When the geneticist Francis Collins was named director of the National Institutes of Health, last summer, he became the public face of American science and the keeper of the world’s deepest biomedical-research-funding purse. He was praised by President Obama and waved through the Senate confirmation process without objection. There also came a peer review of a sort that he’d never experienced, conducted in the press and in Internet science forums. Collins read in the Times that many of his colleagues in the scientific community believed that he suffered from “dementia.” Steven Pinker, a cognitive psychologist at Harvard, questioned the appointment on the ground that Collins was “an advocate of profoundly anti-scientific beliefs.” P. Z. Myers, a biologist at the University of Minnesota at Morris, complained, “I don’t want American science to be represented by a clown.”

The choice of Collins to head the N.I.H. seemed to reflect the President’s own view of the harmony between science and religion. Illustration by Guy Billout

Collins’s detractors did not question his professional achievements, which long ago secured his place in the first rank of international scientists. As a young researcher at Yale, Collins conceived a method of hastening the laborious process of hunting disease-causing genes by skipping across long stretches of chromosomes until the suspect gene’s neighborhood was located. As an assistant professor at the University of Michigan, in the nineteen-eighties, he and collaborators at the University of Toronto employed this method to find the gene that causes cystic fibrosis and, a year later, the genetic flaw responsible for neurofibromatosis. These breakthroughs brought him fame and, eventually, the job of director of the Human Genome Project, which promised to revolutionize medicine by identifying and mapping all the approximately twenty thousand human genes that code for protein.

Thanks to that job, there wasn’t much doubt about Collins’s ability to handle the formidable management challenge of running the N.I.H., which directly employs twenty thousand scientists and staff, funds three hundred and twenty-five thousand outside researchers, and operates twenty-seven institutes and research centers on its campus, in Bethesda, Maryland. A key duty of the N.I.H. director is to justify the agency’s budget and defend before Congress the programs it funds, a duty that requires a skill quite apart from prowess in the laboratory. In fifteen years at the National Human Genome Research Institute, Collins had proved himself an able manager, bringing the Genome Project to a successful conclusion in 2003—two and a half years early and four hundred million dollars under budget. He also won friends in Congress with a genial manner and a gift for conveying complex scientific information in felicitous language.

The objection to Collins was his faith—or, at least, the ardency of it. Collins is a believing Christian, which places him in the minority among his peers in the National Academy of Science. (Of its members, according to a study, only seven per cent believe in God.) After leaving the Genome Research Institute, Collins began drawing large crowds on the college lecture circuit; he created a Web site, BioLogos, to advance his idea of the companionability of reason and faith; and he wrote a best-selling book, “The Language of God,” in which he presented what he claims to be scientific evidence of the existence of God.

President Obama’s choice of Collins for the N.I.H. touched a nerve. The George W. Bush era had been an extraordinarily fractious time in public science, beginning with Bush’s first prime-time address to the nation, in which he announced restrictions on embryonic-stem-cell research. That move, and others that followed, convinced Bush’s critics that the religious right had become the final arbiter of public policy, an impression that Bush seemed little inclined to dispel. “Well, we thought we’d seen the last of the theocracy of George W. Bush, but it apparently ain’t so,” Dr. Jerry Coyne, a University of Chicago professor, wrote when Collins was appointed. “I am funded by the N.I.H., and I’m worried. Not about my own funding (although I’m a heathen cultural Jew), but about how this will affect things like stem-cell research and its funding.”

A year later, Obama’s appointment of Collins seemed an inspired choice. The President had found not only a man who reflected his own view of the harmony between science and faith but an evangelical Christian who hoped that the government’s expansion of embryonic-stem-cell research might bring the culture war over science to a quiet end. On August 23rd, however, Judge Royce C. Lamberth, of the Federal District Court for the District of Columbia, halted federal spending for embryonic-stem-cell research, putting hundreds of research projects in limbo and plunging the N.I.H. back into a newly contentious national debate.

At the N.I.H., the ability to deal with controversies, as a generation of Collins’s predecessors learned, matters at least as much as credentials; political combat comes with the job. Collins does not seem a likely combatant. His physical aspect—gray mustache and hair (cut in an early-Beatles mop top), thin-rimmed eyeglasses, and a distinct pallor—suggests a man best acquainted with a sunless existence in some laboratory. Yet, in a relatively colorless town, Collins has come to be known as something of a character, a model of geek cool. He likes big, noisy motorcycles, and, despite a mild manner, he is famously unself-conscious. At the unlikeliest moments, he will strap on a guitar and accompany himself in song, often a tune he has composed for the occasion.

In dealing with Congress, Collins is less given to sentiment. A few weeks after moving into the director’s office, he received a letter from two Republican congressmen pressing him about a handful of N.I.H. grants “that do not seem to be of the highest scientific rigor.” The lawmakers, Joe Barton, of Texas, and Greg Walden, of Oregon, demanded to know the process by which the agency had funded a $423,500 study of why young heterosexual men did not consistently use condoms during sex. Barton and Walden were also curious about an N.I.H.-funded study investigating substance use and H.I.V.-risk behaviors among female and transgender sex workers in Thailand, and a $29,469 grant to researchers studying patterns of drug abuse in the Brazilian rave culture. The Barton-Walden inquiry was, in practical terms, just a gesture, as the programs in question had already been funded. Sometimes, though, such a gesture hits a vein of real political opportunity.

In November, Barton and Walden sent Collins a second letter, this time focussing on a series of N.I.H. grants investigating gun violence as a health issue. The N.I.H.-sponsored study, if portrayed as a back-door attempt at gun control (as it immediately was by Glenn Beck, on Fox News), threatened an unwelcome contretemps for an Administration fast depleting its political capital.

