"Arik" is a physicist at a US university. Although he is easy-going on most issues, he regards religion as a form of "intellectual terrorism", a "virus" to which he has now become "immune", and he is proud that his children have been "thoroughly and successfully indoctrinated that belief in God is a form of mental weakness".

Far from being worthy of even grudging respect, religion is to "Arik" simply "garbage - the detritus left over from the age of enlightenment and the scientific revolution". Its fierce and inevitable struggle with science counts as "the only realization of the battle between good and evil that I know of".

Much of this is pretty familiar. The notion that religion is perniciously simple-minded and locked in an eternal fight with science has been powerfully argued by a number of atheist thinkers, many of them based in the academy, with the charge led by Richard Dawkins in his 2006 best-seller The God Delusion. But what counts as evidence for such a claim?

One person who has looked closely at this issue is Elaine Howard Ecklund, assistant professor of sociology at Rice University in Texas. She surveyed nearly 1,700 natural and social scientists in elite American universities - "Arik" is a pseudonym for one of the academics she interviewed in depth - and she presents the results in her new book, Science vs. Religion: What Scientists Really Think. By asking them about how religion and spirituality have had an impact on their lives, she hopes to offer "a balanced assessment of information gathered scientifically from scientists themselves".

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Although they are undoubtedly less religious than the American public as a whole, the scientists Ecklund interviewed are far from a uniform band of militant atheists. Only 34 per cent say they concur with the statement "I do not believe in God" (and 30 per cent confess to agnosticism), 71 per cent believe "there are basic truths in many religions" and 18 per cent attend religious services at least once a month. Close to half could be said "to have a religious tradition" in some sense, and the age data in Ecklund's survey suggest that levels of faith among US scientists are rising.

So, many people devote their lives to scientific work but still find - more or less comfortable - ways of combining this with their religious beliefs and practices. Yet this also implies something else. "Arik" may despise religion, but by the sheer law of averages, progress within his discipline, and probably within his department, depends on collaboration between religious, agnostic and atheist scientists.

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Science and religion also seem to have rubbed along well during one of the golden ages of scientific discovery. Peter Harrison is Andreas Idreos professor of science and religion at the University of Oxford. Much of his research has focused on the 17th century, when, he says, "virtually all the key natural philosophers (early scientists) were religious believers. Some were clearly motivated by religious considerations - notably Johannes Kepler and Robert Boyle - although different individuals had different motivations. Most, however, thought that religious beliefs were consistent with their scientific findings, and indeed that religious beliefs and science were mutually reinforcing."

This hardly counts as evidence that religious claims are true. But it surely casts some doubt on the notion that only the "mentally weak" can believe in God or see such a belief as consistent with a commitment to science.

A further point is made by Karl Giberson, professor of physics at Eastern Nazarene College in Quincy, Massachusetts. Despite certain areas of tension, he observes, "most of religion and most of science just don't relate to each other - that's the most common connection, namely a lack of connection".

This all sounds like good news. Neither science nor religion is likely to disappear. And if there isn't a war between them either in the minds of many practising scientists or inside scientific institutions, perhaps they can just be left to peacefully coexist.

But before we get too cheerful, we face an obvious problem. Many people on both sides of the issue are deeply, and often very emotionally, committed to the idea that science and religion are locked in mortal combat.

This is taken to license a good deal of abuse and stereotyping. When the geneticist Francis Collins, a committed Christian, was appointed director of the National Institutes of Health in the US last summer, he was denounced by atheist scientists as a "clown" and as suffering from "dementia".

"You clearly can be a scientist and have religious beliefs," Peter Atkins, professor of chemistry at the University of Oxford, once conceded. "But I don't think you can be a real scientist in the deepest sense of the word because they are such alien categories of knowledge."

This view would, of course, demote Isaac Newton, to name but one, from the ranks of "real scientists". Is such a "conflict model" either accurate or helpful?

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In the US, there are particularly good reasons for scientific anxieties about religion.

"We have significant groups of Christian and Islamic fundamentalists who want to read Scripture in the old-fashioned way," Giberson says. "There are large organisations devoted to creating a replacement science in accordance with the Bible and they see it as a war."

It is pretty much only in America that one can find people such as the "young-Earth creationist" Ken Ham. The president of Answers in Genesis, which defines itself as "an apologetics (that is, Christianity-defending) ministry", Ham is also the driving force behind the Creation Museum in Kentucky. Powerful and well-funded groups such as the Discovery Institute, keen to express their "scientific dissent from Darwinism", together with a media appetite for "alternative viewpoints" and intellectual fisticuffs, mean that Americans often assume that relations between science and religion are always highly conflicted.

