Editor's Note: Excerpted with permission from Imagine There’s No Heaven: How Atheism Helped Create the Modern World, by Mitchell Stephens. Available from Palgrave Macmillan. Copyright © 2014.

Science’s contributions to the spread of disbelief is the least controversial segment of the virtuous cycle for which I am arguing in seventeenth-century Europe. For science’s methods are clearly troublesome for religion. The devout, to begin with, are not wont to view their precepts merely as propositions to be controverted or confirmed. The orthodox, as a rule, are used to arguments being settled by authority, not experiment. The hope belief offers does not always stand up well to observation and experience: life sometimes works out okay; sometimes it doesn’t. Faith, particularly of the “certain-because-impossible” variety, and reason have long been tussling. Miracles are notoriously miserly with evidence. Revelation does not lend itself to experimental verification. And the mystical, by its nature, fails to produce facts.

When it is employed, the scientific method, consequently, has a way of uncovering information that is inconvenient for religion. Conflicts are inevitable with ancient holy books—most of which do end up proclaiming something or other on “how” the earth works or “heaven goes.” Scientists in these centuries diverged from Scripture at their peril. Galileo learned that. But in the end the greater cost would be borne by the holy books. Catholic leaders did indeed have reason to fear that, in taking Copernicus’ theory seriously, Galileo might encourage people to take the Bible less seriously.

Consider, for another example, the questions reason and experience were, cautiously, raising in Europe at this time about the account of Noah’s flood in Genesis: From whence did all that water—enough to cover “all the highest mountains everywhere”—come? Where did it go after those “forty days and forty nights” ended? How could one ark (Genesis specifies its dimensions) hold so many pairs of creatures? Were fish or birds on board? Observations led to more questions: what about all those new animals being discovered in America?

The discovery of fossils of sea animals far from the sea seemed to some scientists to provide a needed boost to the credibility of the flood story. “From all this,” one scientist told the Royal Society at the start of the eighteenth century, “it sufficiently appears, that there was a time when the water overflowed all our earth, which could be none but the Noachian deluge.” One of the seventeenth century’s great fossil collectors and naturalists, John Ray, thought the matter out a little more deeply, however, and noted that a quick flood should have deposed sea animals evenly over the earth, which was not how fossils were distributed. Ray also observed that some of those fossilized sea animals no longer exist. Shouldn’t they have been saved with Noah on the ark?

And with science continuing to pick up speed, new observations kept arriving. The British scientist Edmond Halley undertook some calculations in 1694:

The Rain of forty Days and Nights will be found to be a very small Part of the Cause of such a Deluge, for supposing it to rain all over the Globe as much in each Day, as it is now found to do in one of the rainiest Counties of England in the whole Year, viz. about forty Inches of Water per Diem, forty such Days could cover the whole Earth with but about twenty two Fathom Water, which would only drown the low Lands next the Sea.

Halley did have to abjure. Acting on the advice of “a person whose judgment I have great cause to respect,” he hastily retreated from his incautious analysis. However, the doubts being raised about holy writ by scientifically inclined minds were not so easily eased. John Keill, a scientist with a strong religious bent, saw the danger: “These contrivers of Deluges have furnished the Atheist with an argument which . . . is not so easily answer’d as their theories are made,” Keill concedes.

Religion is resilient, no doubt about that. When discussions in sacred texts become difficult to defend as historical they are defended as metaphorical. Still, seventeenth-century science was increasingly placing religion on the defensive. When biblical tales such as that of Noah are shown to have been unlikely, that makes it a little harder to subscribe to the truth of the Bible and a little easier to dismiss it.

In 1623, Marin Mersenne, a monk who was at the center of a lively and productive intellectual correspondence, insisted that Paris alone harbored 50,000 atheists. In 1652, the English physician and scientist Walter Charleton wrote that his country “has of late produced . . . more swarms of atheistical monsters . . . than any age, than any nation has been infested withal.” Both likely were exaggerating or mislabeling attenuated Christianity as atheism. Europe’s infestation of true, there-is-no-God “atheistical monsters” was probably still rather small.

But disbelief was, indeed, growing. And the science in which both Mersenne, an important correspondent of Galileo’s, and Charleton were participating was taking the lead in that questioning: Did the sun really stop in the sky for Joshua? Was the entire earth actually flooded? If the mathematics of gravity can explain movements of the planets, what need is there for an omnipotent Being?

