The Muir Russell “Contract”

Apparently the U of East Anglia paid the Muir Russell inquiry nearly £300,000. David Holland has requested information on the contractual basis of these payments. Situation normal – the UEA has refused to provide the information and it looks like another appeal to the ICO.
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Shub Niggurath on Archiving Code

Excellent post by Shub Niggurath at his blog here discussing replication problems. It’s interesting to see how the same excuses play themselves out in different fields. Statisticians criticize authors for non-replicability of their results. The authors complain that the statisticians failed to replicate a previously unreported (and usually questionable) methodological procedure. We’ve seen this movie before.

Shub reports that Hothorn and Leisch, Case studies in reproducibility, in Briefings in Bioinformatics noted that one of our papers (MM 2005, EE) even included code in the running text of the paper to clarify certain points:

Acknowledging the many subtle choices that have to be made and that never appear in a ‘Methods’ section in papers, McIntyre and McKitrick go as far as printing the main steps of their analysis in the paper (as R code).

More Stonewalling from UEA

I draw CA readers’ attention to UEA’s continued stonewalling of David Holland – their most recent refusal is online (together with the original request and accompanying correspondence here.)

NOAA Misrepresents Inspector General Report

NOAA’s news release on the IG report contains the following misrepresentation of NOAA’s repudiation of FOI requests:

The report questions the way NOAA handled a response to four FOIA requests in 2007. The FOIA requests sought documents related to the review and comments of part of an Intergovernmental Panel on Climate Change (IPCC) report. NOAA scientists were given legal advice that IPCC work done by scientists were records of the IPCC, not NOAA. The requesters were directed to the IPCC, which subsequently made available the review, comments and responses which are online at IPCC and http://www.hcl.harvard.edu.

“The NOAA scientists responded in good faith to the FOIA requests based on their understanding of the request and in accordance with the legal guidance provided in 2007,” Glackin said.

I reviewed the actual statements in the Inspector General report earlier today here. The Inspector General said that there was a divergence between Solomon’s evidence and the evidence of the NOAA attorneys, the latter denied giving “legal advice that IPCC work done by scientists were records of the IPCC, not NOAA”, with Susan Solomon unable to provide any documentation of ever receiving such evidence.

NOAA’s assertion that Solomon had been “given legal advice that IPCC work done by scientists were records of the IPCC, not NOAA” is not a finding of the report. Solomon claimed that she’d been given such advice, but the NOAA lawyers denied giving it to her, with the IG saying that he was unable to reconcile the divergent claims.

NOAA’s assertion in the press release misrepresents the IG report, a misrepresentation that has been picked up by various news outlets, e.g. CBC here.

Solomon’s “Divergence” Problem

Although NOAA were minor players in the Climategate letters, the recent report from the Inspector General of the US Department of Commerce (re NOAA) is the first report to date in which the investigators made any effort to crosscheck evidence from Climategate correspondents against independent sources.

It does not list the emails that it investigated and its report does not discuss some relevant emails involving NOAA (Tom Karl copied on the post-Arusha discussion that resulted in hide-the-decline; also comments on 1127614205.txt ; 1148307524.txt ; 1182342470.txt;1226451442.txt; 1248902393.txt would have made the report more comprehensive.)

They did an interesting analysis of NOAA’s repudiation of 2007 FOI requests for documents held by NOAA related to IPCC review comments. They rejected NOAA’s assertion that they did not hold any IPCC-related documents (an assertion characterized at CA as “mendacious”) and sought an explanation for the assertion from NOAA employee and IPCC WG1 Co-Chair Susan Solomon, who was specified in the FOI request.

