We are born sun worshippers, or so it seems. Last year’s big show at London’s Tate Modern proved it beyond doubt. Blogs filled up with astonished messages about the experience of visiting the Tate’s huge Turbine Hall, where the Danish artist Olafur Eliasson set up an astounding experiment he called “The Weather Project”. Eliasson likes manipulating light to explore how our ways of seeing the world are always changing, how our eyes deceive us and how light can play tricks.

High up at one end of the Turbine Hall hung scores of sodium lamps radiating nearly monochromatic yellow light. There was no attempt to mislead: visitors could get behind the lamp array to see how its wiring worked. In the hall itself, a hazy mist was blown into the chamber, while its ceiling was entirely covered in mirrors. As the lamplight streamed through these clouds, the lamps turned into a vast sun, and the floor of the hall into a kind of artificial beach, with hundreds of visitors lying on their backs, bathed in a strange glow, gazing up at a reflecting sky.

Watching the show, it was hard to tell whether you were at the seaside or in church.

Light’s like that. It seems always to mix up everyday life with something spiritual. Eliasson’s set-up is a perfect illustration of the long history of experiments on light and the way different societies have used its remarkable properties. His works craftily mimic important scientific experiments and perfectly illustrate sun worship, optical refraction and solar eclipses. They give spectators some feeling for the oddities of vision and the deeper meanings of light itself.

The Book of Genesis tells believers that God’s first words summoned light into existence: “Let there be Light”. And Isaac Newton certainly believed there was a divine explanation. Even so, his optical researches, performed between the 1660s and 1680s, transformed experimental understanding of light. This year marks the third centenary of the appearance of Newton’s masterpiece, Opticks, the most important book published in English on the behaviour of light.

It laid the foundations for a novel way of investigating nature, using careful experiments and ingenious theory to analyse complex phenomena. In later centuries, its techniques would help interpret the spectra of sunlight and starlight, revealing the chemical composition and speed of the most distant celestial objects. Newton had a new and initially dubious doctrine to teach: white light is made of seven different kinds of rays.

Each of these rays bends at a specific unique angle when it is refracted through a prism. And each ray produces a unique, specific colour when it enters our eyes.

Not only was this a startling story about light and colour. Newton wanted to convince his audience by getting them to repeat his experiments. This was controversial. The idea that theories should be believed if the experiments they depend on can be replicated became crucial for all modern science. But there are other questions here, linking Newton’s work with that of “The Weather Project”. For Newton himself had other aims too. His optical experiments may have helped promote a modern and enlightened world; but he first launched them because of his faith in God.

His Opticks gathered together records of experiments he’d done 40 years before its publication. One of Newton’s early set-ups, in 1666, was surprisingly similar to “Your Sun Machine” an installation created by Eliasson in Los Angeles in 1997. The 24-year-old Cambridge student Newton made his own sun machine. He put himself in a closed room with a circular hole drilled in a window shutter to let in the sunlight. Using glass prisms he would now carefully show exactly how sunlight behaved, and, even more amazingly, he would show how we see colours. When Newton did this trial he was an established member of a college dominated by Anglican churchmen who would check every new theory against the principles of their reformed religion.

Newton consulted the most advanced texts in modern optics. He learned from reading the most impressive recent philosophical thinkers, Rene Descartes and Thomas Hobbes, of their ambitions to explain all phenomena in nature without any souls and spirits. According to these men, it seemed as if God had no real power in the world and all could be understood by the motions of brute matter alone.

But Cambridge priests told him how subversive were these arguments to religious faith and Newton agreed. He thought his experiments might show these dangerously mechanistic philosophers were wrong. Newton tried to challenge the threatening idea that everything in the world happens purely mechanically, without any divine intervention and without souls or spirits.

Optical philosophers such as Descartes and Hobbes believed light was just a disturbance propagated along lines of adjacent particles. The disturbance would be produced whenever a light source gave the line a shove; different colours appeared whenever the particles started to spin. Spins would start, so colours would be made, for example when light was bent through glass by refraction. Newton came to see most of this story as bad philosophy and worse theology.

He began to disprove these theories with stunningly dangerous experiments on himself. There must be a way of telling the difference between the mechanical actions and spiritual intervention. When he pushed his eye, he saw things differently from when he simply willed his eye to move. If there was a difference between a physical shove and the action of his mind, then there was something in the world that wasn’t merely mechanical. He started to record what he saw, a red circle inside a blue circle, when he pressed his eyeball with his finger or a brass plate. Newton even used a wooden needle pressed between his eyeball and his skull. Once again, he managed to produce concentric red and blue circles. He was fascinated by these colours. In series of experiments, he stared at the Sun until light bodies turned red and dark ones blue. Then he looked away, into the dark, until the coloured after-images slowly faded away. It took him four whole days sitting in the dark to recover his sight.

