If you could go back and ask Aristotle whether he considered himself more a philosopher or a scientist, what might he say? Probably, he would just be baffled by the question since no such distinction existed for him. In those early days of human inquiry, all inquiries into the universe and our place in it were of equal merit, be they physical investigations or metaphysical speculations. It was only as the body of human knowledge grew beyond what could be understood by a single mind that the need arose to fragment knowledge into ever increasing numbers of disciplines and specialisations. Even comparatively recent thinkers such as Descartes and Leibniz are as famous for their philosophy as for their massive contributions to modern engineering practices.

But what a difference a couple of centuries make. When I entered the world of science and engineering, it was made clear to me that the humanities - philosophy, sociology and other "soft" sciences - belonged to a parallel universe which had nothing to do with the real world that I was learning to deal with. "We" are the ones who understand the universe as it really is, and manipulate and exploit it for the good of all mankind. "They" sit idly back and enjoy the fruits of our labour while simultaneously mocking and cajoling us for the collateral damage we create.

Somehow a gulf of mutual misunderstanding and even contempt had opened up between the sciences and humanities. But is that chasm as real (or as permanent) as some would have it?

I have a picture in my mind of two sailing ships. For centuries, becalmed among the treacherous rocks of religious intolerance, they lashed themselves together for safety and could proceed only at a sea-snail's pace. Each new scientific discovery could only safely be published if accompanied by a philosophical correlation with the church's latest thinking. While mathematicians could chart and predict with great precision the movements of bodies, both terrestrial and celestial, their findings had to be presented with reference to supernatural beings who were the ultimate cause of such regular movements. Even to suggest otherwise could be a costly business, as both Galileo (remembered today as a scientist) and Bruno (known as a philosopher) found out for their open support for Copernicus' theories of the solar system.

But with the dawn of Enlightenment, that first great wave of knowledge sharing based on new information technology - the printing press - religion's grip on teaching was loosened. A safe passage opened up for novel ideas, and our good ships' sails filled with the fresh breath of intellectual knowledge. They loosened their ties and surged forward independently although, for sure, it was the Science that took the lead. As it surged forward, its crew applied their new scientific method to sift through their cargo, identifying the items of real value and jettisoning the worthless. Hopeful but unproven practices such as alchemy were pitched overboard to make room for chemistry to flourish and fuel - literally - the industrial revolution. Superstitious astrology was thrown to the sharks and charlatans, leaving space for astronomy to flourish and teach us our true place in the universe.

Now running ahead of the wind in full sail, the crew of the Science looked forward to a bright new future, with barely a glance back at their old companion. Perhaps they assumed that its assorted collection of pastoralists, poets and philosophers was drifting off, set on in its own, irrelevant, course to oblivion. In any case, they had no need for idle speculation when science was proving itself quite capable of explaining the universe, in its entirety, using its own language. For with each new generation of technology - clockwork, steam, electricity - came new analogies to describe the world and our place in it. Planets moved around the sun like the cogs in a pocket-watch, people and animals were just intricate machines, their minds little more than computers. For a couple of centuries a complete understanding of the universe and an answer to all our questions was always just over the horizon, almost within reach. No need for metaphysical contemplation, just ever refined calculation.

But the end of the nineteenth century brought the first waves of the storm that was about to break. Michelson and Morley's demonstration that the speed of light is independent of both observer and observed, followed by Einstein's theoretical interpretation, opened up a whole new universe of uncertainty. Heisenberg and Shrödinger then really put the cat among the pigeons, publicising this fundamental uncertainty in a way that horrified animal lovers and perplexed the public. Suddenly there were not just things that we didn't know yet, but things that we cannot know at all.

Of course, the good ship Science sailed on, building models of the universe at fantastically big and fantastically small scales with ever greater precision, generating mathematical formulae that predict the existence of phenomena such as particles with stunning accuracy, most spectacularly with the Higgs Boson. But something had been lost. Perhaps like the first sailors who went over the horizon felt, the crew of the Science look back to see their old land of certainties had simply disappeared. Their wonderful mathematics and computer simulations can no longer be explained in ways that make sense to the layman. There are no simple analogies like the old sun-and-planets model to provide intuitive descriptions of the new physical realm of quarks, bosons, spin and strangeness. A void has opened up between what we can know about our world - by which we mean, in scientific terms, what we can model and accurately predict - and what we understand.

When physicsts respond to questions about what it all means with the semi-facetious response that their role is just to "shut up and calculate," they open up the door to all manner of speculation. Speculative fiction, new age religions, conspiracy theorists and maverick scientists all rush to fill the vacuum, so that the popular press and the internet are awash with their compelling - or not so compelling - notions.

How to make sense of it all? What discipline can we apply to sift through all this uncertainty and find something that makes some sense, at least to us? Well, of course, dealing with uncertainty lies at the heart of philosophy, and while the good ship Science has been making its wonderful progress over the last centuries, philosophy, too, has been coming along and has one or two things to say.

So, as the crew of the Science sail into uncharted waters, out of sight of land, they may cast around and find that the Humanities is right behind them after all. Perhaps it's had never been so far away, after all.