When Michael Reiss lost his job as education director at the Royal Society last September, a number of specific allegations were made. He has undoubtedly argued that teachers should be prepared to discuss creationism in science classes, just as they can address pupils' concerns about the paranormal, although even The Guardian backtracked from the implications of its original headline: "Teach creationism, says top scientist."

But equally striking was the tone of the campaign against him, with its suggestion that, as a scientist who had been ordained as a priest, he was simply by definition not the right person for the job.

Nobel laureates Sir Harry Kroto, Sir Richard Roberts and Sir John Sulston sent a letter to the president of the Royal Society saying: "We gather Professor Reiss is a clergyman, which in itself is very worrisome." And Richard Dawkins commented: "A clergyman in charge of education for the country's leading scientific organisation - it's a Monty Python sketch."

In the words of journalist Paul Vallely, do we all need to start looking for "Revs under the bed"? Was Reiss a victim of a mindset that decrees that, despite many examples since the days of Isaac Newton of scientists with religious faith, anyone who is for science must also be against religion?

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Reiss has taught biology in schools and to undergraduates, including six years at ³ÉÈËVRÊÓƵrton College, Cambridge, where he was senior lecturer in biology and then reader in education and bioethics. In his late twenties, he embarked on non-residential training for Anglican ordination.

Now returned to a full-time post as professor of science education at the Institute of Education, University of London, he refuses to discuss the details of what happened at the Royal Society. But he has plenty to say about creationism and the wider relations between religion and science.

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For the record, Reiss believes that literal creationism is "completely mistaken". As someone who studied evolutionary biology and population genetics up to postdoctoral level, he was "utterly reared and continue[s] to live within the framework which sees the evolutionary view as incomparably the best way of understanding the diversity of life and indeed what it to be human".

Nor does he have any time for intelligent design, the notion that the "irreducible complexity" of entities such as the bacterial flagellum points to the existence of a designer.

"The chance that someone will be able to demonstrate that certain features of life today could not have evolved through Darwinian and other evolutionary processes is, in my view, completely negligible," he says.

All this seems pretty clear. If there is a God, he moves, as it were, in Darwinian ways. Creationism is fundamentally mistaken and, whatever a researcher's personal religious views, they can and should be kept out of the laboratory, since certain questions can be usefully addressed only by using standard scientific methods.

So would Reiss want to claim that science and religion essentially operate in separate spheres and that, provided he was fulfilling the terms of his contract at the Royal Society, his private faith was simply no business of Dawkins, Kroto and fellow Nobellists?

This is not the way he sees it. He doesn't view science and religion as independent but as "pretty integrated", because "I have quite a conventional Christian faith that behind and within the observable world there is a God.

"Let me give you a concrete example. Suppose that you and I become great friends as a result of this interview and see each other socially, and then you get knocked down and badly injured in a car crash. My instinctive reaction would be both to pray for you and to hope you got absolutely the best conventional medical attention. I don't sit around asking: is prayer for someone to get better a worse or better idea than medical treatment? They go hand in hand. Part of the way God chooses to act in the world is through doctors and nurses and paramedics and so on."

In relation to sex education, a field in which Reiss edits a journal, he declares himself "broadly happy to say that some of my views are informed by my religious faith".

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For those who assume clerics are likely to be puritanical and illiberal, this may sound ominous. Yet Reiss argued last year in ³ÉÈËVRÊÓƵ that, although "sexual relationships between students and staff are not just a possibility (but) a frequent occurrence", there is no case for a universal ban.

"When I thought about sexuality a good deal about 20 years ago," he adds today, "I came to the conclusion that being gay or lesbian was absolutely as acceptable as being heterosexual."

So was he led to such views by looking at the Scriptures as well as, say, the Kinsey reports? "Yes, and I'm glad to say I've got both somewhere up there on my shelves."

In this area, furthermore, Reiss has a firm belief in dialogue as a means of overcoming inevitable differences of opinion.

"One of the interesting things about sex education is coming up with school policies and practices that work when you have a diversity of pupils. If you can manage to organise to get parents together, you find such high levels of agreement that most people end up leaving incredibly relieved and far more encouraged than before they met."

