Every night, under cover of darkness, boats set out into the Mediterranean Sea to fish illegally. But they can no longer do so invisibly, thanks to a detection system designed and operated by an institute of the European Commission's Brussels-based Joint Research Centre (JRC). The system collects location data signalled to coastal stations from transponders on approved fishing vessels, and combines them in real time with satellite images at a resolution as low as 8 metres that can identify the boats without transponder signals — among which are the illegal fishing ships.

This is just one of several examples of how the JRC's seven institutes develop and apply technologies to support European Union (EU) policies. In the institute devoted to health and consumer protection, for instance, researchers validate methods to replace, reduce or refine the use of animals in safety testing of chemicals; develop tests to detect unauthorized genetically modified organisms in EU markets; and devise the kind of nanoscale measurement methods that will be needed to support future nanoparticle-safety studies.

In some of its research areas, the JRC leads the world — which is all the more striking because the centre, with a budget close to €400 million (US$507 million) and a staff of 2,750, was once deemed to be a sluggish and inflexible body. But in the past 12 or so years it has transformed itself into a sharper and more effective organization that last year won unaccustomed approval from an evaluation panel led by the former UK science adviser David King.

Since then, the JRC has been working to implement King's report recommendation that it should go further still, and have a more proactive role in advising the European Commission, Parliament and Council instead of just responding to their immediate needs. Last week the JRC unveiled its new — and still evolving — decadal strategy for achieving that goal.

But because this comes at a time when commission president José Barroso is planning to create a new, high-level post of chief scientific adviser within his cabinet, a question arises. How should the new adviser and the JRC interact?

It is still early days — the role of the chief scientific adviser has not been defined. But it is clear that the adviser's office will have a small staff, and will thus be dependent on information gathering from elsewhere. The JRC would like to be its major pillar of support, and its 10-year plan includes two activities that could help to achieve this. One is the provision of 'policy options', which would allow policy-makers to base their decisions on dispassionate technical analyses of the pros and cons of each course of action. The other is identifying new issues and technologies — synthetic biology, for example — that might require a policy response in the future.

As valuable as those initiatives might be, however, and as admirable as the JRC's self-reform has been, the chief scientific adviser should not be constrained to listening to any single organization, least of all one that is part of the commission. He or she should be free to seek independent input from anywhere in the world.

The JRC's prime mission must be to remain a world-class technical resource for the EU, helping to protect its people against everything from natural and man-made catastrophes to illegal fishing. If it develops its strategy in the same positive spirit that has animated its reinvention over the past dozen years, the long-awaited chief scientific adviser will no doubt be glad to give its technical input serious weight — without treating it like an absolute mandate.