The holes in the windows, which depict the Magi on their way to Bethlehem, Jesus on a pinnacle and the Transfiguration, are about 5 to 10 inches in diameter, officials said. The windows are about 30 feet off the ground, officials said, suggesting that large rocks were thrown at them.
Duke President Richard Brodhead called the vandalism a "sad, stupid act (that) is an insult to every member of the Duke community." The university is investigating the case to identify the culprits, he said.
Investigators have no suspects, Duke Police Chief John Dailey said, adding that the damage likely occurred during or after an outdoor concert for students.
Duke held a celebration Wednesday night to recognize the end of classes for the spring semester, so hundreds of people were on campus.
There was no estimate on the cost of the damage. Duke routinely hires a contractor to restore the 75-year-old stained glass in the Gothic chapel, and Sam Wells, dean of the chapel, said the firm would likely be brought in to repair the three windows.
"I have no worries that the damage can be repaired," Wells said.
Because of the size of the rocks used and the fact that they had to be hurled with great force and accuracy, Wells said he doesn't consider the broken windows to be "a spontaneous act of vandalism."
Still, he said, he doesn't understand why anyone would damage the chapel windows.
"I don't see that this is necessarily an attack on Christianity or even an attack on Duke," he said. "I think the person who has done it is trying to say something, but what they are trying to say is a mystery to me. It could perhaps even be a mystery to them."
Lauren Sims, a student at the Duke Divinity School, said she was heartbroken to learn about the broken chapel windows.
"This is part of a symbol of what we are as Duke," Sims said, adding that she hopes people's feelings can be repaired as easily as the windows.
"It's not about getting back. It's not about getting even. It's about seeing the hope and working for reconciliation," she said.
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