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David King shot to prominence earlier this year by cutting through the ministerial muddle over foot-and-mouth, but the government's chief scientific adviser had earned a reputation as a truthsayer eight years previously, when he publicised how British scientists were being held back by the desperate state of university laboratories.

Describing his own chemistry department, the Cambridge University professor recalls: "I showed a health and safety officer how bad it was with a TV camera crew present. That made the university sit up and take notice."

King went on to commission a comprehensive refurbishment strategy for the building from Danish architect Erik Sørensen, who had designed the award-winning crystallography department building next door. This gave the department a head start when the government announced its Joint Infrastructure Fund in 1998, in which grants totalling £750m were earmarked for upgrading university laboratory buildings over five years. The department, which boasts more scientific research citations than any other British university, walked off with the largest chunk of round-two JIF money.

Cambridge's chemistry building is currently undergoing the fifth phase of its £34.5m nine-phase refurbishment programme. Although more ambitious than other universities' projects, the refurbishment typifies the problems encountered in upgrading laboratory buildings. The project was taken over by local architect Nicholas Ray Associates, and in one of the old laboratories still awaiting its makeover, Nicholas Ray points out an original fume cupboard built into a corner window. "It discharged noxious fumes straight out of the window into the open air and right next to a window that was used for fresh-air ventilation," he says. "Now we have 10 times as many fume cupboards, and modern health and safety regulations won't allow us to push the fumes out through the windows any more."

In the partly refurbished south wing of the building, a labyrinth of ducts now channels the noxious fumes from the lab fume cupboards to rooftop flues where they can escape safely. These ducts also supply fully conditioned air to the laboratories. The big problem with this solution was how to thread the bulky air ducts through the five-storey building to roof level. Ray's bold solution has been to run the extract ducts out through the external walls and up the south facade to the rooftop flues. To conceal the external ducts, a glazed facade has been created 3.3 m beyond the original brick external wall. Beyond the north wall, a similar facade conceals the supply ducts, which channel conditioned air down from rooftop chillers.

Inside the refurbished labs, the fume cupboards have been banked back-to-back in groups of four and placed at right angles to south-facing windows. Their extract ducts pass through the adjoining window openings, which have now been bricked up. All exhausted air in the air-conditioned laboratories is also discharged through the fume cupboards and out through their external ducts.

"We said that the number of windows should be halved, because the south facade was overglazed and suffered from excessive solar gain," explains Ray, "so we were able to run our ducts in front of alternate windows."

The external curtain wall also plays a role in cutting solar gain and glare, as the frameless glazed panels have been fritted in near-white enamel to leave a dense pattern of tiny transparent "holes". Side panels to the facade are in galvanised steel sheet that has been perforated to match the fritted panels, with holes of the same size and density. Added to that, the glazed facade has "windows" of its own, either as clear-glazed panels or as gaps in the glazing, and these coincide with the windows that have been retained in the original brick external wall behind.

Inside the laboratories, benches alternate with the banks of fume cupboards. Horizontal ducts and other services are concealed within the 1.5 m ceiling void, thanks to generous original floor-to-floor heights. The original chemical-resistant teak worktops have been recycled on top of new proprietary lab benches, and the timber block floors have likewise been relaid. The layout is dense but orderly, and despite the bricking-up of four of the 10 original original windows in each lab and the addition of the extra curtain wall, sufficient daylight penetrates the interior to counteract claustrophobia and provide a view.

Aside from the practical problems of ventilation, the facades and the chimneys, which project 7 m above the roofline near the heart of historic Cambridge, posed a special town-planning challenge.

As part of the planning application, nine high-resolution photomontages were prepared by Miller/Hare at a cost of £10,000 to illustrate the impact of the rooftop chimneys on hallowed views from the city's colleges and parks.

The city planners' response was far from hostile. "Their idea was that, rather than have factory flues, they should be made into sculptural showpieces," recalls King. Ray adds: "Peter Studdart, the chief planner, even suggested coloured ducts like those at the Pompidou Centre in Paris. We argued for patinated copper, as this was an established roofing material in Cambridge."

The rooftop flues take the form of bulky lopsided chimneys in green prepatinated copper, and they certainly live up to their sculptural requirement. Their lopsided shapes bring to mind the heroic designs of the Italian futurist Antonio Sant'Elia before the First World War, but are in fact generated by more mundane kinks in the extract ducts as they bend inwards to bulky fans housed in the rooftop plant room and then back outwards to the new glazed facade. To add to the sculptural effect, notches in a vestigial classical style have been let into the four top corners of each chimney. From the neighbouring classical Downing College, the sculptural green chimneys project a more distinguished skyline than the spindly aluminium flues they replaced.

The glazed north facade below the chimney has a harmonious design to match, with a complex rhythm of fritted panels, clear glazing and gaps. The fritted glass even takes on a slight bluish-green tinge that matches the patinated copper above. One stylistic problem that remains unresolved is that the high-tech glazed curtain wall masks the brick building behind it, which retains its own very different sub-classical integrity. However, no new glazed skins are planned for the front facade or the facade of the north wing, which are the building's more public faces.

Other components of the chemistry building's phased refurbishment include relocating the boilers to rooftop plant rooms, converting the basement vacated to technicians workshops, and adding links between north and south wings to bind the department closer together.

Nicholas Ray believes the scheme is sustainable because the JIF laboratory improvements have been co-ordinated within a comprehensive long-term refurbishment strategy. To David King, the improvements have an even wider significance for his department. "We can now match our main competitors in the USA and Japan. They would have just flattened the building and rebuilt it at a cost we can only dream about," he says.