Berkeley CSUA MOTD:Entry 33835
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2004/9/29 [Science/GlobalWarming, Science/Physics] UID:33835 Activity:high
9/29    What an embarrassment for Nature.  The editors and Mann of global
        warming fame are beginning to look very suspicious.
        http://www.climate2003.com
        http://www.uoguelph.ca/~rmckitri/research/fallupdate04/update.fall04.html
        \_ The editors of Nature are known to be jackasses.  Talk to anyone
           who has been in any field of science at a high level for long
           enough to have dealt with them, and they'll all tell you this.
           And it's not just sour grapes.  I know pleny of people who've
           been published in Nature multiple times who think this.  As far
           as this stupid "dogleg plot" controversy goes, peer review is
           only as good as the peers of the person who submits the paper.
           Some fields have a lot of jackasses in them.  Just for shits and
           grins, you should go through the old copies of Nature from a
           hundred years ago or more in the stacks of a university
           library and see how nasty scientific controversies were back
           then.  Believe it or not, they were worse.
           \_ Were there scientific controversies 100 years ago that were
              used as evidence to promote the wholesale realignment of
              global industrial policy?
           \_ Yeah, there are some pretty horriable peer review stories out
              there.  We had a talk here at LLNL a month or so back about
              using bad computer data in published papers.  The peer review
              process let a lot of really bad science pass.  (Like, you can
              see that this graph increases linearly!  When investigated, it
              turns out they only plotted 2 points. etc.)
        \_ Are you a Republican?
           \_ Why do you ask?  Because only Republicans require good data to
              base their decisions on? -!op
              \_ There's no such thing as "good data".  There's only bias.
                 Once you have determined your bias, then you pick the data
                 to support your bias, and you form your conclusion based
                 on your data.
                 \_ There is good data.  Because of good data, bridges stay
                    up, airplanes fly, and the Internet doesn't grind to a
                    halt.  Nature is not forgiving to bias.  You should
                    maybe read up on this invention called
                    'empirical science.'  (Yes, my sarcasm detector is in
                    the shop). -- ilyas
                 \_ There is good data and there is bad data.  The data in the
                    seminal paper "Electron-Band Structure in Germanium, My
                    Ass" was bad data.
                    \_ And there is even worse than bad data, which is
                       cooked data. At least the E-BSiGMA paper accurately
                       plotted what he observed.
                       \_ I prefer my cooked data with gravy made from the
                          blood of the working man.
                          \_ Mm, one of my favorite recipes from "To Serve
                             Man."
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www.climate2003.com
Comments on MM03 The purpose of this webpage is to provide supplementary information and comments to ongoing research on the use of proxy information to develop temperature reconstructions. The principal focus to date has been on analyzing the reconstruction by Mann et al. Third Assessment Report (2001) to support claims that the 1990s were the warmest decade and 1998 the warmest year of the millennium, and was applied in the main promotional graphics used by IPCC, as shown below. However, we are in the process of examining the other major multi-proxy studies (Jones et al. FIGURE 1 NH Temperature Reconstruction - IPCC Version of MBH98, MBH99 Despite the extensive policy reliance on this presentation, IPCC did not itself audit or verify the data and methods of MBH98 and MBH99. To our knowledge, other than our efforts, no other person or institution has attempted any replication or verification. These errors and defects appeared to include collation errors, use of obsolete data, incorrect principal components calculations for tree ring networks, unjustified truncation or data, geographical mislocations etc. We re-collated tree ring data from original sources and obtained updated versions wherever possible. FIGURE 2 NH Temperature Reconstructions from MM03 MM03 occasioned considerable controversy. argued that they had sent us the wrong data and this compromised the MM03 calculations. Since we re-collated the compromised data, this criticism had no bearing on our own calculations, although it did have a bearing on a couple of our criticisms of MBH98. FTP location said to be the location of MBH98 proxy data. Since November 2003, we have examined this FTP location and found many additional data errors and defects, additional to those described in MM03 Some of these issues have been addressed in the recent Nature Corrigendum; there are many data errors in MBH98 