Even an old atheist like me sees no good in this ignorance of basic Christian myths. How do you make any sense of history, art or literature without knowing the stories and iconography of your own culture and all the world's main religions? Total ignorance of religion and its history could make people more susceptible to the next passing charlatan offering Kwik Save salvation from whatever it is people want to be saved from.

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On Easter Day the National Union of Teachers votes on the same motion debated by the Association of Teachers and Lecturers to end the growth of religious state schools and ban the teaching of "intelligent design" as a valid alternative to evolution. How craftily the creationists have hijacked the word "intelligent" for something so dumb. The teachers are right to join the battle just as the Royal Society gathers up the might of its scientific authority this week to oppose the teaching of creationism: it was the wonderful Steve Jones who said it is like teaching genetics as a theory only as valid as the theory that storks deliver babies.

This is indeed a clash of civilisations, not between Islam and Christendom but between reason and superstition. The wake-up call came with a BBC/Mori poll showing that, even in this least churchgoing nation, science is on the run: 48% believe in evolution, against 39% who believe in creationism/"intelligent design". If even scientists aren't believed then here is fertile territory for any mad and dangerous theories to take hold.

But instead of standing up for reason, our government is handing education over to the world of faith. It's the same government that went to war in Iraq to install the likes of Grand Ayatollah Ali al-Sistani into positions of great power. The man George Bush and Tony Blair see as the best hope for promoting stability and "freedom" in Iraq has just issued a fatwa calling for the killing of all sodomites and lesbians. See www.sistani.org: "Q. What is the judgment for sodomy and lesbianism? A. Forbidden. Punished. The people involved should be killed in the worst, most severe way of killing." The exiled Iraqi gay campaigner Ali Hili reports that these orders are now being obeyed, with an upsurge in beatings and slaughter of gays in Iraq by religious cadres who have declared all unmarried men over 35 "under surveillance".

The Pope may not call for murder, but the Vatican is directly responsible for millions of Aids deaths by refusing to sanction condoms even in parts of Africa where half the population is infected with HIV, putting out deliberate lies that condoms are useless against the virus anyway. Yet here is the Labour government encouraging religions to take over as many schools as they can, promoting the humbug that values and morality only come with the "ethos" of faith.

Remember this: over a third of all state schools are now run by religions. Most are Christian, with some Jewish, Sikh and of other faiths. Under Labour the Church of England is rolling out 100 new secondary schools; half are open already. In Labour's flagship academy programme, 42 of the first 100 belong to Christian sponsors - at least five of them to evangelical creationists. Since Labour came to power six new Muslim state schools have been created; there are another 150 in the pipeline, according to the National Secular Society.

The chief inspector of schools, David Bell, says Islamic schools pose a challenge to social cohesion. "Traditional Islamic education does not entirely fit pupils for their lives as Muslims in modern Britain." The Muslim Parliament itself has just expressed anxiety about sexual abuse and violence in the 700 unregulated madrasas where 100,000 Muslim children go after school. Catholic revelations are a reminder that all religions are at the same risk of abusing women and children wherever there is a secretive spiritual and cultural power over their lives.

Now the teachers' unions fear the faiths will make a grab for many more schools when the education bill puts them all up for potential takeover. Trust status will give sponsors power not just to run the governing body, but to devise their own curriculum. (So forget sex education). Every school that vanishes into the hands of the religions is gone for ever, exceedingly hard for a future government to get back. How can a Labour government be doing this?

It's because religious schools are so popular, the government says, and indeed they are. There may be few bums on seats in pews, but there are queues for the schools whose special "ethos" is called closet selection. God doesn't move in such very mysterious ways: research by the Institute for Research in Integrated Strategies is only the latest to find that C of E and Catholic schools take a lower proportion of free-school-meal children than the average for their catchment area. It means nearby schools have to take more, magnifying the imbalance as an unfair proportion of troubled children congregate in bog-standard schools without the magic "ethos".

Understandably, parents dash for schools where the better-off congregate, but few value religious schools for their own sake. In Northern Ireland, where most schools are breeding grounds for religious sectarianism, the few nondenominational schools are hugely oversubscribed - but sectarian politicians prevent more opening for fear of losing their tribes. The Young Foundation's study The New East End warns that in Tower Hamlets white parents fleeing Bangladeshis have taken over four church secondary schools in which Bangladeshis make up only 3% of the pupils, while they form 90% of pupils in the next-door secular schools. Religion usually means class, race or tribe segregation.

Ask most Labour MPs and they abhor the devious abuse of religious schools and the segregation they cause. It's not "choice", since most parents would never choose faith schools if they were not the flag for assembling the better pupils locally. Baroness Morgan, until last year a close Blair ally as No 10's director of government relations, spoke out boldly against religious schools in the Lords. (Note how everyone leaving No 10 suddenly speaks their mind - and it is rarely the mind of their leader.) ICM polling shows that 64% of voters think "the government should not be funding faith schools of any kind" - a surprisingly strong position. So what on earth is a Labour government up to - and why don't Labour MPs refuse to let this happen?

polly.toynbee@guardian.co.uk