Picture this. I am staying in a remote cottage in Cornwall without a car. I have a temperature of 102, spots on my throat, delirium, and a book to finish writing. My desperate publisher suggests I call Hilary Fairclough, a homeopath who has practices in London and Penzance. She sends round a remedy called Lachesis, made from snake venom. Four hours later I have no symptoms whatsoever.

Dramatic stuff, and enough to convince me that while it might use snake venom, homeopathy is no snake oil designed for gullible hypochrondriacs. Right now, though, a fierce debate is raging between those, like me, who trust homeopathy because it works for them, and those who call it shamanistic claptrap, without clinical proof or any scientific base.

There have been a number of articles in the press recently criticising homeopathic remedies as worthless at best, and potentially lethal at worst, if they are being taken instead of tried-and-tested conventional medicines for conditions such as malaria or HIV.

I have found myself cited, and drawn into this, because I am on record as supporting homeopathic practice in general, and in particular the Maun homeopathy project, a clinic in Botswana set up by Fairclough.

The organisation Sense About Science and journalists such as Ben Goldacre and Nick Cohen are targeting a symposium in London in December that will discuss HIV and Aids and the homeopathic response to such diseases. Of particular concern is a claim by the British homeopath Peter Chapel and his Dutch colleague, Harry Van Der Zee, that Chapel has developed a remedy, PC1, that can be used to treat the HIV virus.

As a patron of Fotac (Friends of the Treatment Action Campaign) that has been fighting President Mbeke's lunatic insistence that HIV sufferers just need Vitamin C and a good diet, I am dismayed by any claim that may deter HIV sufferers from taking anti-retroviral drugs (ARVs). And so is Peter Fisher, an NHS doctor, director of the Faculty of Homeopaths, and, incidentally, homeopath to the Queen. Good homeopaths know the value of conventional medicine and do not seek to undermine that value. Fairclough's clinic, and her talk at the symposium, concentrate on using homeopathy to support the ARV programme by alleviating the side-effects of ARVs, and boosting the patient's immune system so they are better able to fight off the opportunistic viruses that follow behind HIV, and the drugs necessary to suppress it. There is no suggestion that homeopathy can replace ARVs.

Edwin Cameron, a justice of South Africa's supreme court of appeal who is HIV positive, has done much to counter the disastrous Aids denialists there. He visited Maun and agreed in writing that "there are patent health benefits". He also admitted that, although initially sceptical of homeopathy, he had had a persistent mouth and gum disease, untreatable by antibiotics, but which was cleared by homeopathic intervention.

I use the word "intervention" because I admit it is hard to talk about what it is that homeopathy actually does, or why it works. For my part, I want to know more, not less, but I can't dismiss the thing in the way that Sense About Science, many doctors, and some journalists are asking me to.

A recent furore over those homeopaths who offered an undercover journalist alternative remedies for the prevention of malaria has also prompted long-term critics of homeopathy to demand its head on a plate. There will soon be an article in the Lancet calling on doctors to tell their patients that homeopathic medicines offer no benefit. Until now the caveat has been no "proven" benefit. But where is the scientific sense is saying that because we don't understand something, even though we can discern its effects, we have to ignore it, scorn it, or suppress it?

This homeophobia is, I think, a genuine terror of what homeopathy is suggesting; which is that we think differently about the relationship between the cure and the disease. It is not enough to say Disease A is caused by B and can be cured by C. Homeopathy, in common with other holistic approaches, asks that we look at the whole picture - the person, and not just his illness. Specifically, in the case of homeopathy, the remedy picture, which is carefully drawn up after full consultation with the patient, follows the "like by like" premise - that tiny dilutions of the "problem" can prompt the body to effect its own cure. This is why the homeopathic code of practice does not talk about the medicines themselves having a simple causal effect - C cures A. Homeopathy seeks to understand everything we are, everything we do, as a web of relatedness. The reason why I have a recurring sore throat will not be the reason why you have one, and what helps me may not help you.

This seems to be partly why tests used for conventional medicines fail when used to test homeopathy. Sceptics will say it is the medicines that fail, and not the trials, but if the medicines really are ineffective, why is it that so many people who have tried homeopathy have found that it makes a difference to their wellbeing?

As I understand it, homeopathy is not a linear medicine - a drug aiming for a target - nor does it seek to remove the human factor. The patient and the practitioner are both important and relevant when it comes to understanding how humans respond to treatment.

That a good doctor is part of the therapeutic process is commonsense to anyone who has ever visited their GP or been for surgery. We know too that patients heal differently, develop complications or not, secondary infections or not, and so on. The placebo effect that is often cited by detractors as homeopathy's only resource (ie that people like being talked to and then given a pill to take), is common to all therapeutic processes, and it is valuable. We can feel better in the right hands - everyone knows that - and people can shrivel and die in the wrong hands - whatever the treatment.

I am sure that there is a placebo effect in homeopathy, but it is a fact that many of the people who end up visiting a homeopath do so as a last resort, when nothing else is working. That such people often see an improvement suggests that the remedies themselves are contributing to the wellness of the individual.

Objections to homeopathy begin with what are viewed as the impossible dilutions of the remedies, so that only nano amounts of the original active substance remain, and in some cases are only an imprint, or memory. Yet our recent discoveries in the world of the very small point to a whole new set of rules for the behaviour of nano-quantities. Thundering around in our Gulliver world, we were first shocked to find that splitting the atom allowed inconceivable amounts of energy to be released. Now, we are discovering that the properties of materials change as their size reaches the nano-scale. Bulk material should have constant physical properties, regardless of its size, but at the nano-scale this is not the case. In a solvent, such as water, nano particles can remain suspended, neither floating nor sinking, but permeating the solution. Such particles are also able to pass through cell walls, and they can cause biochemical change.

We do not know whether this has a bearing on homeopathic dilutions, but it may well be that nanoparticles offer a clue.

Fisher says that water as a solvent has properties that are not yet understood, and there was great excitement recently when a team of Korean scientists seemed to show that water has "memory". I take New Scientist every week and I am continually amazed at how the seemingly well-known physical world of ours is beginning to show itself as stranger than anyone imagined.

I would like to see homeopathy better regulated. I would like to see the Society of Homeopaths engaging with its critics, as well as initiating more research. There will always be rogue homeopaths and bad homeopaths, but that is true of any profession. Above all we should be careful of dismissing the testimony of millions who say the remedies have worked for them.

· Jeanette Winterson is donating the fee for this article to the Maun homeopathy project.