The evolution-creationism skirmishes that have periodically flared up throughout the past century embody the long historical tension between science and religion. It may surprise you, then, to learn that Charles Darwin matriculated at Cambridge University in theology, and throughout his five-year voyage around the world he was a creationist who regularly attended church services. It was only upon his return home that his loss of faith came about. Nagging doubts about the nature and existence of the deity chipped away at his faith from his studies of the natural world, particularly the cruel nature of many predator-prey relationships. “What a book a Devil’s Chaplain might write on the clumsy, wasteful, blundering low & horridly cruel works of nature!”

Pain and evil in the human world made Darwin doubt even more. “That there is much suffering in the world no one disputes,” he wrote to a correspondent. Which is more likely, that pain and evil are the result of an all-powerful and good God, or the product of uncaring natural forces? “The presence of much suffering agrees well with the view that all organic beings have been developed through variation and natural selection.”The death of Darwin’s beloved 10-year-old daughter Anne put an end to his faith. Yet, he hardly ever spoke or wrote about religion. In 1880, only two years from his death, Darwin explained why: “It appears to me (whether rightly or wrongly) that direct arguments against christianity & theism produce hardly any effect on the public; & freedom of thought is best promoted by the gradual illumination of men’s minds which follow[s] from the advance of science.”

Was Darwin’s approach to science and religion healthy and logical? To answer that question I devised a threetiered model on the relationship of science and religion.

1. CONFLICTING-WORLDS MODEL. This “warfare” model holds that science and religion are mutually exclusive ways of knowing, where one is right and the other is wrong. In this model, the findings of modern science are always a potential threat to one’s faith and thus they must be carefully vetted against religious truths before acceptance; likewise, the tenets of religion are always a potential threat to science and thus they must be viewed skeptically.

2. SAME-WORLDS MODEL. More conciliatory in its nature, this position holds that science and religion are two ways of examining the same reality; as science progresses to a deeper understanding of the natural world it will reveal that many ancient religious tenets are true.

3. SEPARATE-WORLDS MODEL. On this tier science and religion are neither in conflict nor in agreement. Today it is the job of science to explain the natural world, making obsolete ancient religious sagas of origins and creation. Yet, religion thrives because it still serves a useful purpose as an institution for social cohesiveness and as a guide to finding personal meaning and spirituality.

Over the past decade a plethora of books have been written on the relationship of science and religion, most of which may be classified in one of these three categories. The six books under review here are well representative of my three-tiered model (itself presented in my first book in this genre, “How We Believe,” and resurrected in my latest,”Why Darwin Matters”).

“The God Delusion” (Houghton Mifflin, 406 pages, $27), by the Oxford University evolutionary biologist Richard Dawkins, is firmly ensconced in the Conflicting-Worlds Model. Based on his controversial BBC documentary, “The Root of All Evil?,” Mr. Dawkins presents his view of religion as a cultural virus that, like a computer virus, once downloaded into the software of society corrupts almost all programs it encounters. It isn’t hard to find examples to fit this view; one has only to read the dailies coming out of the Middle East to see its nefarious effects. And Mr. Dawkins is so compelling in his narrative — both on camera in his cultured British accent, and in print through a literary style unmatched by any living science writer — that when you reach the end you are convinced that the answer to the rhetorical question posed in the documentary’s title is a resounding yes! Of course, religion is so pervasive around the world and throughout history that it is a twoedged sword that cuts both ways — a force for unspeakable evil as well as unmitigated good. It is Mr. Dawkins’s belief that the former outweighs the latter and that it is time for humanity to grow beyond it.

“Blind Faith” (St. Martin’s, 304 pages, $25.95) by Richard P. Sloan, a professor of behavioral medicine at Columbia University, is also in the Conflicting-Worlds Model, in that the author is critical of attempts to mix religion and medicine, most notably the highly publicized studies on prayer and healing.

