Today secular philosophers call that kind of divine invocation "God of the gaps"—which comes in handy, because there has never been a shortage of gaps in people's knowledge.

As reverent as Newton, Huygens, and other great scientists of earlier centuries may have been, they were also empiricists. They did not retreat from the conclusions their evidence forced them to draw, and when their discoveries conflicted with prevailing articles of faith, they upheld the discoveries. That doesn't mean it was easy: sometimes they met fierce opposition, as did Galileo, who had to defend his telescopic evidence against formidable objections drawn from both scripture and "common" sense.

Galileo clearly distinguished the role of religion from the role of science. To him, religion was the service of God and the salvation of souls, whereas science was the source of exact observations and demonstrated truths. In a long, famous, bristly letter written in the summer of 1615 to the Grand Duchess Christina of Tuscany (but, like so many epistles of the day, circulated among the literati), he quotes, in his own defense, an unnamed yet sympathetic church official saying that the Bible "tells you how to go to heaven, not how the heavens go."

The letter to the duchess leaves no doubt about where Galileo stood on the literal word of the Holy Writ:

In expounding the Bible if one were always to confine oneself to the unadorned grammatical meaning, one might fall into error….

Nothing physical which … demonstrations prove to us, ought to be called in question (much less condemned) upon the testimony of biblical passages which may have some different meaning beneath their words….

I do not feel obliged to believe that the same God who has endowed us with senses, reason and intellect has intended us to forgo their use.

A rare exception among scientists, Galileo saw the unknown as a place to explore rather than as an eternal mystery controlled by the hand of God.

As long as the celestial sphere was generally regarded as the domain of the divine, the fact that mere mortals could not explain its workings could safely be cited as proof of the higher wisdom and power of God. But beginning in the sixteenth century, the work of Copernicus, Kepler, Galileo, and Newton—not to mention Maxwell, Heisenberg, Einstein, and everybody else who discovered fundamental laws of physics—provided rational explanations for an increasing range of phenomena. Little by little, the universe was subjected to the methods and tools of science, and became a demonstrably knowable place.

Then, in what amounts to a stunning yet unheralded philosophical inversion, throngs of ecclesiastics and scholars began to declare that it was the laws of physics themselves that served as proof of the wisdom and power of God.

One popular theme of the seventeenth and eighteenth centuries was the "clockwork universe"—an ordered, rational, predictable mechanism fashioned and run by God and his physical laws. The early telescopes, which all relied on visible light, did little to undercut that image of an ordered system. The Moon revolved around Earth. Earth and other planets rotated on their axes and revolved around the Sun. The stars shone. The nebulae floated freely in space.

Not until the nineteenth century was it evident that visible light is just one band of a broad spectrum of electromagnetic radiation—the band that human beings just happen to see. Infrared was discovered in 1800, ultraviolet in 1801, radio waves in 1888, X rays in 1895, and gamma rays in 1900. Decade by decade in the following century, new kinds of telescopes came into use, fitted with detectors that could "see" these formerly invisible parts of the electromagnetic spectrum. Now astrophysicists began to unmask the true character of the universe.

Turns out that some celestial bodies give off more light in the invisible bands of the spectrum than in the visible. And the invisible light picked up by the new telescopes showed that mayhem abounds in the cosmos: monstrous gamma-ray bursts, deadly pulsars, matter-crushing gravitational fields, matter-hungry black holes that flay their bloated stellar neighbors, newborn stars igniting within pockets of collapsing gas. And as our ordinary, optical telescopes got bigger and better, more mayhem emerged: galaxies that collide and cannibalize each other, explosions of supermassive stars, chaotic stellar and planetary orbits. Our own cosmic neighborhood--the inner solar system--turned out to be a shooting gallery, full of rogue asteroids and comets that collide with planets from time to time. Occasionally they've even wiped out stupendous masses of Earth's flora and fauna. The evidence all points to the fact that we occupy not a well-mannered clockwork universe, but a destructive, violent, and hostile zoo.