Evangelicals reject the idea that faith might be reduced to chemical reactions in the brain. Humanists refuse to accept that religion is inherent in people's makeup. And some scientists have criticized Hamer's methodology and what they believe is a futile effort to find empirical proof of religious experience.
But Hamer, a behavioral geneticist at the National Institutes of Health and the National Cancer Institute, stands by research he says shows that spirituality - the feeling of transcendence - is part of our nature. And he believes that a universal penchant for spiritual fulfillment explains the growing popularity of nontraditional religion in this country and the presence of hundreds of religions worldwide.
''We think that all human beings have an innate capacity for spirituality and that that desire to reach out beyond oneself, which is at the heart of spirituality, is part of the human makeup,'' Hamer, 53, said in an interview at his home. ''The research suggests some people have a bit more of that capacity than others, but it's present to some degree in everybody.''
The God Gene, published in September and featured in Time magazine's Oct. 25 cover story, is a sequel to Living With Our Genes, a 1998 book in which Hamer examined the genetic basis of such behavioral traits as anxiety, thrill-seeking and homosexuality. Hamer said his previous research, most notably his work on anxiety, encouraged him to look into the genetic propensity for religious belief.
What he found was that the brain chemicals associated with anxiety and other emotions, including joy and sadness, appeared to be in play in the deep meditative states of Zen practitioners and the prayerful repose of Roman Catholic nuns - not to mention the mystical trances brought on by users of peyote and other mind-altering drugs.
At least one gene, which goes by the name VMAT2, controls the flow to the brain of chemicals that play a key role in emotions and consciousness. This is the ''God gene'' of the book's title, and Hamer acknowledges that it's a misnomer. There probably are dozens or hundreds more genes, yet to be identified, involved in the universal propensity for transcendence, he said.
Furthermore, the scientific linkage of a gene with chemicals that affect happiness or sadness does not answer the question ''Is there a God?'' but rather ''Why do we believe in God?''
''Our genes can predispose us to believe. But they don't tell us what to believe in,'' said Hamer, whose current research involves HIV/AIDS.
Critics in the scientific community argue that Hamer's conclusions are simplistic and speculative, relying too much on anecdotal evidence and too little on testing of the VMAT2 gene to determine other possible connections to behavior. They also wonder whether his findings can be replicated, a necessity in scientific research.
''The field of behavioral genetics is littered with failed links between particular genes and personality traits,'' said Carl Zimmer, a science author who reviewed the book in last month's Scientific American.
Some religious leaders welcome the idea of a genetic basis for spirituality and say it validates long-held teachings.
''I wondered for a long time why [the concept of] a genetic implant hasn't been put in print or been part of a conversation in the broad theological community,'' said Bishop John Chane, of the Episcopal Diocese of Washington. Chane associates Hamer's findings with the Apostle Paul's statement ''There are a variety of gifts but the same spirit.''
Chane also welcomes the notion of genetic universality as a new, deeper way of promoting understanding among people of different faiths - particularly Judaism, Christianity and Islam, all of which trace their beginnings to the same father, Abraham.
Others, such as Bishop Adam Richardson Jr., of the Washington area district of the African Methodist Episcopal Church, said it's hard to quantify matters of the spirit and that attributing behavior to one's genetic makeup ''can be a frightful thing.'' By analogy, saying that people are predisposed to be spiritual also means that criminals are genetically wired to be criminals and have no hope of rehabilitation.
''Why not just put them in prison and throw away the key?'' he asked.
Richardson said there is also the danger of people losing hope, of believing their genetic makeup limits their development and personal growth. ''In my own system, we do have choice. We always have choice,'' he said.
Hamer said his own religious development began in a Congregationalist church, which he abandoned when he became a scientist. But he discovered new spiritual meaning when he began researching this book - partly through meditative practices he learned at a Zen center near Kyoto, Japan.
He likens spirituality to the capacity for language: Humans are genetically predisposed to have it, but the language people speak and the religion they practice are learned rather than inherited characteristics.
People are designed to communicate through language, but they speak English, French or Chinese because of the part of the world they grew up in. Similarly, genetic makeup urges people to believe in a creator or find spiritual fulfillment, but culture, history and environment determine whether one is a Christian, Hindu, Jew, Buddhist or Muslim.
Although people can change or abandon that religious affiliation, they cannot rid themselves of the genetic propensity to be spiritual. But people can build on and develop that innate spirituality through meditation, prayer and creative arts such as music and painting. These practices can be done inside or outside organized religion, he said.
Hamer said he has received numerous comments from people who say the dichotomy of spirituality and religion makes sense. ''I always knew this, that I was inclined to be spiritual, even though I've always had a problem with religion,'' they tell him.
''I see more and more people doing things like yoga,'' Hamer said. ''They do it initially because they want to get more flexible and look good and feel great. Then they find that once they spend some time sitting on a mat, doing nothing but concentrating on their body and clearing their mind of everything else, they say, 'That feels kind of good.' ''
Such feelings can lead to an intuitive sense of God's presence, Hamer said. ''We do not know God; we feel him.''
Organized religion can become so codified, so caught up with learned rituals, that the focus on spirituality gets lost, Hamer said. The resurgence of Pentecostalism and other emotion-based religions is one sign of the staying power of inherited spirituality, he said.
Megachurches, too, are part of this phenomenon and have widespread appeal because of the emotional aspects of worship, he said. ''They have lots of music, video screens, the whole multimedia thing going on,'' he said. ''They're tapping into that [innate spirituality]. It's fun and allows people to get into that spiritual frame of mind.''