“A clergyman in charge of education for the country’s leading scientific organisation – it’s a Monty Python sketch,” pronounced Britain’s top atheist, Richard Dawkins, recently. How the world turns. In the days of Galileo it was the church which went around persecuting scientists. Now the boot appears to be on the scientific foot. That is how it must feel, at any rate, to Professor Michael Reiss who last month was hounded out of his job as the Royal Society’s director of education by a group of Nobel Prize winners who were outraged not by what he said but by what people might think he had said.

The problem was that Reiss, as well as being an evolutionary biologist and population geneticist, is a non-stipendiary priest in the Church of England. When he said recently that science teachers should answer questions about creationism if pupils asked them he was deemed to have been advocating the idea that British schools should teach the idea that the world was magicked up (complete with fossils and ancient geology) just 6,000 years ago – and then tell pupils to make their own minds up between that and the theory of evolution to which the overwhelming scientific evidence points.

The hapless Reiss made it clear that he insists creationism is scientific nonsense. But a handful of the Royal Society's most eminent members began a campaign to have him sacked. Sir Harry Kroto, Sir Richard Roberts and Sir John Sulston said in a letter to the president of the Royal Society: "We gather Professor Reiss is a clergyman, which in itself is very worrisome." We must all now be on the look-out, it now seems for Revs under the beds.

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The idea that science and religion are incompatible is a fairly recent import into contemporary culture. It has been given huge credence by the 9/11 terrorist attacks on the United States. The pronounced motivation of Islamic fundamentalists in 2001 hammered home that some people are prepared to inflict outrageous acts of inhumanity in the name of religion.

Yet the roots of the shift in attitude go back much further. "It came about because of a perfect storm – a wide range of factors came together," says the atheist philosopher Julian Baggini. Among them were a shift from liberal to evangelical Christianity in Britain, the rise of creationism in America, advances in scientific techniques in biology and changes in public perception on issues as disparate as homosexuality and assisted dying.

But we are leaping ahead here. The relationship between science and religion has had a long and chequered history since the settled days of the medieval consensus, which saw faith and the natural sciences as part of a cosmic whole. Galileo put paid to that with his insistence that the earth revolved around the sun. The Catholic Church, which saw man and his planet at the centre of the universe – and which already felt its authority threatened by the rise of Protestantism – locked horns with him. The clash became a metaphor for the irreconcilability of scientific materialism and biblical literalism.

Things changed with Isaac Newton. His laws of physics led to a world view which relegated God to background status as the designer of a clockwork world which he wound up and then left to its own devices. Newton's celestial mechanics brought an advance in our scientific understanding but didn't really work for a faith that wanted to believe that, through the historical Jesus, God had become, in the words of the song "a slob like one of us".

Next came Darwin. At first many saw his theory of evolution as a threat to religion but mainstream Christianity soon accepted evolution as the answer to the "how" of creation, leaving the "why" questions of meaning and morality to faith. Science and religion exercised authority over two discrete compartments of life between which there could be no link.

But through the latter half of the 20th century a synergy developed. In cosmology the science of the expanding universe and the Big Bang chimed in with a moment of creation. The inherent uncertainty that quantum physics discovered at the subatomic level overturned Newton's mechanics and created room for a "God of the gaps". Process theology embraced evolution and said men and women are called to play a part in an ever-ongoing creation. Advances in neuro-science showed that mental and spiritual phenomena depend upon biological processes, undermining the old dualist notions about body and soul and offering a more holistic body-mind-spirit axis.

"Attacks on religion, when I was a student in the Sixties, were largely on political grounds," says Dr Denis Alexander, the Director of the Faraday Institute for Science and Religion in Cambridge. "It was seen to be on the side of capitalism and the rich." In Anglo-American philosophy, says Baggini, "religion was seen as wrong but as something that didn't really matter much. The world was going secular and eventually it would just die out."

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But the rise of Christian fundamentalism in America in the past few decades – the word fundamentalist in its religious sense was added to the Oxford English Dictionary in only 1989 – was mirrored in a milder way in Britain too. Liberal Christianity, so long in the ascendant in the Church of England, began to lose ground to evangelicalism. "Non-literal Christianity failed," says Baggini, "because it doesn't capture the popular imagination. The certainties of evangelical Christianity appeal more to those for whom the attractions of religion are on a more visceral level." This appeal was symbolised through the 1990s by the Alpha course on the basics of the Christian faith devised in London by a curate at Holy Trinity, Brompton, which has since been used by more than 10 million people in 160 countries. The idea that the miracles of the New Testament may have been metaphors rather than literal truths suddenly went out of fashion in Christian circles.

Throughout this time scientists such as Richard Dawkins had evidenced a disdain for such simple certainties. In his 1976 book The Selfish Gene there were a few side-swipes at religion and in 1986 in The Blind Watchmaker he conducted a sustained critique of the 18th-century deist argument that the world is too complicated to have sprung into existence by accident so a rational observer should conclude that it must have been designed, just as someone finding a watch would conclude that somewhere there must be a watchmaker who made it. And by 1991, in response to the question of why evolution had allowed religion to thrive, he had coined the notion that religion was a virus.