which remain unacknowledged. argued that the differing results could be attributed to different handling of tree ring principal component calculations - in particular, that MM03 had not carried out a "stepwise" calculation - and to our use of a different version of the TTHH tree ring series. They produced the following emulation of our results by changing 3 indicators. As it turned out, this procedure resulted in the NOAMER PC1 and STAHLE/SWM PC1 being unavailable in the AD1400 step. We used a version of the TTHH series which began later (and ended later), because this was the later version archived by Jacoby (which was calculated well before the publication of MBH98). however, since the TTHH series doesn't start until 1459 in the MBH98 version, it is irrelevant anyway. As it turns out, the presence or absence of the Stahle/SWM PC1 has virtually no effect on early 15th century values. The differences between results depend entirely on the calculation of the NOAMER PC1. We have closely examined this matter and have identified an error in the MBH98 procedure for calculating principal components, which we have submitted to a journal. This one error accounts for most of the difference between our results. We have also been able to identify one other data misrepresentation, which accounts for the balance of the difference between our results. We anticipate that these results will soon become public. We have also endeavoured to ensure a complete public record with respect both to MBH98 and other multi-proxy studies. It seems scandalous to us that there should be anything other than copious public disclosure of all data, methods and source code in papers relied upon for major public policy. We have had some partial success in this endeavour with the new SI for MBH98, which provides considerable new information on this study. Nonetheless, the public record remains incomplete and multi-proxy authors have refused to provide key information. We have endeavoured here to provide a complete record of all data and methods used in MM03, including all scripts. See SI to MM03) As noted above, our studies have progressed significantly since MM03 and we hope to be able to comment more fully our submission in review in the near future.
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www.uoguelph.ca/~rmckitri/research/fallupdate04/update.fall04.html
first part concerned the provenance of the data used for our analysis and was released in November 2003. We can now update this process, starting with the latter item first. short article to Nature, arguing that the shape of the MBH98 hockey-stick depended on: transforming each tree ring proxy prior to calculating principal components (PCs) by subtracting its 1902-1980 mean rather than subtracting the mean of the length of the PC itself (e,g, 1400-1980 for AD1400 calculation step), as would be done in usual software and the duplicate use of the same Gasp tree ring series in two locations in the MBH98 data base, and, in one of its duplicate uses, an extrapolation at the beginning to make the series available in AD1400 step calculations, while incorrectly listing the first available date as AD1400, thereby concealing the extrapolation. Although MBH98 claimed great "robustness" for its reconstructions, even claiming robustness to the exclusion of all tree ring data, we showed that its results were not robust to seemingly slight changes in these aspects of the methodology. We also showed that, once these issues were remedied, our results held up even when we included the NOAMER PCs back to AD1400, which had been a specific methodological difference earlier. Our cover letter outlined the purpose of our submission, recognizing that it did not fit neatly into Nature's submission categories, which classify submissions as "Letters", "Articles" and "Communications Arising". "Letters" and "Articles" are reports on "original" work and have longer word limits than "Communications Arising", which may be criticisms. We thought that the submission could be construed as a "letter", although of an unusual type. Our submission was a comment on a publication, but represented a great deal of original work, which obviously no one else had done. Although the content was critical in nature, the topic was of extreme international importance and we stated explicitly that we were open to guidance on editorial format and asked that the submission be valued on its merits. favorable revise and resubmit, at which time we were asked to add additional material in order to respond to referee comments (our paper then standing at 1910 words). Referee #2 stated: The technical criticisms raised by McIntyre and McKritrik (MM) concerning the temperature reconstructions by Mann et al (MBH98), and the reply to this criticism by Mann et al is quite difficult to evaluate in a short period of time, since they are aimed at particular technical points of the statistical methods used by Mann et al, or at the use of particular time series of proxy data. A proper evaluation would require to redo most of the calculations presented in both manuscripts, something which is obviously out of reach in two weeks time. Furthermore, both manuscripts seem to contradict each other in some basic facts. Therefore, my