Here is a postscript version and pdf version of the graphic showing simulated PC1s with a hockeystick shape and the MBH98 Northern Hemisphere reconstruction. Can you find the "real" MBH98 hockeystick? 

The AGU conference is unbelievably big. I'm told there were over 10,000 people there. The printed program is 512 pages long and for individual papers only lists authors and titles. I was surprised how little attention was paid to climate in the last 1000 years. Climate in the past 3 million or 30 million years was a big topic, with many presentations from ODP drilling. There were several presentations on the climate effect of the closure of the Panama Seaway (due to plate tectonics). Impressionistically, the plate tectonics people tend to date this about 4 MM years ago and the ODP climate people about 2.8-3 MM years ago. The closure ended Pacific waters moving into the North Atlantic and bringing heat to the Arctic and initiated a long-term cooling through the Pliocene and Pleistocene. The warming in the Holocene (10000-12000 years), including modern warming, is still well short of the Pliocene warm period. The Pliocene is not dinosaur vintage, but is getting to a recognizably modern configuration. But once the Panama Seaway closed, ocean currents had to re-arrange themselves and ultimately the modern Conveyor Belt was established, in which warm waters now come around the Cape of Good Hope. The re-arrangement is a big job, when you think of it. One of Nof's students presented a poster arguing that one of the big changes in the Holocene has been the opening of the Bering Strait, which even though is very shallow, de-bottlenecks Arctic water.

Bob Carter showed me some very interesting material from his ODP drilling on the east New Zealand offshore. This is the main entry point for cold Antarctic waters into the Pacific - there are surprisingly few entry points. Bob has found that there are fluctuations at all scales - in fact, his data would indicate that changes of 0.8 deg C in a century are pretty much the norm for millions of years and lesser changes (the premise of the hockey stick) would seem to be the exception. 

My poster session was on the Friday afternoon and I was reasonably busy. I talked to about 40-50 people. I had visited the poster session for Nonlinear Methods and quite a few of these mathematically oriented people reciprocated. They got the point of the principal components argument almost immediately and you could almost see them laughing at the punchline. I had printed off the computer program from Mann's FTP site and highlighted the 4 lines that contain the programming error.  

People who were not mathematically inclined were intrigued by a graphic showing 8 hockeysticks - 7 simulated and 1 MBH (the same sort of graphic as the one put up here a while ago, but just showing 1 simulation.) Quantity seems to matter in the demonstration. No one could tell the difference without being told. I'll insert this graphic here in a day or two. 

Again, I was surprised how little was on recent climate. There was very little representation from tree ring people. Casper Amman had a presentation describing his emulation of MBH98; he is planning to web up R code, which should be interesting. He outlined many issues pertaining to problems in emulating MBH98 - most of which will be familiar to any followers of our work, but conspicuously made no reference to our efforts. He said that he could emulate MBH98 results, but made no reference to principal components calculations or such esoterica as the MBH98 editing of the Gaspe series. (I'm still trying to get the new data from Jacoby et al., who say that the old data is more "temperature sensitive" and should be used in preference to the new data, which they refuse to archive. LOL) 

Mann and some of his colleagues have set up a blog at the above address. A couple of Mann's first postings have been arguments against our papers. I'll post up a two quick comments below. I'm going to be in San Francisco at the AFU conference all next week, where I'm presenting a paper [see abstract] and will post some more when I get back.

Dec. 10, 2004   Robustness

If 2 PCs are used in the AD1400 North American network along with conventional (centered) PC calculations, we argued in our Nature submissions that MM-type results are obtained. This is now effectively acknowledged by MBH. To try to salvage MBH98, they now argue that they should be entitled to increase the number of PCs in the AD1400 North American network from 2 to 5 and that our not doing so is "incorrect".  They point out that, using centered PC methods, the PC4 (instead of the PC1) has a hockey stick shape (from the bristlecone pines) and, as long as they can use the PC4, the PC4 now drives world climate history. Doesn't this just seem silly?  Now we're not dealing with a "dominant" pattern of world climate, but a PC4. ROTFLOL.

