My impression from reading the emails is that different standards are being applied to the AGW skeptics because of their conclusions rather than because of their methods. At the same time there is evidence of data massaging and dubious practices around their own methods in order to match their pre-conceived conclusions. The whole process does not look like the disinterested search for truth that is the scientific ideal.

My P(B|E) would be higher if I read emails that seemed to focus on methodological errors first rather than proceeding from the fact that a journal has published unwelcome conclusions to the proposal that the journal must be boycotted.

I do think the likelihood ratio is significantly above 1. This is based off reading some of the emails, documents and code comments in the leaks. Here's a reasonable summary of the emails. It looks like dubious science to me. I find it hard to understand how anyone can claim otherwise unless they are ideologically motivated. If you genuinely can't see it then I'm not really interested in arguing over minutiae so we'll just have to leave it at that.

It seems to me that AGW skeptics made a variety of claims that AGW believers dismissed as paranoid: there was a conspiracy to keep skeptical papers out of the journals; there were efforts to damage the careers of climate scientists who didn't 'toe the party line'; there were dubious and possibly illegal efforts to keep the original data behind key papers out of the hands of skeptics despite FOI regulations. I did not see many AGW believers prior to the climategate emails saying "Yes, of course all of that happens, that's just the way science operates in the real world".

When the CRU leaks became public and substantiated all the 'paranoid' claims above, including proof of illegal destruction of emails and data to avoid FOI requests, I find it suspicious when people claim that it doesn't change their opinions at all. The standard response seems to be "Oh yes, that's just how science works in the real world. I already knew scientists routinely engage in this sort of behaviour and the degree of such behaviour revealed in the emails is exactly in line with my prior expectations so my probability estimates are unchanged". That seems highly suspect to me and looks an awful lot like confirmation bias.

AGW skeptics have often been challenged on the lack of peer reviewed papers in credible climate science journals supporting their arguments. Now it is quite possible that this is the case because skeptical papers have been rejected purely due to being bad science (as is the case with the lack of papers supporting the effectiveness of homeopathy in medical journals). However, the absence of papers from the key journals cannot be treated as independent evidence of the badness of the science if there is a concerted effort by AGW believers to keep such papers out of the journals.

It is legitimate to attack the science the AGW skeptics are doing. It is not legitimate to dismiss the science purely on the basis that they have not been published in peer reviewed journals if there is a concerted effort to keep them out of peer reviewed journals based on their conclusions rather than on their methods. Now I'm sure the AGW believers feel that they are rejecting bad science rather than rejecting conclusions they don't like but emails like the above certainly make it appear that it is the conclusions as much as the methods that they are actually objecting to.

In my opinion the CRU emails mean that it no longer appears justified to ignore claims by AGW skeptics purely because they have not appeared in a peer reviewed journal. They may still be wrong but there is sufficient evidence of biased selection by the journals to not trust that journal publication is an unbiased signal of scientific quality.

Have you followed the climategate email leak story at all? One of the more damning themes in the leaked emails is the discussion of ways to keep dissenting views out of the peer reviewed journals. One of the stronger arguments used against AGW skeptics was that there were not more papers supporting their claims in peer reviewed journals. Given the prevalence of this argument, clear evidence of efforts to keep 'dissenting' opinions out of the main peer reviewed journals is a big problem for the credibility of climate science. For example:

The group also did not approve of the American Geophysical Union (AGU) and its choices allowing opposing views to be heard. The group’s trade publication, Geophysical Research Letters (GRL) was targeted by Michael Mann as he wrote, “I’m not sure that GRL can be seen as an honest broker in these debates anymore.” He however acknowledged the publications importance saying, “We can’t afford to lose GRL.”

Mann seemed particularly concerned about ‘contrarian’ with the name Saiers, presumably James Saiers of the Yale School of Forestry & Environmental Studies. “Apparently, the contrarians now have an “in” with GRL. This guy Saiers has a prior connection w/ the University of Virginia Dept. of Environmental Sciences [where Saiers completed his PhD] that causes m some unease,” Mann wrote.

Tom Wigley, a senior scientist in the Climate and Global Dynamics Division at NCAR, felt though that they could deal with Saiers by getting him removed from the AGU. “If you think that Saiers is in the greenhouse skeptics camp, then, if we can find documentary evidence of this, we could go through official AGU channels to get him ousted.”

And this comment is also rather damning:

This was the danger of always criticising the skeptics for not publishing in the "peer-reviewed literature". Obviously, they found a solution to that--take over a journal! So what do we do about this? I think we have to stop considering "Climate Research" as a legitimate peer-reviewed journal. Perhaps we should encourage our colleagues in the climate research community to no longer submit to, or cite papers in, this journal. We would also need to consider what we tell or request of our more reasonable colleagues who currently sit on the editorial board...

What do others think?

mike

Inspired by reading this blog for quite some time, I started reading E.T. Jaynes' Probability Theory. I've read most of the book by now, and I have incredibly mixed feelings about it.

On one hand, the development of probability calculus starting from the needs of plausible inference seems very appealing as far as the needs of statistics, applied science and inferential reasoning in general are concerned. The Bayesian viewpoint of (applied) probability is developed with such elegance and clarity that alternative interpretations can hardly be considered appealing next to it.

On the other hand, the book is very painful reading for the pure mathematician. The repeated pontification about how wrong mathematicians are for desiring rigor and generality is strange, distracting and useless. What could possibly be wrong about the desire to make the steps and assumptions of deductive reasoning as clear and explicit as possible? Contrary to what Jaynes says or at least very strongly implies (in Appendix B and elsewhere), clarity and explicitness of mathematical arguments are not opposites or mutually contradictory; in my experience, they are complementary.

Even worse, Jaynes makes several strong claims about mathematics that seem to admit no favorable interpretation: the are simply wrong. All of the "paradoxes" surrounding the concepts of infinity he gives in Chapter 15 (*) are so fundamentally flawed that even a passing familiarity of what measure theory actually says dispels them as mere word-plays caused by fuzzy or shifting definitions, or simply erroneous applications of the theory. Intuitionism and other finitist positions are certainly consistent philosophical positions, but they aren't made appealing by advocates like Jaynes who claim to find errors in standard mathematics while simply misunderstanding what the standard theory says.

Also, Jaynes' claims about mathematics that I know to be wrong make it very difficult to take him seriously when he goes into rant mode about other things I know less about (such as "orthodox" statistics or thermodynamics).

I'm extremely frustrated by the book, but I still find it valuable. But I definitely wouldn't recommend it to anyone who didn't know enough mathematics to correct Jaynes' errors in the "paradoxes" he gives. So.. why haven't I seen qualifications, disclaimers or warnings in recommendations of the book here? Are the matters concerning pure mathematics just not considered important by those recommending the book here?

(*) I admit I only glanced at the longer ones, "tumbling tetrahedron" and the "marginalization paradox". They seemed to be more about the interpretation of probability than about supposed problems with the concepts of infinity; and given how Jaynes misunderstands and/or misrepresents the mathematical theories of measure and infinities in general elsewhere in the book, I wouldn't expect them to contain any real problems with mathematics anyway.