PHILADELPHIA -- Elin Danien quietly listens to a meditation tape, eyes closed, as the radioactive tracer is injected into her IV, freezing a picture of the blood flow in her brain. As a research associate at the University of Pennsylvania Museum of Archeology and Anthropology, Danien is sharp enough to organize an upcoming exhibit on the Mayans, but finds herself increasingly forgetful. Now she is part of a study to determine if meditation can improve brain functioning -- to measure how traditional spiritual practices alter the structures of the brain itself.

It is typical work for Dr. Andrew Newberg of the University of Pennsylvania School of Medicine -- perhaps the nation's leading expert on the biological basis for religious experience. More exotic subjects of his brain scans have been nuns at prayer, Buddhist monks during meditation, Pentecostals speaking in tongues and entranced Brazilian mystics who write out messages from the other side.

These subjects share little in common theologically. But the activity of the brain during intense religious experiences is often (though not always) similar. The frontal lobes are activated, indicating attention and focus. The thalamus shuts down normal sensory input. And the parietal lobes -- which ground us in time and space -- are less active. In this state, people describe a sense of timelessness, a suspension of self, a feeling of bliss and oneness with the universe.

What Newberg reveals through what is called single photon emission computed tomography is not religion, but the physical basis for the feeling of transcendence. Meditation appears to heighten this experience over time. But it can also come in milder degrees through rituals of communal worship -- smelling incense, drinking wine, viewing images such as the cross, repeating words, standing, sitting, singing in unison. Or this sense of oneness can be encouraged through the secular rituals of the military -- drumming, walking in cadence, a strict and rhythmic schedule. "All these stimuli have an impact on the brain," Newberg argues. "They drive ideals into the whole body."

Drugs such as Lexapro or peyote have effects that overlap with spiritual experience, but they flood and excite the whole brain while meditation lights up only those portions that encourage the feeling of transcendence. This feeling can be also generated by intense personal suffering, or even by a stroke in certain portions of the brain. (Jill Bolte Taylor's recent, remarkable book, "My Stroke of Insight," tells the story of how her painful stroke also produced an extraordinary sense of euphoria and purpose.)

For individuals, this pioneering research brings bad news and good news. Some people, it turns out, are probably less open to these experiences for genetic reasons. But the brain is more like a muscle than a computer. The spiritual facility can be developed -- and it changes over our lifetime, as our brain ages. In this narrow sense, prayer and meditation work, in the same way that aerobic training works on the heart muscle.

For societies, this biological basis for spirituality provides an explanation for the universality and persistence of religion. Human beings routinely have experiences that are not normally associated with normal consciousness, yet seem more real than normal consciousness. "There is something in the brain that facilitates and rewards that type of experience," says Newberg, "and our brain desires to make sense of it."

This leads some, of course, to reductionism -- the assertion that a physical basis for transcendent experience proves there is no such thing as transcendence. It is an evolutionary joke on mankind -- perhaps useful, but not accurate -- because everything explainable is thus illusory.

But this view is not more "scientific" than other views. It involves a philosophic materialism that is entirely faith-based. We know, for example, that a complex series of physical, hormonal changes helps bond a mother to her newborn child. Does this mean that parental love is a myth? Only according to the philosophic claim that chemicals exhaust reality. Is it not equally possible that a cosmos charged with transcendence might organize itself in such a way that human beings can sense transcendence?

We have seen this debate before. Sigmund Freud believed that a deep, psychological desire for God proved that God is an illusion -- merely the projection of our deepest wishes into an empty universe. But the intensity of a desire or an experience does not make it a lie. And perhaps the frontal lobes and the thalamus and the parietal lobes are responding to a reality, not conjuring it.