Secondly, I defy anyone to show me how the actual retention of PC series in MBH98 can be derived from the Preisendorfer criteria now said to be used in MBH98 for tree ring networks (although MBH98 itself only talked about spatial distributions for tree ring PC retention). Below are two plots made on the same basis as the plot shown at Mann's blog for the AD1400 North American network - only here for the AD1600 Vaganov and AD Stahle/SWM networks. In the first case, MBH98 retained 2 PCS and in the second case, MBH98 retained 9 PC series. I do not believe that there is any rational policy here. I sure can't see how the actual retention can be linked to Preisendorfer. It would be helpful to see some source code here. Maybe there's something weird and inconceivable like their centering method. 

Thirdly, what does this do to their claims of robustness? A robust reconstruction obviously should not stand or fall on whether 2 or 5 PCs are used in the AD1400 North American network - but this is exactly what Mann et al. are saying. Remember all the grandiose claims about MBH98 being robust to the presence or absence of dendroclimatic indicators altogether (see both MBH98 and Mann et al.[2000]). Now it seems that MBH98 is not even robust to the presence or absence of a PC4. Also remember that Mann et al. have known about the lack of robustness to the bristlecones for a long time - look at the PC1 in the BACKTO_1400-CENSORED directory. It's almost exactly the same as ours. Maybe someone can explain to me how you can claim robustness after doing the CENSORED calculations. 

Dec. 10, 2004 Rutherford et al [Journal of Climate 2004]

The Dec. 4 post "False Claims" refers to an article by Mann and his associates [Rutherford et al. 2004], supposedly discrediting our work. There is nothing in this article about the two main points in our Nature submissions: 1) the modification of the PC algorithm such that it produces hockey sticks in the PC1 from red noise; 2) the ad hoc and unique extrapolation of the Gaspe series. It regurgitates the comments made in the Nov. 2003 Internet response in which Mann et al. attributed the difference in PC results to a stepwise procedure used in MBH98, but never previously reported. However, the calculations in our 2004 submissions implemented the stepwise procedures and isolated the difference to a completely different cause: the weird centering method introduced at line 168 of their Fortran program. Rutherford et al [2004] do not discuss this matter, although Mann et al. are obviously aware of the issue, as it is referred to in the first paragraph of the web posting.

It is interesting that this matter is being discussed in a Journal of Climate article. Jones and Mann [Rev Geophysics 2004] refers to a submission by Mann et al. to Climatic Change, which was said to have refuted our first submission. Does it strike anyone as odd that this submission mentioned in print over 6 months ago has not seen the light of day?  Is it possible that something happened to the article at Climatic Change?   

There's a difference between the underlying proxy data, source code and supporting calculations, and the situation is different for each category. 

Proxy data: There is an archive of proxy data located at Mann's FTP site at the University of Virginia and this is not a current problem area. This data has not "always" been available. The FTP site was started on or about July 30, 2002, about 4 years after publication of MBH98, so it was not available prior to then. The proxy data is presently located at the url  <ftp://holocene.evsc.virginia.edu/pub/MBH98> and bears a date stamp from 2002. The FTP site has private areas. For example, the directory presently located at <ftp://holocene.evsc.virginia.edu/pub/MANNETAL98> was formerly located at <ftp://holocene.evsc.virginia.edu/pub/sdr/temp/nature/MANNETAL98> and was not indexed. If you knew the exact url, you could retrieve it, but not otherwise. When the url was changed to its present location, the date stamp for the directory did not change, so it looks like this directory has been public since December 2003, but it hasn't been. (BTW my access to Mann's FTP site from my computer has been blocked, although I can still get to it from computers at the University of Toronto. This seems a little petty.) Prior to publication of our first article, there had been no references to this url, even at Mann's FTP site. I believe that it is quite possible that the directory was re-located - similar to the relocation of the MANNETAL98 directory and was only accessible since Nov 2003. Be that as it may, the proxy data is currently available.