Many, notes Giberson, are left with "the impression that there is a religious objection to every scientific advance. Yet the most aggressive critics of the Creation Museum are more moderate Christians, not militant atheists. They believe young-Earth creationists have to be rejected, for turning Christians into anti-intellectual hillbillies."

Despite all the provocation from Christian extremists, however, Giberson believes that the scientific response has often been unhelpful. He has recently published a book, co-written with the late Mariano Artigas, called Oracles of Science: Celebrity Scientists versus God and Religion. This examines the work of six authors who have been acclaimed for making cutting-edge science accessible to a broad audience: Richard Dawkins, Stephen Jay Gould, Stephen Hawking, Carl Sagan, Steven Weinberg and Edward O. Wilson. All are, or were, at least agnostics verging on atheism. And all chose to write passages or chapters - and, in Dawkins' case, a full-length book - setting out their largely unflattering views on God and the godly.

Given that they have thereby ventured well beyond their central areas of scholarly expertise, Giberson disputes the accuracy of many of their claims.

"Weinberg sees only the negative side of religion," he suggests, "not so much in terms of wrong ideas but as a consistent force for evil. Religious people can't help wondering where he gets that impression. We all know fellow believers who help people out or serve in soup kitchens. That obviously has to be balanced against the real harm that religion can do, but it's so implausible as to be ridiculous to believe that religion does only harm, even though Weinberg is a physicist who knows the importance of evidence.

"Reading the work of the 'celebrity scientists', one never has the sense that they know, at a close personal level, a significant number of religious people who are not terrorists, not opposed to gay marriage, not trying to get evolution out of public schools - although there are plenty of us out there."

This leads to a more important point. Passing remarks such as Weinberg's claim that "the more the universe seems comprehensible, the more it also seems pointless" are widely quoted and, claims Giberson, "lead the religious to believe that scientists are all atheists, which increases their uneasiness about science.

"So you get a situation where both sides stereotype the other. Scientists end up thinking that all Christians believe in a young-Earth creation, while the religious assume that any scientist at a famous university must be an atheist and hostile to religion. Neither is at all accurate.

"There is no truth in the idea that being a scientist means being a crusader for atheism, and even many atheist and agnostic scientists are opposed to Richard Dawkins for making their life more difficult," Giberson adds.

Particularly in a society as religious as the US, scientists who are keen to reach out and share their work risk alienating their audience if they are openly contemptuous of religion. And, despite his trenchant views on religion, Weinberg shared his 1979 Nobel Prize in Physics with Abdus Salam, a devout Muslim who quoted the Koran during his acceptance speech.

There is a simple, predictable view of an inevitable clash," agrees Thomas Dixon, senior lecturer in history at Queen Mary, University of London, and the author of Science and Religion: A Very Short Introduction.

"For some reason, the public and the media like science stories to be about God: the God equation, the God gene, the God particle or the God spot. When Stephen Hawking published a book of unbelievably obscure physics earlier this month (The Grand Design, written with Leonard Mlodinow), his suggestion that it is 'not necessary to invoke God to light the blue touchpaper and set the universe going' led to a discussion on (BBC Radio 4's) Today programme, with representatives of religions queueing up to dispute his claims. The Punch and Judy conflict story seems much easier to process than anything more complex."

Theologians and religiously committed scientists regret that the debates are so heated, so polarised - and so predictable.

Gerard Loughlin, professor of theology and religion at Durham University, believes "the new atheists are resistant to learning about the things they disparage - in, for example, their reading of Genesis, which they take to be an obviously false account of the world's formation. There are of course many Christian fundamentalists who read it in a similar way, only they believe it to be true.

"Both ways of reading Genesis are mirror images of one another, and both are modern reductions of the text to a single meaning (held to be false by one group and true by the other). But earlier Christian thinkers, including some of the most powerful and influential, such as St Augustine, held the Bible to have many levels of meaning, and that the allegorical meanings were often the more important," Loughlin says.

Simon Oliver, associate professor of theology and religious studies at the University of Nottingham, is in no doubt that "science gives us startling accounts of the workings of the universe and gives us enormous power to predict and manipulate nature towards ends that are good and bad. But when science is treated as 'metaphysical' - that is, an account of the way things are that is beyond the physical - then serious questions begin to emerge.