Scientists can, of course, be religious. With rare exceptions (Galileo and Halley possibly among them), the men who made the Scientific Revolution appear to have sensed God behind what they were learning of the natural world. Their increasingly diligent observations, their telescopes and their microscopes enabled them to see what humans had never before seen. Their first reaction was awe, and they understood awe as a religious emotion: “'Tis the contemplation of the wonderful order, law and power of that we call nature,” writes Robert Hooke, inventor of the microscope, “that does most magnify the beauty and excellency of the divine providence, which has so disposed, ordered, adapted and empowered each part so to operate as to produce the wonderful effects which we see.”

The logic of these awe-struck early scientists sometimes appears to have flagged, as the historian Richard S. Westfall has noted: The “beauty and excellency” of the universe are used to prove that there is a God, and He is good. And if we see things that are ugly and unpleasant—such as “mice, cockroaches or snakes”? Well, they simply “serve,” as Walter Charleton put it, “as a foil to set off beauty.” How do we know that? Because, in essence, there is a God and He is good.

A similarly circular path leads to the conclusion that, in the words of that proponent of experimentation Francis Bacon, “the world was made for man.” This happy fact is demonstrated by the world’s multitudes of helpful touches, including, according to one of these scientists, the horse’s ear, which conveniently turns backward to better hear commands. Thus we comprehend God’s plan. And if we happen to see some things that don’t appear to be doing a lot for humankind—distant heavenly bodies, for example, or the aforementioned snakes—well, that’s just a sign that we can never fully comprehend God’s plan.

Isaac Newton, the greatest of these “natural philosophers,” shared the awe felt by his contemporaries and drew similar conclusions from it. (There appears to have been a fair amount of feigning religious belief in the seventeenth century, but it seems unlikely that Newton’s expressions of faith could be explained that way since they appear in numerous private as well as public writings.) Indeed, he added the following line to the second edition of his monumental Philosophiæ Naturalis Principia Mathematica: “This most elegant system of the sun, planets, and comets could not have arisen without the design and dominion of an intelligent and powerful being.” Some scientists at the time found evidence of this “design” in the complexity of the universe; Newton, having worked out his astoundingly powerful means for understanding the universe, marveled, instead, at “the simplicity in all the works of the Creator.”

Yet Newton and these other seventeenth-century scientists generally managed to keep their awe from interfering with their investigations. The first edition of Newton’s Principia, published in 1687, did not contain any discussion of “an intelligent and powerful being.” It does not contain any discussion of theology whatsoever. It was only after his book was criticized by Gottfried Leibniz and others for impiety—for presenting space, gravity and the universe in a way that appeared not to support an orthodox conception of God—that Newton added a section discussing God’s role. Newton believed, but he had initially managed to produce a mathematical understanding of motion, which merely made intelligible the workings of the entire cosmos, without any overt reference to that belief.

The first edition of Newton’s book, with God conspicuously absent, helps form, then, another segment of the virtuous cycle created by science and disbelief (“atheism” would be too strong a word here) in seventeenth-century Europe. The argument is that if Newton had dwelt in his book on God’s role, he might not have done such a magnificent job of working out gravity’s role. If he were more fearful of challenging understandings of God, if he were more content with ceding responsibility to the whims of God, if he thought human reason could never comprehend God’s Creation, Newton might not have been able to outline so persuasively a physics and mathematics that manage to function so impressively on their own.

Isaac Newton was not above dabbling in the occult. He spent decades experimenting with alchemy—making use of mystical sources and hoping to come upon long-lost mystical secrets. The man who devised calculus, understood inertia and quantified gravity also seemed obsessed (a word that often comes to mind with Newton) with uncovering hidden secrets in the Bible, which included, he suspected, a chronology of the past and the future.

Newton was, in other words, ready to use religion in his immense and unceasing efforts to figure things out. But he was less ready to allow religion to interfere with those efforts. “It is the temper of the hot and superstitious part of mankind in matters of religion ever to be fond of mysteries,” Newton writes, “and for that reason to like best what they understand least.”

