The Commonwealth Scientific and Industrial Research Organisation (CSIRO) is the major publicly funded research body in Australia, employing more than 6500 people in almost 60 sites across the nation. Its name is synonymous with science. How could Australians have BBQs if the CSIRO hadn't invented Aerogard? When we use money to pay for things, we hand over CSIRO-devised polymer banknotes; the more technologically savvy use WiFi, purportedly (but disputably) covered by a CSIRO patent.

Other CSIRO achievements have been less well publicised, though they are arguably more important. CSIRO scientists invented the main technique for measuring mercury in fish. It is measured at levels reminiscent of needles in haystacks: fractions of parts per million. And the CSIRO is a critical part of the international team monitoring methane levels in the atmosphere, measured in even smaller units: parts per billion (PPB). The current level is 1774 PPB, more than double what it was 200 years ago - something to which I will return.

The CSIRO, in short, has a well-justified reputation for scientific excellence.

In late May 2005, this prestigious scientific organisation launched a diet book, The CSIRO Total Wellbeing Diet. Despite attracting criticism from nutritionists, including Rosemary Stanton, for its high protein content and its research basis, the Total Wellbeing Diet was a dazzling commercial success, for a time even outselling Harry Potter.

Not a year later, in March 2006, four scientists published a short paper in a scientific journal. Three of the four worked for the CSIRO then, and all work for the CSIRO now. The article begins simply:

Colorectal cancer is a socio-economically important disease in affluent societies and epidemiological data suggest that dietary composition is a major factor in its etiology. Earlier reports suggested that high intake of red or processed meats could be a risk factor. Three large [human] population studies have recently confirmed those earlier reports.

This is just one of a number of papers by CSIRO researchers on the link between red meat and colorectal cancer.

The four scientists, having described the state of research in the area, continue with a description of an experiment. Groups of rats were fed various diets with and without red meat, and with and without a special form of starch. There was nothing unusual about the meat: the authors described buying it at Adelaide's central market. But the starch was special. It's part of the much-touted nutraceutical industry - designer foods with heavily hyped health benefits that attract a premium price. The CSIRO has a number of patents in this area.

Why were the scientists doing this research?

Because DNA damage is an early step in the initiation of cancer, these findings suggest that increased DNA damage due to high dietary protein as cooked red meat or casein could increase colorectal cancer risk but inclusion of resistant starch in the diet could significantly reduce that risk.

Put simply, if the DNA damage in rats eating red meat with special starch is less than the damage in the rats eating red meat alone, then a resourceful marketing department can say things such as, "Years of research by CSIRO scientists have given us an improved form of starch that dramatically increases bowel health." A statement like this, linked to the respected CSIRO brand, is a recipe for mega-dollars.

But doesn't this involve the CSIRO in a serious contradiction? On the one hand, it is lending its name to a diet high in foods that damage colon DNA in ways that could go on to become colorectal cancer. On the other, its researchers are developing and patenting products to reduce that DNA damage.

Documents obtained under Freedom of Information legislation in late February 2008 show that the CSIRO board was informed of the work of its bowel-health researchers at its April 2006 meeting. It was told: "Recent findings from [CSIRO] scientists have established that diets high in red meat, processed meats and the dairy protein casein can significantly increase the risk of bowel cancer."

In late October 2006, in time for Christmas shoppers, the second edition of The CSIRO Total Wellbeing Diet was released, at a launch attended by Julie Bishop, the then federal minister for science. The second edition contains a page discussing red meat and colorectal cancer, including this statement: "Studies have shown that fresh red meat (beef and lamb) is not a significant risk factor for colorectal cancer."

Why the clear discrepancy between what the organisation's researchers were telling it privately and its advice to the public? Had any new evidence emerged to alter the opinions of its researchers? Certainly the board and CEO documents don't mention any new research containing contrary findings.

The CSIRO was clearly concerned about the research findings because it set up a team to act as a "translator" of the science of this complex area for the public. It took heart from the findings of a special CSIRO working group: "Specifically, in relation to the association between red meat and processed meat and colorectal cancer, the CSIRO working group did note that the magnitude of effect was small and that population studies had not always adjusted for potential confounders."