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For decades, sociologist Margaret Poloma struggled against the tone-deafness to spirituality that rules her discipline; she wanted to study prayer, to measure divine love, to "see God as an actor." In the meantime, having held a tenured post at the University of Akron since 1970, she built a respectable career with a long list of journal articles and books to her name. She became an authority on Pentecostalism and on the family lives of modern women. But all along, Poloma says, "I felt like I was swimming alone upstream."

That changed in the early 1990s, when she found an ally in David Larson, a psychiatrist who longed to integrate religion into the practice of medicine. He was in the process of founding the National Institute for Healthcare Research (NIHR); what the National Institutes of Health (NIH) is to medicine writ large, the NIHR would be for "the forgotten factor" of faith. In 1995 Larson brought Poloma to a conference organized by his funder: the John Templeton Foundation, established by the eponymous investor who died in July 2008 at 95. "That conference was a magical experience for me," Poloma remembers. It was there that she met Stephen Post, a bioethicist who would later create the Institute for Research on Unlimited Love with Templeton money. With Post she began receiving grants from the foundation. By 2007 she was co-director of the Flame of Love Project, administering $2.3 million from Templeton to establish "a new interdisciplinary science of Godly Love," with a focus on the Pentecostal tradition.

Other scholars aren’t quite sure what the "science of Godly Love" means, exactly. Anthea Butler, a historian of Pentecostalism at the University of Pennsylvania, remembers that when Poloma’s Flame of Love request for proposals appeared, "nobody in the field could figure out what the hell she was talking about." Many applied anyway. "She went from being an outsider to someone with tons of money who can set the terms of discussion," says Butler.

"This grant is something I would never have dreamed of," Poloma told me. "I feel like I’m soaring like an eagle." For her, all gratitude is due to the funder. "Where but Templeton would you find that kind of dialogue going on?"

Nowhere—and that’s what has some people so concerned. The kind of research Poloma and her colleagues propose, however empirical and peer-reviewed, seems to come as an affront to centuries of purported progress in disentangling natural science from supernatural belief. Depending on whom you ask, Templeton represents either the hijacking of nothing less than the meaning of life, or the restoration of its luster, which has been dulled by politics and cynicism.

Poloma’s story repeats itself throughout the cluster of academic fields that the Templeton Foundation has chosen to flush with money. This past January $4.4 million went to a project on free will, headed by philosopher Alfred Mele at Florida State University. In a particularly arresting case, between 2006 and 2009 MIT physicist Max Tegmark received $8.8 million to set up the Foundational Questions Institute (with the dashing acronym FQXi), which funds first-rate scientists to explore basic problems about time, space and the origin of the universe. Its conferences have been "a coming-out-of-the-closet experience," says Tegmark. "Lots of people reconnect with the real reasons they started doing science in the first place."

Templeton has a history of seeding fields of study almost from scratch. After the foundation’s initiative for research on forgiveness began in 1997, the number of psychology journal articles on the subject went from fewer than fifty per year to more than 100 in 2000 and nearly 250 in 2008. When Templeton first financed Larson’s NIHR in the early 1990s, the number of medical schools with courses on religion could be counted on one latex glove. Now, according to Dr. Christina Puchalski of the Templeton-funded George Washington Institute for Spirituality and Health, three-quarters of US medical schools have brought spirituality into their curriculums.

What connects, say, unlimited love with string theory? According to the foundation, they are among life’s "Big Questions," the exploration of which constitutes its mission. Templeton money supports other causes, like promoting virtue, encouraging gifted youth and fostering free enterprise, but its core concerns are more cosmic: "Does the universe have a purpose?" "Does science make belief in God obsolete?" "Does evolution explain human nature?" As the advance of knowledge becomes ever more specialized and remote, these questions seem as refreshing as they are intractable; the foundation wants them to be our culture’s uniting, overriding focus. For those who work on matters of spirituality and science today, Templeton is around every turn, active in disciplines from biology and cosmology to philosophy and theology. Many leading scholars speak of it with a tone of caution; some who have not applied for grants expect to do so in the future, while a few have taken a principled stand against doing so.

Like debates about religion broadly, debates about Templeton often get mapped onto the culture wars in black and white, or red and blue. It doesn’t help that the foundation is a longstanding donor to conservative think tanks like the Heritage Foundation and the Cato Institute. And while its founder preferred eternal questions to worldly politics, the son who has succeeded him, John Templeton Jr.—Jack—is a conservative Evangelical who spends his personal time and money opposing gay marriage and defending the Iraq War. Since his father’s death, concerns have swirled among the foundation’s grantees and critics alike that Jack Templeton will steer the foundation even further rightward and, perhaps, even further from respectable science.

