Seventeen miles of underground tunnel, thousands of superconducting magnets, and protons whipped to a fraction below light speed have given the Large Hadron Collider a reputation that borders on myth.

At CERN’s Large Hadron Collider on the edge of Geneva, scientists have reported a surprising twist in the behavior of matter.

The long circular tunnel beneath the pine barrens in Upton, New York, came to a halt on a calm winter morning. For 25 years, ...