Emily Shuckburgh spends much of her time wrapped up against the cold on the far side of the world, measuring atmospheric and ocean eddies for the British Antarctic Survey. But over the past few months she has been rolling up her sleeves and travelling across the UK to confront the public heat over climate change.

With support from Living With Environmental Change, a partnership between government departments and funding agencies, she has run a series of focus groups exploring people’s views on media coverage of science. She endorses projects such as oldweather.org, an attempt to engage the public directly in analysing historical sea temperature data. On secondment to the Department of Energy and Climate Change, she has also been posting videos on YouTube and engaging with “sceptics” via blogs.

“It’s quite clear there has been a breakdown of trust between scientists and the public, and it’s important that we try to articulate more clearly what our processes are,” she says. “I’ve been working hard to find ways to communicate our findings. A lot of climate science is difficult and counter-intuitive. We really have to put more effort into explaining our work and making it understandable and relevant.”

Shuckburgh is in the vanguard of a new generation fighting back against those who reject mainstream science, actively taking on criticism in fields from genetically modified food and nuclear power to vaccination and animal testing. The weapon of choice has been the internet. Both sides use websites, e-mails and Twitter to inform and unite previously isolated individuals. The tactics deployed by the “sceptics” range from overwhelming Freedom of Information requests on climate scientists to financially crippling libel lawsuits against critics of alternative medicine.

No controversy has been more high profile than global warming, where public suspicion has been stoked by the alleged manipulation of temperature records exposed in the leaked “Climategate” e-mails from the University of East Anglia, and questions over the reliability of the predictions in the Intergovernmental Panel on Climate Change reports. It is a debate in which the very word “sceptic” has formed part of the battle, seized as their own by those who question global warming.

“Scepticism is a major part of science, and it’s a shame it has been appropriated,” says Shuckburgh. “That leads to a lot of confusion. If we could reclaim the word … that would be progress.” She could be a poster-child for the findings of Sir Muir Russell’s report on Climategate, which rejected any suggestion of lack of rigour or dishonesty by the researchers. Instead it called on scientists generally to be more open in the way research is conducted, make their results and models available to other interest groups, and engage with critics in the blogosphere.

Many feel much more still needs to be done. Writing in a blog about scepticism in New Scientist in February, Sir John Beddington, the UK government’s chief scientific adviser, warned: “It is time the scientific community became proactive in challenging misuse of scientific evidence. We must make evidence, and associated uncertainties, accessible and explicable. In a world of global communication, we cannot afford to speak only to ourselves.”

Bob Ward, policy and communications director at the London School of Economics Grantham Research Institute on Climate Change and the Environment, argues: “The key problem has been not so much what people accept about science but whether they trust the researchers … Scientists are not very good at framing the unknowns in ways that are meaningful to the decision-making process. Too often when you are trying to bring your research into the policymaking domain, uncertainty can be used as [an] excuse for inaction. Some have downplayed uncertainties not because they are trying to pull the wool over your eyes but because they are afraid they would be amplified by those who have vested interests in resisting potential policy responses. We need to get better at explaining uncertainties.”

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At London’s Grange Hotel in the shadow of St Paul’s Cathedral earlier this month, Bill Gates, the billionaire co-founder of Microsoft, looked content as he shared a platform with a dozen health and development ministers. They had just concluded a meeting which generated $4.3bn in additional donations for the Global Alliance for Vaccines and Immunisation, designed to buy and distribute vaccines to children in the world’s poorest countries.

Outside the building, a group of protesters gathered to raise their concerns over the safety of vaccines, reflecting discredited claims first made in 1998 by Dr Andrew Wakefield of a link between autism and the measles, mumps and rubella jab, which triggered a slump in child immunisation by concerned parents in the UK and the US. Inside, when a journalist raised the issue, Gates politely but curtly dismissed the concerns with the words: “I don’t know if there is any medical question that has been more studied.”

In February, at the World Economic Forum in Davos, he had been still more blunt when asked to comment on the link between autism and vaccines. “It’s an absolute lie that has killed thousands of kids. Because the mothers who heard that lie, many of them didn’t have their kids take either pertussis [whooping cough] or measles vaccine, and their children are dead today. And so the people who go and engage in those antivaccine efforts, you know, they, they kill children.”

