In a unique experiment, The Guardian published online the full manuscript of its major investigation into the climate science emails stolen from the University of East Anglia, which revealed apparent attempts to cover up flawed data; moves to prevent access to climate data; and to keep research from climate sceptics out of the scientific literature.

As well as including new information about the emails, we allowed web users to annotate the manuscript to help us in our aim of creating the definitive account of the controversy. This was an attempt at a collaborative route to getting at the truth.

We hoped to approach that complete account by harnessing the expertise of people with a special knowledge of, or information about, the emails. We wanted the protagonists on all sides of the debate to be involved, as well as people with expertise about the events and the science being described or more generally about the ethics of science. The only conditions are the comments abide by our community guidelines and add to the total knowledge or understanding of the events.

The annotations - and the real name of the commenter - were added to the manuscript, initially in private. The most insightful comments were then added to a public version of the manuscript. We hoped the process would be a form of peer review.

The response of the science establishment to the hacking is set to become a case study in public relations disasters. One PR figure from a major environment group said: "Their response will be taught in university communications courses - because I'm going to make sure it is."

The initial response from both the emailers and their employers was to condemn the hackers and ignore what they hacked. Michael Mann at Penn State University called the affair "a high-level orchestrated smear campaign to distract the public about the nature of the climate change problem." Phil Jones, holed up in the Climatic Research Unit at the University of East Anglia, called most of the charges against them "ludicrous". Kevin Trenberth at the National Centre for Atmospheric Research in Boulder, Colorado, and IPCC chairman Rajendra Pachauri both said they saw it as an attempt to undermine the Copenhagen climate conference, that was due to take place two weeks later.

Ben Santer from the Lawrence Livermore National Laboratory in California called Jones "one of the gentlemen of our field". He was standing firm in the face of "the vilest personal attacks" from "powerful forces of unreason." Bob Ward of the Grantham Institute for Climate Change at the London School of Economics said Jones and Mann "have been subjected to a co-ordinated campaign of personal attacks on their reputation." The UEA put out a statement saying that "the selective publication of some stolen emails and other papers taken out of context is mischievous and cannot be considered a genuine attempt to engage with the issues in a responsible way."

But the contents of the emails was not edifying for anyone. And the sceptics were making hay. They gleefully blogged that the emails revealed extensive data manipulation. The Daily Telegraph published a blog by a former news reporter on the paper, James Delingpole, claiming the affair "exposed the conspiracy behind the anthropogenic global warming myth", adding for good measure that "this scandal could well be the greatest in modern science."

The Daily Express ran a long story headlined: "100 reasons why global warming is natural". It said the list came from a "dossier" issued by the European Foundation, a UK-based right-wing group that campaigns mostly against European integration. But two months on, the dossier has not been published. Most of the hundred reasons were either meaningless or scientific nonsense, according to New Scientist magazine, which gave up after debunking the first 50.

In the US, sceptical physicists used the moment to revive a campaign to overturn a 2007 declaration by the American Physical Society that evidence of man-made climate change was "incontrovertible". Their letter began: "By now everyone has heard of... ClimateGate, which was and is an international scientific fraud, the worst any of us have seen."A picket formed outside the offices of NCAR in Boulder, where Tom Wigley, Trenberth and other emailers worked. Wigley was among a number of climate scientists who say they received death threats.

Many who might have been expected to defend Jones and his colleagues were silent. Most environmentalists sat on their hands, awaiting events. An exception was Elizabeth May, head of the Canadian Green party. She said she had read all the emails and declared: "How dare the world's media fall into the trap set by contrarians without reading the whole set." For her "the enormous volume of emails give a picture of thoroughly decent scientists increasingly finding themselves in a nightmare. They write each other in disbelief, protesting 'I have never been political. I am an honest scientist'." But four days after the leak, the environmental commentator George Monbiot said that Jones should resign.

The mood changed. Even Mann, whose words featured prominently in early soundbites published from the emails, began an op-ed in the Washington Post with the words: "I cannot condone some things that colleagues of mine wrote." The website that Mann co-hosts, RealClimate, offered the half-apologetic insight that the emails offered "a peek into how scientists actually interact and the conflicts show that the community is a far cry from the monolith that is sometimes imagined... For instance, we are sure it comes as no shock to know that many scientists do not hold Steve McIntyre in high regard." The post went on, "Gravity isn't a useful theory because Newton was a nice person."

But such guarded apologies didn't turn the tide of invective. A survey in the US found that 49% of respondents claimed to have followed news of climategate "very closely or somewhat closely", and 59% found it "very likely or somewhat likely" that some scientists have falsified research data in order to support their own theories and beliefs about global warming.

