Like all historic private universities, Baylor University – chartered in 1845 by the Republic of Texas – has its share of beloved traditions.

One of them is that public prayers during graduation ceremonies are given by Baylor staff members, faculty and, when possible, ministers who are the parents of graduating seniors. That’s why the Rev. Dan Freemyer of Broadway Baptist Church in Fort Worth, Texas, stepped to the microphone on May 18 to deliver the benediction at one of Baylor’s spring graduation rites.

God is doing new things in today’s world, he said, while offering blunt prayer requests on behalf of the graduates.

“God, give them the moral imagination to reject the old keys that we’re trying to give them to a planet that we’re poisoning by running it on fossil fuels and misplaced priorities – a planet with too many straight white men like me behind the steering wheel while others have been expected to sit quietly at the back of the bus,” said Freemyer.

It’s crucial to know that Freemyer serves as the “missional engagement” pastor at Broadway Baptist, a progressive congregation that in 2010 voted to leave the Baptist General Convention of Texas in a dispute over the moral status of homosexual behavior. Baylor retains BGCT ties, but – for many decades – has had many connections to Broadway Baptist.

Ending his prayer, Freemyer stated: “God, you are doing a new thing. Praise be! … It springs forth, and we can feel it.”

This prayer drew scattered applause, in part because it came days after Baylor regents declined to meet with leaders of the campus LGBTQ group Gamma Alpha Upsilon, which has been seeking formal recognition from school administrators. That recognition would give the group, once known as the Sexual Identity Forum, access to student-fee funds and, more importantly, this would indicate that Baylor leaders believe its work is in accord with the school’s “unapologetically Christian” mission.

The Freemyer prayer yanked years of conflicts back into the open, igniting debates during graduation events and, later, online.

Baylor President Linda Livingstone released a statement noting that she was “caught off guard … as this prayer is intended to focus on the graduates as they leave Baylor University and make a mark around the world, not to communicate any kind of political statement.” She stressed that the prayer had not been “scripted by anyone” in the administration and that Baylor leaders will “review our internal procedures moving forward to ensure the Benediction is offered as intended” at future rites.

Baylor’s doctrinal statement on marriage and sexuality has made headlines, in part because of tensions with activists at some state universities in the Big 12 athletic conference. Meanwhile, key Baylor leaders have struggled to affirm their LGBTQ community – without erasing centuries of Christian moral theology.

The bottom line: This struggle is about doctrine, not politics or football.

That current doctrinal statement promises that Baylor “welcomes all students into a safe and supportive environment in which to discuss and learn about a variety of issues, including those of human sexuality. The university affirms the biblical understanding of sexuality as a gift from God. Christian churches across the ages and around the world have affirmed purity in singleness and fidelity in marriage between a man and a woman as the biblical norm. Temptations to deviate from this norm include both heterosexual acts outside of marriage and homosexual behavior.”

Recently, 3,000 Baylor insiders – including some faculty, former regents and donors – signed an “open letter” urging the administration to change its stance denying official recognition to the campus LGBTQ group. Making this change would not signal that “Baylor University condones all aspects of the organization,” stated these “members of the Baylor family.” Baylor leaders, they concluded, will not want to “look back in a few years and realize that we were on the wrong side of an issue of basic compassion and human dignity.”

In response, a “Save Baylor Traditions” petition urged regents and administrators to “stand strong” and retain ties to mainstream Texas Baptists.

“It is certainly within the best interest of the university to abide by traditional Christian principles,” stated this petition. “If this is unacceptable to some, they are free to associate themselves with a school which more closely aligns with their position.”

Terry Mattingly is the editor of GetReligion.org and Senior Fellow for Media and Religion at The King’s College in New York City. He lives in Oak Ridge, Tennessee.