"For example, Dawkins takes an account of the physical process of genetic reproduction or the spread of viruses and turns this into a 'metaphysical' account that explains something like religion. But isn't this a huge category mistake, which reflects a kind of fundamentalist approach to evolutionary biology - that is, the view that it can explain not only biology, but everything, because in the end everything can be reduced to biology?"

If we require an example of what Oliver calls "scientism" and "vulgar materialism - a sense that the only questions worth asking are those that concern material reality" - we could cite other comments by Peter Atkins. Religion, he has written, is "armchair speculation well fitted to adipose brains", which relies on an "inwardly directed sentimental glow". Science, on the other hand, "can lead to an understanding of the entire physical world" - which, he goes on to argue, amounts to "the entire world".

But what about the aspects of life, such as "love and aesthetic appreciation", which many people find important? Atkins will "grant that these qualities, or at least their physiological appurtenances, exist". But is it really the job of chemists to pronounce on whether love exists, or any wonder that such "scientism" alienates many readers?

Harrison has a number of theories about "why there is still a widespread belief in the notion that science and religion are necessarily locked in a to-the-death struggle".

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"One is the seductive but mistaken idea", he suggests, "that religion is primarily to do with offering explanatory hypotheses about the universe. On this view, religion and science will necessarily come into conflict because they compete for the same explanatory territory.

"Related to this is a belief in progress that sees religion as a kind of primitive science, destined in time to be replaced. A further point is the polarisation of 'reason' and 'faith', which sees science as the omni-competent embodiment of reason that is capable of answering all legitimate questions. The assumption is that reason plays no role in religious belief, and that faith is a stubborn refusal to take cognisance of the relevant facts.

"All this is underpinned by a mythology about the past in which events such as the Galileo affair (when he was sentenced to imprisonment, later commuted to house arrest, by the Inquisition in 1633 for correctly arguing that the Earth revolves around the Sun) are taken to exemplify some general historical principle about science and religion. This mythology is very difficult to dislodge because it confirms a position that has already been adopted."

David Wilkinson, principal of St John's College at Durham University, is the kind of person whose very existence seems to baffle and offend Richard Dawkins, Peter Atkins and their like: a scientist, with a background in theoretical astrophysics, who has become a theologian and a Methodist minister.

"I became a Christian at the age of 17," he recalls, "at the same time as I began to study physics at Durham, so my faith and science have grown up together. Any doubts I have had don't come from the laboratory but from age-old philosophical challenges such as the prevalence of evil and suffering in the world, to which I don't have any easy answers. Science has enriched my faith and theology far more than it has raised difficult questions.

"There is an unhelpful model of the inevitable conflict between science and religion that comes out of 19th-century debates and particularly the interventions of (Darwin's most pugnacious advocate) Thomas Huxley, yet the history is really much more complex and fruitful for both sides. The legacy of the post-Darwinian controversies is still working its way out within Western cultures.

"The conflict hypothesis is simple and can be entertainingly argued, so it works much better on television and in the popular media than people trying to hammer out areas of agreement. But it doesn't reflect my experience. I have worked with Hindu scientists in India, with Muslim scientists, and with scientists who are very open to the faith of others even if they don't have faith themselves."

The situation on today's campuses, with students from many different backgrounds and a huge spectrum of religious and irreligious convictions, poses a number of concrete problems for administrators. But all-out wars between neighbours tend to be pretty unpleasant, and the reality is that atheistic scientists have to share space within universities with scientifically literate religious believers and religiously committed scientists.

Although they may find plenty to disagree about or find each other's beliefs stupid or ridiculous, can it really help to see them as being at each other's throats? Might it not be time, rather, to declare peace and break open the champagne?

MORE LIGHT, LESS HEAT: Institutions look to strengthen lines of communication about religious issues on campus

When most British vice-chancellors entered the academy, there was a widespread assumption of secularisation. To put it bluntly, religion was thought to be on the way out.

But this notion was never very plausible beyond Europe and now seems hopelessly inadequate. Like it or not, universities and their leaders must engage with the many issues raised by the broad spectrum of religious belief (and disbelief) on most campuses.

What will it mean, for example, when the parts of June and July normally used for exams or re-sits coincide with Ramadan from 2013 to 2016? How far do legitimate security concerns, robust debate about the political situation in Israel-Palestine, or even freshers' week events involving alcohol, create an uncomfortable environment for certain students?

