Kiddies, gather round and let me tell you another chapter in the story of "If you irritate people, they act irritated."

Let's begin with a recap: just before the Copenhagen climate conference, a large wodge (that's a technical term) of e-mails from the Climate Research Unit at University of East Anglia magically appeared in public. Those e-mails contained all the makings of a false controversy. And, as you can imagine, anyone who had been grinding an axe wasted no time in placing said axe vigorously into the back of any climate scientist they could find.

The first target was Phil Jones, head of the Climate Research Unit. The colloquial language used in his e-mail correspondence was trumpeted as fraud, while he also showed that his response to harassment (and there is no doubt that he was being harassed) was to become belligerent and petty-minded. Jones was cleared by not one, not two, but three separate enquiries.

Target number two was Michael Mann at Penn State in the US. He had corresponded with Phil Jones and, of course, in the leaked e-mails much of that correspondence became public. Skeptics swung into action and rained complaints down on Penn State. Although no formal accusations of fraud were made, the tone of the e-mails was apparent and Penn State launched its own enquiry.

The first problem is that there was no specific complaint, so one had to be constructed. The university eventually used the e-mails to construct a single complaint that covered the general themes. These complaints were:

Allegation 1: "Did you engage in, or participate in, directly or indirectly, any actions with the intent to suppress or falsify data? " Allegation 2: "Did you engage in, or participate in, directly or indirectly, any actions with the intent to delete, conceal or otherwise destroy emails, information and/or data, related to AR4 [a particular dataset whose handling had been questioned in the enquiries that Phil Jones went through], as suggested by Phil Jones?" Allegation 3: "Did you engage in, or participate in, directly or indirectly, any misuse of privileged or confidential information available to you in your capacity as an academic scholar?" Allegation 4: "Did you engage in, or participate in, directly or indirectly, any actions that seriously deviated from accepted practices within the academic community for proposing, conducting, or reporting research or other scholarly activities?"

To determine if there was any truth behind these allegations, the university assembled a team of academics from both within and outside the university. The individual committee members reviewed relevant "...e-mail correspondence, journal articles, Op-Ed columns, newspaper and magazine articles, the National Academy of Sciences report entitled 'Surface Temperature Reconstructions for the Last 2,000 Years,' ISBN: 0- 309-66144-7 and various blogs on the Internet."

From this, they drafted an additional 15 more specific questions that needed to be answered in addition to the four general allegations. Mann answered these and follow-up questions in a two-hour interview. He was then asked to provide all e-mails related to the fourth IPCC report—these are the e-mails that Phil Jones had requested be deleted—which he did, along with a file that indexed the e-mails and a further 10 pages of supplemental information.

One of the hurdles with any enquiry into a scientific topic is trying to interpret the data and analysis methods. Each branch of science has built up its techniques through years of testing, and it takes a long time to master and understand why things are done the way they are done. To cope with this particular hurdle, the committee consulted an outside expert. However, as we will see, they felt that this was not a sufficiently close examination.

The conclusion of this investigation was that Mann had not suppressed or falsified data. Nor had he deleted e-mails and/or data related to AR4. And Mann had not misused privileged information. In other words, Mann had been above board for allegations one, two and three. Decision four was to launch another enquiry:

Decision 4: The Inquiry Committee determined that "given that information emerged in the form of the e-mails purloined from CRU in November 2009, which have raised questions in the public's mind about Dr. Mann's conduct of his research activity, given that this may be undermining confidence in his findings as a scientist, and given that it may be undermining public trust in science in general and climate science specifically, an Investigatory Committee of faculty peers from diverse fields should be constituted under RA-10 [university regulation] to further consider this allegation."

Thus, with this short paragraph the enquiry spawned another enquiry. The second enquiry interviewed both Mann and a number of other scientists to determine Mann's view on data sharing, code sharing, and manuscript sharing. This was then compared to the views of other scientists, including Richard Lindzen, a well known critic of Mann's.

What was found was that Mann was exactly in line with the community as far as data sharing goes: the collector gets first use, after that the data is placed in a repository that allows public access. The processed data gets presented in papers, while the in-between steps are not made public.

Code sharing was uncommon for a variety of reasons in the past, but is now more common. It is, however, performed on a collegial basis, rather than through repositories. All scientists, except one, felt that the methods section of the paper was sufficient to replicate results, negating the need for code sharing as a rule. Although the other scientists had a range of views, Mann was pretty much right in line with the majority of the scientists consulted.

The only place where Mann found himself near one end of the spectrum was on sharing papers that were still going through peer review. He had, in the past, shared papers that he had peer reviewed but were not yet published. In these cases, the papers were authored by scientists that he had close contact with and were sent to other close contacts with the stipulation that they were not to be passed on. He said that although he did not have explicit permission, he understood that he had implicit permission (e.g., he felt that his friends trusted his judgment). The other scientists offered a mix of opinion on this, with some specifically requiring explicit permission, while others did not.

The end result: Mann is a scientist who behaves like a scientist. He is above board and, given his record, an extremely good researcher.

Further reading: Final report.