When a man in the cheap seats near the top of Notre Dame's Joyce Center interrupted President Obama's commencement speech, shouting "Abortion is murder," the crowd boo'd loudly, then errupted into the cheer, "We are ... ND!" To which Obama responded, "We're not going to shy away from things that are uncomfortable."
Obama tackled the controversy surrounding his speech  at the Catholic university directly, calling for "fair-minded words" and a "presumption of good faith" to those with whom we disagree. Applause for this line: "Those who speak out against stem cell research may be rooted in admirable conviction about the sacredness of life, but so are the parents of a child with juvenile diabetes who are convinced that their son’s or daughter’s hardships might be relieved." (Read the complete text. )
Jenkins also mentioned the controversy in his introduction of Obama, but stressed the importance of dialogue, especially at a Catholic university. The crowd burst into applause when Jenkins pointed out that most of the attention has focused on Notre Dame's invitation to Obama, but little attention on his decision to accept.
"President Obama has come to Notre Dame, though he knows well that we are fully supportive of church teaching on the sanctitity of human life (interupted by applause) and we oppose his policies on abortion and embrynoic stem cell research. Others might have avoided this venue for that reason. But President Obama is not someone who stops talking to those with differ with him. (More applause) Mr. President: This is a principle we share." (Applause)
The cheers and standing ovation that greeted the president when he entered the Joyce Center were repeated when Obama recieved his honorary degree, which specifically cited his "willingness to engage with those who disagree with him and encourage people of faith to bring their beliefs to the public debate." The yellow crosses and baby's feet on the top of the caps of about a dozen students protesting the president's appearance disappeared during the degree conferral, as those students remained seated.
A man tried to shout down the president and was escorted from the center, just as the president joked that honorary degrees are "pretty hard to come by. So far I'm only one for two as president" (a refererence to Arizona State University's decision to not give him an honorary degree). He also joked again about his willingness to join the Bookstore basketball team named after him. "Next year, if you need a 6'2" forward with a decent jumper, you know where I live."
The third interruption, again from the seats near the press box where parents and guests were seated, came, somewhat ironically, as Obama was saying, "Your generation must find a way to reconcile our ever-shrinking world with its ever-growing diversity: diversity of thought, of culture, and of belief. In short, we must find a way to live together as one human family."
His speech closed with a story--on this, the anniversary of Brown v. Board of Education--about the Civil Rights Commission, which included former ND president Father Ted Hesburgh (who received almost as much applause as Obama). As the story goes, the group had difficulty finding a hotel or restaurant that would serve the black and white members of the commission together. So Father Ted flew the group to the university's retreat house in Wisconsin, where they hammered out what would eventually become the Civil Rights Act of 1964.
"Years later, President Eisenhower asked Father Ted how on Earth he was able to broker an agreement between men of such different backgrounds and beliefs," Obama said. "And Father Ted simply said that during their first dinner in Wisconsin , they discovered that they were all fishermen. And so he quickly readied a boat for a twilight trip out on the lake. They fished, and they talked, and they changed the course of history."
Obama implored the graduates to remember that lesson. "Remember that in the end, in some way we are all fisherman," he said. "If nothing else, that knowledge should give us faith that through our collective labor, and God’s providence, and our willingness to shoulder each other’s burdens, America will continue on its precious journey towards that more perfect union."