The public health minister, Anna Soubry, has commented that the poor are more likely to be obese. It is well known that social status is linked to health, but her comments were also motivated by a mentality that victimises the most vulnerable. She should really be directing her criticism at the food industry. There is no doubt that an oversupply of cheap junk food fuelled by unregulated and irresponsible marketing limits our ability to make healthy choices. But there is an equally important question that merits attention: are we being given the wrong dietary advice?

A patient recently came to see me for a cardiovascular evaluation. He was particularly baffled as to why he had gained a stone in weight several months after he had followed a dietician's instructions to lower his blood cholesterol by eating "low fat" products. How could this have happened?

This week the British Medical Journal's front page asked: "Is sugar the real culprit in the obesity epidemic?", a response to a study published in the same edition that concluded that cutting sugar intake led to significant weight loss. A paediatric endocrinologist, Prof Robert Lustig, has highlighted the toxic, addictive and appetite-driving properties of sugar. His 90-minute lecture has attracted worldwide attention with over 3m views on YouTube. But the dangers of sugar is not news to the scientific community. A British professor and nutritionist, John Yudkin, believed that sugar, not fat, was the biggest culprit in heart disease and in 1972 set this out in his book, Pure, White and Deadly.

Research has moved on a great deal, and recent research has revealed that saturated fat from dairy products in particular may actually be protective against heart disease and stroke. Dairy products are exemplary providers of Vitamin A and D in which many British people are deficient. Calcium and phosphorus, also found in dairy products, may be beneficial to health through blood pressure-lowering effects. Vitamin D deficiency has been strongly associated with cardiovascular death.

Highly processed foods advertised as "low fat" are often loaded with cheaply added excess sugars and preservatives. Cereals and flavoured yogurts are just a few examples. I have started to advise my patients to eat butter instead of margarine and just eat real food. But even doctors' own dietary beliefs are strongly influenced by industry advertising. I was recently surprised to discover that there was no scientific basis to the heavily promoted claims made on behalf of a well-known sports drink that I had been taking on my daily visits to the gym – that it has performance-enhancing qualities. Instead of wasting £7,000 in the past 15 years buying a product loaded with sugar, I would have been better off drinking tap water.

There is universal scientific consensus that trans fats found in fast food and processed foods such as biscuits, crisps and frozen pizza are detrimental to health and may even increase the short-term risk of a heart attack. The British Medical Association has rightly called for a reduction of trans fats, salt and sugar in pre-prepared foods.

And as to "saturated fat" and weight gain? Prof David Haslam, chair of the National Obesity Forum, says that all calories are not created equal. "It's extremely naive of the public and the medical profession to imagine that a calorie of bread, a calorie of meat and a calorie of alcohol are all dealt in the same way by the amazingly complex systems of the body. The assumption has been made that increased fat in the bloodstream is caused by increased saturated fat in the diet, whereas modern scientific evidence is proving that refined carbohydrates and sugar in particular are actually the culprits."

Big tobacco was able to stall government intervention by planting doubt in relation to smoking and lung cancer for half a century and "big food" continues to deny that sugar is harmful. The academic vice president of the Royal College of Physicians, John Wass, is right to suggest that medical students should have more lectures on nutrition. But the advice doctors give when dealing with overweight patients should be based upon the best available scientific evidence, not what the food industry wants us to believe. As an isolated voice, Yudkin, who died in 1995, may have lost the battle with the sugar industry four decades ago, but big food will find it more difficult to silence his growing army of disciples whose only incentive is to expose what's right for public health.