I asked a much-acclaimed headteacher the other day about the secret of his success. Consistency, he said. Schools did best when they had consistent approaches to behaviour, teaching and learning. People thought consistency was dull; in fact, it was exciting, even sexy.

We did not then go on to discuss whether creationism and intelligent design should be taught alongside evolution in school science lessons. But it later struck me that to continue as we are - teaching one version of the world in one classroom and a quite different version across the corridor - is hardly consistent. That is why I have some sympathy with Professor Michael Reiss, the Church of England minister who has stepped down as director of education at the Royal Society after arguing "there is much to be said for allowing students to raise any doubts they have [about evolution]" in science lesson.

I am an atheist, though not quite a practising one. By that, I mean I sometimes attend church services, albeit only for aesthetic and cultural reasons. I have no problem with marking births, marriages and deaths in Christian services, because the churches have developed effective, time-honoured rituals for these milestones. I think children should read the King James Bible because it is one of the glories of our language and its influence on English prose style is comparable to that of Mozart on European music. But I do not like faith schools or the teaching of religion in schools as a discrete subject. To me, intelligent design is an attempt to reintroduce creationism in a more plausible form, having got round the manifest falsehood that the world began in 4004BC. It is a theory, but it happens to be wrong, while Darwin's theory of natural selection, overwhelmingly supported by evidence, is right.

Christians - at least C of E members - may agree. The Church's website assures us there is nothing in natural selection that "contradicts Christian teaching". I beg to differ: Christianity demands a rational being capable of moral choices. It can accept that such a being may take time to evolve and share ancestry with chimpanzees. It can even accept that the being might not take a human form, though I'm not sure what that does to the stuff about "made in the image of God". But unless something like us comes along eventually, and unless things are designed for us to emerge, the doctrine of redemption is meaningless. Anyone who understands natural selection knows there was nothing inevitable about the arrival of Homo sapiens, and we should not imagine evolution was always striving to this end. All organisms face extinction if they fail to adapt to environmental changes. It will almost certainly happen to us, perhaps quite soon.

The C of E says it objects only to social Darwinism, which "elevates selfishness into a virtue". Our social relationships and moral choices are not dictated by our genes, it insists. This, to my mind, is true, but a cop-out. The difficulty with mainstream evolutionary theory for Christians is not that it denies that humans are free moral agents, but that it denies such agents are a necessary outcome. It leaves them with a God who, after setting a universe in motion, sits twiddling his thumbs for aeons on the off-chance that beings capable of sin and of appreciating his works come along. This insouciant God is as implausible as the hyperactive God of Genesis.

Physics presents no comparable difficulty. On the contrary, because the laws of physics favour the development of matter, suns, planets and, ultimately, life, a supreme being calibrating the controls fits quite nicely. That is why religious folk never try to interfere with physics lessons.

So what should schools do? Keeping religion and biology separate, as though one has no bearing on the other, is intellectually incoherent. Brighter pupils will detect the inconsistency.

My answer is to take religion out of RE lessons (or whatever they are now called) and integrate it with other subjects. It is impossible to understand history, music, art, architecture and literature without understanding the role of religion. The same applies to science, which proceeded for centuries within an intellectual framework based on faith. Children should learn how Darwin developed his theory, how it was later tested and elaborated, how and why the Victorian churches opposed it, the spiritual anguish of many Victorians, and how some people, in defiance of evidence, have recently invented intelligent design to rescue a lost cause.

If that is what Michael Reiss wants, I support him. Pupils will have to learn that the theory of natural selection conflicts with one aspect of religious doctrine. But that is a problem for Reiss and his Church, not for educators.