"It is fairly clear what my advice on homeopathy is. But sometimes other factors come into play in determining how ministers treat scientific advice."

Sir John Beddington is relaxed about the limitations of his influence as the government's chief scientific adviser. The former professor of applied population biology at Imperial College London described his approach to the post he took up at the beginning of 2008 as "collegiate".

Indeed, many observers point to a marked contrast with his predecessor, Sir David King, who made forceful public interventions on issues such as climate change, organic foods and the Iraq War.

But Sir John insisted he was merely going about his business in the way that came naturally to him.

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"People have different personalities," he told Times ÖйúAƬ. "But I don't feel I've had a particularly low profile. Where there is a particular problem I'm happy to talk (to the media) about it, whether it is the machinery of government or major international issues such as climate-change scepticism or food and water security."

Sir John is also conscious of his "fairly substantial responsibility" to "make science and engineering work in government".

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One key step in realising that aim was the Principles of Scientific Advice to Government that he drew up after last year's acrimonious sacking of David Nutt as head of the Advisory Council on the Misuse of Drugs.

For that reason, some observers were surprised that Sir John did not speak out earlier this month when news broke that the home secretary, Theresa May, had abolished the legal requirement to have a minimum of six doctors and scientists on the council.

But that, he said, was because the media had "misapprehended" the government's intention, which was merely to make the scientific membership of the panel more flexible.

"I was consulted about it and it seemed quite a good idea, because in one situation you might want a toxicologist, while in another you might want a sociologist or someone who understands behaviour under stress," he said.

Group thinking

Sir John's focus on integrating science into the government's internal machinery has also resulted in every department except the Treasury acquiring its own chief scientific adviser. The advisers meet every week as a group - sometimes in the presence of David Willetts, the universities and science minister.

Sir John said that this was an effective way to ensure scientific input on cross-governmental issues, such as the impact on the UK's research capacity of the government's proposed immigration cap.

As for the Treasury, Sir John said that now the Comprehensive Spending Review is over, he will raise the issue again. However, he was confident that the lack of a chief scientific adviser had not made it any less receptive to the evidence submitted to the CSR about science's value to the economy. He was "delighted" by the flat-cash, ring-fenced research budget.

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He said his own role in the CSR process was not so much to lobby for science as to "give advice to everybody from the prime minister downwards on a number of points", including the risk that fixed commitments in certain areas of the research budget would magnify the size of cuts in others.

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Sir John admitted that he had "focused less" on the capital budget, and described the expected 44 per cent cut as "obviously a problem".

"But it could have been a lot worse. If there had been cuts in the basic science budget and in the capital spend, that would have been extraordinarily difficult," he said.

Sir John is conscious that the Department for Business, Innovation and Skills is not the only state source of research funding. He said he will work with a team from the Treasury to check that the budgetary plans of each department do not contain "disproportionate" cuts in spending on research, development and analysis, cuts that "although optimal for (them) would have ramifications for other departments".

Like many other senior figures, he believes the "special protection" given to the research budget imposes an obligation on the science community to "try to make savings and operate in a cooperative and sensible way".

Although he said that he was unaware of any Treasury pressure for more money to be spent on applied research, Sir John said there were likely to be more programmes addressing "grand challenges" such as food security and living with environmental change, which attract funding from both research councils and government departments.

"That is a good way of having research council funding directed at solving particular problems that the government also wants to see investigated," he said.

Nor does he refrain, in such cases, from offering his advice to the research councils about what specific questions should be addressed.

But he said he will not lose sight of the Haldane principle, which states that research funding allocations should be made by researchers rather than politicians.

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"I'll tell the research councils that I think it is important that they think about these problems, but the decision will be taken by them," Sir John said. "That's the kind of sensible dialogue you would expect."

paul.jump@tsleducation.com.