The nineteenth-century German theologian Rudolf Otto, in his book The Idea of the Holy, popularized the term "numinous", an adjective describing the sense of mystery and wonder that purportedly stems from the presence of a deity. According to Otto, the sense of the numinous had two main characteristics: the mysterium tremendum, the sense of fear and trembling that comes from the presence of that which is wholly other, and the mysterium fascinas, the sense of fascination and curiosity that such an experience evokes.

Otto's theology concisely sums up the categories of religious experience. But the problem with his conception of the numinous is that it lacks one very important quality - understanding.

For Otto, as for many theists, the numinous is not something we should seek to comprehend. We should cower in its presence, or chase after it, or both, but there is no mention of penetrating the mystery, learning what it truly is and how it works. There is no mention made of pulling back the curtain of our ignorance, nor of plumbing the depths of the strange and unknown until it becomes known and familiar.

This idea may seem sacrilegious to theists, but I answer that it's what humanity has been doing throughout its history: piercing the mysteries that surround us, drawing them back one by one, and learning ever more about who we are and what our place in the world is. We are great solvers of mysteries; we have never been content to live in ignorance.

After all, to primitive people, the world was a strange and terrifying place ruled by forces they could not comprehend. To them, everything they encountered was a mysterium tremendum et fascinans: thunderstorms and lightning, sunrise and sunset, the cycle of the seasons, the fall of the rains and the coming of prey, the growth of crops and the bearing of children. Every one of these things, and many more besides, was once a religious mystery before which we worshipped in terror and awe.

But through science and reason, we have pierced the veil of these mysteries. We have learned that natural forces, which once must have seemed like mighty and capricious gods, were in reality grand clockworks, controlled by the predictable unfolding of the mathematical laws that govern the cosmos.

Thunder and lightning are not the spears of the gods, before which we cower in terror; they arise from the buildup of electric potential between cloud and ground, and the shock wave caused by the rapid superheating of air when that potential is discharged. The seasons come from the earth's axial tilt as it orbits the sun. Fertility is no longer a compelling mystery, but a section of the evolutionary trajectory of life as it perpetuates itself. These mysteries and many more we have solved, setting aside primitive superstitions of ritual and sacrifice, and learning through reason how to use the laws of nature for our benefit.

What, then, of the numinous? Is every religious experience doomed to fade as our understanding grows?

I think not. Or, rather, I think the religious experiences of our childhood, born of superstition and fear, will die - but when understanding comes, they can be reborn in a stronger and purer form. Far from science robbing the world of awe and wonder, I think it's only science that makes true awe and wonder possible at all.

I remember standing in the rain of El Yunque, touching the leaf of a plant and contemplating our kinship, our both belonging to that unbroken tree of evolutionary history that unites all life on Earth. My sense of the transcendent was not undermined, but deepened and magnified by that knowledge, the insight into the vastnesses of time and space and the twisting paths of contingency that led to we two living things side by side in the rainfall. I look at my hands with the knowledge that they are shaped from the dust of exploded stars, and that looking up at the night sky, I am looking at the place of my origin. Many more examples like this could be given, proving that true understanding does not diminish awe, but enhances it immeasurably.

The religious experience is, at best, a stunted variety of this feeling. Awe without understanding, or at least the desire for understanding, degenerates into mysticism: viewing a mystery not as a challenge to be solved, but something to be worshipped for its own sake. Mysticism states that ignorance is a desirable condition, a state we should glory in. This attitude only keeps us frightened and ignorant, and worst of all, robs us of the deeper and more genuine awe that comes with comprehension. I say, let us explore. There may be problems too high or too deep for us, mysteries we cannot penetrate - but so far, we haven't found any, and if there are any, they will not need to be protected from our investigations.

The story goes that the renowned physicist Richard Feynman was once asked to summarize the most important finding of modern science in a single sentence. Feynman replied, "The universe is made of atoms."

Although there are many other scientific discoveries that are arguably of equal importance, Feynman's choice makes a lot of sense. The discovery of atoms is so familiar to us that it's easy to overlook its breathtaking significance. We know, at the smallest scale where it still makes sense to talk about distinct objects, what are the fundamental building blocks that matter is made of, and we have described their interactions with astounding precision. Our understanding of everything from why the stars shine, to how DNA replicates, to why a table is solid, relies on our knowledge of the way atoms behave.