Of all the contemporary polemics in which scientists engage, doubts over the safety of vaccines raise one of the greatest short-term threats to human life. The slump in MMR take-up in the UK following Wakefield’s claims has triggered a surge in infections – in addition to current high-level outbreaks in Europe and the US as well as Africa – which can be fatal or lead to sterility. But with so many people directly confronting the issue of vaccination for their own children, and the consequences so great, the rhetoric is also intense.

“Gates’ comments should be perceived as hate speech,” says Mary Hooper, a lawyer who helped organise a protest rally in response outside Microsoft’s New York headquarters. As someone who spent periods as a child in the Soviet Union, she draws a parallel between the “pro-vaccine” lobby and totalitarianism. “There is a very rigid party line, with four oligopolistic vaccine manufacturers,” she says. “If you dissent, you are branded as a heretic. There is a lot of self-censorship.”

Much of her argument is based not on the overwhelming scientific case, which rejects a link to autism, but on a smaller number of dissenting studies and compensation paid in the US to parents whose children suffered side-effects that judges implied could have been the result of vaccination. “The science is so unsettled,” she says. A book that she co-edited this year positions the debate between “pro and antivaccine” camps, rebranding some scientists as “vaccine injury denialists”.

Such views continue to find resonance in the media. Sir Colin Blakemore, professor of neuro­science at the University of Oxford, says: “There is increasing respect for the authority of science, and increasing understanding of the scientific method and its limitations. The opposition is more vocal because of the internet, but I don’t think it’s having a greater impact.” He argues it was the mainstream media that stoked up concern over autism, and that its search for “balance” is partly at fault. “The public is capable of making decisions if the data are presented honestly. The pressure should be on the national press.”

The challenge is how best scientists can engage with this press. Professor Paul Offit, chief of the Division of Infectious Diseases at the Children’s Hospital of Philadelphia, says: “We have a duty to explain why vaccination is important. But at no point in your training are you educated about how to deal with the media. The media is required to compress issues into a soundbite. In politics, you lie, are mean, attack the other person and get away with whatever you can. I’m so hardened to it, but scientists are certainly not trained for this. We picked this gentle job, spending 10 years in a windowless room inoculating mice.”

He has been a tireless advocate, appearing frequently in the media and writing a book, Deadly Choices, which attacks the antivaccine movement. He sees room for optimism, citing a series of recent legal challenges in the US overturning “personal belief” exemptions that allow parents to avoid mandatory vaccination of their children in schools. But he also points to a very practical reason for the shift, more evident in vaccination than in many other controversies. “The pendulum is swinging back. The reason is outbreaks. In 2010, we had the biggest pertussis outbreak in California since 1947.”

David Salisbury, head of immunisation at the Department of Health in the UK, is also optimistic that the debate on vaccines is being won, while stressing: “It’s much more complicated than a pro/anti stance. It’s about individual perceptions.” He cites not only a resurgence in uptake in basic vaccinations, but also opinion polls asking mothers whether they automatically vaccinate their children or agonise over a decision. A decade ago, just half did so without question. Now, three-quarters do not hesitate. “We have learnt to engage, but subtly,” he says. “You don’t counter one threat with another, balancing a fear of the consequences of vaccination by saying that measles can also be very serious. Parents want more information on side-effects.”

While officials were slow to react to the MMR scare after Wakefield, Salisbury argues that today there is much more active and sophisticated engagement. He cites the recent uptake of the HPV vaccine in the UK to protect against cervical cancer, which used social media including chatrooms. When one girl died shortly after receiving a jab, he stresses that the Department of Health refrained from comment until verifying that it was the result of an unrelated condition, then spoke out. But the battle is far from won. When pandemic flu spread around the world two years ago, desperate efforts to identify sufficient quantities of the vaccine were soon displaced by concern over extremely low take-up. Only about 40 per cent of frontline healthcare workers were vaccinated despite the risks of infection. Some polls suggested suspicion and fear of side-effects as the reason.