According to American science historian Spencer Weart, the frenzied assaults on climate scientists were unprecedented. "We've never before seen a set of people accuse an entire community of scientists of deliberate deception and other professional malfeasance. Even the tobacco companies never tried to slander legitimate cancer researchers."

One PR operator for a leading environmental organisation in Britain told me: "The emails represented a seminal moment in the climate debate of the last five years, and it was a moment that broke decisively against us. I think the CRU leak is nothing less than catastrophic."

The next recourse was to an investigation. Jones stood down while the University of East Anglia's pro-vicechancellor Trevor Davies, who himself had been director of CRU from 1993 to 1998, launched an independent inquiry to be headed by senior civil servant, Sir Muir Russell. The IPCC's chairman Rajendra Pachauri initially said the affair was "a serious issue and we will look into it in detail". But later made clear he would only be looking for lessons to learn and would not investigate the affair itself separately from the University of East Anglia and the Norfolk constabulary. In January the House of Commons Science and Technology Committee announced its own investigation.

The emails made little impression at the UN climate negotiations in Copenhagen in early December. This was about raw politics and not climate science. A few sceptics such as Senator Inhofe and Danish economist Bjørn Lomborg were present giving media interviews, and others such as Lord Monckton caused offence by declaring that young climate activists were akin to "Hitler youth". Saudi Arabia's lead climate negotiator Mohammed Al-Sabban, claimed on the opening day that "it appears from the details of the scandal that there is no relationship whatsoever between human activities and climate change" — a view that not even the most sceptical scientists would endorse.

But lobbyists were busy organising. In Britain, Lord Lawson launched the Global Warming Policy Foundation (GWPF) four days after the story broke. Lawson had been chancellor of the exchequer in 1989, when Margaret Thatcher assembled her entire cabinet to hear a seminar on climate change at which Tom Wigley, then director of CRU, was the star perfomer. But Lawson now opposes measures to fight climate change.

The GWPF's stated purpose is to "bring reason, integrity and balance to a debate that has become seriously unbalanced, irrationally alarmist, and all too often depressingly intolerant". But its trustees and academic advisers do not reflect that balance. Most have a public record as making sceptical comments about climate science. Lawson appointed as the foundation's director Benny Peiser. He is a social anthropologist, part-time lecturer at the School of Sport and Exercise Sciences at Liverpool's John Moores University, and long-standing co-editor of the journal Energy and Environment. The journal is trashed by Jones in the emails as "the worst journal in the world" for its patronage of what he regarded as poor-quality papers by sceptics. Even Peiser's co-editor Sonja Boehmer-Christiansen, a geographer from the University of Hull, admits that it espouses what she calls a "political agenda" but she has defended the journal, saying that, "it's only we climate sceptics who have to look for little journals and little publishers like mine to even get published." When asked by the Guardian to answer Jones's specific comment she did not respond.

Within hours of his appointment, Peiser had begun what became a frequent media presence on the increasing number of occasions when editors needed a sceptical voice in their climate coverage.

The BBC and the media reponse



One of the most significant outcomes – and perhaps a bellwether of public mood – has been the response of the media. "The CRU hack shifted the balance of legitimacy in newsrooms," says Ben Stewart, media officer at Greenpeace UK. Many newspaper began to probe the sceptics' case more thoroughly. Viewers of the BBC watched a crashing of editorial gears. For several years most of its coverage of climate change has been based on the scientific consensus that warming is real and that mankind is to blame. This had been reinforced by a study for the BBC Trust that concluded in 2007: "The weight of evidence no longer justifies equal space being given to the opponents of the consensus."

But even before "climategate", the BBC had been reviewing both its climate and science coverage. Deputy director-general Mark Byford organised an editorial seminar on climate change in September 2009. Insiders say the seminar followed an in-house trawl to find out how much coverage news bulletins gave to climate sceptics. It had been called after an MP complained that sceptics didn't get a hearing, and it discovered that very often they did not. After the seminar, deputy editor of news Steve Mitchell sent round a memo advising of the "need to reflect deniers in run-up to Copenhagen". One straw in the wind was the awarding of a Leeds-based BBC weather man with mildly sceptical views, Paul Hudson, with the title "climate correspondent" – to the chagrin of news correspondents covering that beat. In October he began posting blogs on the BBC website.

The ripples of the Mitchell memo spread through the BBC. Radio 4's Today raised eyebrows when, days before the climategate emails leaked, it interviewed an Australian climate change denier, geologist Ian Plimer, giving him what one critical insider called "the easiest of rides" for a string of highly contentious claims. And after climategate the change became even more visible to viewers and listeners. Reports say they have been under pressure from editors to "get more sceptics on". One major beneficiary has been Benny Peiser from the Global Warming Policy Foundation, who has made repeated appearances of prime-time BBC news. "We are," one correspondent said privately, "back to the false balance days that chiefs swore had been left behind."

