Here are 2 examples:
From the hacked email:
Phil Jones writes to University of Hull to try to stop sceptic Sonia Boehmer Christiansen using her Hull affiliation. Graham F Haughton of Hull University says its easier to push greenery there now SB-C has retired.
Ok, seriously? Did you read the e-mails? Sonia Boehmer Christiansen, who is, it seems, a professor emeritus, sent out an e-mail in which she admitted that she isn't qualified to judge what she's talking about, but then went on to, evidently, support ClimateAudit, and use her status as a professor emeritus at the University of Hull to lend credibility to her arguments. This email was brought to the attention of Phil Jones, a climatologist. Jones was offended by the dishonesty of the content of the e-mail, and brought the matter up to Graham Haughton, a professor at the University of Hull, to inform him of the misrepresentation of the facts, inform him that SB-C is using her affiliation with University of Hull as a credibility prop, and state his opinion that "science should be undertaken 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."
In short, he seems to be informing a colleague of the situation. He clearly feels that the original e-mail was inappropriate, and is questioning whether University of Hull wants to be associated with such things.
I seem to recall similar questions over William Dembski's use of his affiliation to Baylor University, when he used said affiliation to promote "intelligent design" (aka creationism).
Regardless, Haughton replies that he'll talk to her about it, but that she is technically entitled to use her title in such a manner.
Jones replies, saying he appreciates the reply, and commiserating with how busy they both are, and don't really have time to be dealing with nonscience, even if they feel obligated to do so. He then shares an observation regarding the journal that she is an editor for, is not regarded as a quality peer-reviewed journal (indeed, this is true; ISI's journal citation reports doesn't even list Energy and Environment, which would seem to indicate that it is not looked upon very well by others). He then comments that he's just venting frustration, and agrees that Haughton's reply is correct. Haughton's final reply mentions that SB-C, before her retirement, provided an 'ongoing critique of my motives and supposed misguidedness' with regards to Haughton's environmental interests (Haughton is a professor of Human Geography, so environmental concerns are not the only thing he could be primarily studying).
Does this really seem like such an outlandish and unreasonable discussion to you? I don't know what branch of theoretical physics you're in, or at what level, but you've never complained to someone else about how you feel that someone else is unfairly criticizing your research because of personal prejudices? Of course, the part where Jones complained about her use of her affiliation with University of Hull is unlikely to have any equivalents in your field, as I doubt there are professional (or retired) physicists who frequently comment in the sphere of public opinion rather than scientific discussion about how your (personally, your) research is completely backwards and accused you of dishonesty. And use their former affiliation with reputable universities to make their ignorant critique sound more informed.
From the hacked email:
Michael Mann discusses how to destroy a journal that has published sceptic papers
This is doubly untrue. His reason for opposing the journal isn't that they have 'published skeptic papers', as many prominent journals have, in fact (I believe Nature has published a few...), but that the papers they are publishing are not fit to pass peer review, and so the problem is their peer review process. Secondly, he doesn't advocate "destroying" the journal, but rather, as sometimes happens when journals become a venue for advocacy rather than science, that scientists stop recognizing it as a peer-reviewed journal. As a non-peer-reviewed journal, scientists would not cite articles from it or submit their articles to it as part of the scientific literature. Do you submit your articles to, or cite articles from, the International Journal for Creation Research?
Incidentally, the paper which prompted this e-mail, Proxy climatic and environmental changes of the past 1000 years (Soon and Baliunas, 2003), was horribly flawed, and indeed, never should have been published. Shortly after the publication, half of the editorial board of Climate Research resigned over the matter. One of those who resigned was the Von Storch mentioned in the email as a possible skeptic. Von Storch had just been promoted to Editor-in-Chief, and attempted to publish an editorial against the paper in question, the publisher, Otto Kinne, decided that the editorial could only be published with the consent of all of the editors of Climate Research (including the one who approved the Soon and Baliunas paper). The editorial would not be published, and Von Storch resigned a few days before his promotion from editor to the newly created position of editor-in-chief was to take effect.
Futhermore, 13 authors of papers cited in the Soon and Baliunas paper wrote a letter in which they criticized the paper on three main grounds: Soon and Baliunas used data reflective of changes in moisture, rather than temperature; they failed to distinguish between regional and hemispheric temperature anomalies; and they reconstructed past temperatures from proxy evidence not capable of resolving decadal trends.
When two other climatologists repeated the study, but without making the mistakes of Soon and Baliunas, they came to... let's just say, a rather different result. In short, peer-review at the journal Climate Research actually had failed badly, and Mann was, in fact, correct to come to the conclusion that he did.
Each "scandalous" email is dissected here:
Summary of notable emails from the CRU hacking scandal : science
Stop the personal attacks or there will be further consequences.
