From the very beginning, the conflict between religion and modern science was couched in extreme, even apocalyptic rhetoric. Thomas H Huxley, who popularised the Origin of Species, insisted that people had to choose between faith and science; there could be no compromise: "One or the other would have to succumb after a struggle of unknown duration." In response, conservative Christians launched a crusade against Darwinism. After the first world war, the Democratic politician William Jennings Bryan claimed that there was a direct link between evolutionary theory and German militarism: the notion that only the strong could or should survive had "laid the foundation for the bloodiest war in history. The same science that manufactured poisoned gases to suffocate soldiers is preaching that man has a brutal ancestry."

The struggle continues - nowhere more so than among the Christian right in the US, who still regard the evolutionary hypothesis as surrounded by a murderous nimbus of evil. In 1925, they tried to ban the teaching of evolution in public schools and developed creation science, based on a literal reading of the first chapter of Genesis. More recently, they have tried to introduce into the school curriculum the teaching of intelligent design (ID), which claims that the irreducible complexity of micro-organisms could not have evolved naturally but must be the result of a single creative act. The issue splits the nation down the middle: fundamentalists want to win a battle for God; liberals and secularists are fighting for truth and rationality.

The same passions are likely to be aroused by President Bush's decision last week to veto the Stem Cell Research Enhancement Act, which would have loosened the restrictions on federal funding for stem cell research. "This bill would support the taking of innocent human life in the hope of finding medical benefits for others," Bush said. "It crosses a moral boundary that our decent society needs to respect."

His opponents point out that while the president zealously champions the rights of the unborn, he is less concerned about the plight of existing American children. The US infant mortality rate is only the 42nd best in the world; the average baby has a better chance of surviving in Havana or Beijing; infant mortality rates are unacceptably high among those who cannot afford adequate healthcare, especially in the African-American community. And, finally, at the same time as Bush decided to veto the stem cell bill, Israeli bombs were taking the lives of hundreds of innocent Lebanese civilians, many of them children, with the tacit approval of the US.

Is there a connection between a religiously motivated mistrust of science, glaring social injustice and a war in the Middle East? Bush and his administration espouse many of the ideals of the Christian right and rely on its support. American fundamentalists are convinced that the second coming of Christ is at hand; they have developed an end-time scenario of genocidal battles based on a literal reading of Revelation that is absolutely central to their theology. Christ cannot return, however, unless, in fulfilment of biblical prophecy, the Jews are in possession of the Holy Land. Before the End, the faithful will be "raptured" or snatched up into the air in order to avoid the Tribulation. Antichrist will massacre Jews who are not baptised; but Christ will defeat the mysterious "enemy from the north", and establish a millennium of peace.

This grim eschatology, developed in the late 19th century, was in part a reaction to the "social gospel" of the more liberal Christians, who believed that human beings were naturally evolving towards perfection and could build the New Jerusalem here on earth by fighting social injustice. The fundamentalists, however, believed that God was so angry with the faithless world that he could save it only by initiating a devastating catastrophe; they would see the terrible battles of the first world war, which showed that science could be used to lethal effect in the new military technology, as the beginning of the End.

The fundamentalists' rejection of science is deeply linked to their apocalyptic vision. Even the relatively sober ID theorists segue easily into Rapture-speak. "Great shakings and darkness are descending on Planet Earth," says the ID philosopher Paul Nelson, "but they will be overshadowed by even more amazing displays of God's power and light. Ever the long-term strategist, YHVH is raising up a mighty army of cutting-edge Jewish End-time warriors." They all condemn the attempt to reform social ills. When applied socially, evolutionary theory "leads straight to all the woes of modern life", says the leading ID ideologue Philip Johnson: homosexuality, state-backed healthcare, divorce, single-parenthood, socialism and abortion. All this, of course, is highly agreeable to the Bush administration, which is itself selectively leery of science. It has, for example, persistently ignored scientists' warnings about global warming. Why bother to implement the Kyoto treaty if the world is about to end? Indeed, some fundamentalists see environmental damage as a positive development, because it will hasten the apocalypse.

This nihilistic religiosity is based on a perversion of the texts. The first chapter of Genesis was never intended as a literal account of the origins of life; it is a myth, a timeless story about the sanctity of the world and everything in it. Revelation was not a detailed programme for the End time; it is written in an apocalyptic genre that has quite a different dynamic. When they described the Jews' return to their homeland, the Hebrew prophets were predicting the end of the Babylonian exile in the sixth century BC - not the second coming of Christ. The prophets did preach a stern message of social justice, however, and like all the major world faiths, Christianity sees charity and loving-kindness as the cardinal virtues. Fundamentalism nearly always distorts the tradition it is trying to defend.

Whatever Bush's personal beliefs, the ideology of the Christian right is both familiar and congenial to him. This strange amalgam of ideas can perhaps throw light on the behaviour of a president, who, it is said, believes that God chose him to lead the world to Rapture, who has little interest in social reform, and whose selective concern for life issues has now inspired him to veto important scientific research. It explains his unconditional and uncritical support for Israel, his willingness to use "Jewish End-time warriors" to fulfil a vision of his own - arguably against Israel's best interests - and to see Syria and Iran (who seem to be replacing Saddam as the "enemy of the north") as entirely responsible for the unfolding tragedy.

Fundamentalists do not want a humanly constructed peace; many, indeed, regard the UN as the abode of Antichrist. The willingness of the US to turn a blind eye to the suffering of innocent people in Lebanon will certainly fuel the rage of the extremists and lead to further acts of terror. We can only hope that it does not take us all the way to Armageddon.

· Karen Armstrong is the author of The Battle for God: A History of Fundamentalism

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