Beyond the two tribes



What about science itself? Science is about producing findings that others can test by trying to replicate or falsify them. That is how theories and bolstered, how bad theories discarded and how knowledge is advanced. Some experiments are easy to replicate. All you need is a lab. Others are more complicated. And few are more complicated than those based on huge amounts of data assembled from all over the world over many decades. Both Jones's temperature data and Mann's proxy data of past temperatures fall into this category. That is one reason why sceptics, rightly or wrongly, have been able to claim that bad science has proliferated in climate research.

That is why the demands for scientists to release their data, even to people outside the research community, have grown. But it is also why researchers who have spent years, sometimes decades, assembling their data, are unwilling to hand it out to the first blogger to ask for it under a Freedom of Information request.

For sceptics like Steve McIntyre, the central issue is the principle that scientific findings are only valid if they can be replicated. And some scientists recognise that. Stephen Schneider of Stanford University in California and editor of the Climate Change journal, said in an email to CRU scientists and others in January 2009: "Our best way of dealing with this issue of replication is to have multiple independent author teams, with their own codes and data sets, publishing independent work on the same topics... That is how credible scientific replication should proceed."

But is it enough to ensure replication among the close network of scientists? Do non-scientists, or amateur scientists, or scientists who run politically charged blogs, have an equal right to share scientific data? Jones believes not. In October 2009 he wrote an email to Graham Haughton, a geographer at the University of Hull, about how "science should be conducted through the peer-review literature, as it has been for over 300 years. The peer-review system is the safeguard science has developed to stop bad science being published."

But many are beginning to disagree. In the world of the internet and freedom of information laws, the balance is shifting towards more open access. Some believe that Jones's cherished peer-review system is itself in jeopardy.

And not before time, says McIntyre. "I don't think there should be any issue of drawing up special rules for outsiders. I simply ask that scientists live up to their own policies," he says.

"There is an unseemliness about scientists willingly providing data to their friends and resisting the provision of data to people who are perceived as critics."

One in the mainstream who agrees is Judy Curry, a climate scientist at the Georgia Institute of Technology. She cut her teeth in public debate after publishing a paper on climate change and hurricanes shortly after Katrina hit New Orleans. She says much greater efforts are needed to open up science to outsiders.

Reviewing the saga of the leaked emails, she said the various datasets connected to Mann's hockey stick studies and Jones's CRU temperature data "stand out as lacking transparency. The raw data behind the key graphs in the climate debate "were not preserved" by the analysts, she said, though it "presumably is available from the original sources". Rather than being stuck in the archives, it needs reprocessing and reanalysing, she believes.

She didn't blame anyone for this state of affairs, but said "given the growing policy relevance of climate data, increasingly higher standards must be applied." In an open letter to young scientists involved in climate research, she said she was "trying to figure out how to engage sceptics effectively... I have received significant heat from some colleagues for doing this (I've been told that I am legitimizing the sceptics and misleading my students)."

Far from it, she said. "Ignoring sceptics from outside the field is inappropriate. Einstein didn't start his career at Princeton, but rather at a post office. Scientists claim they would never get any research done if they had to continuously respond to sceptics. The counter to that argument is to make all of your data, metadata and code openly available. Doing this would keep molehills from growing into mountains."

Curry says climate science has fallen victim to tribalism. "Climate tribes were established in response to the politically motivated climate disinformation machine...The reaction of the climate tribes... has been to circle the wagons and point the guns outward in an attempt to discredit misinformation."

She had found herself in a political storm after publishing a paper on how the number of hurricanes had doubled in 35 years – probably due to rising sea temperatures. By chance, the paper came out days after hurricane Katrina hit New Orleans. "I and my colleagues were totally bewildered and overwhelmed by the assault we found ourselves under" from sceptics, she says. "Associating with a tribe where others were more experienced and savvy about how to deal with this was a relief and very helpful at the time."

Unlike another victim of the hurricanes fracas. Kevin Trenberth, Curry does not appear in the leaked CRU emails. She says that she subsequently fell out with some of her fellow tribes-people after congratulating McIntyre for his work on freeing up data. And the hacked emails, she says, have reinforced her fears about "the systematic and continuing behaviour from scientists that hold editorial positions, serve on important boards and committees and participate in major assessment reports."

Other leading figures are also looking for ways to defuse the tribalism. Hans von Storch, a German meteorologist, often tries to arbitrate between sceptics and mainstream scientists. In December 2009, he wrote in the Wall Street Journal: "We need to repair the damage and heal the public's new mistrust of the workings of climate science.... The core of the knowledge about man-made climate change is simple and hard to contest. [Nonetheless] data must be accessible to adversaries; joint efforts are needed to agree on test procedures to validate, once again, already broadly accepted insights." He denounced the "CRU cartel" for their efforts to suppress open access to data.

