The Protestant Reformation led to the Enlightenment, which had a lot of advantages but also had the disadvantage of “science” increasingly replacing religion over the following centuries—not science, which is the facts and only the facts, but “science,” which is a certain kind of religion masquerading as science. That is, the Protestant Reformation, which challenged the traditional religious authorities, led to the Enlightenment, which in turn led to scientism. Ultimately, the best answer to the Protestant-Reformation-Enlightenment question isn’t atheistic science. Why? Because atheistic science is impossible in the long term; atheistic science is the death of religion, and from the meaninglessness of atheism is born the next religion.

The best answer to the Protestant-Reformation-Enlightenment question is to purify science of religion, purify religion of science, and then make religion and science like the left and right sides of the brain: semi-autonomous, but communicatively connected.

Modern science is in part a degenerate manifestation of physicalism. Traditional optics has as its epistemological foundation introspection into the subjective experience of light; the congenitally blind, who lack that kind of subjective experience, wouldn’t be able to understand. But modern optics, being physicalist, doesn’t rely on introspection, doesn’t rely on subjective experience. For modern optics, like modern science in general, the different sensory modalities are interchangeable. The congenitally blind, despite not being able to see the physical world, even in their mind’s eye, can nevertheless understand it. They can touch it, for instance.

There’s nothing degenerate about that, of course, the degeneracy coming only later: when it got popular, especially in the late-19th and early-20th centuries, not only to think of physical science as the only legitimate kind of science but also to make a religion out of it.