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In Benedict’s letter, the pope emeritus takes Mr. Odifreddi to task for what he said was the “aggressiveness” of his book, and responds to many of the arguments raised with piqued criticism himself.

“What you say about the figure of Jesus isn’t worthy of your scientific standing,” wrote Benedict, who authored a highly praised, three-volume work on the Jesus Christ during his pontificate.

He similarly criticizes Mr. Odifreddi’s “religion of mathematics” as “empty” since it doesn’t even consider three fundamental themes for humanity: freedom, love and evil.

On evolution, he wrote: “If you want to substitute God with Nature, the question remains: What does this Nature consist of? Nowhere do you define it and it appears rather like an irrational divinity that doesn’t explain anything.”

Mr. Odifreddi, for his part, wrote in an accompanying piece Tuesday that he was stunned to have received the letter, though he said he wrote the book precisely in hopes Benedict might read it. He said he sought, and obtained, Benedict’s permission to publish the letter.

He said he planned to reissue his book with Benedict’s letter included: “an unprecedented dialogue between a theologian pope and an atheist mathematician, divided in most everything but drawn together by at least one objective: the search for Truth.”