There is no cover up. If you're trying to cover something up it's generally not a good idea to publish papers about it, especially in
Nature. What there is is a smear campaign. There are very clear and unequivocal explanations behind almost all of the high profile emails that were released and they only hint at malfeasance if you intentionally ignore the context.
Of course peer review is necessary, which was exactly why the scientists were discussing what to do about the journal
Climate Research. At least 4 sub-par papers (at least one of which was funded by the American Petroleum Institute) were funneled into publication through a single editor who was known to be sympathetic to the "skeptical" cause. The situation came to a head in 2003 when a particularly bad paper funded by the API was published. No new research was performed in the paper. It was simply a review of previous studies done by other researchers. 13 of the researchers cited in the paper responded saying that their work was misrepresented. That one paper was so bad that half of the editorial board resigned in protest of its publication. The incoming editor-in-chief, Hans von Storch also resigned after his attempt to publish an editorial rebutting the paper was blocked. It's worth noting too that he is quite clearly not on friendly terms with Mike Mann or Phil Jones (two of the major players in the emails). Even the director of the publishing company admitted that the paper had been handled improperly. NONE of these events or the reaction of the climate science community were a secret back when the events were unfolding. Coincidentally, I was reading about the whole fiasco just a few weeks ago, before the emails came out. It wasn't a secret then either. Why is it suddenly a sinister revelation?
A recounting of the events from one of the editors who resigned (published Nov. 2003).
http://www.sgr.org.uk/climate/StormyTimes_NL28.htm
The version from the editor-in-chief (published on his website in 2003).
http://coast.gkss.de/staff/storch/CR-problem/cr.2003.htm
The publisher's comment on the issue (published in
Climate Research Aug. 2003)- the author's expertise is in scientific review.
http://www.int-res.com/articles/misc/CREditorial.pdf
The response by 13 of the authors who were cited in the paper who say that their work was misrepresented (published in the journal
EOS in 2003).
http://www.geo.umass.edu/faculty/bradley/mann2003a.pdf
So how was this covered up and what was improper about scientists deciding not to cite or submit to the journal anymore? Do you expect them to treat a journal with a demonstrably flawed review process as equal to other prestigious journals?
As for keeping original data- the CRU analyzes data; they don't collect original data themselves. Their raw data are COPIES of the meteorological data archived by national meteorological organizations. Even if the CRU deleted ALL of their data, none of the original raw data would be lost because it doesn't reside at the CRU. That also means they don't own the raw data they use, so they cannot give it to you no matter how many people you get to pester them with FIO requests. If you want it, you have to settle for the 98% of so of it that is publicly available or you have to go to the national meteorological service that originally collected it. So again, what is sinister about getting rid of copies of data that you have already processed when the original still exists? What is sinister about refusing to release data that you do not have the legal right to disseminate?
Your last claim I assume is something about the Yamal analyses, but I'm not sure because none was based on 3 trees. The original analysis used 241 from a total of about 2000 samples. Other analyses used various subsamples of those 2000. The Briffa paper McIntyre raised a huge stink about claimed to use 611 trees. McIntyre claims that the actual value couldn't have been more than about 250 (though he also originally claimed only 10 trees were used), but the values in the graph indicate that the actual number was almost definitely at least 200, which is plenty to get a statistically meaningful result.
There are lots of good reasons to exclude trees and they have nothing to do with confirming a pre-determined conclusion. Arbitrarily ditching most of the dataset so you can replace it with one of a different size and of unknown quality isn't one of them. First of all, once you get beyond a certain sample size, additional samples have very little effect on the result, so it doesn't make much sense to waste the time and money processing a lot more samples. Second, any trees that have been damaged by fire, wind, lightning, stripped bark, etc. may have missing or damaged rings. You also don't have a single tree that spans 2000 years. You get the series by matching up overlapping dates from multiple trees. Not all trees will have identifiable overlaps with other trees, so they can't be placed in the series and you have to toss them. Last but not least, not all trees make good proxies because their growth doesn't always correlate well with temperature. If that's the case, you can't use them, at least for the period where there is no correlation. That's the "divergence problem" with tree ring proxies.
Which brings us to "the decline" that was "hidden." Just from the context of the email alone it's clear that it's talking about the divergence problem. First of all it says that the real temps were added to the end of each series, which should be a dead giveaway that "the decline" was not in temperature, otherwise adding in real temps would not hide it. Also, we know from the other instrumental and satellite records that temps didn't decline from 1961-1999. As it turns out, "Keith" would be Keith Briffa, the guy who published a paper in Nature a year earlier showing the divergence problem, wherein from 1961 onward, the data from SOME trees indicated a decline in temperature, while most other trees, other proxies, the instrumental record, and the satellite record indicated continued warming. Not surprisingly, most of the leaked data files concerning processing of tree rings say things within the code such as- "Specify period over which to compute the regressions (stop in 1960 to avoid
the decline)." Again, if you're trying to cover something up, a paper in
Nature isn't a great way to do that and you probably shouldn't comment about it repeatedly in your code.
The paper:
http://www.nature.com/nature/journal/v391/n6668/abs/391678a0.html
I just ran a search on ISI for "climate, tree, divergence" and got 79 hits over the past 10 years, most of which seem to discuss "the decline" as well, so like the rest of the "proof" of a coverup it doesn't seem to be a very well-hidden either.
The bottom line though is that none of the emails change any of the science on the issue and there is nothing in them to show scientific misconduct. Are some of them rude? Absolutely, but as scientists we aren't payed to be nice and we certainly aren't paid to indulge the whims of idiots. Probably most telling is the fact that even when they think they're having a private conversation they STILL think McIntyre and the like are annoying idiots. They STILL complain about the efforts to misrepresent their work. They STILL think a lot of the "skeptical" papers are crap. They aren't saying "McIntyre is too smart. He's onto our fraud" or "I can't believe they buy this hoax" or "We need to make this scarier so we can get more money."