"I never sought to conceal these things," the pope said of cases of clerical abuse, and lamented the scholar depicting the church as the only place where such "deviation" and "filth" occur.

The publication of the retired pope's comments Sept. 24 to an atheist scholar came the same month a written letter by Pope Francis to an Italian journalist concerning dialogue with nonbelievers was published. Both letters were published, with the two popes' permission, by the Italian daily La Repubblica.

The paper released long excerpts of Pope Benedict's original 11-page response to Piergiorgio Odifreddi, a prolific science writer who authored the book, "Dear Pope, I Write to You" in 2011. The book, presented as a letter to Pope Benedict, proposes the superiority of a worldview in which belief should stem only from things that can be understood and empirically known over worldviews that include belief in things that cannot be fully understood or known.

The pope's response, dated Aug. 30, thanked Odifreddi for seeking to juxtapose his ideas against the pope's own writings "and, thus, with my faith."

The pope, who has long engaged in dialogue with nonbelievers, most notably with his "Courtyard of the Gentiles" initiative and his 2011 Assisi gathering, said he appreciated Odifreddi's efforts to engage in a frank and open dialogue with the Catholic faith.

However, the pope said he met "with deep dismay" Odifreddi's unspecified comments about the clerical abuse scandals.

The pope, who was the first pontiff to meet with abuse victims, had spoken out forcefully against "the filth" in the church, clarified church laws to expedite cases, and mandated bishops' conferences put in place stringent norms against abuse, among a number of other initiatives.

In his letter, the pope said he never tried to cover up allegations.

"That the power of evil seeps all the way into the inner world of the faith is a source of suffering for us." Not only must the church bear the burden of this evil, but it also must "do everything possible so that such cases never repeat themselves," he wrote.

While there "is no reason to find solace in the fact that, according to research by sociologists, the percentage of priests guilty of these crimes is no higher than those present in other similar professional fields," neither should people "ostensibly present this deviation as if it were filth pertaining only to Catholicism," Pope Benedict wrote.

Just as it is wrong "to be silent about the evil in the church," it is wrong to remain silent about the good, holy and loving service the church has offered, he said.

Pope Benedict said he read Odifreddi's book "with pleasure and benefit."

However, he also offered some sharp criticisms against Odifreddi's arguments as well as his neglect of and lack of explanation for very real and observable phenomena such as love, liberty and evil.

The pope said it was curious that someone like Odifreddi, who considers theology to be nothing but "science fiction," would even consider the pope's works as "worthy of such a detailed discussion."

The retired pope said one of the things the two men have in common is a belief in a First Cause to the universe, only Odifreddi replaces God with "Nature" as the origin.

"But the question remains, who or what is this nature," the pope asked.

Nowhere does the scholar offer a definition, making "it appear, therefore, as an irrational divinity that explains nothing."

Concerning Odifreddi's "religion of mathematics," the pope said nowhere does this belief system consider three major human realities: "freedom, love and evil."

"I'm amazed that with just one stroke you eliminate freedom, which has existed and is the fundamental principle of the modern era."

"Whatever neurobiology says or doesn't say about freedom, this is present as a decisive reality in the actual unfolding of our history, and it must be taken into consideration."

Odifreddi's religion of mathematics also lacks any thought or discussion about love and evil, too, the pope said.

"A religion that neglects these fundamental questions remains empty," he said.

The pope, who has also long-supported the compatibility of faith and science as both being dedicated to the truth, underlined that the task of theology is to keep religion and reason closely connected.

One without the other will lead to certain dangerous "pathologies" in either religion or reason, he said.

Pope Benedict said science fiction exists in many areas of science, especially in some theories about the beginning and end of the world.

"I would define (Odifreddi's thoughts on this) as science fiction in the good sense of the word -- they are views and forecasts in order to reach real understanding, but they are, in fact, only (products of) imagination with which we try to get closer to reality."

The pope also gave Odifreddi some recommended readings to address the mathematician's doubts about being able to know anything for certain about the historical figure of Jesus.

Just because there is shoddy research out there "doesn't compromise the importance of serious historical research," which has brought real and certain knowledge about the figure of Jesus, the pope said.

He said "historical-critical exegesis is necessary for faith, which doesn't propose myths" out of historical figures and events, but demands a history that is based on truth and facts, and presents such findings with scientific rigor.

"All of my efforts have been aimed at showing how the Jesus described in the Gospels is also the real historical Jesus; that it is history that has really taken place," Pope Benedict said, referring to his writings on Jesus of Nazareth.

The pope ended his letter admitting he may have been harsh in some of his criticisms, but that "frankness is part of dialogue."