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All week long, the president of Emory, James W. Wagner, had been trying to rewind a column that he had written for the university magazine. In it, he praised the 1787 three-fifths compromise, which allowed slaves to be counted as three-fifths of a person as a way to determine how much Congressional power Southern states would have, as an example of how polarized people can find common ground.

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

A faculty group censured him last week for the remarks. And 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," Dr. Wagner acknowledged both the nation's ongoing education in race relations and his own.

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

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

About 45 protesting students showed up at the reception, silently holding signs that read "This is 5/5 outrageous" and "Shame on James" as Dr. Wagner; Representative John Lewis of Georgia, a veteran of the civil rights movement; and leaders of the S.C.L.C. spoke about the fight for racial equality.

Whether the cuts, which include the elimination of physical education, visual arts, journalism, and graduate programs in economics and Spanish, disproportionately affect racial minorities is in dispute at the university, whose student body is 31 percent minority.

Certain programs that focused on or made recruiting minorities a priority have been shifted to other departments or eliminated, but university officials say the numbers are not as drastic as protesters believe.

Savings from the reorganization 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 around the country, said Phil Kleweno, a consultant at Bain & Company 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, Dr. 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 incident 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 the 20th best university in the nation in U.S. News and 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 grappled over whether to allow Chick-fil-A, whose conservative Christian owners have donated large sums of money to organizations opposed to gay marriage, to serve food on campus.

And in October, Dr. Wagner officially apologized to Jewish dental students who had either been failed, harassed or both under John E. Buhler's reign as dean of the dental school from 1948 to 1961.

Many had seen the apology for that chapter in Emory's history, when as many as 65 percent of Jewish students had to redo coursework or were failed, as a forward-thinking and healing move in keeping with the culture of the university, which has devoted years to studying its own racial history, both the good and the bad.

The school, which is 177 years old, was named for John Emory, a slave owner. Although many of its leaders favored segregated education, the school decided in 1962to 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 history and literature, including what is arguably the nation's most complete database documenting American slave trade routes.

"Emory is a community that airs its laundry," Dr. Wagner said, calling that a strength and a demonstration of its ability to evolve with its student body.

"We've had several wounds this year," he said. "This one is a particularly painful wound for me because it was self-inflicted."

Jovonna Jones, 19, the president of the Black Student Alliance at Emory, said she forgave Dr. Wagner for his transgression.

"As an African-American woman who has gone to predominately white institutions since middle school, I've had lots of incidents like this," she said. "It's hard to be shocked any more."

People keep asking her if she thinks the university president is a racist, Ms. Jones said.

"I don't think that's the real question," she said. "The important question is: What does it mean to embrace and value a diverse student body? What are the values of the school?"

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

In his column, Dr. 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, said Dr. Harris.

"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 S.C.L.C., whose records are housed in Emory's Manuscript, Archives, and Rare Book Library, the protesters at the reception were a welcome sign.

"I love it," said Brenda Davenport, once the national volunteer and youth organizer for the S.C.L.C. "Where else would you want protesters to show up but at something that is about the value of protesting?"