But it was the terrorist attacks in 2001 that turned Dawkins into an Alpha atheist and transformed him from an academic backwater into a populist ideologue. Before 9/11, he said, religion may have appeared a "harmless nonsense". But the attacks in New York showed it to be a "lethally dangerous nonsense". Previously, he said, "we all bought into a weird respect, which uniquely protects religion from normal criticism. Let's now stop being so damned respectful!" The gloves were off.

But another prominent atheist, medic and secularist, the Liberal Democrat MP, Dr Evan Harris, is not so sure that 9/11 was the nodal point. "It's not the main thing to scientists," he insists. "When you talk to them the thing that comes up most often is the influence religion has had on science in America under George Bush." Religious pressures there have had direct impacts on a wide range of policy – from a ban on public money being put into stem cell research to a refusal to allow US aid programmes to hand out condoms to fight Aids in Africa. "Scientists who are publicly funded can't go to conferences and speak without being obliged to stick to the Bush line," says Harris.

Advances in bio-technology have opened up new areas for disagreement. Test tube babies, embryo selection, saviour siblings, stem cell research and animal-human cybrids have all created new battlegrounds between those who think that an embryo is a person from the moment of conception to those who think it is merely a cluster of cells before implantation or even birth – and all variety of opinions in between.

"There is a definite danger of our desire for research outstripping our capacity to anticipate the ethical implications of those advances," says the feminist theologian, Tina Beattie, whose book The New Atheists argues that Dawkins & Co misuse Darwin and evolutionary biology as much as the Christian fundamentalists misuse the Bible. "Some scientists experience religion as merely an irritating brake on their striving to do new things." The public, after a list of scientific disasters from thalidomide and nuclear weapons to BSE and the stealing of dead children's organs at Alder Hey, are much more suspicious, judging that "scientists have problems policing their borders".

From a very different perspective Andrew Copson, the director of education for the British Humanist Association, agrees. "Scientists are fearful so the issue has become very emotive," he says. "They fear that, behind what people like Michael Reiss say, there lies a Trojan horse." It is perhaps significant here that the two main instigators of the campaign to have Reiss ousted from his Royal Society job, Sir Harry Kroto and Sir Richard Roberts, are now based in the United States where creationism is a major phenomenon. Polls suggest that around 45 per cent of Americans are creationists with 40 per cent believing that God worked through evolution and just 10 per cent saying it was nothing to do with a God.

The experience of being a secularist in the US is clearly a radicalising one. "I don't know if it is too late to stop the slide in Britain but I think it is in the US where [the religious right] have now almost complete control over politics, the judiciary, education, business, journalism and television," Kroto, who won the Nobel Prize for Chemistry in 1996, has said, adding darkly: "The Royal Society does not appreciate the true nature of the forces arrayed against it."

The position in the UK is nothing like that, though the statistics are unclear. A 2006 BBC poll claimed that 48 per cent of the British public accepted evolution with 22 per cent preferring creationism but the definitions it used were so sloppy as to be almost meaningless. A survey of schoolchildren has suggested that more than 10 per cent now believe in creationism. But the Evangelical Alliance, whose members now number around 3 per cent of the UK population, reckons that only a third of its members – about 1 per cent of the population – are creationists. About a third think Genesis is merely symbolic, and a third believe that God worked through evolution but is still capable of intervening in specific ways. Its most recent, unpublished, survey shows that the proportion seeing the Genesis account as symbolic is increasing, the EA's Head of Theology, Dr Justin Thacker, says.

Evan Harris accepts that the number of British schools teaching creationism is tiny. But, as an MP, he is worried about the increasing activity of religious lobby groups in public life. "Groups like the Evangelical Alliance, the Christian Institute and Christian Action Research and Education are now all much more organised and active in seeking to change public policy. They are making the running in parliament, much more than the leadership of the Catholic Church. The Church of England's bishops are much more evangelical too; their centre of gravity has changed form the days when liberals ruled the roost. And the C of E has been much more active in Parliament."

All this is having a real impact, Dr Harris suggests. "In the days of Thatcher all the mainstream Tories voted in favour of embryo research. Twenty years on most of the new suave modernising Cameroonian Tories vote against it." Academics detect a similar shift. Professor Steve Jones, of University College London, who has been teaching genetics and evolutionary biology for 30 years, has said that religious students – even those studying medicine – are becoming increasingly vocal in their opposition to evolution, demanding to be exempted from classes and exam questions on the subject.

Creationism, like Coca-Cola, came here from the United States. The American lobby group Answers in Genesis, with its $13m annual budget, now has an office in the UK from where staff go round giving illustrated talks about how humans and dinosaurs roamed the earth together. Another conservative group, Truth in Science, has adopted a strategy of lobbying for schools to "Teach the Controversy" in an attempt to get Intelligent Design, a spin-off of creationism, taught alongside evolution in school science lessons. In 2006 it sent resource packs to the heads of science of all British secondary schools; New Scientist claims that 59 schools have used, or plan to use, them.