Source code: There is source code at Mann's FTP site for the calculation of tree ring principal components only. There is no source code for the calculation of reconstructed principal components, for the calculation of NH average temperature, for the Preisendorfer-type simulations, etc. etc. We have requested source code and been refused; we have sought intervention from Nature and the U.S. National Science Foundation without success. For the calculations where code is available and a full reconciliation is possible, there were obviously major discrepancies between the procedures as described in Nature and the procedures as actually used. Who would ever have thought that they used an uncentered algorithm on de-centered data? There were also material discrepancies between the series listed as used and the series actually used. Who would have expected this? Mann et al. have provided a vast new Supplementary Information attached to the July 2004 Corrigendum, which Nature has stated to us finally provides a complete and accurate description of their procedures. Since Nature has not obtained the source code and reconciled it, how can they possibly know that the SI is an accurate description. (By the way, the Supplementary Information was not edited by Nature and almost certainly not peer reviewed.)

Supporting calculations:  The supporting calculations that I most want to see are the calculations for the AD1400 step which is in controversy. The only information available on this step is an RE statistic (of 0.51). Nature has refused to provide supporting calculations for the RE statistics. It is significant that the R2 and other verification statistics have not been provided. My calculations indicate that the R2 and other verification statistics are embarrassingly low, which is probably why no one wants to disclose them or to provide the supporting calculations from which they can be conclusively calculated. The attitude of Nature is that an interested party can calculate their own values. This is hardly an adequate response both given the widespread reliance on this study and the prior track record of inaccurate disclosure of both data and methods. I'd like to see the exact calculation and the refusals make me all the more interested.

So while quite a bit of new information has been provided, there's a lot of material which has not. It should be easy to simply archive the programs. You'd think that it would be easier to archive the source code than to fight about it.  

We are sometimes asked about other multiproxy studies which are held to somehow support Mann. A couple of comments. First, if Mann's calculations are wrong, the fact that other studies get similar results is neither here nor there. Equally, a critique of MBH98 doesn't refute these other studies, nor have we claimed this. Second, I'm not convinced that these studies are anywhere near as mutually supporting as claimed. When I get to it, I'm going to try to quantify exactly what is supposedly being shown by the spaghetti diagrams and see if they rise statistically above spaghetti diagrams from our simulated hockey sticks (see the Oct. 25 comment for an example). Third, the record for other multiproxy studies is, in all but one case, worse than MBH98. Here is a brief summary:

These studies are less "independent" than they appear. Many proxies recur in nearly all studies (e.g. Tornetrask, Polar Urals, Tasmania). If you look at all the authors, there is much overlap. Mann is in 4 of the studies; in addition to Jones et al 1998 and the two articles with Mann, Jones is a co-author in Briffa et al. 2001 and supplied much of the data to Crowley and Lowery. Bradley and Jones have been frequent co-authors. 

On July 16, 2004, Stephen Schneider posted up the MBH reply to our first Nature submission here: Reply to MM04a, Mar.  2004 which may interest readers. This was presumably sent to Schneider in support of a still unpublished submission by MBH to Climatic Change. Some of the comments in our re-submission addressed points raised in this reply, especially in connection with bristlecone pines. M pointed out that 14 sites made a material contribution to their PC1 - not just Sheep Mountain. When we investigated these 14 sites, we found that they were all bristlecone and foxtail pine sites, collected by Donald Graybill and reported in Graybill and Idso (1993). There is a rich irony in these sites turning up in their new alter ego as the MBH98 PC1. These sites also enabled an explanation of the BACKTO_1400-CENSORED subdirectory at Mann's FTP site. There is no explanation of this directory, but we found that this contained PCs calculated without 20 (nearly all) bristlecone pine sites, getting a PC1 virtually identical to ours. MBH98 did not report these calculations.

Responding to a recent challenge, I did the following experiment: I added 0.5 for the period 1400-1450 to 50 North American tree ring series (normalized in MBH98 to mean of 1) (the 50 which were in the BACKTO_1400-CENSORED subdirectory) without adding 0.5 to the 20 (mostly) bristlecone pine series. The graphic below shows the impact on the PC1 for a centered PC calculation and for the MBH98 de-centered calculation (all smoothed to 21 years). Above: PC1 using centered calculation: solid - base case; dashed - with arbitrary addition of 0.5 to 50 non-Graybill sites. This behaves as expected. Below: PC1 using MBH98 decentered method: solid -as archived; dashed - with arbitrary addition of 0.5 to 50 non-Graybill sites as above. This unexpectedly and perversely reduces the PC1 in the 1400-1450 period. Carried through to the NH temperature index, the NH temperature index is reduced in the 1400-1450 period by this increase of ring width in 50 series. Pretty strange. 

