"I have deep respect for those who do not agree with some of the provisions in the bill because of religious conviction," wrote Gordon Brown the day before Monday's Commons vote on hybrid embryos. "But I believe that we owe it to ourselves and future generations to introduce these measures and, in particular, to give our unequivocal backing, within the right framework of rules and standards, to stem-cell research."

In those two sentences Brown managed to capture all that is wrong in how we approach public debates about bioethics.

Brown's words are typical of the way religious views are "respected", only so that they can then be ignored. The debate then proceeds on fatalistic, utilitarian premises: there is no other option; we have to do this for the greater good. Both these moves are not so much steps forward as sideways, avoiding the tough issues and disagreements.

Take the engagement with religion first. There is a curious implicit pact here, whereby atheists, agnostics and believers alike all accept that faith stands somehow to one side of rationality. The devout gain respect and immunity from rational prosecution, at the price of being excluded from intellectual debate. Non-believers get to keep the civic sphere entirely secular, at the price of having to back off from believers. At one level, this is right. Much religious belief is a matter of faith, as impervious to rational scrutiny as the Vatican is to women. However, when it comes to specific matters of morality, the idea that religious convictions need respect, not interrogation and defence, is absurd. The world's major religious texts have nothing to say about stem cells, not least because those words do not appear in any of them. It may be a matter of faith that Christ rose from the dead, but Christians have to defend anything they say about the first stages of life.

For example, in his Easter Sunday sermon, Cardinal Keith O'Brien quoted from a letter he and several other church leaders had signed: "This bill goes against what most people, Christian or not, reckon is common sense. The idea of mixing human and animal genes is not just evil. It's crazy!" It is not good enough, on reading this, simply to nod sympathetically and say, "I respect your view." For one thing, the respect is not reciprocated: scientists and supporters of the bill are being accused of doing great evil. What we should do is demand that the central claims be substantiated, which, in this case, they are not. As a matter of fact, opinion polls repeatedly show that most members of the public do approve of embryo research, interspecies or otherwise. More importantly, if anyone other than a church leader accused something of being evil and crazy, we would want to see some reasons why we should agree. Instead, we smile, and move on.

Once religion is set aside, the debate then tends to proceed in a crassly simplistic way. Most of the time, the argument is no more than the claim that the benefits of the research will be enormous, and therefore we must do it. But this is far too quick. Using the terminally ill for experiments might teach us things future generations will benefit from, but that doesn't mean we should do it.

Yet it suits people to stop the debate here, because the real issue is much more complex: What is the moral status of embryos? Bishops simply assert they are as precious as full-grown human beings, scientists avoid answering the question altogether, and between the two camps, the fundamental issue is passed over in silence.

This fudge suits the religious lobby more, for it leaves unchallenged the view that cells from which human beings grow are precious. A similar silence has occluded the morality of abortion for decades. But if we thought 14-day-old embryos and aborted foetuses were as fully human as we are, then no appeal to the balance of costs and benefits could justify their routine killing. People talk as though foetal life has an important moral status, but act as though it does not.

Artificial divide

The contradiction can be resolved in one of only two ways: either we agree the bishops were right all along, or we face the facts squarely and stop the pretence that anything growing in the womb is important, and as human, as a tiny baby. The latter need not lead us down a slippery slope where human life in general is granted less respect. Nor would it entail treating stem cells with no respect: it is good for us to practise reverence for life even if, on reflection, we do not always think it is worth preserving.

But how can we debate these deeply divisive issues, when people's fundamental convictions are so different? What is needed is a way to bring religious perspectives into public discourse without diluting the essentially secular nature of the public square. This might sound impossible, as it is too often assumed that a secular politics requires people to leave their religious beliefs behind them. But that is a mistake. Democratic politics in a pluralist age requires, not that people set aside their fundamental commitments, but that they discuss their differences in a common language. The absence of God will inform someone's opinions on morality, but one cannot expect arguments in public debate to carry any weight if they start with an assertion of atheism. Catholicism may inform someone's beliefs on birth control, for instance, but we cannot be expected to agree with them on the basis of what the Pope says.

What both sides must do is to make their case in terms the other can assess and understand. Arguments for stem-cell research need to appeal to facts about the actual, not imagined, nature of early embryos, as well as serious thought about the potential social consequences of entirely new ways of doing science. Arguments can also draw on religious insights, just as long as they do not assume any particular theological framework. One can talk about the need for humility, deep respect for human life and the dangers of hubris without invoking St John's Gospel.

The justifiable desire to keep religious dogma out of public life has led to an unjustifiable tendency to treat religious views as a whole as separable from civic life. It is in the interests of everyone, believer or not, to end this artificial divide and start a real intellectual tussle in which secular and sacred views battle it out, rationally and in the open.

Julian Baggini is editor of The Philosophers' Magazine