Soon after David Solomon arrived at Baylor University in 1960, he realized that one of his new friends had a problem -- this rancher's kid had spent his life in boots.

"That's all he had," said Solomon, a philosopher who leads the Notre Dame Center for Ethics & Culture. "We went out and he bought his first pair of lace-up shoes. ... That's what Baylor was about, back then. Baylor was supposed to take Baptist kids from small-town Texas churches, knock the dust off them and hit them with the Enlightenment. You know, civilize them."

Texas has changed. But anyone digging beneath the headlines about the Waco wars over faith and learning will find that the past has power. The old assumption was that students arrived rooted into a brand of faith that was rich and rigid. Thus, Solomon said most of his professors set out to "shake everybody up" and teach students a more complex, progressive set of beliefs than what they learned at home and church.

Baylor life was baptized in faith, symbolized by chimes that played hymns as students -- like me, during the 1970s -- walked to chapel.

But in the classrooms, most professors assumed that piety was a good thing, but had little to do with the wisdom in secular textbooks, said Solomon, who has stayed active in debates at his alma mater. Thus, the world's largest Southern Baptist school was a "university with a Christian atmosphere," but not a "Christian university" that blended ancient faith and modern learning.

This worked for decades, until reports about sex, drugs and nihilism pushed millions of parents to hunt for distinctively Christian campuses. As the Wall Street Journal recently noted, enrollment in the 105 members of the Council for Christian Colleges and Universities -- an organization in which I teach journalism -- soared 60 percent between 1990 and 2002, while numbers at public and secular private schools edged up or stayed level.

Recently, Baylor has steered toward "Christian university" status, led by its regents and an academic team headed by a brash president named Robert Sloan.

The result was Baylor 2012, a controversial plan calling for a larger endowment, a 36 percent tuition hike, more scholarships, 230 new faculty positions and a wave of construction, most noticeably a $103 million science building. Sloan's team also began asking prospective professors -- Protestants, Catholics and Jews alike -- to explain how faith affected their teaching and research. This was a direct challenge to the "Christian atmosphere" tradition, with its separate zones for faith and learning.

Sloan fought for a decade, before the Jan. 21 news that he will step down to become chancellor. Baylor's civil war had become national news, especially when combined with a tragic basketball scandal.

While Sloan made painful mistakes, Baylor 2012 provoked a public statement of support from an ecumenical coalition of Christian educators -- including Solomon -- from Notre Dame, Yale, Harvard, Duke, the University of Chicago and elsewhere.

"Baylor has charted a bold course," it said. "It has strengthened the mission entrusted to it by its founders, preserving its Baptist heritage while making it intellectually relevant. ... In matters of faculty hiring and curricular innovation Baylor has assumed a leadership role among the remaining Christian colleges and universities."

News reports have often linked the Baylor controversy to decades of conflict between Southern Baptist "moderates" and "fundamentalists." But what Sloan and the regents say they want is a "big tent Christian orthodoxy" that transcends Baptist politics, according to Robert Benne of Roanoke College.

These are fighting words to many Baylor loyalists.

"Above all, traditional Baptists disagree with Sloan's contention that Christianity has intellectual content," argued Benne, writing in the Christian Century. "In the view of Baylor's new leaders, faith is more than atmospheric. There is a deposit of Christian belief that all Christians should hold to. On the basis of that belief they should engage the secular claims of the various academic disciplines."

This attempt to wed soul and intellect encouraged, or infuriated, many educators in postmodern America, said Solomon.

"We can no longer assume that our students know much at all about the faith once delivered to the saints," he said. "It's a new world, even for church kids. The days of bringing boys in off the farm are gone."