Storch advised that "the authors of the damaging emails would be wise to stand back from positions as reviewers and participants in the IPCC process. The journals Nature and Science must review their quality-control measures and selection criteria for papers." Meanwhile, he told the media and politicians: "You have the knowledge you need for the political decisions. Let us [scientists] sit in our studies and discuss the remaining issues... Give us time to consider, to test alternative hypotheses, to falsify theories – to do our work without worrying if the results support our causes. Science is a valuable and unique societal institution, but not if it is consumed by short-sighted political goals."

And one of Jones's former senior colleagues, ex-CRU research scientist Mike Hulme, joined with Oxford science philosopher Jerry Ravetz to write: "Climate scientists will have to work harder to earn the warranted trust of the public – and maybe that is no bad thing." But to do that, they said, science itself might have to change. "This event might signal a crack that allows for processes of restructuring scientific knowledge of climate change. It is possible that some areas of climate science have become sclerotic... too partisan, too centralized. The tribalism that some of the leaked emails display is something more usually associated with...primitive cultures."

Hulme and Ravetz called for a "major change in the relationships between science and the public", with wider public scrutiny of its findings and methods using "the proliferating new communication media...Science is a deeply human activity, and we need to be more honest about what this entails."

Ravetz goes further. He told the Guardian: "In retrospect, it is clear that the Norwich group were practising evangelical science. For them there was a simple truth that would save us, and all naysayers were evil." After the war on drugs and the war on terror, we now had a war on carbon. He called the "extended peer community" on the blogosphere "necessary for the health of science. In spite of all the hazards of any extension of democracy, the rejuvenating effects must be good."

"Climategate" seems set to lead to far greater openness about research data. RealClimate, the climate science blogsite part-run by Mann, is promising to publish more data and relevant computer codes. "We have set up a page of data links to sources of temperature and other climate data, codes to process it, model outputs, model codes, reconstructions, paleo-records, the codes involved in reconstructions etc," it announced within a week of the leak.

"The climate science community fully understands how important it is that data sources are made as open and transparent as possible, for research purposes as well as for other interested parties... The providers of these online resources are very interested in getting feedback on any of these sites and so don't hesitate to contact them if you want to see improvements." That is a sea-change from the days in the CRU bunker.

In response to the saga, Britain's Met Office announced that it was putting into the public domain data on climate change from 1,700 stations round the world. This was not as big a deal as it sounded. Jones had told Nature magazine he was working on this back in July 2009. And, as the Met Office admitted, a lot of it was old data already "publicly available" through the World Meteorological Organization. And, while it might disseminate foreign data, it wants to hang to much of its own data because, according to its spokesman David Britton, "We at the Met Office have to offset our costs for the benefit of the taxpayer, so we have to balance that against freedom of access."

Like other recent battles over access to publicly held information, from lists of paedophiles to school league tables, those demanding freedom of information are winning. But there look like being many battles ahead.

There is a separate question for the scientific journals themselves. How much data should they require that scientists provide when they publish. There seems little agreement on that at present. The big two, Nature and Science, are relatively relaxed and demand little on top of what is required to allow the paper to pass muster with reviewers. Schneider asked his board at Climate Change to consider the matter after McIntyre asked him for personal computer codes. They decided that enough data should be provided to allow others, with the skill to write their own codes to replicate the findings. But no more.

Others are tougher. The Royal Society in London demands full data disclosure from contributors to its Philosophical Transactions.

Schneider told the Guardian there might be some middle ground – especially over researchers' highly prized and personally written computer codes. Maybe, like commercial patents, they should be allowed exclusive use of their own codes, as their own intellectual property, for two or three years. That, he said, would be time enough to "publish the initial papers using their hard work". But after that, the codes should all be disclosed. He added: "This broad discussion about the boundaries of data transparency, personal codes and exclusive rights... may be the only positive that might emerge from this unfortunate incident."

But many sceptics are not satisfied with such half-way houses. Many sceptic bloggers are in full cry against the entire peer review process. They talk about "peer-to-peer" review. Meaning an end to centralised control through journals and a free for all in which everything is published and anyone can comment on anything. A journalist active in this movement, the West Coast former street artist and radical arts critic Patrick Courrielche, claims: "Climategate... triggered the death of unconditional trust in the scientific peer-review process, and the maturing of a new movement of peer-to-peer review."

Can an entirely free intellectual market deliver better science? Can the pioneers of scientific review on the blogosphere do better than the journals? Would this ensure quality control or shatter it? Should the Jeffrey Archers of the scientific world have as much access to the journals as the Nobel laureates? They may shudder in the labs, but we may one day find out.