The stakes are high. The Templeton Foundation holds assets valued at around $1 billion, a sum that will likely swell to $2.5 billion in the years to come as John Templeton Sr.’s estate is settled. That would put it squarely among the richest twenty-five foundations in the country, somewhere between the Rockefeller Foundation and the Open Society Institute. The foundation dispenses about $70 million in grants annually, the bulk of which goes to programs in the religion-and-science orbit, from an eight-year, $9.8 million grant to Duke University’s Center for Spirituality, Theology and Health to $25,000 for a 2007 conference on Carl Linnaeus and religion in Sweden. For the often-fledgling, cash-strapped areas it funds, nothing else can compete.

But what makes the foundation more influential than its deep pockets is the combination of elite research and broad dissemination. As a memo signed by John Templeton in 1995 put it, "The main purpose of the John Templeton Foundation is to encourage the top 1/10 of 1% of people and thereby encourage all people to think that progress in spiritual information is possible, desirable, can be done and will be done." The "top 1/10 of 1%" part happens in projects like the Humble Approach Initiative, a series of high-level interdisciplinary seminars that since 1998 have covered topics such as "Universe or Multiverse?" and "Faith, Rationality, and the Passions." At each step, the foundation tries to keep a wider audience abreast. Along with advanced research, it funds public essay contests and lectures. A series of periodicals, including In Character and Science & Spirit, have tried to build readerships around Templeton’s favorite topics—the former was even, for a time, sent to every member of Congress. The foundation supports the annual World Science Festival in New York and takes out lavish ads in magazines and newspapers to showcase handpicked intellectuals answering Big Questions about God, science and markets.

The founder’s flagship program, though, is the Templeton Prize, usually handed out each year by Prince Philip at Buckingham Palace. The first went to Mother Teresa in 1973; this year’s laureate is biologist and former Catholic priest Francisco Ayala. Winners have run the gamut from Aleksandr Solzhenitsyn to physicist Freeman Dyson. The award’s value is consciously pegged to be bigger than that of the Nobel Prize.

The zoologist and author Richard Dawkins quipped in his 2006 book The God Delusion that the Templeton Prize goes "usually to a scientist who is prepared to say something nice about religion." He and others among the so-called New Atheists have been the foundation’s most strident critics lately; they believe Templeton is corrupting science by trying to inject it with religious dogma and, in turn, misrepresent science to the public. The advance of science steamrolls over religion, they say, and Templeton is deluding people into thinking otherwise.

These are no minor charges. Recent years have witnessed political and religious campaigns to both undermine and co-opt scientific authority on matters ranging from climate change to sex education to evolution. Organizations like Answers in Genesis, which advocates for young-earth creationism, and the Discovery Institute, which orchestrates the intelligent-design movement, have been trying to squeeze creationism into public school science classes. Within this environment, Templeton has struggled to maintain a delicate balance between alarmed scientists on one side and its mission to bring religion into conversation with science on the other.

In the past the foundation has funded book projects related to intelligent design by theorists William Dembski and Guillermo Gonzalez, who were affiliated with the Discovery Institute when they received Templeton grant money. By then, though, Templeton had already begun funding a program that opposes creationism at the American Association for the Advancement of Science. "We do not believe that the science underpinning the intelligent-design movement is sound," wrote one foundation official in a 2007 letter to the Los Angeles Times. Templeton has since taken pains to promote evolutionary theory among Christians, such as through the BioLogos Foundation, which was headed by geneticist Francis Collins until President Obama appointed him director of NIH. Still, Templeton continues to find itself in murky waters; in May, for instance, it supported a conference celebrating the retirement of the eminent philosopher Alvin Plantinga, who also happens to have been a sometime ally of intelligent design.

Indeed, the larger the foundation becomes, the harder it is to pin down. "They’ve become fuzzier and fuzzier," says California Institute of Technology astronomer Sean Carroll, one of Templeton’s more outspoken critics. Even Jeffrey Schloss, a Templeton trustee who is part of the new $10 million grant project on evolutionary biology based at Harvard, admits that without the foundation "there’d be a bit less accommodationist fluff that proposes integration [between religion and science] at the expense of rigor."

Nonreligious scientists who accept Templeton grants—like biologist David Sloan Wilson and psychologist Jonathan Haidt—insist that the money comes without strings attached. "No coercion, no corruption," Haidt says. But Nobel Prize–winning chemist Harry Kroto won’t accept that. "They are involved in an exercise that endangers the fundamental credibility of the scientific community," he contends. Kroto has taken to organized resistance; in 2007, when the Royal Society of London considered accepting Templeton money for one of its programs, he was among eleven fellows, five of them Nobel laureates, who successfully lobbied against the plan. Since a Templeton lecture series in 2004, the Royal Society hasn’t worked with the foundation, though some fellows and its president, astrophysicist Martin Rees, have done so individually.

