The GM controversy has divided society into two warring blocs. All those who see genetically modified food as a scary prospect - "Frankenstein foods" - are pitted against the defenders who see them as one of great achievements of the late 20th century. But beyond the for and against arguments, there is something politically important happening here. I refer not to the "Monsanto tendency" of new Labour, or the victimisation of a key scientist, or even the suppression - it is euphemistically called "extended gestation" - of critical documents. All of these only bring back the sort of Schadenfreude that we've missed since May 1997. What is really important is that, in the eyes of the public, science has totally lost its innocence. It has been politicised so much that it will never be the same again.

The popular image of science has always included such figures as the noble discoverer and the mad inventor. But in the GM controversy, the noble discoverer has taken a fatal beating at the hands of consumers and their champions. The way many scientists see themselves, as good people doing good work for ultimate human benefit, will henceforth always be open to question. Moreover, the model of science commonly used for its defence has been demonstratively shown in the GM affair to be less then satisfactory.

This model starts with independent discovery, proceeds to criticism by peers, publication for the common good, and then eventual application under an appropriate regulatory regime. It goes without saying that the scientist will be socially responsible and warn whether his or her discoveries can be put to bad as well as good use. Indeed, this picture may still apply to non-industrial scientific research, but in crucial cases like GM, it has a hollow ring.

Consider the case of Dr Arpad Pusztai, the scientist who first (allegedly) showed that rats suffered a reduction in brain size, liver damage and a weakening of their immune system after being fed GM potatoes. Pusztai went public a year ago, then had his funding withdrawn (so much for "independence"), then went public again, was accused of unspecified malpractice and sacked. As part of that process, he was then gagged.

One eminent critic asked why Pusztai didn't publish like a real scientist - that is, submit his research for publication in a reputed journal. But scientists working in corporations or government institutions cannot automatically do so without the consent of their institution. As Pusztai himself explained, his report to the Rowett Research Institute went down the bureaucratic memory chute.

In retrospect, we discover that this same institute is doing contract research for Monsanto, the corporation with most to gain from GM foods. And there are other interlocking commercial interests involved, not least those of the science minister, Lord Sainsbury, that prevented Pusztai from taking the normal route to publication. If we had waited for scientific journals to tell us about his results, we'd still be waiting.

So we now have to recognise a new sort of scientist, and with it a new sort of science. To some significant degree, the scientists working for publicly funded institutions are proletarians. They are hired and fired by convenience, they are assigned tasks set by their bosses, and they have few rights, or none, to the intellectual property of their work. And their employers may be engaged in work that involves risks, small, great or unquantifiable. If the scientist-worker doesn't like it, he can, like Pusztai, choose to be a whistle-blowing martyr or he can search for another career. The difference in the situation of the "independent" university-based scientists is only of degree, not of kind; they all need grants. And, as the GM affair shows so clearly, industry-based scientists have influence in high places - they move in the corridors of government. What then is the price of criticism?

So we must adjust our image of science. First, disinterestedness and integrity are no longer to be assumed, either by scientists or the public. Rather, they must be fought for and defended against inherently hostile interests, just as much as the liberty of the citizen against public and private corporate powers. Second, the myths that have sustained so much of the image-making of science, handed out in schools and fed to the public, will need a drastic overhaul. The traditional certainty and objectivity of scientific facts are guaranteed only in those cases where they are unimportant. Third, the public will play an increasing role in shaping science policy. With the GM affair, consumers have discovered their true power. As science-based technology raises ever more dangers inseparable from its benefits, there will be increasing public participation in issues of science and its policy. We can now take it as a given that science, politics and lifestyle are totally interconnected and inseparable from each other.

The scientific world we have lost (which of course existed but imperfectly) rested on a sort of normality, where everyone could do the job they were called to. Scientists researched and discovered; technologists applied and developed; industrialists made and sold; and governments promoted and regulated. The general public was the passive beneficiary, both in its cultural and material wellbeing.

The great achievements of that system have led, in dialectical fashion, to its present crisis. Science has made life more secure and comfortable, so that now people expect to be safe - and indeed demand safety from the system. But the very powers of the scientific system, which is now invading natural systems and even creating new natures, have compromised that safety. We do not know, we cannot know, how safe we will be when the new technologies come in.

So the scientific system, an integral part of our technology, culture and polity, is now caught in a contradiction. Its clients among the public demand more safety of the kind it has delivered up to now just as it becomes increasingly incapable of delivering it in the future. Of course, there should be more regulation by less supine governments. But let's be realistic. We have a globalised production of science and it will not be possible to regulate every aspect of science everywhere. If this is a genie, it really is out of the bottle.

This is not a cheering prospect. But the GM scare may just be an overture to what is coming next, in the manipulations of the human body. The real scare stories have yet to come. So, unless the politics of science catches up, and soon, we may find ourselves in a situation where the Sorcerer's Apprentice is not the little Mickey Mouse of Fantasia but the mightiest of the global corporations.

All this puts those who speak for science, such as the Royal Society, in a new and challenging position. Up to now they have been firmly a part of the establishment, rather like the church in its way. But just as the church is no longer the Tory party at prayer, the Royal Society can no longer be simply the great and good of the labs. Next month it is hosting a meeting on "Science, Technology and Social Responsibility", and although the organisers include propagandists of science such as Lewis Wolpert, the voices of dissent - Jonathon Porritt, Steven Rose and others - will have a prominent place. For only when institutions such as the Royal Society come to terms with the new politics of science, and involve concerned citizens in their deliberations, can science start to take its rightful place in the postmodern world.