Just when you thought it was safe to go out – hands scrubbed, festooned in condoms, vaccinated up to the eyeballs, choosing a nice lull between the threat of death by bird flu or polonium poisoning – stop! A new health scare has arrived.

The land on which we are now merrily building homes for the next generation could damage our health. Yes, the brave new world of the Olympics, regenerated northern cities and smart new-builds contains a cocktail of toxic chemicals whose safety has started to worry scientists. Only last week Gordon Brown ordered another three million homes to be built on mostly brownfield sites. If previous health scares made you nervous about going out, this makes you nervous about staying in.

“As you go to build on that brownfield land, you start finding things in the soil,” Pat Troop, chief executive of the Health Protection Agency, said. “And our knowledge of the effects of chemicals on health is very limited.”

When Professor Troop talks about what she does know, it can sound quite alarming. Her responsibility is to protect Britain against killer diseases, from measles to the effects of fallout from a dirty bomb. When a lethal flu pandemic sweeps the country, the first in the front line will be this grandmotherly type in a retro1970s twinset, Yorkshire’s answer to Miss Ellie from Dallas. Yet it is when she discusses what she does not know that the hairs prickle on the back of your neck. She trusts us enough to tell us about the dangers that we are blind to, or unprepared for. But can she trust us to find this reassuring rather than frightening?

Take contaminated land. This is the unexpected answer to our question: what threat is as yet relatively unknown, but serious? “The areas I think that are growing in their importance are environmental issues. People need houses and here are some sites for them to build on. But it’s just making them safe.”

The only land that we have left to build on is often contaminated by industrial chemicals that are known to be harmful. Although efforts are made to clear the worst of it, no one knows what effect the residues have on the humans moving in. “You know that somewhere above a certain level of a chemical you can get acute problems, from our experience in industry. What we haven’t got very much understanding of is the very low levels over a long period. That’s really what’s missing,” Professor Troop said.

She has funded a toxicology unit in Newcastle upon Tyne to begin studies, but the task is mammoth. Not only must they look at the effects from contaminated land, but also from the everyday chemicals that we come into contact with, from cleaning products to make-up. And the results may not be known for many decades.

“There are so many chemicals circulating. There are, I think, about 100,000 in use. There’s such a backlog. People are tolerating very low levels. But if you ask, ‘What long-term health effect has it caused?’, at the moment we don’t know those answers,” Professor Troop said. “So the research programme goes right back to very basic stuff about what kind of mechanisms it’s causing in the body. Does it affect DNA or not?”

Relax. A bird-flu pandemic may get you first. Has she privately stockpiled Tamiflu, the drug to lessen the flu virus, to save her family? “No,” she said. “I wouldn’t go against our own guidelines. We have a normal first-aid kit at home.”

But one of the first measures that Professor Troop would put in place during a pandemic is “home quarantine”. This requires those with the disease stay at home with their families. She hopes they will comply. “We haven’t had an equivalent scenario with a massive disease right across the country,” she said. “We really just don’t know exactly how it’s going to pan out.”

Eek. More immediate have been the vicious personal attacks on her by the antiMMR lobby. Professor Troop’s previous job, as deputy chief medical officer, was to persuade parents to give their children the MMR jab; now she monitors the growing measles outbreaks caused by those that didn’t. The doctor who started the scare over the jab appeared before the General Medical Council this week, reminding her of a bruising time. “It was very critical, as if we weren’t human beings and parents who cared.”

When her children were small, Professor Troop was offered a full-time job, and they decided that her husband would abandon his new business and become a house-husband, as well as looking after their 20 acres of fenland.

She is less conventional than she appears. When we ask her if she had taken drugs, the question of the week, she smiled nostalgically: “Let’s just say I was a student in the Sixties.”

She sails as often as she can – she even commutes to work from her flat in London on the Thames ferry. But she is concerned about those of us who take our holidays farther afield – especially since we increasingly book online, to exotic places, and at the last minute.

She has in her sights the new travel websites that, irresponsibly in her opinion, don’t tend to give health warnings about jabs and pills.

“It’s particularly people who go online last minute. We’ve had problems with malaria. It’s partly that they don’t get the advice.”

When Professor Troop started out she specialised in surgery, the quick-fix branch of medicine. But when your patient is the public at large “you have to have the eye of faith, because some things take 10, 20 years before you see any change”.

Does she know that she has made any difference? There was a long, long pause. “It’s difficult to disentangle,” she said.

She mentioned just two projects from early in her career that she could be certain about. Professor Troop may have saved thousands more; she may end up saving us all. Like her, we just don’t know.

Pat Troop: CV

Born
April 5, 1948, Rotherham

Family
Married, two grown children

Career
University of Manchester medical school;
Stockport and Cambridge health authorities until 1988, chief executive in 1990;
Regional director of public health for East Anglia, 1993;
Deputy chief medical officer, Department of Health, 1999;
Chief executive of the Health Protection Agency, March 2003.
Appointed CBE in 2001

Interests
Sailing, cricket, horses

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