Solomon said that she did so on the basis of legal advice from NOAA attorneys. However, the attorneys denied that they had given Solomon such advice. They asked Solomon for evidence that she had received such advice and she was unable to provide any such evidence. They say observe dryly:

“we were unable to reconcile the divergent accounts [of Solomon versus the NOAA attorneys]”

The section deserves careful reading as it also contains important statements on IPCC process. Continue reading

New Light on “Delete Any Emails”

New light today on Phil Jones’ notorious request that Mann, Briffa, Wahl and Ammann “delete any emails”. Continue reading

Judy Curry on Hide the Decline

Huge comment traffic at Judy Curry’s discussion of Hide the Decline here and here

“we could only do this back to about 1700”

Here is a longer excerpt from the July 19, 2000 Raymond Bradley Climategate email posted earlier today:

[……At this point Keith Alverson throws up his hands in despair at the ignorance of non-model amateurs…]

But there are real questions to be asked of the paleo reconstruction.

First, I should point out that we calibrated versus 1902-1980, then “verified” the approach using an independent data set for 1854-1901. The results were good, giving me confidence that if we had a comparable proxy data set for post-1980 (we don’t!) our proxy-based reconstruction would capture that period well. Unfortunately, the proxy network we used has not been updated, and furthermore there are many/some/ tree ring sites where there has been a “decoupling” between the long-term relationship between climate and tree growth, so that things fall apart in recent decades….this makes it very difficult to demonstrate what I just claimed. We can only call on evidence from many other proxies for “unprecedented” states in recent years (e.g. glaciers, isotopes in tropical ice etc..).

But there are (at least) two other problems — Keith Briffa points out that the very strong trend in the 20th century calibration period accounts for much of the success of our calibration and makes it unlikely that we would be able be able to reconstruct such an extraordinary period as the 1990s with much success (I may be mis-quoting him somewhat, but that is the general thrust of his criticism). Indeed, in the verification period, the biggest “miss” was an apparently very warm year in the late 19th century that we did not get right at all. This makes criticisms of the “antis” difficult to respond to (they have not yet risen to this level of sophistication, but they are “on the scent”).

Furthermore, it may be that Mann et al simply don’t have the long-term trend right, due to underestimation of low frequency info. in the (very few) proxies that we used. We tried to demonstrate that this was not a problem of the tree ring data we used by re-running the reconstruction with & without tree rings, and indeed the two efforts were very similar — but we could only do this back to about 1700.

Whether we have the 1000 year trend right is far less certain (& one reason why I hedge my bets on whether there were any periods in Medieval times that might have been “warm”, to the irritation of my co-authors!). So, possibly if you crank up the trend over 1000 years, you find that the envelope of uncertainty is comparable with at least some of the future scenarios, which of course begs the question as to what the likely forcing was 1000 years ago. (My money is firmly on an increase in solar irradiance, based on the 10-Be data..).

Another issue is whether we have estimated the totality of uncertainty in the long-term data set used — maybe the envelope is really much larger, due to inherent characteristics of the proxy data themselves….again this would cause the past and future envelopes to overlap.

In Ch 7 we will try to discuss some of these issues, in the limited space available. Perhaps the best thing at this stage is to simply point out the inherent uncertainties and point the way towards how these uncertainties can be reduced. Malcolm & I are working with Mike Mann to do just that.

In an earlier post, I criticized the repugnant attitude in which Bradley sneered at “antis” who had not yet reached the “level of sophistication” sufficient to disentangle adverse results that Bradley and coauthors had failed to report, but were “on the scent”.

In the present post, I wish to focus on a different point, the one referred to in the following paragraph:

Furthermore, it may be that Mann et al simply don’t have the long-term trend right, due to underestimation of low frequency info. in the (very few) proxies that we used. We tried to demonstrate that this was not a problem of the tree ring data we used by re-running the reconstruction with & without tree rings, and indeed the two efforts were very similar — but we could only do this back to about 1700. [my bold]

It seems certain to me that Bradley is here referring to the analysis in Mann et al 2000( Earth Interactions), which had an online version at NOAA here. The published version of this article states that it was “Received 11 May 1999; accepted 31 May 2000. (in final form 15 June 2000) ]”. Thus it was very recent (to say the least) at the time of Bradley’s July 10, 2000 email. It is my surmise (though this is just a surmise) that this article combined with the interactive web presentation was what Bradley was referring to in the closing paragraph of his July 20, 2000 email (though nothing turns here on the correctness of this surmise):

Perhaps the best thing at this stage is to simply point out the inherent uncertainties and point the way towards how these uncertainties can be reduced. Malcolm & I are working with Mike Mann to do just that.

