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ATLANTA — A reception Friday at Emory University to celebrate the work of the Southern Christian Leadership Conference (SCLC) in the years after the assassination of the Rev. Martin Luther King Jr. could have been more poorly timed, but not by much.

All week long, the president of Emory, James Wagner, had been trying to rewind a column he had written for the university magazine. In it, he praised the 1787 three-fifths compromise — which allowed each slave to be counted as three-fifths of a person in determining how much congressional power Southern states would have — as an example of how polarized people could find common ground.

It was, he has since said, a clumsy and regrettable mistake.

A faculty group censured him last week for the remarks. In a speech at Friday’s reception for the campus exhibition, “And the Struggle Continues: The Southern Christian Leadership Conference’s Fight for Social Change,” Wagner acknowledged the nation’s continuing education in race relations and his own.

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“I know that I personally have a long way to go,” he said.

His article has been seized upon by students and faculty members who say it was one more example of insensitivity from the Emory administration, which in September announced sweeping cuts that some say unfairly targeted programs popular with minorities.

About 45 students showed up to protest at the reception, silently holding signs that read “This is 5/5 outrageous” and “Shame on James” as the fight for racial equality was discussed by Wagner; Rep. John Lewis of Georgia, a veteran of the civil-rights movement; and leaders of the SCLC.

Whether the cuts — which include phasing out the departments of physical education and visual arts, the journalism program, and graduate programs in economics and Spanish — disproportionately affect racial minorities is in dispute at the university, where minority members make up 31 percent of the students.

Certain programs that focused on or made recruiting minority members a priority have been shifted to other departments or eliminated, but university officials say the impact will not be as drastic as protesters think.

Savings will be reinvested in other departments, including neurosciences, studies of contemporary China and new-media studies.

Such academic realignment is starting to happen at liberal-arts colleges nationwide, said Phil Kleweno, of global consulting firm Bain, who specializes in higher education.

“Not every school can excel in every subject,” he said. “Given where we are financially, these are wise decisions for many universities to make.”

In an interview Friday, Wagner said neither the cuts nor his self-described gaffe in Emory Magazine was intended to hurt what he described as a vibrant multicultural environment at the college.

The president’s misstep was only the latest episode in what one Emory administrator called “quite a challenging year” for the private university, which some call the Harvard of the South. (Emory boosters prefer to call Harvard University the Emory of the North.)

Although still listed as the 20th-best university in the nation in U.S. News & World Report’s latest ranking, Emory admitted in August that it had intentionally sent incorrect test scores to the magazine and the Department of Education for more than a decade.

The university has also debated over whether to allow Chick-fil-A, whose conservative Christian owners have donated large amounts of money to organizations opposed to same-sex marriage, to operate on campus.

In October, Wagner officially apologized to Jewish dental students who had been failed, harassed or both under John Buhler’s tenure as dean of the dental school from 1948 to 1961.

Many saw the apology for that chapter in Emory’s history, when up to 65 percent of Jewish students had to redo course work or were failed, as a healing move in keeping with the culture of the university, which has devoted years to studying its own racial history, the good and the bad.

The school, which is 177 years old, was named for John Emory, a Methodist bishop who owned slaves. Although many of its leaders favored segregated education, the school decided in 1962 to sue the state for the right to enroll students regardless of race.

More recently, the school has dealt with a fraternity that flew a Confederate flag and an anthropology professor who used a racial epithet in class. But it also houses significant collections of African-American historical artifacts and literature, including what is thought to be the nation’s most complete database documenting U.S. slave-trade routes.

“Emory is a community that airs its laundry,” Wagner said, calling that a strength and a demonstration of its ability to evolve with its students.

“We’ve had several wounds this year,” he said. “This one,” he added, referring to the magazine column, “is a particularly painful wound for me because it was self-inflicted.”

Leslie Harris, a history professor and the director of a series of campus events that for five years examined issues of race at Emory, said she was troubled by the intellectual holes in Wagner’s argument.

In his column, Wagner used the congressional fight over the national debt to muse on the importance of compromise, which he called a tool for noble achievement.

“The constitutional compromise about slavery, for instance, facilitated the achievement of what both sides of the debate really aspired to — a new nation,” he wrote.

That is a deep misunderstanding of history, Harris said.

“The three-fifths compromise is one of the greatest failed compromises in U.S. history,” she said. “Its goal was to keep the union together, but the Civil War broke out anyway.”

To members of the SCLC, whose records are housed at Emory’s Manuscript, Archives, and Rare Book Library, the protesters at the reception were a welcome sign.

“I love it,” said Brenda Davenport, who has served as the national volunteer and youth organizer for the SCLC. “Where else would you want protesters to show up but at something that is about the value of protesting?”

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