Cardinal Winning, the leader of Scotland's Catholics, has become the most important churchman in the country. For a land which gave birth to John Knox and where sub sects of devout Protestantism still thrive this is a remarkable event. But all the old certainties are being overturned as Scotland establishes a new identity.

The story of how a cardinal became dominant in one of Europe's bastions of the Protestant faith is also the story of how the Irish immigrant population slowly integrated into the neighbouring Celtic culture.

It wasn't the Irish farm workers of the last few centuries who brought Catholicism to Scotland. The Scots had been divided on religion for a long time. Protestants hoped they'd won when Bonnie Prince Charlie fled to Italy after the failed Highland rising of 1745. With the Catholic pretender to the crown gone, the Protestant majority had a safe superiority.

When potato pickers were needed for the fields of lowland Scotland, extra hands were recruited from Ireland. A two-way trade in labour and goods existed between the two countries for centuries. It wasn't until the industrial boom of the British Empire coincided with the Famine that large, permanent communities of Irish immigrants took root. They went where the jobs were, which was chiefly in and around Glasgow. The city was becoming the "workshop of the Empire" and needed all the hands it could get.

Like Liverpool, Glasgow developed a particular character influenced by the new arrivals. The Irish were joined by Highland Scots, who also fled famine conditions for the hope of work. However, it was an overwhelmingly Protestant character. British identity was undergoing a vigorous reinvention, designed to justify its colonial expansion. The religion of choice was Protestant, which meant the Church of Scotland.

There was a strong link between Protestantism, industrial employment and political conservatism. At the turn of the century, when Scotland was the richest country on the planet, as measured by wealth per capita, it seemed like a pretty successful formula. Many of the factories and skilled labouring jobs were barred to Catholics.

Despite the discrimination, Scotland is possibly the only country to experience a large influx of Irish immigrants without a network of Irish clubs or associations growing up. The only club they could call their own was Celtic Football Club, formed in 1888. To this day it is still where Tricolours fly and young Glaswegians learn the words to The Soldiers' Song, even if the reasons behind these traditions are fading and losing their power.

The protector of the Irish Catholic population came in the form of the Labour Party. It wooed the Catholic vote and so formed an alliance which lasted a century. The Labour Party opened a door into municipal politics that gave Catholics a means of self-improvement and climbing the social ladder. The Labour Party also fought for separate Catholic schools in Scotland, which still exist. The schools meant not only education, but also good middle-class jobs as teachers for the Irish community.

It was no accident that as recently as 1990 the leader of Glasgow City Council, held by Labour for more than 60 years, was also a director on the board of Celtic. Ironically, given the chants in the football ground, the bond between Labour and the Catholic community was strengthened by the rise of nationalism in Scotland. The Scottish National Party (SNP) was seen as a Protestant movement that would enforce a religious purity upon the country, much as de Valera wanted a rustic purity for Ireland.

The overwhelming majority of Catholics voted No when Scottish devolution was first offered in 1979. But then things changed, a process that continues and grows more interesting by the day. The general increase in living standards and the erosion of old professions and identities weakened the link between Labour and Irish Catholics.

No longer was the Catholic population to be found only around Glasgow, but evenly spread across the country. It no longer feared the nationalists, who desperately worked to reinforce their non-discriminatory and inclusive politics. Most importantly, Irish Catholics were to be found in every economic bracket. They had escaped the poverty of the past.

When the 1997 referendum was held on the creation of a Scottish parliament, the people said Yes by 80 per cent. Within that landslide were the majority of Irish Catholic votes. Constitutional change was no longer a threat to religion, but rather seen as essential for economic development. That transformation in attitude from the 1970s to the 1990s also occurred on a cultural level. It's no longer valid to speak of an Irish community with a separate identity. Opinion polls show fourth-generation Donegal families think of themselves as Scottish first and foremost.

Despite the fall in church attendance, which puts the number of active Catholics at about 200,000 in a population of 800,000, Cardinal Winning has risen to prominence. The Parliament may temporarily sit in the Church of Scotland's assembly building, but it is only the cardinal who can bring out the sweat on a cabinet minister's brow. Against a background of the steady decline of religion's significance, he has taken moral stands on issues which have found favour beyond his flock.

In the mid-1990s he began a scheme in Glasgow whereby young mothers would be offered cash support to have their babies rather than have an abortion. It ran counter to Labour Party policy and caused a split between the two bodies.

Outrage was provoked this year when a 12-year-old girl used the scheme. A new religious order, backed by the cardinal, has now been created to carry on this work. It is called the Sisters of the Gospel of Life.

When the Scottish coalition government announced it was going to scrap Section 28, which banned local authorities from publicising homosexuality, it was Cardinal Winning who raised the first objections. He has since been joined by an array of fundamental Protestants and social conservatives in one of the most ill-tempered policy debates Scotland has had for decades.

While the Church of Scotland and the Catholic Church in England pursue tolerance and harmony in their social views, Winning has become a lone figure of moral certainty in a pragmatic age.

Now the cardinal steps ever closer to officially endorsing the SNP, having been actively courted by its leader, Mr Alex Salmond.

In a land rejecting religion and the old political allegiances, the cardinal remains the one church leader a politician needs on side to avoid suffering the wrath of outraged tabloid headlines.

For the nationalists and Catholics to be so close is a sign that Scotland has changed irrevocably.