When I asked Collins about the Barton-Walden inquiries last winter, his response was polite but dismissive. “These grants, like all of our grants, go through this rigorous, two-level peer-review process,” he said. “And you can go back with any grant, and you can see, O.K., who was the peer-review group that looked at this? O.K., these are the leaders of their field. And what kind of evaluation did they give it? Well, it got funded, which means it was in the top twenty per cent of grants that that group looked at.” That was the message Collins conveyed to Barton and Walden in his written response to their queries, and the issue faded away.

The Barton-Walden exchange reflects a paradox faced by any director of the N.I.H.: the public (and, therefore, Congress) likes the idea of spending tax money on medical discoveries, but often recoils when presented with details of the research (especially research outside the laboratory) that it’s bought. The N.I.H. was a politically obvious choice when the Administration and congressional Democrats were dispersing stimulus money, and the Institutes received ten billion dollars to spend over two years. But, inevitably, some of that money went toward projects that made easy targets for Republicans. This summer, Senators John McCain and Tom Coburn issued a list of “stimulus projects that give taxpayers the blues,” and the N.I.H. found itself under attack for a $180,935 grant to the University of Missouri to find better ways to freeze rat sperm.

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“Now, why would anybody spend money on freezing rat semen?” Collins asks. “Well, I’ll tell you why. We have all these incredibly valuable rat strains that represent particular models of human disease, like hypertension or heart disease. But you don’t necessarily want to keep them running around in cages gobbling up rat food at extreme expense, year after year, if you’re not sure that strain is something you’re going to want to study five years from now. If you just freeze the sperm, you can re-create that rat when you’re ready, and it saves us a huge amount of money. Knowing how to do that effectively is a pretty good investment. But, of course, nobody bothered to find out the reason for this. They just thought it sounded weird and bizarre and like a waste of money.”

The man who holds the most powerful job in American science came from an unusual background. During the Depression, Collins’s parents, Fletcher and Margaret Collins, became part of a short-lived West Virginia project—sponsored by Eleanor Roosevelt, and with financial help from Bernard Baruch—that attempted to create an ideal community for a group of impoverished miners near Morgantown.

Fletcher was the project’s music director, with the mission of helping the homesteaders recover their cultural heritage. He had a gift for coaxing from the mountain people the nearly forgotten old fiddle tunes, folk songs, and square-dance calls that had been, he wrote, “very much in their blood,” but “layered over by coal dust.”

After the war, the Collinses bought a ninety-four-acre farm in the Shenandoah Valley, near Staunton, Virginia, determined to derive a livelihood from the land without modern agricultural machinery. They kept chickens, sheep, cows, and two workhorses, who pulled the plow and old wagon that carried the harvest from the hilly fields to the barn. The four Collins children, all boys, served as farmhands, collecting eggs, milking the cows, and shucking corn. When the alfalfa needed to be mowed and baled, amused neighbors would stop by with their tractors and help out. Once a week, the family drove into Staunton, where Margaret’s parents lived, and the boys had a bath; in the summertime, they bathed in the cow trough. After a few years, Fletcher took a position as drama instructor at the local women’s college, Mary Baldwin (“My cash crop,” he’d say), but the family was relatively poor. The younger boys wore their brothers’ hand-me-downs, and by the time the clothes reached Francis, the youngest, they were threadbare.

The Collinses’ household, known as Pennyroyal Farm, became the center of a vibrant arts community in Staunton. (It’s still thriving.) “Musicians would come and crash there for a couple of weeks because they’d run out of money,” Collins recalls. “They’d play great music, and then finally they’d move on.” Bob Dylan was among those who came to Pennyroyal. “Margaret and Fletcher were sort of hippies before there were hippies,” the singer Linda Williams recalls. “They were back-to-the-landers, and saw things the way people did in the seventies, only they’d done it in the thirties.”

For Francis, it was an enchanting, if arduous, childhood, part Boys’ Life and part Woodstock. He could set a barn door and knew how to predict weather by reading the sky over the distant Alleghenies. He did not see the inside of a schoolroom until sixth grade, because Margaret taught her boys at home. “There was no schedule,” Francis recalls. “The idea of Mother having a lesson plan would be just completely laughable. But she would get us excited about trying to learn about a topic that we didn’t know much about. And she would pose a question and basically charge you with it, using whatever resources you had—your mind, exploring nature, reading books—to try to figure out, well, what could you learn about that? And you’d keep at it until it just got tiresome. And then she’d always be ready for the next thing.”

Collins doesn’t recall ever seeing a Bible among the books in his parents’ house, and the only time they sent him to church it was for the choir music, and with the admonition “You should be respectful of what they’re doing, even if the stuff they’re talking about doesn’t make a lot of sense.” He was an agnostic when he went off to the University of Virginia, and by the time he was studying physical chemistry as a graduate student, at Yale, he’d become what he calls a “fundamentalist” atheist—the sort of non-believer who would share his dining table with a believer, just for the chance to expose the folly of faith. “I was fairly obnoxious about it,” he says.

Collins’s academic career was a sprint. He published his first research paper while still an undergraduate at Virginia. The summer after his junior year, he married Mary Lynn Harman, a struggling math student he’d tutored in high school, and they soon had two children. (They have since divorced, and Collins has remarried.) Collins was breezing through a doctoral program in theoretical chemical physics at Yale when he realized that a professor’s life in that field was not at all what he wanted. He decided instead to become a physician, and enrolled at the University of North Carolina School of Medicine.