Now Dawkins and Kroto, with eight other advisory board members of Project Reason, founded by New Atheist author Sam Harris in 2007 to promote secularism, are at work on another offensive. Project Reason hired British science journalist Sunny Bains to investigate Templeton and build a case against it. Her unpublished findings include evidence of pervasive cronyism: more than half of the past dozen Templeton Prize winners were connected to the foundation before their win, and board members do well obtaining grant money and speaking gigs. Bains also argues that the true atheistic tendencies of leading scientists were misrepresented in the foundation’s Big Questions advertisements. Templeton’s mission, Bains concludes, is to promote religion, and its overtures to science are an insidious trick with the purpose of sneaking in God.

Though some critics refuse to go near anything associated with Templeton, others are forced by its ubiquity to make compromises. Sean Carroll, for one, will work only on scientific projects funded by Templeton (such as the FQXi) that aren’t solely under the foundation’s banner. "It represents a serious ethical dilemma," says A.C. Grayling, a British philosopher and former columnist for New Scientist magazine; he accuses the foundation of "borrowing respectability from science for religion."

These critiques have taken a toll on the Templeton brand. "I don’t think Templeton money is dishonorable, and I have taken it myself," says Michael Ruse, a philosopher of science at Florida State University. But Ruse expresses relief that his latest book wasn’t funded by any Templeton grants. "The whole business has become so politicized and open to attack by the New Atheists—they would claim that I am just a paid spokesman."

In response to its critics, the foundation cites the careful peer review process its projects go through and the integrity of the leading institutions with which it partners. "The goal is to insist that the scholarship that is done in theology and philosophy is scientifically informed, and that the research done on the scientific side is conceptually rigorous and clear," explains Michael Murray, a Templeton Foundation vice president. In many cases these protocols and elite affiliations are enough to persuade eminent scientists, like Rees and Carroll, to put aside their misgivings and participate in Templeton projects.

Still, few Templeton grantees are fully aware of the breadth of the foundation’s activities, much less the quixotic vision of its founder, John Templeton—or, as friends of the foundation have called him since he was knighted by Queen Elizabeth II in 1987, "Sir John."

In the foundation’s boardroom, no one can hide from Sir John’s gaze. His bust is mounted above the far end of a long meeting table, and his portrait hangs on a long wall. The offices are in one of a cluster of new towers scattered among industrial relics and hillside homes in West Conshohocken, Pennsylvania, fourteen miles up the Schuylkill River from downtown Philadelphia. There, away from the distractions of big-city political and intellectual life, John Templeton’s legacy is meant to carry itself out, unadulterated. As the foundation grew larger, it became increasingly concerned that it not stray from the mission he gave it. By the time he died, an elaborate audit system had been put in place to ensure that his wishes would forever be its holy writ.

Templeton’s own spirituality was eclectic. Though a lifelong Presbyterian, he imbibed the wisdom of religions both Eastern and Western, ranging from his friend Norman Vincent Peale, the prophet of the organization man, to Ramakrishna. Early on, his mother exposed him to the Unity School of Christianity, a turn-of-the-century movement that emphasized positive thinking and healing through prayer. The Unity School considered itself progressive and even, loosely speaking, scientific: a practical application of Christianity to modern life.

Out of his humble origins in small-town Tennessee, Templeton built a career as one of the great architects of globalization—"the dean of global investing," Forbes once dubbed him. As he grew older, though, his wealth ever multiplying, Templeton began turning his attention away from business. "All my life I was trying to help people get wealthy, and with a little success. But I never noticed it made them any happier," he told Charlie Rose in a 1997 interview. "Real wealth is not in money; it’s in spiritual growth."

When Templeton created his foundation in the mid-’80s, conventional wisdom still largely held that religion would retreat as science secularized the world. But in Templeton’s eyes, this made religion the perfect investment. "To get a bargain price," he would say, "you’ve got to look for where the public is most frightened and pessimistic." Religion’s potential value far exceeded the asking price; a lot could be done with a little. Templeton would rhapsodize about science’s amazing progress in virtually every area of knowledge over the past century—except in spirituality, which he believed had remained stagnant. "It is no small wonder, then," Templeton wrote in his manifesto, The Humble Approach, "that some people believe religion is gradually becoming obsolete." The answer he envisioned wasn’t simply a louder, timelier enunciation of familiar doctrines but a new posture he called "humility theology," an outlook that emphasizes how little is known about the divine and how much believers need to question and test their beliefs, as scientists do. Templeton thought that science could get religions out of their rut.

