Jones was assigned to the "Kitzmiller v. Dover Area School District" bench trial, the first direct challenge brought in the federal courts against a school district that mandated the teaching of intelligent design. He was praised by Tom Ridge, former Pennsylvania Governor and former head of the Department of Homeland Security, who said that "I can't imagine a better judge presiding over such an emotionally charged issue ... he has an inquisitive mind, a penetrating intellect and an incredible sense of humor."