Francisco J. Ayala pulls open the top drawer of a black cabinet and flips through nearly a dozen files, all neatly titled by publication and due date. These are the essays on evolution he has been churning out over the past six to eight weeks for popular books and magazines. “Hack jobs,” he calls them with a smile, bragging that each one takes only a day or two to complete.

After some 30 years of proselytizing about evolution to Christian believers, the esteemed evolutionary biologist at the University of California, Irvine, has honed his arguments to a fine point. He has stories and examples at the ready, even a shock tactic or two at his fingertips. One out of five pregnancies ends in spontaneous miscarriage, he often reminds audiences. Next he will pointedly ask, as in an interview with U.S. Catholic magazine last year, “If God explicitly designed the human reproductive system, is God the biggest abortionist of them all?” Through such examples, he explains, “I want to turn around their arguments.”

The 74-year-old Ayala is preparing for an exceptionally busy 2009. The year marks the bicentennial of Charles Darwin’s birthday and the sesquicentennial of the publication of On the Origin of Species, and the battle over the teaching of evolution is sure to heat up. Ayala says the need is especially great for scientists to engage religious people in dialogue. As evidence, he lugs over the 11-by-17-inch, 12-pound Atlas of Creation mailed out by Muslim creationist Adnan Oktar in Turkey to scientists and museums across the U.S. and France. This richly illustrated tome not only attacks evolution but also links Darwin’s theory to horrors, including fascism and even Satan himself.

In the U.S. the intelligent design–promoting Discovery Institute in Seattle has published biology textbooks questioning evolution and has promoted the 2008 film Expelled: No Intelligence Allowed to make the case that anti-Darwinist scientists are persecuted. (For a rebuttal, see “Ben Stein’s Expelled: No Integrity Displayed,” by John Rennie, and related articles.) Republican vice presidential candidate Sarah Palin has said she believes that creationism should be taught alongside evolution in schools. One in eight high school biology teachers already treat creationism as a valid alternative, according to a Pennsylvania State University poll.

Despite outreach efforts by scientists and constitutional rulings against them, creationists and intelligent design advocates “are not getting weaker,” Ayala says. “If anything, they’re more visible.”

But Ayala thinks that scientists who attack religion and ridicule the faithful—most notably, Richard Dawkins of the University of Oxford—are making a mistake. It is destructive and gives fodder to the preachers who insist followers must choose either Darwin or God. Often students in Ayala’s introductory biology class tell him that they will answer test questions as he wishes, but in truth they reject evolution because of their Christian beliefs. Then, a couple of years later, when they have learned more science, they decide to abandon their religion. The two, students seem to think, are incompatible.

That saddens him, Ayala says. Instead he would like believers to reconcile their faith with science. Drawing on five years of study in preparation for ordination as a Dominican priest, Ayala uses evolution to help answer a central paradox of Christianity—namely, how can a loving, all-knowing God allow evil and suffering?

Nature is poorly designed—with oddities such as blind spots built into the human eye and an excess of teeth jammed into our jaws. Parasites are sadists. Predators are cruel. Natural selection can explain the ruthlessness of nature, Ayala argues, and remove the “evil”—requiring an intentional act of free will—from the living world. “Darwin solved the problem,” Ayala concludes. He refers to science-savvy Christian theologians who present a God that is continuously engaged in the creative process through undirected natural selection. By addressing religious people on their own terms, Ayala aims to offer a better answer than intelligent design or creationism.

Ayala straddles science and religion by speaking both languages extremely well (and with a Castilian accent). Despite his prolific—and time-consuming—activity in the public arena, he keeps his molecular genetics at the cutting edge. As in his theological debates, he enjoys challenging accepted scientific ideas. Ayala’s early work was the first to demonstrate the extensive nature of genetic variation and the action of natural selection at the protein level. His measures led to important modifications to the theory of the uniform “molecular clock,” which is used to time when species diverged from a common ancestor, based on differences in either protein structure or DNA. He no longer maintains a wet lab but collaborates extensively.

Ayala graduated in physics at the University of Madrid, then worked in a geneticist’s lab while studying theology at the Pontifical Faculty of San Esteban in Salamanca, Spain. By his ordination in 1960 he had already decided to pursue science instead of a ministerial role. At the monastery Darwinism had never been perceived as an enemy of Christian faith. So a year later, when Ayala moved to New York City to pursue a doctorate in genetics, the prevailing U.S. view of a natural hostility between evolution and religion was a shock.

Ever since, Ayala has attempted to address religious skepticism about Darwin’s theory. At first, he recalls, his scientific colleagues were wary and took the position that researchers should not engage in religious discussions. By 1981, when the Arkansas legislature voted to give creationism equal time in schools, the mood began to change. The National Academy of Sciences prepared an amicus curiae brief for a Supreme Court case on the Louisiana “Creation Act” and asked Ayala to lead the effort. The booklet became the 1984 Science and Creationism: A View from the National Academy of Sciences.

For the second edition in 1999 Ayala presented the idea of incorporating the words of some theologians but recalls, “I was almost eaten alive.” In the third edition, published this year, one section features statements by four religious denominations and three scientists on the compatibility of evolution with religious beliefs.

Ayala is again giving his colleagues pause by sitting on the advisory board of the John Templeton Foundation, which paid out $70 million in grants last year alone for research and scholarly programs “engaging life’s biggest questions.” Some scientists complain that the organization’s main mission is to inject religion into science. But Ayala defends Templeton’s interest in connecting science to religious life. The foundation has “started to do very good things in recent years,” he explains.

Even so, some philosophers of science, such as Philip Kitcher of Columbia University, have come to believe that evolution and belief in a providential creator cannot coincide. Kitcher admires Ayala but complains that “he has residual supernaturalist tendencies.” For others, Ayala’s approach of debating theological questions and clearly explaining the science is not enough. When two thirds of the public profess a commitment to creationism, argues Stanford University evolutionary biologist Joan E. Roughgarden, the situation is dire. In 2006 Roughgarden wrote what she calls a “religious book” that detailed ideas and examples of evolution written in the Bible. The daughter of Episcopalian missionaries, Roughgarden says she meets believers on their turf—and has even given sermons on evolution from the pulpit. The heart of the debate rests not in theological concepts like explaining evil, she insists, but in the pews.

Sometimes Ayala sounds ready to go there, as when he talks about the vision of God as the author of the universe. But he is unwilling to affirm or deny a personal belief in God, preferring to stick with philosophy. Smart people are being told their faith is incompatible with science. It is his goal, Ayala says, to help believers see evolution as an ally.

Note: This story was originally published with the title, "The Christian Man's Evolution".