MBH98 had stated that “the long-term trend in NH is relatively robust to the inclusion of dendroclimatic indicators in the network”. No supporting evidence is given for this statement in MBH98. The only support appears to come from the Mann et al 2000 article, which gives the following summary statement:

We have also verified that possible low-frequency bias due to non-climatic influences on dendroclimatic (tree-ring) indicators is not problematic in our temperature reconstructions.

Note that this statement is much broader and much more categorical than the one in Bradley’s email, where he admitted to insiders that their results not hold up for the pre-1700 networks.

This statement in Mann et al 2000 linked to a NOAA webpage http://www.ncdc.noaa.gov/paleo/ei/ei_nodendro.html, which has itself attracted considerable commentary over the past few years. It stated:

MBH98 argued, furthermore, that biases unique to a particular type of proxy indicator (e.g., tree-ring widths) are less problematic for “multiproxy”-based reconstructions that make use of the complementary information in a diverse proxy network. MBH98 found through statistical proxy network sensitivity estimates that skillful NH reconstructions were possible without using any dendroclimatic data, with results that were quite similar to those shown by MBH98 based on the full multiproxy network (with dendroclimatic indicators) if no dendroclimatic indicators were used at all. We show this below for annual-mean reconstructions of Northern Hemisphere mean temperatures.

[my bold]

They illustrated this “finding” with a graphic showing their AD1760 reconstruction. They continued with a similar statement as above, but this time include the qualification that the graphic only shows the similarity for “the period in question”.

Also shown is the reconstruction based ONLY on dendroclimatic indicators (ie, no coral, ice core, or historical or instrumental indicators). Again, the primary features of the reconstruction are very similar. Whether we use all data, exclude tree rings, or base a reconstruction only on tree rings, has no significant effect on the form of the reconstruction for the period in question.[my bold] This is most probably a result of the combination of our unique reconstruction strategy with the careful selection of the natural archives according to clear a priori criteria. Furthermore, we note that Jones et al. (1998), get similar results for the recent changes using an almost completely different tree-ring network based on wood density from high latitude trees. These comparisons show no evidence that the possible biases inherent to tree-ring (alone) based studies impair in any significant way the multiproxy-based temperature pattern reconstructions discussed here.

The above statements, both individually and collectively, give an entirely different impression to the reader than Bradley’s email to Oldfield.

The argument in http://www.ncdc.noaa.gov/paleo/ei/ei_nodendro.html has continue to be cited, most recently in Hughes’ evidence to the Muir Russell Committee in early 2010. Hughes stated that it was “it was possible to make this comparison only for the period AD 1750 to 1980” – a point obviously contradicted by Bradley’s email noting (adverse) results for earlier networks:

We published a comparison of our results including and excluding tree rings in the online journal Earth Interactions in 2000 http://www.ncdc.noaa.gov/paleo/ei/ei_nodendro.html showing that the decadal course of reconstructed temperatures was largely insensitive to the inclusion or exclusion of tree-ring data, including after 1960. At that time (in 2000), it was possible to make this comparison only for the period AD 1750 to 1980 because many of the records we used ended by 1980, and because, although there were plenty of tree-ring records before 1750, that was not true of the non-tree-ring data at that time.

The webpage http://www.ncdc.noaa.gov/paleo/ei/ei_nodendro.html was cited in Mike Mann’s well-discussed Sep 22, 1999 email 136. 0938018124.txt, leading up to hide the decline (though no attention was paid to this point in my earlier discussions of IPCC and the Trick). This was the email in which Mann noted “everyone in the room at IPCC was in agreement that this [the Briffa reconstruction] was a problem and a potential distraction/detraction from the reasonably concensus viewpoint we’d like to show w/ the Jones et al and Mann et al series”, later adding that he didn’t want to give “fodder” to the skeptics.