comments are based on my impression of the consistency of the results presented, but there is a wide margin of uncertainty that could be resolved only by by looking in detail into the whole data set and the whole software used by the authors. In general terms I found the criticisms raised by McIntyre and McKritik worth of being taken seriously. They have made an in depth analysis of the MBH reconstructions and they have found several technical errors that are only partially addressed in the reply by Mann et al. We had pointed to the overwhelming weighting given to one hockey stick-shaped North American tree ring series (Sheep Mountain CA) as a result of the subtraction of the 1902-1980 mean. which we found interesting was that their PC1 did not just depend on Sheep Mountain, but 14 other sites had at least 25% of the contribution of Sheep Mountain. re-submitted in late March, adding a new paragraph showing that these 14 highly weighted sites in the PC1 were all from a group of specialized and controversial high-altitude bristlecone pine series, studied by Graybill and Idso (1993), exhibiting an anomalous 20th century growth spurt, which yields hockey-stick shaped growth series. Graybill and Idso stated that explicitly that the 20th century growth could not be explained by local or regional temperature; co-author Hughes in Hughes and Funkhouser (2003) said that the anomalous growth was a "mystery". NOAMER/BACKTO_1400-CENSORED subdirectory at Professor Mann's FTP site. The PC1 in this subdirectory proved to be virtually identical to the one we calculated using standard PC methods on the entire North American network. Carrying these PCs forward into an NH temperature index led to a reconstruction almost the same as ours! Nature then asked us to reduce the paper down to 800 words. final version was within the 800-word limit and was submitted on April 9 We did not hear the results of the re-submission for four months. When we inquired about delays, Nature said that they had not heard back from reviewers. It turns out that Nature had added a third reviewer, which may have contributed to the delays. The main reason was that the issues raised are too technical to resolve in the now 500 word space available: In the light of this detailed advice, we have regretfully decided that publication of this debate in our Brief Communications Arising section is not justified. This is principally because the discussion cannot be condensed into our 500-word/1 figure format (as you probably realise, supplementary information is only for review purposes because Brief Communications Arising are published online) and relies on technicalities that do not bring a clear resolution of the underlying issues. This decision primarily reflected the views of the new reviewer, who stated: Generally, I believe that the technical issues addressed in the comment and the reply are quite difficult to understand and not necessarily of interest to the wide readership of the Brief Communications section of Nature. I do not see a way to make this communication much clearer, particularly with the space requirements, as this comment is largely related to technical details. This reviewer did not object to any of our findings per se. Readers may share our surprise that the matters raised are "too technical" for consideration in a science journal; additionally, whether or not the matters were of interest to a "wide readership" (and we believe that they are), potential defects in MBH98 affect Nature's publication record and require disclosure. Our old referees again commented on the difficulty of resolving who was right and who was wrong. Referee #2 (Referee #1 of the first round) remained sympathetic, and stated: The amount of material, often contradictory, is simply too complex and lengthy to resolve all the rights and wrongs in a realistic length of time" Only a reader with several days to spare (longer if they are unfamiliar with the area), to chase references and probably the authors, could hope to come close to a full understanding of the arguments. I started my original review by saying that I found merit in the arguments of both MBH & MM To rewrite this, I believe that some of the criticisms raised by each group of the other's work are valid, but not all. I am particularly unimpressed by the MBH style of 'shouting louder and longer so they must be right'. However, Referee #3 (Referee #2 of the first round) was impressed by some of the new arguments of Mann et al. In his new comments, he expressed concern about whether the points could be made within the space limitations and stated: I see some merit in MM04 and I would encourage them to pursue their testing of MBH98, and by the way other reconstructions. As I wrote in my first evaluation, this should be a normal and sound scientific process that should not hampered. For instance, questions that seem to be quite critical, such as the sensitivity of the MBH98 reconstructions in more remote periods to changes or omissions in the proxy network or the dependency of the final results to the rescaling of the reconstructed PCs, have become clearer to me now. At the moment, my opinion is that the present MM04 manuscript could be of interest just for the bunch of specialist working exa...