There are many possible responses to these challenges, says Adam Dinham, director of the Faiths and Civil Society Unit at Goldsmiths, University of London. However, they are often vitiated by "the lamentable quality of the conversation" about religion in much of the academy. "We are much worse at talking about religion", he suggests, "because we thought we'd done away with it."

Dinham is also the programme director of Religious Literacy Leadership in ºÚÁϳԹÏÍø, an organisation funded by the ºÚÁϳԹÏÍø Funding Council for England that offers research, resources and training to bridge this intellectual gap. The organisation held an event in London this month that brought together 25 of Britain's vice-chancellors. Another in York assembled about the same number of senior managers, chaplains and deans and experts on diversity.

Religious issues have gone up the agenda in the academy largely because of concerns about equality legislation, questions of diversity and social mobility, and the increasing sense that there is a need to enhance the student experience.

The events, explains Dinham, were not designed "to produce expert theologians or more religion but to set the tone for a conversation that can generate more light than heat".

"Universities can take any position they want on religious literacy issues," he elaborates, "provided they do so from an informed perspective. Some try to be neutral towards religion, while one vice-chancellor expressly described his institution as 'secular and therefore needing to defend that'. You can just respond to what the law demands, or you can look to the underlying questions of social justice and human rights embodied in the law."

Religious diversity can be seen as a time-consuming irritant, as enriching the student experience or even (particularly in universities that themselves have religious foundations) as part of a spiritual, "whole-person" philosophy of education.

So how do these broad themes play out on the ground in the universities where the delegates to the York workshop are employed?

One reported "a lack of clear leadership on the issue", with "no references to religion in our strategic plans". Another regretted that any initiatives in the area seemed to be "bolted on, (to be) things we have to do" because of legal requirements rather than part of a carefully thought-out policy. A third worried about "conversations being stifled by people not wanting to say or do the wrong thing".

A chaplain mentioned a successful campaign to prevent his university officially describing itself as a secular institution. (Those institutions that do have a proud tradition of secularism have been known to resort to ruses such as refusing to use the phrase "prayer room" even when a room is specifically set aside for prayers.)

The activities of religious societies can lead to tensions, not least within their own faith groups. The Roman Catholic chaplain at one institution reportedly felt harassed by the Christian Union. Such unions also sometimes came into conflict with the main students' union, if, for example, they rely on prayer rather than voting to determine their leadership.

There seemed to be general agreement that religious societies should be allowed to "set out their stalls but not buttonhole students" on campus.

Questions were raised, however, about why it was permissible to "proselytise" about ecology or human rights and not about religion. And it was also asked whether there wasn't a danger of overprotecting students, given that many will have faced (and presumably survived) people trying to convert them by accosting them in the street or by knocking on their doors at home.

The Religious Literacy Leadership programme has compiled a set of case studies that formed the basis for small-group discussions at York. One concerned a medical degree that required students to attend classes in a local hospital on Saturdays, making it impossible for Orthodox Jews to graduate.

Delegates suggested that the university should enter into discussions both with the hospital and with Jewish groups to see whether there was any possibility of compromise. If not, it was only fair to inform applicants to the course clearly and up-front what would be required of them and why.

Such frankness could be helpful even in relation to the difficult dilemmas surrounding security. It was right to tell students in advance, for example, if a threat of terrorism was believed to justify breaches of confidentiality such as the disclosure of membership lists.

According to participants at the York event, some universities had come under strong pressure to monitor Friday prayers, and one had banned outsiders from attending events organised by religious societies.

In a case in which perpetrators of a terrorist attack did have links to a particular university, the institution had yielded to pressure from Special Branch to reveal the names of the members of the Islamic Society. Although this certainly led to acrimony, reported one of the women involved, "there was no breakdown in communications - they came in and yelled at us every day!"

She also stressed the importance of reassuring Muslim parents that their children were unlikely to be led into extremism when attending the institution, and emphasised the importance of the press office in helping student societies and unions deal with enquiries from journalists.

Despite the many difficulties, one delegate applauded the goals of religious literacy initiatives that would "help outsiders understand the lived experience of religion, and believers understand their own traditions beyond their inherited practices" - and help both, ideally, to thrash out issues of the common good.

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Universities are wrong, in Dinham's view, to "regard themselves as 'post-religious', which is taken to mean secular and therefore neutral. We want society more generally to think more about religion as something happening within it. Universities are well placed to lead that wider conversation."