The fear generated by such tactics is what did for Michael Reiss. "Even if he doesn't support all this, what he said might be seen to give succour to it," says Andrew Copson of the British Humanist Association. "I can understand why alarm bells go off with people who are familiar with 'Teach the controversy' tactics of people who want to baby-step creationism into our science classrooms."

All of this mystifies the vast majority of the nation's Christians who have been taught since the time of St Augustine, who died AD430, that where there appears to be a conflict between demonstrated knowledge and a literal reading of the bible then the scriptures should be interpreted metaphorically. They see no conflict between faith and reason because, as Pope John Paul II put it: "God created man as rational and free, thereby placing himself under man's judgement." Just last month the present Pope reiterated the same line, warning of the dangers of fundamentalist readings of the Bible. Each generation, he said, needs to find its collective interpretation of the text. For this task of interpretation – which can never be never completely finished – science offers a major tool.

It all perplexes academics who specialise in the interplay between science and religion too. Creationism doesn't just involve many scientific errors, it relies on a major theological one too. "When Robert Burns tell us his love 'is like a red, red rose', we know that we are not meant to think that his girlfriend has green leaves and prickles," says the particle physicist and Anglican priest, Sir John Polkinghorne. Why, he wonders, would any rational person want to read the Bible in that way?

The world of science he encounters is a much more subtle one. "There's a cosmic religiosity among physicists," he insists, though "biologists see more ambiguity, perhaps because they look at the wastefulness of nature, and perhaps because sequencing the human genome has made them triumphalist." It is more complex even than that: the head of the Human Genome Project, Dr Francis Collins, last year published a book about his journey from atheism into faith arguing that science and religion, far from being irreconcilable, are in fact in deep harmony.

In the past 30 years an area of inter-disciplinary activity has opened up to explore this. Areas of research include cognitive neuro-sciences and issues like freewill and consciousness and whether human minds are merely matter or something more. In evolutionary psychology they have also explored together questions like the origins of altruism – asking whether evolutionary biology can give an adequate account of why people are willing to sacrifice themselves on behalf of others. In paleobiology they are asking questions like how eyes evolve in different lineages – suggesting that evolution isn't a random or chance process but is channelled by certain chemically-determined pathways. In cosmology there is a universe versus multiverses debate.

"All that going on, but all the public knows about is Dawkins," says Dr Denis Alexander of the Faraday Institute in Cambridge. "Academic discussion on the relationship between science and religion is genuinely exploratory, not polarised. To most people in it Dawkins just sounds rather odd."

John Hedley Brooke, who recently retired as the first Professor of Science and Religion at the University of Oxford, is more sanguine. "These eruptions take place from time to time historically," he shrugs. "Dawkins is just a throwback to 19th-century rationalism. He has a strong emotional antagonism that is very indiscriminate and treats all kinds of religion the same. A lot of fine distinctions that get lost in the polemics. The problem is that it is all a cumulative process in which the extremes feed off one another."

"Paradoxically, Dawkins is the biggest recruiter for creationism in this country," says Denis Alexander. Recently, he says, Bill Demcksi, a leading US creationist, e-mailed Dawkins to thank him for his assistance. "The danger is that all this polarisation will make some believers more anti-science which is not a clever move tactically." He hopes that whoever succeeds Dawkins as Oxford's Professor of the Public Understanding of Science is more interested in promoting science than in attacking religion.

On the other side of the argument Evan Harris is unapologetic about contributing to what Julian Baggini waggishly calls this "assertiveness inflation". "It's good that there's this tension," the MP says. "These debates need to be had in public. Science has nothing to fear from them. I don't think we're winning; we've won a few battles; but there's a war to be fought." He concedes that Michael Reiss may have been sacked unfairly – saying that the "overstrong line" taken by Kroto and Co should not be taken as representative of all on the secular side – but points out that employment injustices are perpetrated every time a church school refuses to appoint a maths teacher because she doesn't "have Jesus in her heart".

The danger is that between the strident secularists and the fanatical fundamentalists some important middle ground is being squeezed out. "Dawkins sees religion as credulous, superstitious and prejudiced but mature religious traditions teach people to challenge all that," says Tina Beattie. "Science will never offer an answer to the parents of Madeleine McCann. Nor will it ever be irrational to go to a Mozart concert, though science can never explain the genius of his music. The new atheism completely misunderstands the way that human beings experience the poetry and narrative of life."

Perhaps the conflict is not between science and religion but between good and bad ways of doing both. In all of us there will always be a struggle between the craving for certainty, purity and closure and the acceptance of mystery, brokenness and provisionality. At their best, both scientists and people of faith are in a permanent state of awe-struck humility before the wonder and strangeness and messiness of things. At their worst, they are arrogant, dogmatic, and incurious. There's a bit of both in all of us, of course.