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So Reiss is a believer in a pragmatism and mutual respect based on his first-hand educational experience. But what happens when creationists turn up in classrooms or, even stranger, in lecture halls, where one might expect students of geology or biology to have implicitly signed up to learn about evolution?

"Having a religious faith strengthens the quality of what I can write or discuss in this area," declares Reiss. "It's an advantage, because I think I can empathise with some of the creationists' fears about evolutionary thinking, even though I've never been a creationist - and I can empathise with the worries of atheistic scientists if creationism became more prominent, both because I'm a scientist and because I was an agnostic/atheist until I was an undergraduate."

This in no way implies a retreat from the duty to teach the basics of evolutionary theory. "I believe that everybody, by the time they are 16, should have been taught some evolution, as it's such a core part of science. It's there on the syllabus - I'd like more of it there - but evolution and the history of the origin of the universe is such a crucial way of understanding ourselves that I believe you should do it before the age of 16, whether or not you go on to higher education."

Yet Reiss feels this can and should be combined with respect for religious convictions and for the comfort some pupils get from ritual, prayer and worship - and their fear science may deprive them of such things.

"Some atheists and agnostics don't understand that under much fundamentalist religious belief is a deep, deep fear about what would happen to individuals and the world if religion were no longer held to be true - a fear of moral collapse, a fear that there is nothing in the world to come, a fear that humans will be revealed to be mere beasts."

For some pupils, Reiss has written, "scientific ideas are incongruent enough to pose cognitive challenges that teachers need to help (them) negotiate". Creationism and intelligent design "should be handled in a way that is respectful of students' views, religious or otherwise, while clearly giving the message that the theory of evolution and the notion of an old Earth/Universe are supported by a mass of evidence and fully accepted by the scientific community".

This is obviously a delicate path to tread, but Reiss believes it is the best means of "promoting cultural tolerance and individual autonomy" while "ensuring that students at the very least learn what evolution is".

"One of the sad things is when science attacks people's religious beliefs," he adds, "which I think is a bit pointless and not really the job of science."

Might this be taken as a criticism of Richard Dawkins, who was so gratuitously rude about Reiss and used his position as the University of Oxford's first Charles Simonyi professor of the public understanding of science to launch a ferocious attack on all religious belief in The God Delusion (2006)? Reiss is far too diplomatic to be drawn on this question and says only that, despite their differences of opinion, he hugely admires Dawkins' books such as The Extended Phenotype (1982) and is fully committed to academic freedom of expression.

And where does religious education fit in? "It is very appropriate for RE teachers", says Reiss, "to want to get pupils to understand a bit about the various world Scriptures."

This can lead to a danger of proselytising, but the guidance on creationism and intelligent design issued in 2007 by the Department for Children, Schools and Families, which Reiss helped put together for the Qualifications and Curriculum Authority, should guard against this. It pulls few punches ("Creationism and intelligent design are sometimes claimed to be scientific theories. This is not the case ...") and has been broadly welcomed by atheists as well as others.

Yet the unsurprising limitations of many RE teachers is one of the things that leads Reiss to believe that creationism shouldn't be a total no-go area in science classes.

"Because they (RE teachers) usually have a good understanding of theology," he argues, "they are immediately able to make students understand that the Scriptures are read in a range of different ways by different people. They are less good at knowing the science. That's why it can be appropriate to discuss the issues pupils raise about creationism in a science lesson, by looking at the scientific evidence about the history of the world." This clearly doesn't imply "teaching creationism".

Compared with the issues creationism raises in schools, universities are in a much easier position and can pursue a much stronger line.

"Steve Jones (head of the biology department at University College London) is right," says Reiss. "Creationism is becoming more and more of an issue in universities. If you do go on to higher education to study geology or cosmology, you have to an extent signed up - and that gives lecturers a bit more freedom to assume you're going to take seriously the standard working assumptions within the discipline. But lecturers have a duty, which they often enjoy, to passionately argue about the evidence for those assumptions. On a scientific course, students have to respond in scientific terms - it's not enough for them to quote things like the way they understand Scripture.

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"I've got much more sympathy with being impatient with a group of 19-year-olds in HE than a group of 14-year-olds. That's simply because, by the time you are 19, you are more robust, and less likely to be traumatised by having an intelligent adult argue with you."