In 1999, Mr. Sloan published a definitive critique of such studies in the prestigious British medical journal Lancet, and his book elaborates on these and the studies in this field published since. Mr. Sloan notes that many of these distant intercessory prayer studies — in which religious strangers pray for patients to be healed — failed to control for such intervening variables as age, sex, education, ethnicity, socioeconomic status, marital standing, degree of religiosity, and the fact that most religions have sanctions against such insalubrious behaviors as sexual promiscuity, alcohol and drug abuse, and smoking. When such variables are controlled for, the formerly significant results disappear.

Mr. Sloan also explains that different studies show different outcomes. In one of the most highly publicized studies of cardiac patients prayed for by bornagain Christians, 29 outcome variables were measured, but on only six did the prayed-for group show improvement. In related studies, different outcome measures were significant. To be meaningful, the same measures need to be significant across studies, because if enough outcomes are measured, some will show significant correlations by chance.

Not only is this bad science, Mr. Sloan says, but trying to quantify God is bad religion. For example, are Christian, Jewish, Muslim, Buddhist, Wiccan, and Shaman prayers equal? Are two 10-minute prayers equal to one 20-minute prayer? Is one priestly prayer identical to 10 parishioner prayers? If God is omniscient, does he need to be reminded that someone needs healing?

In the Same-Worlds Model, both “God’s Universe” (Harvard University Press, 139 pages, $16.95) by the Harvard astronomer and historian of science, Owen Gingerich, and “The Language of God” (Free Press, 294 pages, $26) by the director of the Human Genome Project, Francis Collins, present compelling arguments for people who already believe in God that their faith is not ungrounded.

Both authors accept all of the major theories and findings of science, reject Intelligent Design as a political movement, and are not only not threatened by science but use it to bolster their faith, particularly the fine-tuned nature of the universe that allows for the evolution of complex intelligent life. Predictably, the astronomer Mr. Gingerich focuses on the universe and the geneticist Mr. Collins concentrates on the complexity of life; both are presenting modern variations on the ancient arguments from design and purpose for God’s existence.

In my opinion, these are the best arguments to be made in the Same-Worlds Model, and believers will not find two more stellar names in science to back them.

Nevertheless, we nontheists have perfectly good counters to these arguments (which I present in detail in “Why Darwin Matters”). First, the universe is not so finely tuned for life. The vast majority of the universe is empty space, and the vast majority of what little matter there is, is completely inhospitable to life, including most planets. In its 13.7 billion year history, the fine-tuned conditions for life were nonexistent.

Second, our universe is not finelytuned for us, we are finely-tuned for it, which is what the theory of evolution predicts. It is entirely possible that a completely different form of life could be based on another type of physics.

Third, our universe may not be that exceptional. String theory, for example, allows for 10500 possible worlds, all with different self-consistent laws and constants. That’s a 1 followed by 500 zeroes possible universes (12 zeroes is a trillion!). If true, it would be miraculous if there were not intelligent life in a number of them.

Fourth, there may be an underlying principle behind all the fine-tune equations and relationships that will be forthcoming when the grand unified theory of physics is discovered.

Fifth, we may live in a multiverse, in which our universe is just one of many bubble universes, all with different laws of nature. Those with physical parameters like ours are more likely to generate life.

To explain the complexity of life, we turn to the properties of self-organization and emergence that arise out of complex adaptive systems. Self-organization means that the system requires only an input of energy into it in order to generate an action, which comes from within the system itself. An emergent property is one that is more than the sum of its parts: Water is a self-organized emergent property of a particular arrangement of hydrogen and oxygen molecules; consciousness is a self-organized emergent property of billions of neurons firing in patterns in the brain; language is a self-organized emergent property of thousands of words spoken in communication between language users; the economy is a self-organized emergent property of millions of people pursuing their own self-interests; life is a self-organized emergent property of prebiotic chemicals; complex life is a self-organized emergent property of simple life, where simple cells self-organize to become more complex cells; multi-cellular life is a self-organized emergent property of single-celled life; and so on up the chain of complexity.