Atomic theory is now so well-established, and so widely accepted, that it's easy to forget how controversial a notion it originally was. In fact, atomism was once synonymous with atheism, and it was the bête noire of Western religion not just for centuries, but for millennia.

It was in the fifth century BCE that the Greek philosophers Leucippus and Democritus first proposed the idea that matter was composed of indivisible particles called atoms. But these ideas came to their fullest flowering in the mind of their successor, Epicurus, who lived around 300 BCE. In Epicurean philosophy, the world was ultimately comprised of atoms and the void. All that exists and all that occurs - from flowing water to burning fire to human thought - is due to the movement and collision of atoms and the endless, ever-changing array of patterns they arrange themselves in. The ruling principles of the Epicurean cosmos are natural law and random chance, not purpose or plan, and we who live in it and are part of it can find happiness by learning to accept whatever happens with virtue and tranquility. Epicurus did believe that the gods existed - he saw this as the only way to explain the widespread dreams and visions of them - but in his philosophy, they were not supernatural spirits but material beings composed of atoms, just like humans. More importantly, they did not take any interest in human affairs; they were more like images than actual persons.

In scientific terms, it's impressive how much Democritus and Epicurus got right. They correctly anticipated the very discovery that Richard Feynman called the most important element of modern science. Epicurus even believed that atoms sometimes exhibited "random swerves", a startling point of agreement with modern quantum mechanics. If he had claimed that a god told him all this, it would have been by far the most impressive example of theism anticipating later scientific discovery, and genuinely difficult for an atheist to explain.

Yet to the theologians and churchmen who came after him, Epicurus' ideas were the depths of heresy. His materialist notion of the cosmos - no creator deity, no life after death, everything that exists made of patterns of atoms - was anathema to the monotheist conception of an orderly cosmos arranged and guided by God. For centuries, being accused of "Epicureanism" was a very serious charge indeed. For example, the Jewish writings known as the Mishnah, in 200 CE, had this to say:

And these are the people who do not merit the world to come: The ones who say that there is no resurrection from the dead, and those who deny the Torah is from the heavens, and Epicureans.

Indeed, the Jewish word for "heretic" - apikoros - appears to be a Hebrew transliteration of "Epicurean". The Hebrew benediction known as the Amidah, which is recited three times daily by observant Jews, contains a prayer which asks that "may all the apikorsim be destroyed in an instant" (source).

As Christianity became ascendant, it treated Epicureans no less kindly. Acts 17:16-18 records how the first Christians viewed them:

"Now while Paul waited for them at Athens, his spirit was stirred in him, when he saw the city wholly given to idolatry. Therefore disputed he in the synagogue with the Jews, and with the devout persons, and in the market daily with them that met with him. Then certain philosophers of the Epicureans, and of the Stoicks, encountered him. And some said, What will this babbler say? other some, He seemeth to be a setter forth of strange gods."

Early Christian apologists such as Tertullian, Jerome and Augustine reviled Epicurus, calling him a "pig" and an advocate of "depravity and gluttony", and his philosophy a "frigid conceit" (source; see also).

Throughout the Middle Ages, as Christianity gained secular power, the ridicule and persecution grew worse. The Byzantine emperor Justinian I, who actively suppressed non-Christian faiths, closed down the philosophy schools of Athens, including the Epicurean Garden, which had survived for eight hundred years. The twelfth-century philosopher Nicholas of Autrecourt, who taught an atomist doctrine similar to Epicurus', was condemned and forced to recant and burn his writings. In the Divine Comedy, Dante depicts Epicurus and all his followers "who with the body make the spirit die" as imprisoned in flaming tombs for all eternity. As late as the 1600s, Epicurean theories were reviled, as one pamphleteer wrote: "Let that beastly Epicure's mouth be now sealed up in dumb silence."

Yet Epicurus, that sly old Greek, had the last laugh. The church persecuted his followers and sought to stamp out his teachings, but not only did Epicureanism survive, it was vindicated. The universe is made of atoms after all. Natural phenomena like weather, the growth of crystals, even the currents of human motion and thought can be traced back to patterns of atoms and their ceaseless ebb and flow. As in many other areas, this is one where religion arrogantly thought to wade in before science had had its say, and was forced to retreat. We do not live in the medieval church's world, where our bodies are just so much fleshly dust powered by immaterial currents of spirit, and the heavenly bodies move in spheres of celestial ether. We live in a grand cosmic clockwork of atoms and molecules, a vast mesh whose unfolding is determined by random chance and the immutable laws of cause and effect. We live in Epicurus' world.