At the heart of the MMR vaccine controversy is an attempt to blind people with science. Proponents of the vaccine say science has proved it is safe and that those who deny this are scientifically illiterate. This argument has been used to tell parents that the evidence of their own eyes is not true. While the vast majority of children have had no problem with the MMR vaccine, a small proportion of parents found that after vaccination their children developed bowel problems, an allergic reaction to various foods, and a halt to their behavioural development that produced the symptoms of autism.

Their concerns were dismissed by the medical profession. One doctor who did take them seriously was a gastroenterologist, Andrew Wakefield. In a Lancet paper he said the children were suffering from a new disease, autistic enterocolitis; at a press conference he suggested that to be safe children should have single jabs instead of the triple MMR.

Since then the government has pointed to a succession of epidemiological studies that, it says, prove that MMR is safe. A recent meta-study by the Cochrane Library was likewise reported to have said that fears about the vaccine were based on "unreliable evidence".

But the study itself did not say this. On the contrary, it found that nine of the most prominent epidemiology studies that are employed to attack Wakefield's research were unreliable. Since it did not look at Wakefield's research, it did not address the questions raised over the vaccine in the first place. The report therefore could not bear the conclusion attributed to it that MMR was safe.

When I pointed this out in the Daily Mail last week, I was attacked in these pages by Dr Ben Goldacre, who said I did not understand how science worked. On the contrary, it is Goldacre who is ignoring the evidence, and his errors go to the essence of the MMR controversy.

Like the government, Goldacre believes clinical findings are trumped by epidemiology, which he says is "evidence-based" medicine. But the attempt to refute Wakefield by epidemiology is a category confusion. Epidemiology looks at patterns of disease in a population. It cannot prove or disprove cause and effect in individual patients.

A paper published in the Journal of American Physicians and Surgeons says epidemiology "cannot establish a causal association unless other biological evidence backs it up", and does not meet a scientific standard of proof since it is prone to bias - the very criticism that the Cochrane report made of the epidemiological studies of MMR and autism.

Having accused me of misunderstanding "real" science, Goldacre then claims that I have fallen for pseudoscience by believing evidence that has never been peer-reviewed. Bizarrely, he asserts that I have relied upon research that has been published only in the "in-house magazine of a rightwing US pressure group well known for polemics on homosexuality, abortion and vaccines".

What on earth is he talking about? The devastating finding of measles virus in the cerebro-spinal fluid of some autistic children who had been given the MMR vaccine has been peer-reviewed in the Journal of American Physicians and Surgeons.

He claims that Wakefield's term "autistic enterocolitis" has appeared in no other studies that have endorsed it. But Wakefield's core finding of a unique gut-brain disease has been replicated in peer-reviewed papers in the Journal of Paediatric Neurology, Neuropsychobiology, the Journal of Paediatrics, the Journal of Clinical Immunology and the American Journal of Gastroenterology.

So what is this sinister "rightwing" organisation upon which I am supposed to have relied? Alas, Goldacre does not tell us. So let us guess. Might it be, perhaps, the Association of American Physicians and Surgeons, which published the evidence of measles virus in cerebro-spinal fluid? Or might it be the American Institute of Medicine, which said that any evidence that symptoms worsen after booster jabs (as has been claimed with MMR) was real evidence of a link between a vaccine and a disorder?

Goldacre's case boils down to evasiveness, ignorance, misrepresentation and smear. Are these really the attributes of a scientific vocabulary? Is this really "evidence-based medicine"? Of course, it is important to vaccinate children against dangerous diseases. But if even a small subsection of children is badly affected - which is all that is being claimed over MMR - the balance of risk dramatically changes.

The government and the medical establishment deny the evidence of any such effect. They claim that science has shown there is no case to answer. But it depends on which type of science, and whether it is being used appropriately. The fact is that scientists are making progress in deciphering the mysterious relationship, which Wakefield first identified, between a new type of bowel disease and brain disorder. The connection between this relationship and the MMR vaccine is far from proven. But legitimate scrutiny of the real questions that have been raised are being stifled by the government and a medical establishment that have behaved recklessly and spinelessly, and are busy suppressing all attempts to hold this up to the light.

· Melanie Phillips is a Daily Mail columnist

melanie@melaniephillips.com