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At the headquarters of the John Templeton Foundation, a dozen kilometres outside Philadelphia, Pennsylvania, the late billionaire seems to watch over everything. John Templeton's larger-than-life bust stands at one end of the main conference room. His life-sized portrait smiles down from a side wall. His face peers out of framed snapshots propped on bookshelves throughout the many offices.

It seems fitting that Templeton is keeping an eye on the foundation that he created in 1987, and that consumed so much of his time and energy. With a current endowment estimated at US$2.1 billion, the organization continues to pursue Templeton's goal of building bridges between science and religion. Each year, it doles out some $70 million in grants, more than $40 million of which goes to research in fields such as cosmology, evolutionary biology and psychology.

As generous as the foundation's support is, however, many scientists find it troubling — and some see it as a threat. Jerry Coyne, an evolutionary biologist at the University of Chicago, Illinois, calls the foundation "sneakier than the creationists". Through its grants to researchers, Coyne alleges, the foundation is trying to insinuate religious values into science. "It claims to be on the side of science, but wants to make faith a virtue," he says.

But other researchers, both with and without Templeton grants, say that they find the foundation remarkably open and non-dogmatic. "The Templeton Foundation has never in my experience pressured, suggested or hinted at any kind of ideological slant," says Michael Shermer, editor of Skeptic, a magazine that debunks pseudoscience, who was hired by the foundation to edit an essay series entitled 'Does science make belief in God obsolete?'

The debate highlights some of the challenges facing the Templeton Foundation after the death of its founder in July 2008, at the age of 95. With the help of a $528-million bequest from Templeton, the foundation has been radically reframing its research programme. As part of that effort, it is reducing its emphasis on religion to make its programmes more palatable to the broader scientific community.

Like many of his generation, Templeton was a great believer in progress, learning, initiative and the power of human imagination — not to mention the free-enterprise system that allowed him, a middle-class boy from Winchester, Tennessee, to earn billions of dollars on Wall Street. The foundation accordingly allocates 40% of its annual grants to programmes with names such as 'character development', 'freedom and free enterprise' and 'exceptional cognitive talent and genius'.

Unlike most of his peers, however, Templeton thought that the principles of progress should also apply to religion. He described himself as "an enthusiastic Christian" — but was also open to learning from Hinduism, Islam and other religious traditions. Why, he wondered, couldn't religious ideas be open to the type of constructive competition that had produced so many advances in science and the free market?

That question sparked Templeton's mission to make religion "just as progressive as medicine or astronomy". He started in 1972, by endowing the Templeton Prize for progress in religion. He stipulated that the cash value should always be higher than that of the Nobel Prizes; it currently stands at £1 million (US$1.6 million). Early Templeton prizes had nothing to do with science: the first went to the Catholic missionary Mother Theresa of Calcutta in 1973.

By the 1980s, however, Templeton had begun to realize that fields such as neuroscience, psychology and physics could advance understanding of topics that are usually considered spiritual matters — among them forgiveness, morality and even the nature of reality. So he started to appoint scientists to the prize panel, and in 1985 the award went to a research scientist for the first time: Alister Hardy, a marine biologist who also investigated religious experience. Since then, scientists have won with increasing frequency. In 2010, the prize went to Francisco Ayala, a geneticist at the University of California, Irvine, and a former Dominican priest who has spent 30 years fighting the teaching of creationism and intelligent design in schools as alternatives to evolution.

The prize has come in for some academic scorn. "There's a distinct feeling in the research community that Templeton just gives the award to the most senior scientist they can find who's willing to say something nice about religion," says Harold Kroto, a chemist at Florida State University in Tallahassee, who was co-recipient of the 1996 Nobel Prize in Chemistry and describes himself as a devout atheist.

Scientists as allies

Yet Templeton saw scientists as allies. They had what he called "the humble approach" to knowledge, as opposed to the dogmatic approach. "Almost every scientist will agree that they know so little and they need to learn," he once said.

