The battle over the compound fructose now reaches new levels of obfuscation. The food industry is a strong – and loud, and rich – proponent, hard to ignore. The European Food and Safety Agency has just weighed in, in favour of the substitution of sucrose (table sugar: a disaccharide composed of the monosaccharides glucose and fructose) with fructose alone, the sweeter of the two – even to the point of allowing health claims for fructose on the packaging of processed foods.

And yet the scientific data on fructose says it is one of the most egregious components of the western diet, directly contributing to heart disease and diabetes, and associated with cancer and dementia. Nature magazine has just published a scathing indictment of fructose by Dr Lewis Cantley, one of the US's leading cancer researchers. But the EFSA says it sees no harm, justifying its stance on the basis that fructose has a lower glycaemic index than glucose.

The concept of glycaemic index is simple. This is how high your blood glucose rises after ingesting 50 grams of carbohydrate in any specific food, which is a measure of a food's generation of an insulin response, and is used as a way of showing a food's potential for weight gain. Glycaemic index is a proxy for how high your insulin level will rise, which determines whether that blood glucose will get shunted to fat cells for storage. Low-glycaemic-index diets promote blood sugar stability and are associated with weight loss. But the EFSA has missed the point. Glycaemic index is not the issue.

Glycaemic load is where it's at. This takes into account how much of a given food one must eat to obtain 50 grams of carbohydrate. The perfect example is carrots. Carrots have a high glycaemic index – if you consume 50 grams of carbohydrate in carrots, your blood sugar will rise pretty high. But you would have to eat 1.3lbs – 600 grams – of carrots to get 50 grams of carbohydrate. Highly unlikely. Any high-glycaemic-index food can become a low-glycaemic-load food if it's eaten with its inherent fibre. That means "real food". But fructose is made in a lab. It's anything but "real".

Yes, fructose has a low glycaemic index of 19, because it doesn't increase blood glucose. It's fructose, for goodness sake. It increases blood fructose, which is way worse. Fructose causes seven times as much cell damage as does glucose, because it binds to cellular proteins seven times faster; and it releases 100 times the number of oxygen radicals (such as hydrogen peroxide, which kills everything in sight). Indeed, a 20oz soda results in a serum fructose concentration of six micromolar, enough to do major arterial and pancreatic damage. Glycaemic index is a canard; and fructose makes it so. Because fructose's poisonous effects have nothing to do with glycaemic index; they are beyond glycaemic index.

The food industry is fond of referring to a 1999 study showing that liver fat generation from oral fructose occurs at a very low rate (less than 5%). And that's true, if you're thin, insulin sensitive, fasting (and therefore glycogen-depleted), and given just fructose alone (which is poorly absorbed). Conversely, if you're obese, insulin resistant, well fed, and getting both fructose and glucose together (like a sizable percentage of the population), then fructose gets converted to fat at a much higher rate, approximating 30%. In other words, the toxicity of fructose depends on context.

The industry points to meta-analyses of controlled isocaloric "fructose for glucose" exchange studies that demonstrate no effect from fructose on weight gain or other morbidities. Perhaps one reason for this is because crystalline fructose is incompletely absorbed. When that happens, residual fructose in the gastrointestinal system causes pain, bloating, and diarrhoea: ask any child the morning after Halloween in between trips to the bathroom relieving his diarrhoea. Furthermore, those meta-analyses where fructose was supplied in excess do show weight gain, high levels of lipids in the blood, and insulin resistance. The dose determines the poison.

The EFSA has boosted the position of the sugar industry, either through incompetence or collusion. But it is clear that this recommendation is scientifically bogus. Nutritional policy should be based on science – not pseudoscience, as we have seen over the past 30 years.