When I was a medical student at Cambridge in the Sixties, I walked to lectures past the forbidding exterior of the Cavendish Laboratory, as famous for Crick and Watson's unravelling of DNA as for Rutherford's splitting of the atom. One day, scrawled on the wall, was a supreme example of Cambridge graffiti: "CRICK FOR GOD".

No surprise that pivotal advances in science provoke religious metaphors. Crick and Watson's discovery transformed our view of life itself - from a manifestation of spiritual magic to a chemical process. One more territorial gain in the metaphysical chess match between science and religion.

Charles Darwin's theory of evolution was certainly a vital move in that chess game - if not checkmate. In an interview for God and the Scientists, to be broadcast tonight in Channel 4's series on Christianity, Richard Dawkins declares: "Darwin removed the main argument for God's existence."

That wasn't, of course, Darwin's intention. In 1827, he scraped into Cambridge to study for the church. But by 1838, with the wealth of experience from the Beagle's voyage inside his head, Darwin had conceived the idea that natural selection - survival of the fittest - had created new species. Even after she accepted his marriage proposal, Darwin's cousin Emma, a strict Unitarian, fretted that his heretical theories would lead to their separation in the afterlife!

Darwin agonised for more than 20 years before publishing On the Origin of Species, and another two before he could say, in The Descent of Man, that "Man must be included with other organic beings in any general conclusion respecting his manner of appearance on Earth". In the final words of that transcendent book, Darwin couldn't avoid the religious metaphor: "Man with all his noble qualities... with his god-like intellect which has penetrated into the movements and constitution of the solar system - with all these exalted powers - Man still bears in his bodily frame the indelible stamp of his lowly origins."

Throughout the love-hate relationship between science and Christianity, the idea that human rationality is a gift from God has frequently been used as a justification, or an excuse, for scientific inquiry. Pope Benedict XVI has gone further. In a speech read at La Sapienza University in Rome last year (in the face of opposition from the academic staff) he argued: "If, however, reason ... becomes deaf to the great message that comes from the Christian faith and its wisdom, it will wither like a tree whose roots no longer reach the waters that give it life." What on earth was the Pope saying? That only Christians can be good scientists? Sorry, Pythagoras; sorry, Galen; sorry, Einstein; sorry, Crick.

Science has rampaged over the landscape of divine explanation, provoking denial or surrender from the church. Christian leaders, even the Catholic church, have reluctantly accommodated the discoveries of scientists, with the odd burning at the stake and excommunication along the way.

But I was astounded to discover how topical the issue of Galileo's trial still is in the Vatican and how resistant many Christians are to scientific ideas that challenge scriptural accounts. More than half of Americans, even a third of Brits, still believe that God created humans in their present form.

The process of Christian accommodation is a bit like the fate of fieldmice confronted by a combine harvester, continuously retreating into the shrinking patch of uncut wheat.

Ten days ago, on Darwin's birthday, Richard Dawkins, Archbishop of Atheism, and Richard Harries, former Bishop of Oxford, conducted a public conversation in the Oxford University Museum, where Bishop Sam Wilberforce and Darwin's champion, Thomas Henry Huxley, had debated Darwin's ideas in 1860. The two Richards were more civilised. But inevitably, Richard H claimed for religion a territory that science can never invade, a totally safe sanctuary for Christian fieldmice. Science is brilliant at questions that start "how", but religion is the only approach to questions that start "why". Throughout history, human beings have asked those difficult "why" questions.

It's true that spiritual beliefs of one form or another are universal, almost as defining of humanity as language is. But the universality of language and the fact that bits of the human brain are clearly specialised to do language suggest that our genes give us language-learning brains. Is the same true of religion?

Brain scanning has indeed shown particular bits of the brain lighting up with activity when people pray, look at pictures of the Virgin Mary or recollect intense religious experiences. Richard Harries said: "It would not be surprising if God had created us with a physical facility for belief."

But there is another interpretation, which might eventually lead to the completion of the scientific harvest.

Human beings are supremely social animals. We recognise people and judge their feelings and intentions from their expressions and actions. Our thoughts about ourselves, and the words we use to describe those thoughts, are infused with wishes and wants. We feel that we are the helmsmen of our actions, free to choose, even to sin.

But increasingly, those who study the human brain see our experiences, even of our own intentions, as being an illusory commentary on what our brains have already decided to do.

Perhaps we humans come with a false model of ourselves, which works well as a means of predicting the behaviour of other people - a belief that actions are the result of conscious intentions. Then could the pervasive human belief in supernatural forces and spiritual agents, controlling the physical world, and influencing our moral judgments, be an extension of that false logic, a misconception no more significant than a visual illusion?

I'm dubious about those "why" questions: why are we here? Why do we have a sense of right and wrong? Either they make no sense or they can be recast as the kind of "how" questions that science answers so well.

When we understand how our brains generate religious ideas, and what the Darwinian adaptive value of such brain processes is, what will be left for religion?

• Colin Blakemore's God and the Scientists is on Channel 4 at 7pm tonight