'There could be nothing but shame . . . if we appear to forsake our own mandate, mission and values.' (St. John's Seminary)

The Rev. John A. Farren, a conservative and occasionally controversial Dominican friar, warned in the letters last month that the "doctrinal integrity" of St. John's is at risk because of increased proximity to two Jesuit-run Catholic institutions, Boston College and Weston Jesuit School of Theology, which are expected to move into buildings currently held by the seminary.

Farren did not cite specific issues, saying only that Weston Jesuit employs "self-professed gays or lesbians" as faculty members and that several faculty members there have been questioned by the Vatican.

Weston Jesuit and Boston College are generally considered liberal institutions open to a wider range of theological views than St. John's. Under Farren's leadership, several members of the seminary faculty perceived as liberal were ousted.

The letters, one sent to the seminary board and the other to Cardinal Sean P. O'Malley, provide an extraordinary window into the deep ideological tensions within the Roman Catholic Church's leadership. They also shed light on the slow but dramatic transition taking place at the seminary, which once trained priests in relative isolation from the larger community, but which has seen a relatively dense residential neighborhood spring up around it and now faces the prospect of sharing facilities with college students.

Read Rev. Farren's letters
[  • Response of Rector to Proposal (May 23, 2007)
   • Letter to Cardinal O'Malley and Trustees (May 24, 2007)]

The archdiocese, though refusing to criticize Farren, strongly disputes his conclusions. In response to Farren's criticism, O'Malley sent e-mail to priests in the archdiocese defending the proposed sale, and the archdiocese's vicar general said in an interview that the changes will strengthen, not weaken, the seminary.

"We do not believe that the sale of additional property from our Brighton campus will harm or hinder the essential work of St. John's," O'Malley wrote.

The dispute -- unusual in a clerical subculture in which deference is generally paid to the decision of a cardinal-archbishop -- stems from O'Malley's May 24 decision to sell 18 acres in Brighton, much of it belonging to the seminary, for $60 million to Boston College. The sale will leave the seminary owning just half a building, St. John's Hall, and will result in BC managing the seminary's library, food service, and other functions.

BC, which bought an adjoining 43-acre property three years ago, has said it intends to relocate some religious studies programs to the Brighton property. Weston Jesuit, now located in Cambridge, plans to affiliate with BC and move onto the campus.

Farren was scheduled to leave at the end of June but quit May 24 over the sale. He raised financial and legal concerns about the transaction and said he believes it will lead to the eventual demise of St. John's Seminary.

St. John's is expected to have about 50 seminarians this fall, about 20 from Boston and the rest from other New England dioceses and two Vietnamese dioceses.

"If we are urged to reduce expenses by mutual collaboration, this would induce asphyxiation, with the remedy worse than the affliction," Farren wrote to the seminary board. At another point in the letter, he wrote, "As the archdiocese prepares for its bicentennial, there could be nothing but shame and embarrassment if we appear to forsake our own mandate, mission and values for 30 pieces of silver."

Farren wrote that at Weston Jesuit "opinions of every kind are propagated without adequate identification of the binding articles of faith."

"A sign of this is found in the fact that several professors of WJST are currently under investigation by the Congregation for the Doctrine of the Faith," he wrote, referring to the Vatican agency that investigates theologians accused of doctrinal error. "Several professors at WJST are self- professed gays or lesbians. Collaboration at such an institution is not good policy for St. John's Seminary."

The president of Weston Jesuit could not be reached for comment yesterday, but the president of Boston College reacted sharply to Farren's allegations.

"It was very unfortunate that this letter was written," said the Rev. William P. Leahy, BC's president. "No one should be concerned about Weston students and St. John's students being on the same campus. The close proximity will yield many positives, intellectually, socially, and in the sharing of library resources."

The archdiocesan vicar general, Rev. Richard M. Erikson, strongly defended the proposed sale. Erikson, a onetime professor at St. John's, said that seminary students have long been able to take classes at BC, Weston, and area divinity schools, and said he himself took courses at those institutions when he was a student.

He also pointed out that although some seminaries are "totally separate from university or community," there are multiple American seminaries located on Catholic campuses, in Maryland, Minnesota, and two in Texas, for example.

"The history of St. John's is that we've been moving gradually from the model of the separate oasis . . . to the midst of the city and of the campus, and part of it is simply because of the expansion of Brighton around us," he said.

"We are preparing men for ministry in the 21st century in an extraordinarily diverse diocese of 144 communities, 2 million Catholics, and many urban centers, and if our seminarians don't face these challenges and issues as seminarians, they will the day they're ordained. I'm not afraid that having a very diverse and wide experience at seminary is somehow going to corrupt our seminarians."

Farren did not respond to messages left at the seminary and at his religious order in New York, his new assignment. His superior, the Rev. D. Dominic Izzo, declined to comment.

The Globe also offered several seminary trustees, students, and faculty members an opportunity to comment; all declined.

Michael Paulson can be reached at mpaulson@globe.com