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When Professor David Jentsch, a medical researcher at the University of California Los Angeles, opened a letter last October, a pile of razor blades fell out along with a death threat. It was the latest salvo in a campaign of intimidation that began in 2006 with an attempted firebombing of a colleague. It escalated to an explosion that destroyed his own car in 2009. But instead of being put off, he launched a campaign on the importance of animal testing in medical research.

“They didn’t blow up my car to frighten me but to frighten everyone else,” he says. “When you are sitting at your desk, there has to be a pretty big motivational urge to get you away from your computer, and if you needed any reason not to find the motivation, the threat would have done it. But I can balance violence with my own advocacy. It spurred me into actions that we should have been doing anyway.”

Once a month, a dozen demonstrators gather outside his house, shouting obscenities, disturbing his neighbours and bearing photographs of tests which, he says, bear no relation to his work or his laboratory. But Jentsch has organised a counter group, with 40 scientists recently showing up in solidarity to block his gate and hold a party. He has also been stepping up meetings around the US to establish links with funders, science organisations and animal care providers, as well as to convince fellow researchers to rebut claims by animal rights groups. “The vast majority of rights activists don’t want an argument and will not cede. They will succeed when they prevent the argument being had.”

His organisation, called Pro-Test for Science, was inspired by an equivalent group in the UK called Pro-Test, originally launched by Laurie Pycroft, a teenager frustrated by demonstrators objecting to the construction of a new animal laboratory at the University of Oxford. The difference is that Jentsch’s organisation is dominated by scientists themselves, talking about their work.

Such a response would have seemed unthinkable a few years ago. In the UK, animal rights extremism has subsided after belated advocacy by drug companies and academics helped lead to injunctions and criminal prosecutions. In the US, Jentsch says similar approaches are hindered by complex legislation including a strong constitutional defence for freedom of speech. Prosecutions have also largely been unsuccessful. But he believes advocacy by scientists like himself has had a significant effect.

“There’s no control group but, after a period of three years in which violence was escalating, there hasn’t been a single violent reaction. I don’t think it’s a coincidence,” he says.

“Writing a paper is not necessarily the end of being a scientist,” Jentsch adds. “It’s important to show our trainees that it’s also about being a teacher and a communicator of research. I want us to increasingly treat it as part of our job … It’s pragmatic as well as being the right thing to do .”

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Despite the rhetoric, there are signs that trust in science remains strong and may even be improving, while the intensity of polemic in the media and online is having less impact than many believe. The latest in a regular series of polls by Ipsos-Mori showed 83 per cent of the public trusted scientists working for universities “a great deal” or “a fair amount”, although 70 per cent felt there was “so much conflicting information it is difficult to know what to believe”, and just 43 per cent believed they were informed about science.

Professor Mark Maslin, head of the geography department at University College London, argues: “Climategate didn’t really do any damage to climate science. Many people are unaware how much climate change policy is already in the British system, whether in regulations for buildings, waste management or energy supply systems. While the sceptics argue about climate change, there is a multi-billion-euro carbon trading scheme in Europe which will soon include 55 per cent of all global aviation emissions.”

But he, too, argues for more public engagement while stressing that “not all brilliant scientists are brilliant communicators” and that there can be problems when some scientists talk outside their area of expertise. Still, Maslin believes that science should bring in researchers and practitioners from different fields (such as the social sciences and law) and encourage much more engagement by those “on the frontline”. He cites a recent conference on population growth that included many speakers from the developing world; and a presentation on a new study on the impact of the 2010 drought on the Amazon, which gave prominence to Brazilian researchers. “It gives so much more legitimacy than a white middle-aged male scientist.”

Andy Stirling from the University of Sussex cautions against the recent calls for scientists to be intolerant of dissent, stressing that there has always been dissent: “Calling for gross intolerance of scepticism is antiscientific. There is no doubt [that] there are some irrational rejections of science. But sometimes there is a rather hubristic dismissal of areas where there is quite a lot of uncertainty. We should start having grown-up debates.”

The challenge is that many scientists remain ill-trained, ill-suited and under-rewarded for speaking out more widely and effectively. But a growing number do seem increasingly willing to fight back against ill-founded criticisms, not only in their laboratories but in the mainstream and online media, as they seek to win over not only their peers but also public opinion.