It has been a good year for atheists. Richard Dawkins’s book The God Delusion has sold more than a million copies, and between April and June was Britain’s fourth best-selling title, beaten only by two Harry Potter books and Gordon Ramsay. Christopher Hitchens, whose God is Not Great also excoriates religion as poison, has been given free rein on television and in debating halls. The success of the filmThe Golden Compass has provoked anguish among Christians over what is perceived as the atheist message at the heart of Philip Pullman’s His Dark Materials. Authors such as Sam Harris and Daniel Dennett have found that atheism sells on both sides of the Atlantic. Among both Christians and Muslims, Ayaan Hirsi Ali’s impassioned denunciation of the restrictions of Islam in Somalia have stirred sympathy as well as anger. And the new leader of the Liberal Democratic Party has admitted something unsayable only a decade or two ago: that he does not believe in God.

Not since Victorian times has there been such an intense and sustained debate about religious belief. It has been a curiously bad-tempered argument: the books that have spearheaded the militant new atheism have not sought to persuade, reach out or reason. Instead, in the name of reason, they have heaped scorn and ridicule on those stupid enough to believe the myths and the obscurantist cosmology of religion. Believers, Dawkins asserts, are “malevolent... vicious, sado-masochistic and repellent... dodgy, perniciously delusional... sanctimoniously hypocritical... cockeyed”. The atheists have characterised all religions by their most extremist exponents – the fundamentalists and the literalists, the holy warriors and the narrow-minded zealots – and denounced them as the bringers of war and suffering, the dividers and the oppressors, the antithesis of civilisation and the Enlightenment.

The argument has become highly political. Much of the animus driving the prophets of godlessness is a hatred of the American Christian Right and a fear of its power or a disgust with the terrorism and repression of militant Islamism. Many believers as well as agnostics share that disgust, swelling the atheist camp and magnifying its voice. But as faith issues have emerged at the centre of British and global politics, what was once a tolerant debate between believers and unbelievers, respectful and accommodating of each other’s views, has become a vicious dogfight. Dawkins claims that religion, because of its irrationality, can lead to extreme violence; ergo, faith instruction to the young is worse than paedophile abuse.

How should believers respond to this on-slaught? For some, the immediate reaction has been embattled outrage. Donning the shining armour of belief, they have sought to smash down the atheists’ contentions, one by one. Science, they point out correctly, does not have a monopoly on progress, nor religion on backwardness. Were not the two greatest monsters of the 20th century, Hitler and Stalin, both driven by what they believed a “scientific” ideology: the purging of “healthy” races from dangerous impurities, in Hitler’s case, or Stalin’s violent attempt to reconstruct society according to a flawed understanding of genetics? Defenders of the faith have also accused the atheists of the same fundamentalism that they impugn to their enemies: a dogmatic refusal to admit that “progress” has often been the achievement of profoundly religious people – including the atheists’ iconic Isaac Newton – who have been pioneers in science, democratic idealism and human rights.

There has also, however, been a more thoughtful and useful response, which admits the force of many of the atheists’ arguments and asks whether faith has been too arrogant or believers too naively narrow in their convictions. Among Christians, there is no doubt that confusion and disillusion are causing considerable anguish.

Whether it is on the issue of Biblical authority, human sexuality, church democracy or evangelical absolutism, almost all churches in Britain, and indeed beyond, have been riven by uncertainty. For some, the instinct has been to deny division, suppress debate and corral the faithful behind the stockade of religious orthodoxy. It is this very division and doubt, however, that ought to be a strength to underpin faith. For doubt admits the viability of other views, and that is the basis of wisdom and tolerance. Faith has to accommodate to the world around – to the evils, the uncertainties, the depths of human misery. Totalitarianism can be as much a danger to faith as it can be to secular society.

This, surely, is where the new militant atheism is wrong. It is totalitarian in its prescription for human happiness. It would deny as unscientific the spiritual dimension that is as truly Darwinian in its evolution and persistence as patterns of behaviour or genetics. Above all, an ideology – for atheism is an ideology – that cannot see its own scientific limitation cannot claim to be scientific. Those modish atheists who claim to understand the panoply of religious experience, or myth as they would have it, are, in the words of a critic, like “someone holding forth on biology whose only knowledge of the subject isThe Book of British Birds”. Similarly, a claim to know what Einstein admitted was the unknowable about the existence of the universe cannot be made by anyone who is himself a human and therefore part of that universe.

The spiritual dimension goes far beyond mere awe at the sublime, whether it be inspired by nature, beauty, music or human passion – something any sentient atheist can, and will, admit to. Faith admits to both doubt and unknowingness. It is not a provable dimension. But it is one of extraordinary power and potential. Symbolically, it is renewed each Christmas, with reverence and humility. This is the fact we celebrate tomorrow.