The scientific attitude informed the motto that Templeton crafted for his foundation: "How little we know, how eager to learn."

The foundation began with just two employees in a room above the garage of his oldest son, Jack Templeton, in Bryn Mawr, Pennsylvania. The foundation's initial activities were also modest: administering the Templeton Prize, funding science and religion courses at universities and seminaries, and sponsoring essay contests.

"But the foundation was a research project in his mind," says Jack Templeton, who retired from his career as a paediatric and trauma surgeon in 1995 to become the organization's president. The slowly growing staff was bombarded with ideas and directives in a near-daily stream of faxes from Lyford Cay in the Bahamas, where the elder Templeton had lived since 1968.

Templeton's interests gave the resulting list of grants a certain New Age quality (See ). For example, in 1999 the foundation gave $4.6 million for forgiveness research at the Virginia Commonwealth University in Richmond, and in 2001 it donated $8.2 million to create an Institute for Research on Unlimited Love (that is, altruism and compassion) at Case Western Reserve University in Cleveland, Ohio.

"A lot of money wasted on nonsensical ideas," says Kroto. Worse, says Coyne, these projects are profoundly corrupting to science, because the money tempts researchers into wasting time and effort on topics that aren't worth it. If someone is willing to sell out for a million dollars, he says, "Templeton is there to oblige him".

But Templeton wasn't interested in funding mainstream research, says Barnaby Marsh, the foundation's executive vice-president. Templeton wanted to explore areas — such as kindness and hatred — that were not well known and did not attract major funding agencies. Marsh says Templeton wondered, "Why is it that some conflicts go on for centuries, yet some groups are able to move on?"

At the same time, says Marsh, the 'dean of value investing', as Templeton was known on Wall Street, had no intention of wasting his money on junk science or unanswerables such as whether God exists. So before pursuing a scientific topic he would ask his staff to get an assessment from appropriate scholars — a practice that soon evolved into a peer-review process drawing on experts from across the scientific community.

Because Templeton didn't like bureaucracy, adds Marsh, the foundation outsourced much of its peer review and grant giving. In 1996, for example, it gave $5.3 million to the American Association for the Advancement of Science (AAAS) in Washington DC, to fund efforts that work with evangelical groups to find common ground on issues such as the environment, and to get more science into seminary curricula. In 2006, Templeton gave $8.8 million towards the creation of the Foundational Questions Institute (FQXi), which funds research on the origins of the Universe and other fundamental issues in physics, under the leadership of Anthony Aguirre, an astrophysicist at the University of California, Santa Cruz, and Max Tegmark, a cosmologist at the Massachusetts Institute of Technology in Cambridge.

The design Debate

But external peer review hasn't always kept the foundation out of trouble. In the 1990s, for example, Templeton-funded organizations gave book-writing grants to Guillermo Gonzalez, an astrophysicist now at Grove City College in Pennsylvania, and William Dembski, a philosopher now at the Southwestern Baptist Theological Seminary in Fort Worth, Texas. After obtaining the grants, both later joined the Discovery Institute — a think-tank based in Seattle, Washington, that promotes intelligent design. Other Templeton grants supported a number of college courses in which intelligent design was discussed. Then, in 1999, the foundation funded a conference at Concordia University in Mequon, Wisconsin, in which intelligent-design proponents confronted critics.

Those awards became a major embarrassment in late 2005, during a highly publicized court fight over the teaching of intelligent design in schools in Dover, Pennsylvania. A number of media accounts of the intelligent design movement described the Templeton Foundation as a major supporter — a charge that Charles Harper, then senior vice-president, was at pains to deny.

Some foundation officials were initially intrigued by intelligent design, Harper told The New York Times. But disillusionment set in — and Templeton funding stopped — when it became clear that the theory was part of a political movement from the Christian right wing, not science. Today, the foundation website explicitly warns intelligent-design researchers not to bother submitting proposals: they will not be considered.

