatment of the topic. Many leading scientists, from Francis Crick to Hawking, have argued that free will is an illusion, as much so as God and ghosts. This perspective, it seems to me, stems from a cramped, hyper-reductive view of causality, which I wish Nagel had opposed more vigorously.

These qualms asides, I recommend Nagel's book, which serves as a much-needed counterweight to the smug, know-it-all stance of many modern scientists. Hawking and Krauss both claim that science has rendered philosophy obsolete. Actually, now more than ever we need philosophers, especially skeptics like Socrates, Descartes, Thomas Kuhn and Nagel, who seek to prevent us from becoming trapped in the cave of our beliefs.

Lehrer alert: This review was originally published in the Canadian newspaper The Globe & Mail.