In the Separate-Worlds Model of science and religion,”The Creation” by the Harvard evolutionary biologist E.O. Wilson (Norton, 175 pages, $21.95) and “The Varieties of Scientific Experience” (Penguin, 284 pages, $27.95) by the late Cornell University astronomer Carl Sagan, are two of the most thoughtful and respectful books I have ever encountered in the genre.

Mr. Wilson’s narrative is in the form of a “letter to a Southern Baptist Pastor” (Mr. Wilson’s own faith growing up in the South), and it is a passionate appeal to Christian conservatives to “conserve” nature. Mr. Wilson is willing to set aside the fundamental differences between theists and nontheists on the matter of God’s existence or the divinity and resurrection of Jesus in the hope of finding common ground to solve our most pressing environmental problems — most notably global warming and species extinction.

“The defense of living Nature is a universal value,” he writes. “It doesn’t rise from, nor does it promote, any religious or ideological dogma. Rather, it serves without discrimination the interests of all humanity.” Always the big picture theoretician, Mr. Wilson realizes that if we want to save the world we need the five billion believers on the side of science, not against it.

Sagan predates Mr. Wilson in his clarion call for unity of science and religion in the cause of saving the planet, and his “The Varieties of Scientific Experience” (Penguin, 288 pages, $27.95) is based on lectures written and presented at the University of Glasgow for the 1985 Gifford Lectures on Natural Theology. In her introduction to the volume, Sagan’s longtime collaborator and wife Ann Druyan writes: “Carl Sagan was a scientist, but he had some qualities that I associate with the Old Testament. When he came up against a wall — the wall of jargon that mystifies science and withholds its treasures from the rest of us, for example, or the wall around our souls that keeps us from taking the revelations of science to heart — when he came up against one of those topless, old walls, he would, like some latter day Joshua, use all of his many strengths to bring it down.”

Ms. Druyan attended every lecture, “and more than 20 years later what remains with me was his extraordinary combination of principled, crystal clear advocacy coupled with respect and tenderness towards those who did not share his views.” Those who recall the inimitable voice of Sagan, with his punched syllables and dramatic pauses, will hear it again in these chapters. “There was plenty of laughter during these lectures,” Ms. Druyan recalls, “but also the kind of pin drop silence that comes when the audience and the speaker are united in the thrall of an idea.” There is, arguably, no more enthralling an idea than that of God, which Sagan characteristically addressed in a rigorously logical and scientific manner.

Darwin’s Separate-Worlds approach to science and religion worked well for him, but it still leaves open the deeper question about whether one can logically believe in God and science. Belief in God depends on religious faith. Acceptance of science depends on empirical evidence. This is the fundamental difference between religion and science. If you attempt to reconcile religion and science on questions about nature and the universe, and if you push the science to its logical conclusion, you will end up naturalizing the deity; for any question about nature, if your answer is “God did it,”a scientist will ask: “How did God do it?, What forces did God use? What forms of matter and energy were employed in the creation process?” The end result of this inquiry can only be natural explanations for all natural phenomena. What place, then, for God?

The problem with attempts at blending science and religion may be found in a single principle: A is A. Or: Reality is real. To attempt to use nature to prove the supernatural is a violation of A is A. It is an attempt to make reality unreal. A cannot also be non-A. Nature cannot also be non-nature. Naturalism cannot also be supernaturalism. Believers can have both religion and science as long as there is no attempt to make A non-A, to make reality unreal, to turn naturalism into supernaturalism.

The Separate-Worlds Model is the only way to do this. Thus, the most logically coherent argument for theists is that God is outside of time and space; that is, God is beyond nature — super nature, or supernatural — and therefore cannot be explained by natural causes. This places the God question outside the realm of science.

Mr. Shermer is the publisher of Skeptic magazine, a monthly columnist for Scientific American, and the author of “Why People Believe Weird Things.” His just-released book is “Why Darwin Matters.”