I wouldn't focus on individual issues as that will cause a backfire effect. He's probably familiar with the data and either rejects the source or rejects that it leads to a certain conclusion.

In that case, go an abstract route and ask him to articulate his philosophy of science. Follow up with questions that avoid the hot-button topics of evolution or parapsychology. As he's a doctor, I'd stick with his home turf, medicine--no one wants to be wrong in their own field. e.g. if science and religion are the same, why should we prefer antibiotics over exorcisms? If his philosophy of science requires no falsifiability, would he prescribe ionic bracelets? Then let him draw his own conclusions on the other issues. You can lead a surgeon to the OR but you can't make him operate.