Through his mostly self-published writings, Templeton developed an idiosyncratic vocabulary, speaking of the search for "spiritual information" and of God as "Unlimited Creative Spirit." But many of Templeton’s books are less properly theological than they are well-meaning self-help texts with a metaphysical bent. Uneasy with conventional meanings for "God" and "religion," he speculated in a 1990 document that "maybe God is providing new revelations in ways which go beyond any religion." Concerning atheism, Templeton seems to have thought that if religion were more sophisticated, the line between belief and unbelief might disappear. He once mused, "Could even atheists, who deny the reality of a personal God, begin to worship fundamental reality or unlimited mind or unlimited love?"

At worst, Templeton could be called heterodox and naïve; at best, his was a mind more open than most, reflective of the most inventive and combinatorial strains of American religious thought, eager to radically reinterpret ancient wisdom and bring it up to speed with some version from the present.

In 1996 Charles Harper, a planetary scientist from Harvard and NASA with a graduate education in cosmology and theology from Oxford, joined the foundation as its executive director. A forceful—and by many accounts difficult—personality with a visionary streak, Harper shaped John Templeton’s dream into a package of programs that could begin to look credible to the scientific community.

A decade later, phrases that Templeton used, like "spiritual realities," "progress in religion" and even the foundation’s official motto, "How little we know, how eager to learn," were hiding behind a more presentable formula: "Supporting science, investing in the Big Questions." By no means, though, was the spiritual sidelined under Harper’s leadership. "Rigorous, advanced research in science in certain areas," he wrote me, "can be supported and engaged as a form of theologically- significant research adventure." Harper shared with his boss the hope of making questions of faith part of the scientific conversation, and for years they funded innovative ways of doing so.

But in May 2009, less than a year after Templeton’s death, Harper was fired. Those at the foundation are reluctant to explain why; Harvard astronomer and longtime advisory board member Owen Gingerich attributes it to "a difference of opinion about who could best understand Sir John’s intentions" between Harper and Jack Templeton. Above all, "there was a clash of personalities."

Jack Templeton is little like his father. While the elder Templeton’s writings venture into the poetic and speculative, his son’s read like a medical report. Jack displays admirable filial loyalty, evident most of all in his decades-long leadership of the foundation under his father’s guidance; he has been president since it began, serving full time since he left a successful pediatric surgery practice in 1995. His memoir begins and ends with lessons his father taught him and is suffused by, as he put it, "a struggle to find acceptance and approval in my father’s eyes."

Only now, though, are we beginning to learn how that struggle will express itself in his father’s absence. With Harper gone, and his replacement yet to be announced, there is a vacuum at the top. It is, says physicist and trustee Paul Davies, "an anxious time." What seems to have people there most on edge right now, though, is not so much science as politics. In this respect too, the younger Templeton differs in kind from his father. He has financed a right-wing organization of his own, Let Freedom Ring, which once promoted the "Templeton Curve," a graph he designed to advocate privatizing Social Security. Now Let Freedom Ring lends support to the Tea Party movement. Jack Templeton’s money has also gone to the Swift Boat Veterans for Truth and to ads by the neoconservative group Freedom’s Watch. In 2008 he and his wife gave more than $1 million to support California’s Proposition 8, which banned same-sex marriage.

According to his lifelong friend Jay Norwalk, Templeton "is exceedingly scrupulous about keeping his personal life separate from the foundation." By most accounts, this has been the case. Physicist Karl Giberson, a self-described liberal who has been a close collaborator on various foundation projects, adds, "To me, Jack Templeton represents the way you want conservatives to be." (Jack Templeton declined requests for an interview, and the foundation’s chief external affairs officer, Gary Rosen, a former editor at Commentary, instructed foundation leadership to conduct interviews with The Nation only in writing.)

"Conservative," though, hardly encompasses what the Templeton Foundation is about. The founder’s relationship to the notion was especially paradoxical; in The Humble Approach, Templeton writes, "Rarely does a conservative become a hero of history." Although Templeton could be nostalgic, harking back to time-tested values and homespun sayings, he wanted above all to move the world forward, not hold it back. Yet he was, in political parlance, a conservative: a voting (and donating) small-government, probusiness Republican. More George H.W. than Dubya, his values bear little resemblance to the sex-centered prohibitions of today’s religious right. His foundation’s charter speaks instead of "love," "forgiveness," "generosity," "creativity," "thrift" and "awe."