Newton reckoned these coloured after-images could not be due to something in light itself. Colour changes and after-images, which he began to call “phantasms”, were made at the back of his eye, at the retina. These colours could not be a mechanical property of mere bodies, certainly not some kind of spin. They must be more spiritual. Religion was saved. So the young Newton concluded that the best modern philosophers were wrong. Different light rays were not intrinsically coloured. Instead, they simply made the impression of colours in your mind.

But then Newton had a big new puzzle: if they weren’t due to mechanical pushes and spins, where did the different colours made by these rays actually come from? This was when he decided to build his dark room with the hole to let in sunlight, his “Sun Machine”. This kind of dark room has a very long history. From its Latin name, we still call the dark room a camera obscura, or simply a camera for short. You can use a shoebox with a pinhole to perform the trick. There is exactly such a camera obscura in Edinburgh, another at Greenwich, and a temporary one on the balcony of the Hayward Gallery’s “Eyes, Lies and Illusions” exhibition, inside which you can see buses on Waterloo Bridge, speeding past your eyes but upside down.

Since at least the time of Euclid, writing in Alexandria 300 years before Christ, it had been known that when light enters a dark space through a small hole, an upside-down image will be formed opposite the hole. Experts in geometry worked out that the effect depended on the fact that light moves in straight lines. From the early 17th century, it was claimed that the human eye functioned exactly like a camera obscura. The lens at the front of the eye, so it was argued, helped sharpen the image onto the retina, which played the part of the screen.

Several theologians said this showed God’s wisdom and ingenuity in designing such a perfect reliable instrument for communicating information about the world around us. The camera seemed to guarantee that we see the world rightly. Descartes even cut off the back of an ox’s eyeball, then used it as part of a camera experiment, just to show the mechanism of vision. Once inside a darkened room carrying this eye you should “cut away the membranes at the back”, Descartes told his readers. “No light must enter this room except what comes through this eye. Once you’ve done this, if you look at a white sheet you will see there, perhaps with pleasure and wonder, a picture representing in natural perspective all the objects outside”.

When the makers of our TV series Light Fantastic got hold of a bull’s eye from Smithfield meat market and tried Descartes’ experiment at an optical lab nearby, it worked like a charm. And so when Newton turned his own room into a camera, then stood inside it, he was in fact standing inside a huge model of the human eye. This made perfect sense. He had already defended the true religion, as he saw it, by experimenting on his own eye. Now he would experiment inside the eye itself. Instead of a lens, Newton decided to put a prism inside his camera.

Prisms were widely seen as playful tricks, commonly known as “fools’

paradises”, sold cheaply at fairs and by pedlars. By scouring the Cambridge markets, Newton assembled a number of glass prisms, veined and uneven, but fit enough for his purpose. Then he put a prism in the way of the sunlight.

Newton wanted to show that prisms do not make colours, they just separate rays, because each different colour-making ray bends at a different angle through a prism.

But who would believe that bright sunlight really contains all the colours of the rainbow, and always bends at the same angle through glass? He threw the colours onto the opposite wall of his room more than 20 feet away. The prism was set at the position of minimum deviation, so that the light entered and left it at the same angle. This is the only position in which the shape of the hole and of the coloured image should have been the same were there no different refraction for each ray. “The colours should have been in a round circle were all the rays alike refracted, but their form was oblong” - a coloured image five times longer than wide.

This was the first time Newton ever allowed sunlight to shine through a prism and display the image on a screen or wall. So it was the first time he did an experiment which could be simultaneously witnessed by others, an experiment fit for publication, an experiment which might convince the doubters. Within 18 months, he quickly designed more complex techniques for this trial and used better ways of bending light, through water-filled glasses rather than prisms.

He coined the word “spectrum”, in other words “ghost”, to name the sun’s image cast through the prism onto the wall, as though he never wanted to forget the spiritual purpose which first guided his research. And he tried a fairly simple experiment, based on the first one, in which he held a second prism about six yards from the initial prism. He showed that if it was well separated, then each ray would bend just as much through the first as through the second prism, and also that the colour each ray made did not change. Angles and colours, he believed, were specific for each primitive ray. This was his great new result.

Between the 1670s and the 1720s, Isaac Newton’s new story about light and colours was greeted with a mixture of hostility and incomprehension by some of his readers. Just because sunlight threw a coloured image when passed through a prism, it didn’t seem necessarily to mean there were seven different colour-making rays inside the sunlight. But once Newton was treated as being in touch with the truths of creation, it became harder to deny the truth of his prism experiments.

Newton’s almost divine reputation went hand in hand with the triumph of his optics. He became head of the Royal Society, the most famous experimenter in Europe. When Newton was buried in Westminster Abbey, he had already become something like a saint. Through him we witnessed one of the very finest achievements of experimental science. An achievement linked with religious belief and artful design. And so, just after the great man’s death in 1727, the poet Alexander Pope wrote: “Nature, and Nature’s Laws, lay hid in Night: God said, ‘Let Newton be,’ and all was Light.”

Simon Schaffer is professor of the history of science at the University of Cambridge and presents Light Fantastic, a new four-part TV series which starts on BBC4 on Wednesday, December 1 at 9pm