The third largest denomination in the United States, the Methodists, has become the latest church to come out against gays. Their General Conference 10 days ago reaffirmed an earlier court ruling that bishops could not appoint a minister who is a "self-avowed, practising homosexual." In their sights was a lesbian minister in good standing but unprepared to be silent about her sexual orientation. The pro-gay lobby lost vote after vote.

The third largest denomination in the United States, the Methodists, has become the latest church to come out against gays. Their General Conference 10 days ago reaffirmed an earlier court ruling that bishops could not appoint a minister who is a "self-avowed, practising homosexual." In their sights was a lesbian minister in good standing but unprepared to be silent about her sexual orientation. The pro-gay lobby lost vote after vote.

They lost too in Britain, where the High Court last month rejected an attempt by trade-union groups to overturn the decision by the Government to exempt churches from new regulations outlawing anti-gay discrimination in the workplace. The judge upheld the legality of the Government's 2003 Employment Equality (Sexual Orientation) Regulations, which makes being gay a sackable offence in religious organisations. Although the regulations do not apparently apply to teachers in faith schools, gays working for faith-based employers other than schools are liable to dismissal.

How have the churches got themselves into this mess? Some might think that it is fair enough for churches to make rules for their members, which have the backing of law. But what this overlooks is that for decades the churches have been extolling the rhetoric of human rights and urging its enactment in law. As long ago as 1961, Pope John XXIII described the modern church as "dominated by one basic theme - an unshakeable affirmation and vigorous defence of the dignity and rights of the human person." The World Council of Churches campaigns for the legislative enforcement of human rights.

And yet when this rhetoric threatens to become a reality, what do we find? Nothing less than an attempt by the churches to sustain their own discriminatory practices. When push comes to shove, they behave like any other human institution in defending their own perceived interests. In doing so, they make a mockery of human-rights legislation. Sadly, there is little appreciation among church leaders of how serious this situation is, and its corrosive effect on the credibility of the church. What should worry the churches is the gap between what they profess and how they actually behave.

In the past, it was thought that Christianity was a repository of humane and compassionate values to which most people would want to aspire. Today, however, the churches are under judgment, and rightly so. On a raft of issues from child protection, women's rights, the status of animals, to the treatment of gays, people are no longer prepared to give church positions even nodding assent. Church leaders excel at criticising contemporary society as "selfish" or "greedy", but they fail to see the moral critique that can be raised against their own traditions.

Archbishop Rowan Williams in the past few weeks has lamented the Government's lack of "attentiveness to truth". Christian political obedience, he said, must rest on confidence "in openness to a truth that goes beyond power and interest". Ironically, the Government could level the same charge against the church and remind it that its own credibility is at stake when it seeks exemption from human-rights legislation based on calculations of its own interest.

But the issue of discrimination against gays isn't just one of credibility, it is one of theology. Those who want gays out of Christian ministry point to scriptural justification and the weight of tradition, as if those things (even if they were sufficiently clear) settled the matter. On this account, churches are set to endlessly repeat themselves whatever new circumstances arise, and Christian ethics becomes little more than an exercise in archaeology. This model presupposes that all truth is to be found in the past and that there is nothing new to discover.

The deficiency of this position is shown in the Christian doctrine of God as Father, Son, and Holy Spirit; not all truth is given in the past, the Spirit has something to give us in the present. It is untrinitarian to consistently oppose God's work in the past to what we may learn here and now. The dominical promise is that the Spirit "will guide you into all truth" (John 16.13). If scripture and tradition were our only guides, we would still have slavery, the subordination of women, and there would be no declaration of human rights.

Of course it doesn't follow that everything in contemporary culture is the work of the Spirit, and it doesn't mean that the church should simply underwrite a liberal agenda. There needs to be fidelity, but also discernment. But one thing seems sure: whenever the church finds its doctrines are a source of injustice and suffering, the Spirit has more to teach us.

Professor Andrew Linzey is Senior Research Fellow, Blackfriars Hall, Oxford University