The foundation's critics are unimpressed. Avowedly antireligious scientists such as Coyne and Kroto see the intelligent-design imbroglio as a symptom of their fundamental complaint that religion and science should not mix at all.

"Religion is based on dogma and belief, whereas science is based on doubt and questioning," says Coyne, echoing an argument made by many others. "In religion, faith is a virtue. In science, faith is a vice." The purpose of the Templeton Foundation is to break down that wall, he says — to reconcile the irreconcilable and give religion scholarly legitimacy.

Foundation officials insist that this is backwards: questioning is their reason for being. Religious dogma is what they are fighting.

That does seem to be the experience of many scientists who have taken Templeton money. During the launch of FQXi, says Aguirre, "Max and I were very suspicious at first. So we said, 'We'll try this out, and the minute something smells, we'll cut and run.' It never happened. The grants we've given have not been connected with religion in any way, and they seem perfectly happy about that."

John Cacioppo, a psychologist at the University of Chicago, also had concerns when he started a Templeton-funded project in 2007. He had just published a paper with survey data showing that religious affiliation had a negative correlation with health among African-Americans — the opposite of what he assumed the foundation wanted to hear. He was bracing for a protest when someone told him to look at the foundation's website. They had displayed his finding on the front page. "That made me relax a bit," says Cacioppo.

Yet, even scientists who give the foundation high marks for openness often find it hard to shake their unease. Sean Carroll, a physicist at the California Institute of Technology in Pasadena, is willing to participate in Templeton-funded events — but worries about the foundation's emphasis on research into 'spiritual' matters. "The act of doing science means that you accept a purely material explanation of the Universe, that no spiritual dimension is required," he says.

It hasn't helped that Jack Templeton is much more politically and religiously conservative than his father was. The foundation shows no obvious rightwards trend in its grant-giving and other activities since John Templeton's death — and it is barred from supporting political activities by its legal status as a not-for-profit corporation. Still, many scientists find it hard to trust an organization whose president has used his personal fortune to support right-leaning candidates and causes such as the 2008 ballot initiative that outlawed gay marriage in California.

Templeton worried that the word 'religion' was alienating too many good scientists. ,

Scientists' discomfort with the foundation is probably inevitable in the current political climate, says Scott Atran, an anthropologist at the University of Michigan in Ann Arbor. The past 30 years have seen the growing power of the Christian religious right in the United States, the rise of radical Islam around the world, and religiously motivated terrorist attacks such as those in the United States on 11 September 2001.

Given all that, says Atran, many scientists find it almost impossible to think of religion as anything but fundamentalism at war with reason. They have a reflexive reaction against the idea, espoused by Templeton, that progress in spirituality can help to solve the problems of the world.

The big questions

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Towards the end of Templeton's life, says Marsh, he became increasingly concerned that this reaction was getting in the way of the foundation's mission: that the word 'religion' was alienating too many good scientists. This prompted a rethink of the foundation's research programme — a change most clearly seen in the organization's new website, launched last June. Gone were old programme names such as 'science and religion' — or almost any mention of religion at all (See 'Templeton priorities: then and now'). Instead, the foundation has embraced the theme of 'science and the big questions' — an open-ended list that includes topics such as 'Does the Universe have a purpose?'

Under this umbrella come new programmes in such areas as mathematical and physical sciences, life sciences, and philosophy and theology — each, for the first time, with its own team of programme officers. The peer-review and grant-making system has also been revamped: whereas in the past the foundation ran an informal mix of projects generated by Templeton and outside grant seekers, the system is now organized around an annual list of explicit funding priorities.

It remains to be seen how reassuring these changes will be for scientists still sceptical of the foundation — although Marsh notes that last year's inaugural announcement of 13 funding priorities drew some 2,500 submissions.

The foundation is still a work in progress, says Jack Templeton — and it always will be. "My father believed," he says, "we were all called to be part of an ongoing creative process. He was always trying to make people think differently."

"And he always said, 'If you're still doing today what you tried to do two years ago, then you're not making progress.'"