"Education: Elitist activity. Cost ineffective. Unpopular with Grey Suits. Now largely replaced by Training." Michael O'Donnell, in A Sceptic's Medical Dictionary (BMJ publishing, 1997)

The enlightenment was a beautiful thing. People cast aside dogma and authority. They started to think for themselves. Natural science flourished. Understanding of the real world increased. The hegemony of religion slowly declined. Real universities were created and eventually democracy took hold. The modern world was born. Until recently we were making good progress. So what went wrong?

The past 30 years or so have been an age of endarkenment. It has been a period in which truth ceased to matter very much, and dogma and irrationality became once more respectable. This matters when people delude themselves into believing that we could be endangered at 45 minutes' notice by non-existent weapons of mass destruction.

It matters when reputable accountants delude themselves into thinking that Enron-style accounting is acceptable. It matters when people are deluded into thinking that they will be rewarded in paradise for killing themselves and others. It matters when bishops attribute floods to a deity whose evident vengefulness and malevolence leave one reeling. And it matters when science teachers start to believe that the Earth was created 6,000 years ago.

A minor aspect of the endarkenment has been a resurgence in magical and superstitious ideas about medicine. The existence of homeopaths on the high street won't usually do too much harm. Their sugar pills contain nothing and they won't poison your body. The greater danger is that they poison your mind.

It is true that consulting a homeopath could endanger your health if it delays proper diagnosis, or if they recommend sugar pills to prevent malaria, but the real objection is cultural. Homeopaths are a manifestation of a society in which wishful thinking matters more than truth; a society where what I say three times is true and never mind the facts.

If this attitude were restricted to half-educated herbalists and crackpot crystal gazers, perhaps one could shrug it off. But the endarkenment extends to the highest reaches of the media, government and universities. And it corrupts science itself.

Even respectable newspapers still run nonsensical astrology columns and respected members of parliament seem quite unaware of what constitutes evidence. Conservative MP David Tredinnick advocated homeopathic treatment of foot and mouth disease and Lord Hunt, as health minister, referred to 'psychic surgery' as a "profession" in a letter written in response to question by a clinical scientist.

Under the influence of the Department of Health, normally sane pharmacologists on the Medicines and Health Regulatory Authority, which is meant to "ensure the medicines work", changed the rules to allow homeopathic and herbal products to be labelled with "traditional" uses, while requiring no evidence to be produced that they work.

Tony Blair himself created religiously divided schools at a time when that has never been more obviously foolish, and he defended in the House of Commons, schools run by "young-earth' creationists", the lunatic fringe of religious zealots.

The Blairs' fascination with pendulum wavers, crystals and other new-age nonsense is well known. When their elders set examples like that, is it any surprise that more than 30% of students in the UK now say they believe in creationism and intelligent design? As the biologist Steve Jones has pointed out so trenchantly, this makes it hard to teach them science at all.

Homeopaths and herbalists may be anti-science but they are not nearly as worrying as universities who try to justify the awarding of bachelor of science degrees in subjects that are anti-science to their core.

The University of Bedfordshire accredited a foundation degree course in nutritional therapy, at the Institute of Optimum Nutrition (IoN). The give-away is the term "nutritional therapy". Such therapists can claim, with next to no evidence, that changing your diet, and buying from them a lot of expensive "supplements", will cure almost any disease.

The IoN was founded in 1984 by Patrick Holford, whose qualification in nutrition is a diploma awarded by this institute in 1995. His advocacy of vitamin C as better than conventional drugs to treat Aids is truly scary.

The documents that relate to this accreditation are mind-boggling. One of the recommended books for the course, on "Energy Medicine" has been reviewed by the Skeptic magazine thus: "This book masquerades as science, but it amounts to little more than speculation and polemic in support of a preconceived belief."

The report of the university's Teaching Quality and Enhancement Committee (May 24th 2004) looks terribly official, with at least three "quality assurance" people in attendance. But the minutes show that they discussed almost everything about the course apart from the one thing that really matters, the truth of what was being taught. The accreditation was granted. It's true that the QAA criticised the university for this, but only because they failed to tick a box, not because of the content of the course.

The University of Central Lancashire's justification for its BSc in homeopathic medicine consists of 49 pages of what the late, great Ted Wragg might have called "world-class meaningless bollocks". All the buzzwords are there: "multi-disciplinary delivery", "formative and summative assessment", log books and schedules. But there is not a single word about the fact that the course is devoted to a totally discredited early 19th century view of medicine, not a word about truth and falsehood. Has it become politically incorrect to question things like this?

These examples, and many like them, result, I believe, from the bureaucratisation and corporatisation of science and education. Power has gradually ebbed away from the people who do the research and teaching, and become centralised in the hands of people who do neither.

The sad thing is that the intentions are good. Taxpayers have every right to expect that their money is well spent, and students have every right to expect that a university will teach them well. How, then, have we ended up with attempts to deliver these things that do more harm than good?

One reason is that the bureaucrats who impose these schemes have no interest in data. They don't do randomised tests, or even run pilot schemes, on their educational or management theories because, like an old-fashioned clinician, they just know they are right. Enormous harm has been done to science by valuing quantity over quality, short-termism over originality and, at the extremes, fraud over honesty.

Science, left to itself, and run by scientists, has created much of the world we live in. It has self-correcting mechanisms built in, so that mistakes, and the occasional bit of fraud, are soon eliminated. Corporatisation has meant that, increasingly, you are not responsible to your conscience, just to your line manager. The result of this, I fear, is a decrease in honesty, and in the long run, inevitably, a decrease in quality and originality.

If all we had to worry about was a few potty homeopaths and astrologers, it might be better to shrug, and get on with some real science. But now the endarkenment extends to parliament, universities and schools, it is far too dangerous to ignore.

David Colquhoun is a pharmacologist at University College London who writes the Improbable Science blog and website, where you can find more details on the issues discussed above