"Observations do not show rising temperatures throughout the tropical troposphere unless you accept one single study and approach and discount a wealth of others. This is just downright dangerous."

• Peter Thorne, research scientist, Met Office Hadley Centre, to Phil Jones, UEA, 4 February 2005 (email 1939)

Having been asked to look over an early draft of part of the latest IPCC report, Thorne expresses concern that it over-simplifies or even dismisses uncertainty about temperature rises in the atmosphere. The fact Thorne was asked to comment is part of the process intended to make sure such omissions or distortions do not get published, and his reponse demonstrates the openness with which the scientists debate those issues. The resulting public review drafts and final report in 2007 reflected much more observational uncertainty, in line with Thorne's comments.

"Getting people we know and trust [into the IPCC report team] is vital."

• Phil Jones, UEA, to Kevin Trenberth, NCAR, 15 September 2004 (email 714)

In an earlier email in the thread, Jones refers to two scientists he does not "trust". He does not say why, but does not say because he does not agree with them. He and Trenberth discuss a huge range of names as possible contributors, from several countries, and are keen to widen the net.

"Mike, the figure you sent is very deceptive ... there have been a number of dishonest presentations of model results by individual authors and by IPCC."

• Tom Wigley, University Corporation for Atmospheric Research, US, to Michael Mann, Penn State University, US, and others, 14 October 2009 (email 2884)

Wigley is referring to a graph on the Real Climate blog by climate scientist Gavin Schmidt. On Wednesday Schmidt responded, again on the blog, saying he "disagreed (and disagree) with Wigley", and replied at the time to say so. The general allegation about dishonest presentations is uncomfortable, but these are often scientifically difficult judgements, and are being argued out.

"The trick may be to decide on the main message and use that to guide what's included and what is left out."

• Jonathan Overpeck, University of Arizona, to Ricardo Villalba, IANIGLA-CONICET, Argentina, 16 December 2004 (email 4755)

Overpeck is advising Villalba on how to edit something down to a half-page summary, in which context his advice looks less conspiratorial. Notably, he goes on immediately to say: "For the IPCC, we need to know what is relevant and useful for assessing recent and future climate change. Moreover, we have to have solid data – not inconclusive information."

"I find myself in the strange position of being very skeptical of the quality of all present reconstructions, yet sounding like a pro-greenhouse zealot here!"

• Keith Briffa, UEA, to Edward Cook (probably Edward R Cook at the Earth Institute, Columbia University), 20 January 2005 (email 2009)

Briffa explained to the Guardian: "I am trying to reinforce the request to my co-author to provide a strongly critical review of the draft text. I believed that I had taken account of the considerable uncertainties in the evidence when producing the draft and still came to the conclusion that the late 20th century was unusually warm." This explanation is backed up by the email thread, in which he writes: "Really happy to get critical comment here." Not in keeping with the idea that the scientists were only interested in opinions that agreed with theirs.

Waspishly, Briffa does also suggest however that another climate scientist, Kevin Trenberth, is "extremely defensive and combative when ever criticized about anything because he figures that he is smarter than everyone else and virtually infallible." That does not make Trenberth unique!

"We're choosing the periods to show warming."

• Phil Jones, UEA, to Kevin Trenberth, NCAR, and others, 21 December 2004 (email 2775)

On the surface this was one of the more damaging excerpts. But Jones explained at briefing in London on Wednesday that he was referring to the colour scheme and scales on graphs showing temperature records from 1901 to 2005 – the last century – and 1970 to 2005 – the period for which satellite records are available. "Those periods show warming. They were not pre-selected to show warming," he added.

"My most immediate concern is to whether to leave this statement ["the last two decades of the 20th century were probably the warmest of the last millennium"] in or whether I should remove it in the anticipation that by the time of the 4th assessment report we'll have withdrawn this statement."

• Peter Stott, Met Office Hadley Centre, to Phil Jones and others, 8 September 2004 (email 4923)

Stott is preparing for a meeting with the ecologist David Bellamy, who has publicly called global warming "poppycock", and is being cautious about not overstating the evidence in case ongoing research shows it to be untrue. In the event the IPCC report in 2007 still suggests they were the warmest decades, despite the previous extra research.

"We don't really want the bullshit and optimistic stuff that Michael has written ..."

• Phil Jones, UAE, to Jonathan Overpeck, Arizona University, 8 February 2008 (email 3062)

Jones is referring to new research by Michael Schultz of the University of Bremen – not, as many at first assumed, Michael Mann. Jones said on Wednesday he was not confident enough in Schultz's early work on a new way of reconstructing ancient climate through the oceans. Interestingly, Jones's email then asks Overpeck to write something and adds: "What we want is good honest stuff, warts and all, dubious dating, interpretation marginally better etc."

"The results for 400ppm [parts per million carbon in the atmosphere] stabilization look odd in many cases ... As it stands we'll have to delete the results from the paper if it is to be published."

• Rachel Warren, UEA, to Rita Yu, UEA, 19 August 2008 (email 310)

This is a clear illustration of the danger of people posting excerpts online using ellipsis (...). What Warren actually wrote was: "The results for 400ppm stabilization look odd in many cases as I have commented before. I would like to try to understand why, before we finish the paper. As it stands we'll have to delete the results from the paper if it is to be published." Warren has seen an anomoly in Yu's results; Yu is a PhD student and she is being asked to give more detail before an unexplained anomoly is written up in a journal paper.

"What if climate change appears to be just mainly a multidecadal natural fluctuation? They'll kill us probably ..."

Tommy Wills, Swansea University to the mailing list for tree-ring data forum ITRDB, 28 Mar 2007 (email 1682)

Wils' email is part of an exchange about whether and how to respond to climate sceptic criticisms. It appears to be a point made for more for rhetorical effect than anything else. As one contributor on the blog Quark Soup by David Appell put it: "Well, at least they considered it as an option."

"There shouldn't be someone else at UEA with different views [from "recent extreme weather is due to global warming"] – at least not a climatologist."

• Phil Jones, UEA, to Melissa Murphy, UEA, 23 Aug 2004 (email 1788)

The TV programme Tonight with Trevor Macdonald is going to feature a colleague of Jones, David Viner, arguing that (then) recent extreme weather was a result of global warming. Jones is responding to a request via the press office for another member of the Climatic Research Unit to appear making the opposite argument. Jones is arguing it would "look odd" if two people with opposite views were from the same department and suggests the TV production team "could easily dredge someone up" from elsewhere.

"I doubt the modelling world will be able to get away with this much longer."

• Tim Barnett, Scripps Institution of Oceanography, US, to Gabi Hegerl, Duke University, US, 18 May 2007 (email 850)

This is during a discussion about information a group of scientists wants to request from climate modellers to improve their understanding of the models – and presumably improve the models themselves. Barnett says getting forcing data is "a must" because many climate models, when tested against history, produced results close to observed temperatures, despite making different assumptions about "forcing" (probably radiative forcing, the net difference between heat radiation entering the earth's atmosphere and leaving it).

"All models are wrong."

• Phil Jones, UEA, to Timothy Carter, Finnish Environment Institute, 11 Mar 2004 (email 4443)

Jones's statement would be dynamite if he was referring to all climate models. Actually, he said on Wednesday, he was referring to new attempts to average existing models, which he did not believe were complex enough. The UEA said that those early averaging models were not subsequently published because of continuing concerns.