Graphic updated on Dec. 5, 2004

The script to do the simulations showing that MBH98 short-segment standardization consistently yields hockey-sticks from red noise with the persistence properties of the North American tree ring network is here.  This loads and uses functions where are located here and a matrix of North American tree ring site chronologies, which was previously collated from versions at Dr. Mann's FTP site. The figure below shows the distribution of the difference between the 503:581 mean and the 1:581 mean divided by the 1:581 standard deviation using arfima modeling. A 1-sigma hockey stick is produced over 99% of the time and a 1.5 sigma hockey stick over 72% of the time using arfima modeling. With AR1 modeling, a 1 sigma hockey stick is produced 80% of the time, but a 1.5 sigma hockey stick is almost never produced.  

I've been trying to get the data for Crowley and Lowery (2000) for nearly a year. The majority of the series are not archived at WDCP, but, even if they were, one needs to look at the version used in the multi-proxy study since, as seen with MBH98, the versions can differ and the differences can be material. I've sent Crowley over 20 emails. Last June, he promised to archive the data at WDCP by the end of August. This didn't happen. Then he promised to send me the data by the end of September. This didn't happen. On Oct. 15, 2004, he finally sent smoothed and scaled versions of his data. When I asked for the actual data, he said that he "wasn't sure where they are, or even if [he] had them". I'll post some comments on data sources for some of the other multi-proxy studies.  The time series from the composite in the email looks like it's different from the time series which he archived in 2000.  It will be interesting to see why.

Maybe I'll start blogging some odds and ends that I'm working on. I'm going to post up some more observations on some of the blog criticisms.

One of the most common arguments against our criticism of MBH98 is that it is supported by other multi-proxy studies. This "support" is usually shown by "spaghetti diagrams", usually showing the results on an almost unintelligible scale. Here's an oddity from spaghetti diagrams from Briffa et al. (2001) and Jones and Mann (2004). In the Briffa et al. spaghetti diagram, the Crowley-Lowery reconstruction is the "coldest" in the 17th and 18th centuries and does not intersect the MBH99 reconstruction. In the Jones and Mann spaghetti diagram, the Crowley-Lowery reconstruction intersects the MBH99 reconstruction in the late 17th century.

Figure 1. Spaghetti Diagram, Briffa et al. (2001)). <http://www.ngdc.noaa.gov/paleo/pubs/briffa2001/plate3.gif>. The Crowley-:Lowery (2000) reconstruction is in a orange-brown and is the lowest strand in the 17th and 18th centuries,  lower than MBH98/99 (purple) or Briffa et al (2000) (green). 

Figure 2. Spaghetti Diagram, Jones and Mann (2004). Here Crowley-Lowery (2000) is in black In this diagram, it intersects MBH99 in the late 17th century and is consistently above Briffa et al. (2001).

In the Jones and Mann spaghetti diagram, the reconstructions were "scaled by linear regression against the smoothed instrumental NH series over the common interval 1856-1980, with the exception of Briffa et al (2001), which has been scaled over the shorter 1856-1940 interval owing to a late 20th century decline in temperature response in some of the underlying data". This supposed "decline in temperature response" is an interesting story in itself. The Briffa spaghetti diagram states that all values are re-expressed relative to a 1961-1990 mean (see y-axis label). I'm not expressing any views on this right now, merely noting it.

Oct. 25. 2004 A COMMENT ON CONNOLLEY

A sci.environment posting by William Connolley has been circulated by Tim Lambert, Brad DeLong and David Appell, as somehow contradicting the point cited by Muller. 