“The progress of religion is defined,” writes the early-twentieth-century philosopher Alfred North Whitehead, “by the denunciation of gods.” Gods become fewer in number until there is only one—or a Father, Son and Holy Ghost adding up to one. And the qualities of the lonely God that is left are also denounced. He loses His home: God is no longer to be found inside a temple or even, after airplanes, enthroned atop a cloud. He loses His physical form: His beard, His voice, perhaps His body or even His gender. He is neither seen nor heard in public. He grows wispier, more abstract.

Newton, the scientist, probably was responsible for subtracting—denouncing—among the most important of God’s qualities: his daily responsibility for the workings of the heavens. And in his private scribblings on religion, Newton engaged in a fair number of additional denunciations, too.

This mathematician, who taught at Cambridge’s Trinity College, was, for example, offended by the odd arithmetic of the Trinity—insisted upon by Anglicans as well as Catholics. He inclined, in his private writings, toward a view of Jesus as human rather than as one of three parts of one God. In addition, this physicist was suspicious, as was Spinoza, of the idea that miracles “are the works of God” rather than just rare and poorly understood phenomena. Like Spinoza, Newton, when writing for himself, also had no use for a corporeal view of God. Indeed, Newton—when not looking for hidden predictions, at least—was partial to Spinoza’s reading of the Bible as a human document.

In the historian Richard S. Westfall’s view, Newton was a “religious rationalist.” He was looking for a stripped-down version of religion: one compatible with his physics. He was also looking for the principle that all religions have in common: “the law of righteousness and charity,” he called it. A religious rationalist, however, is not an easy thing to be.

To maintain a rational view of “the Author of the system” it would be necessary, for example, to resolve the contradictions that seem inherent in most conceptions of God. There is, for example, that old conundrum about omnipotence—given a twenty-first-century formulation on The Simpsons: “Could Jesus microwave a burrito so hot that He Himself could not eat it?” There is also Carneades’ argument, presented in chapter 2, that a being without flaws or weaknesses couldn’t exhibit virtues. One question Newton and his contemporaries certainly struggled with was what role a Perfect Being would have after a presumably perfect Creation. Wouldn’t He be redundant post-Genesis—after functioning as the First Cause? Wouldn’t Jehovah end up resembling one of the Epicurean gods—left with no responsibility but to enjoy Himself?

A “religious rationalist” would also somehow have to get right the relationship between the natural and the supernatural: what status would natural laws have if a Being exists who is outside of them and violates them at least for the Creation? It would be necessary, too, to square science’s methods with any sort of reliance upon religious authority, including that Bible whose secrets Newton was so interested in revealing. In addition, to be a “religious rationalist,” in Newton’s sense, would require precipitating “righteousness and charity” out of holy texts that do not always seem to embody them and out of a universe that does not always seem to display them.

These tasks may have been beyond the abilities of even this most able of men. Newton wrote out his private treatises on religion—and then rewrote them and rewrote them again. One appeared in at least five versions. As an old man, the Isaac Newton who had gotten the physics of the heavens right was still trying to get this rational view of Christianity right.

But by then Newton had denounced enough to leave a rather hazy, unobtrusive God. In Newton’s understanding, and that of many of his scientifically inclined contemporaries, God was losing not only eyes, a nose, bluster and his two other manifestations, but the inclination to fiddle with natural laws.

So although he was a believer, Newton and his contemporaries help demonstrate what disbelief—or, in his case, limited belief—can contribute to science. His rejection of some of the more mystical and intrusive conceptions of God was probably necessary in order to give the sun and the planets leave to abide by equations. Newton’s physics, the point is, benefited from the rejection of some religious belief.

Science usually does. Its progress, we might say, is “defined” by the diminution of God. Science requires some separation from church. This was, after Galileo, becoming available in Europe in the seventeenth century. Hobbes and Spinoza—however wary they may have been about speaking too “boldly”—helped. And the tendency of scientists—Newton among them—to push aside assumptions they considered irrational or unhelpful certainly helped. Newton’s ability to leave God entirely out of the first edition of Principia Mathematica greatly helped.

A distinguished nineteenth-century atheist, Charles Bradlaugh, deserves the honor of making this point: “It is certainly a clear gain to astronomical science,” Bradlaugh writes in an essay, “that the church which tried to compel Galileo to unsay the truth has been overborne by the growing unbelief of the age, even though our little children are yet taught that Joshua made the sun . . . stand still.”