Charlie Hebdo has suddenly become the best-known example of a venerable French tradition: vituperative and unrelenting anti-religious satire, a provocative yet regular phenomenon of French public life. And now—not, alas, for the first time in that nation’s history—it has occasioned actual bloodshed.

Lampooning of the Bible, Christian doctrine, and clergy dates back almost 400 years to the “strong thinkers,” French learned skeptics in the 16th century. The primary target of anti-religious satire was France’s official religion, Catholicism, the Church’s ties to the state, and its control over education. And the ridiculing wit long directed against these targets would eventually play a central and crucial role in reducing the status and influence of religion in the French Republic.

This tradition began among a small number of French theology students studying in Italy, where they encountered Renaissance humanism—free of the magisterial synthesis of Aristotelianism and Catholicism provided by St. Thomas Aquinas. Reading Aristotle, and newly re-discovered ancient materialists like Epicurus and Lucretius, as rejecting the immateriality and immortality of the soul, Pietro Pompanazzi (1463–1525) and Cesare Cremonini (1550–1631) fomented skepticism among their French students.

But unlike the editors of Charlie Hebdo, these men did not wear their irreligiosity on their sleeves. Cremonini’s motto was “think inwardly as you like, but conform outwardly to custom.” Public irreligion, Cremonini understood, was too dangerous, as the executions of Etienne Dolet (in Paris in 1546) and Cesare Vanini (in Toulouse in 1619) made all too clear. Skepticism was therefore limited to trusted and learned circles.

Gabriel Naudé (1600–53) imported a version of Paduan Aristotelianism to France, and became part of a small number of self-described “strong thinkers,” polymaths who did not flinch from rejecting popular beliefs, including religion. He wrote subtly, hiding impiety through double entendre, indirect Biblical criticism, and erudition....