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 will be a form of peer review.

Almost all the media and political discussion about the hacked climate emails has been based on soundbites publicised by professional sceptics and their blogs. In many cases, these have been taken out of ­context and twisted to mean something they were never intended to.

Elizabeth May, veteran head of the Canadian Green party, claims to have read all the emails and declared: "How dare the world's media fall into the trap set by ­contrarian propagandists without reading the whole set?"

If those journalists had read even a few words beyond the soundbites, they would have realised that they were often being fed lies. Here are a few examples.

The most quoted soundbite in the affair comes from an email from Prof Phil Jones, director of the Climatic Research Unit at the University of East Anglia, to Prof Mike Mann of the University of Virginia in 1999, in which he discussed using "Mike's Nature trick" to "hide the decline". The phrase has been widely spun as an effort to prevent the truth getting out that global temperatures had stopped rising.

The Alaska governor Sarah Palin, in the Washington Post on 9 December, attacked the emailers as a "highly politicised scientific circle" who "manipulated data to 'hide the decline' in global temperatures". She was joined by the Republican senator James Inhofe of Oklahoma – who has for years used his chairmanship of the Environment and Public Works Committee to campaign against climate scientists and to dismiss anthropogenic global warming as "the greatest hoax ever perpetrated on the American people". During the Copenhagen climate conference, which he attended on a Senate delegation, he referred to Jones's "hide the decline" quote and said: "Of course, he means hide the decline in temperatures."

This is nonsense. Given the year the email was written, 1999, it cannot be anything of the sort. At that time there was no suggestion of a decline in temperatures. The previous year was the warmest on record. The full email from Jones says: "I've just completed Mike's Nature trick of adding in the real temps to each series for the last 20 years (ie from 1981 onwards) and from 1961 for Keith [Briffa]'s, to hide the decline."The decline being referred to was an apparent decline in temperatures shown in analysis of tree rings, which have historically correlated well with changes in temperature. That relationship has broken down in the past half century. The reasons are still debated.

The "trick" was a graphic device used by Mann in a 1998 paper in Nature to merge tree ring data from earlier times with thermometer data for recent decades. He explained it in the paper. Jones was repeating it in another paper. "This is a trick only in the sense of being a good way to deal with a vexing problem," Mann told the Guardian. Clearly, this problem with modern tree data raises questions about older data – at least until the reason for the divergence is nailed down. But it is not clandestine data ­manipulation, or, as claimed by Palin and Inhofe, a trick to hide global cooling. That charge is a lie.

While he was in Copenhagen, Inhofe made a link between the "trick" to "hide the decline" and the second most popular soundbite. He said that "of course [Jones] meant hide the decline in temperatures, which caused another scientist, Kevin Trenberth of the National Centre for Atmospheric Research in Boulder, Colorado, to write: 'The fact is we can't account for the lack of warming at the moment and it is a travesty that we can't.'"

The link is bogus. The two emails were 10 years apart. Unlike Jones, Trenberth's remark from October 2009 was indeed about the slackening of the warming trend that some like to interpret as cooling. That much is agreed. But Inhofe and other sceptics latched on to Trenberth's "travesty" phrase as a revelation that scientists were trying to keep cooling secret because it undermined their arguments about global warming.

Again this is demonstrably false. Nothing was hidden. For months, Trenberth had been discussing publicly his concerns about the inability of scientists to pin down the precise reason for the "absence of warming" since 1998. He had argued in the journal Current Opinion in Environmental Stability in early 2009 that "it is not a sufficient explanation to say that a cool year [he had 2008 in mind] is due to natural variability (pdf)". Such explanations "do not provide the physical mechanisms involved". This was the "travesty" he was referring to in his email. He wanted scientists to do better.He said the best way to improve the explanation and make it more specific was to make better measurements of the planet's energy budget. This would allow scientists to distinguish between any changes in the greenhouse effect, which would result in more or less heat overall in the atmosphere and oceans, and short-term natural cycles of variability, which merely redistribute heat. He was debating this with the former head of the Climatic Research Unit Tom Wigley, who took a different view. But their genuine scientific discussion has, since the publication of the emails online, been hijacked by ignorant or malicious invective.

Several other soundbites were subject to perverse or dishonest interpretations by commentators. Patrick Michaels, the climatologist and polemicist for the rightwing Cato Institute, published a long op-ed piece in the DC Examiner, slamming Mann for an email quote about keeping sceptics' papers out of the IPCC report "even if we have to redefine what the peer-reviewed literature is".

Michaels is an old foe of Mann's, but this genuinely damaging statement was actually made by Jones.

In another case George Will, celebrated in some circles as an intellectual, told ABC's This Week programme that Mann had said in an email that he wished to "delete, get rid of, the medieval warming period". No such words appear anywhere in the emails. What Mann said was that "it would be nice to try to 'contain' the putative 'MWP'". And an intellectual like Will should have known that, in this context, "contain" means to understand its dimensions – how warm it was and how long it was. Mann explained as much to anyone who asked. Verdict: not guilty.

Annotations

The text below consists of invited comments made on the Climate wars articles. They can be accessed in the main body of the article by clicking on the text to which they refer, which is highlighted in yellow.