For the first time in a generation, archaeologists have begun to sift through the most sacred soil in Britain, in search of the secret of Stonehenge.

The full artillery of modern science will be trained on a trench of earth, measuring 11 feet long and eight feet wide, inside the great stone circle. Pollen grains, tool fragments, snail shells, and chips of the original bluestone pillars will all be carbon- dated, to try to answer a question that had intrigued thinkers since medieval times: how and why, some 4,500 years ago, did our ancestors bring 80 stones, weighing up to three tonnes each, from the Preseli Hills in southwest Wales to Salisbury plain?

The archaeologists believe that science will unlock the secret of Stonehenge, once and for all. I doubt it, for the myth of Stonehenge may be more powerful even than science.

Stonehenge is one of those historical artefacts whose beauty and inspiration lie in their mystery. The great stone circle has forged more stories, unleashed more flights of spiritual speculation, more sheer imagination than perhaps any other place on earth, precisely because of its inexplicability.

There may be a single “true” reason for Stonehenge: it may have been a druidical temple, a centre for magic arts, an observatory, an oracle, a pilgrimage site, a shrine to the dead or, as the archaeologists now working there believe, a place of healing, the Lourdes of ancient Britain. But there is another sort of historical truth associated with Stonehenge: the beliefs, legends, superstitions and ideas that have clustered around the place because no one knew for certain what it was. Science can answer certain historical questions with unerring accuracy, but at an imaginative cost.

Science and technology have unlocked mysteries that were once thought to be permanently immune to human understanding. The unknowable has become explicable.

The Titanic has been found and explored. The lost city of Heraklion has been located off the coast of Egypt. Was Napoleon poisoned with arsenic? Last month Italian scientists bombarded Napoleon's hair samples in a nuclear reactor, and concluded that he was not. Satellite technology was critical to finding the lost city of Ubar in the Arabian Empty Quarter, said to have been destroyed by Allah to punish its people for their sins. Computers have recreated the night sky in order to identify the day (June 29, 3123 BC) when an asteroid slammed into the Austrian Alps at Köfels, probably taking out Sodom and Gomorrah en route.

Such scientific discoveries add to our understanding of the past, but they remove an element of uncertainty and wonder that is also part of the past, by making the world a little more prosaic, a little more predictable, reducing history to the application of chemistry and physics.

The French writer-pilot Antoine de Saint Exupéry left an airbase in Corsica in July 1944, and was never seen again. That disappearance was part of his mystique, one reason why so many millions of copies of his enchanting story, The Little Prince, sold around the world. My heart sank a little when Saint Exupéry's plane was discovered in 2000 using scientific methods; and it sank a little further last month, when a former Luftwaffe pilot finally admitted he had shot the plane down. Another potent mystery crashed to earth.

In some respects, science enriches, clarifies and even salves the past: identifying the remains of the despicable Josef Mengele, ensuring the Unknown Soldier is finally known, tracing the orphans of the disappeared in Argentina. DNA testing has proved a useful tool for historical debunking, exposing numerous frauds. But by destroying forever the mystery of identity, DNA testing has removed some of the romance of history.

The persistent belief that one of the Romanovs survived the massacre at Yekaterinburg has been destroyed by science. Posthumous DNA testing proved that Anna Anderson, who always insisted she was the Grand Duchess Anastasia, was really a Polish peasant named Franziska Schanzkowska. The parade of Romanov hoaxers offered a picaresque history of their own, but also a window into the Russian soul, a residual hankering for the tsars.

The imaginings that cluster around the unknown and the uncertain are as fascinating as any historical truth, and of nowhere is this more true than Stonehenge. What different people chose to believe and invent about Stonehenge is just as important, historically, as what it was really for.

According to one Greek legend, the Oracle of Delphi took a sort of winter holiday, during which Apollo operated from northern climes, possibly Stonehenge. Geoffrey of Monmouth described how the wizard Merlin ordered the bluestones to be removed from Ireland, where giants had brought them from Africa for their healing properties. Inigo Jones depicted the stones as a druid's temple. Or perhaps Stonehenge was the shrine to the sun described by a Greek historian in the first century BC.

According to one folk tale, the Devil brought the great stones to the plain simply in order to confuse people as to how they got there. He succeeded, and the various stories that have accumulated around the enigma of Stonehenge offer a strange and wonderful human archaeology of changing attitudes, dreams and beliefs.

The latest scientist-archaeologists hope to prove, definitively, that Stonehenge was a Bronze Age healing centre, “the A&E ward of the South West”, in the words of one of them. Perhaps the latest diggers will be able to proclaim that the riddle has been solved at last. But more likely the scientific explanation will simply lie on top of all the other, unscientific, explanations that have preceded it, another layer in an ancient and never-ending mystery story written in stone.

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