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Dr. Samuel Wilkinson was in his first year of medical school at Johns Hopkins University when the question that was percolating in his mind came to a head: Was his belief in God compatible with the theory of evolution? This question stirred up a kind of existential debate in Wilkinson, who at the time had just graduated from Brigham Young University, gotten married and moved to Baltimore. “The theory of evolution has been a stumbling block — more than a stumbling block — for people of faith for a long time,” said Wilkinson, an associate professor of psychiatry at Yale School of Medicine.