John Templeton once told Harper that he read only the news in the paper, never the editorials; the fray of partisanship and policy didn’t interest him. He wanted to keep his foundation away from party politics, just as he kept its offices away from downtown philanthropic circles. He loved undertakings, like a mission to the moon or a mutual fund, that would unite people around a common transcendent purpose.

In the minds of some, he succeeded. Conservative Christian columnist and blogger Rod Dreher, upon beginning his new job as the foundation’s director of publications at the start of this year, had a revelation. "I didn’t realize how burned out with and depressed by politics I had become," he wrote me. Working at the Templeton Foundation, he believes, gave him a chance to grow in a way that political editorializing would never allow. "I’ve become ever more convinced that the more important questions facing us are cultural, not political," Dreher explains.

Templeton has long maintained relationships with a network of right-wing organizations that share its interest in open markets, entrepreneurship and philanthropy. The Heritage Foundation, for instance, received more than $1 million between 2005 and 2008, and the Cato Institute, more than $200,000 in the same period. Templeton’s charter stipulates that the chief executives of the Atlas Economic Research Foundation and the Acton Institute for the Study of Religion and Liberty are entitled to be members of the foundation, and both have received hundreds of thousands of dollars in Templeton grants in recent years. Those organizations also receive contributions from Big Oil and take part in the campaign to distort the scientific consensus on global warming.

Exceptions to the rightward trend abound: psychologist and Templeton trustee David Myers penned What God Has Joined Together: The Christian Case for Gay Marriage; just last year the foundation treated the Marxist literary theorist Terry Eagleton to a Templeton Book Forum event at the Harvard Club in New York—the list goes on. Grants to conservative think tanks are a comparatively minor part of the foundation’s overall giving, but they send a strong signal nonetheless. "There is no getting around the fact," declared a glowing 2007 National Review article, "that it [Templeton] has quickly become a major force in conservative philanthropy."

This is even more the case today. Jack Templeton announced, in the 2008 Capabilities Report, a "fresh endeavor" on free enterprise, the area of the foundation’s work closest to his own predilections. Mauro De Lorenzo, hired as a vice president to lead the initiative, still retains a post at the neoconservative American Enterprise Institute (AEI), which Templeton has also funded. When I asked him about the foundation’s think tank portfolio, De Lorenzo said, "We would be delighted to fund work at so-called left-of-center think tanks, so long as it meets the donor intent." That they haven’t funded such organizations yet, he continued, is just a matter of "not knowing each other."

There is another glaring omission in Templeton’s funding record: the foundation has yet to break ground on one of the six principal causes that John Templeton stipulated—education about voluntary family planning. Gary Rosen explains that this program "is still in development" though it has been in the charter for more than a decade. It is also an area where the foundation’s mission could come into tension with its political and religious allies.

Treading carefully over such theologically fraught ground is a practice that goes back to the founder. His writings might have been iconoclastic, but his deeds were mainly establishmentarian, keeping him in good standing with the religious powers that be. Templeton money has supported a wide range of pious causes, from the American Bible Society to awards for "wholesome" filmmaking (including, controversially, The Passion of the Christ). Templeton Prizes have gone to evangelists Billy Graham and Bill Bright, as well as Watergate conspirator turned Evangelical activist Charles Colson and AEI theologian Michael Novak.

John Templeton built a place where the right’s hardened partisans, like Dreher and Rosen, can settle down and turn to life’s real Big Questions, in peace, for all mankind. But the foundation meanwhile has associated itself with political and religious forces that cause it to be perceived as threatening the integrity of science and protecting the religious status quo. This is quite the reverse of the founder’s most alluring hope: a spirituality finally worthy of our scientific achievements. As a result of such alliances, though, the foundation is also better positioned than most to foster a conservatism—and a culture generally—that holds the old habits of religions and business responsible to good evidence, while helping scientists better speak to people’s deepest concerns. On issues that range from climatology to stem cells, science has too often taken a back seat to the whims of politics, and Templeton’s peculiar vision offers a welcome antidote to that. To live up to this calling, Big Questions are one thing; but the foundation will have to stand up for tough answers, too, as it did when announcing the findings of a major study that intercessory prayer doesn’t improve medical outcomes, or when rebuking intelligent design.

John Templeton did want to hijack the meaning of life; he meant to remake the human race’s moral and cosmic toolbox in some scientific revolution of the spirit. His money has given new life to ancient questions that matter to all of us. But there is also an inescapable curiosity—or for some, like Margaret Poloma, good luck—in the idea that how we think about the most lofty things has become so much at the mercy of an eccentric investor’s later-life dreams.