Mann supported his email with a reference to the supposed nodendro argument as follows:

One other key result with respect to our own work is from a paper in the press in “Earth Interactions”. An unofficial version is available here: http://www.ngdc.noaa.gov/paleo/ei/ei_cover.html

The key point we emphasize in this paper is that the low-frequency variability in our hemispheric temperature reconstruction is basically the same if we don’t use any dendroclimatic indicators at all (though we certainly resolve less variance, can’t get a skillful reconstruction as far back, and there are notable discrepancies at the decadal and interannual timescales). A believe I need to add a sentence to the current discussion on this point, since there is an unsubstantiated knee-jerk belief that our low-frequency variability is suppressed by the use of tree ring data.

We have shown that this is not the case: (see here: http://www.ngdc.noaa.gov/paleo/ei/ei_datarev.html and specifically, the plot and discussion here: http://www.ngdc.noaa.gov/paleo/ei/ei_nodendro.html

Ironically, you’ll note that there is more low-frequency variability when the tree ring data *are* used, then when only other proxy and historical/instrumental data are used!

SO I think we’re in the position to say/resolve somewhat more than, frankly, than Keith does, about the temperature history of the past millennium.

Tim Lambert and others have attempted to argue that this is adequate disclosure. They point to the qualification in the commentary that the result applies only for the “period in question”, disregarding the failure of Bradley and others to report the opposite results in earlier periods. Due to the Climategate email, we now know that Bradley and coauthors were aware of the adverse results in earlier periods (notwithstanding Hughes’ evidence to the Muir Russell panel.) Once again, we see the differences between “full, true and plain disclosure” and Team practices. In a “full, true and plain disclosure” regime, Bradley and co-authors would be obliged to disclose the adverse results for the networks prior to AD1700.

“On the Scent”

Here is an excerpt from a troubling Climategate email that hasn’t been discussed much (if at all) – from Raymond Bradley to Frank Oldfield of PAGES (172. 0963233839.txt) on July 20, 2000. I’m presenting only an excerpt today, but will discuss more from this email on another occasion.

Bradley stated of MBH98-99 results:

in the verification period, the biggest “miss” was an apparently very warm year in the late 19th century that we did not get right at all. This makes criticisms of the “antis” difficult to respond to (they have not yet risen to this level of sophistication, but they are “on the scent”).

In a system of “full, true and plain disclosure”, such as that governing the offering of securities to the public, it is the responsibility of the author to report adverse results. The “biggest miss” in the verification period was something that concerned Bradley; it was his responsibility to disclose it. “Antis” should not have been obliged to try to figure out material adverse results that Bradley and his coauthors had failed to report.

And, needless to say, when someone did achieve the “level of sophistication” to figure out what they were doing, the Team did what they could do delay and obfuscate.

The MBH decision to withhold verification r^2 statistics for early periods looks even worse in the context of this email. Withholding low verification r^2 statistics and withholding information about “big misses” both suppressed verification period problems and both kept “antis” “off the scent”. I’ve commented on other occasions about MBH withholding adverse verification r^2 results for early periods (even though they published a colorful map of verification r^2 statistics in the AD1820 step when they were favorable, they did not report verification r^2 statistics for earlier steps when the statistics were adverse).

In my opinion, the philosophy and attitudes expressed here – concerns about potential critics being on “the scent” – and the associated conduct – withholding adverse information about verification r^2 statistics and big misses – are far more repugnant than revealing the identity of a peer reviewer. However, while the community has taken umbrage at the revelation of the identity of a peer reviewer, they remain unoffended by conduct designed to keep critics off “the scent” through withholding adverse results.

Speculating Privately

Iridge versus TTLS. What if a key text on this conundrum of the day resided in an anonymous open peer review? Would we, within the ethical standards of modern climate science, be entitled to speculate on the identity of the author of these pearls? Or would that be an ethical violation “as bad as possible”? Even if we merely speculated privately, alone here on the internet, just you and I, dear reader? Sometimes truth is stranger than fiction.
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