In our description of the idiosyncratic MBH98 data transformation prior to principal components calculation (in a submission constrained by word length), we said that the series:

“were first scaled to the 1902-1980 mean and standard deviation, then the PCs were computed using singular value decomposition (SVD) on the transformed data…”

Connolley's posting  said:

So we need to look at MBH’s software, not M&M’s description of it. MBH’s software is here, and you can of course read it yourself… Fortran is so easy to read…What they do is (search down over the reading in data till you get to 9999 continue):

1. remove the 1902-1980 mean
2. calc the SD over this period
3. divide the whole series by this SD, point by point

At this point, the new data are in the situation I described above: datasets that trend upwards at the end have had their variance reduced not increased. But there is more…

4. remove the linear trend from the new 1902-1980 series
5. compute the SD again for 1902-1980 of the detrended data
6. divide the whole series by this SD.

This was exactly what I was expecting to see: remove the linear trend before computing the SD.
Then the SVD type stuff begins. So… what does that all mean? It certainly looks a bit odd, because steps 1–3 appear redundant. The scaling done in 4–6 is all you need. Is the scaling of 1–3 harmful? Not obviously.

Perhaps someone would care to go through and check this. If I haven’t made a mistake then I think M&M’s complaints are unjustified

Connolley makes it seem that we did not cite the location of MBH's PC software; in fact, he used our citation. He also makes it seem that we did not describe the method accurately. We were writing for 800 words and the description was terse, but I fail to see any inconsistency between our description of the method and Connolley's description of the method. In fact, our description of the previously unreported transformation is almost exactly echoed by Mann et al. in the Corrigendum SI as follows:

All predictors (proxy and long instrumental and historical/instrumental records) and predictand (20th century instrumental record) were standardized, prior to the analysis, through removal of the calibration period (1902-1980) mean and normalization by the calibration period standard deviation...  The results are not sensitive to this step (Mann et al, in review).  

Obviously we disagree with the last sentence of this paragraph. More on this later. Nature's policies say that SI's are peer reviewed. However, I was informed by a Nature editor that the Corrigendum SI by Mann et al. was not edited by Nature. 

In Connolley's terms, our claim is that the scaling in step 1 (removal of the 1902-1980 mean) is harmful. Connolley does not disprove this; he merely says that this is not "obvious". Given the tentativeness of Connolley's observations, it is curious to see how rapidly it has circulated in the blogosphere as supposedly disproving our findings. In fact, one of the Nature referees - the one who was an expert in principal components - took a different view than Connolley. In his first review, he expressed his concerns about  "short segment standardization" (which is what MBH98 does) and in his second review said that he was very "unimpressed" with Mann et al. "shouting louder and longer so they must be right". 

The effect may not be "obvious", but Rich Muller understood it exactly. Just because it is not "obvious" to Connolley also does not mean that the effect is not real. Below are two graphs: one is a simulated PC1 using the MBH98 method on a network of red noise with the persistence properties of the North American tree ring network (modeled with fractional differencing not AR1). Can you tell which is the "real" hockey stick? 

In 10,000 simulations, we obtained a PC1 with a 1902-1980 mean over 1 sigma away from the 1400-1980 mean in over 99% of the cases (about half the time upside-up and half the time upside-down, but this doesn't matter for regressions). We have described this in detail in a submission to another journal. Our claims are easily verified and rather than arguing about it, I will put up scripts (in R) in a few days, showing the simulations and enabling anyone to test these results.

Connolley's argument was picked up and added to by Brad DeLong as follows:

But Connolley argues--I think correctly--that McKitrick and McIntyre are simply confused: the normalizations diminish the influence of series that show a recent uptrend

I don't see how Connolley's argument supports DeLong's final clause. However, be that as it may, the supposed conclusion is incorrect and it is DeLong who is confused. The short-segment standardization enhances the influence of series with a strong 20th century trend (it can be either upward or downward, with the PC weighting changing the sign).

In fact, in unpublished responses submitted to Nature, Mann et al. have acknowledged two ways in which short-segment standardization affected the North American PC1. First, they have acknowledged that, without the MBH98 data transformation, the controversial bristlecone pine series (which account for over 99% of the variance in the MBH98 PC1) are not overweighted in the PC1, but are overweighted in the PC4 rather than the PC1. Secondly, they acknowledged that the eigenvalues for the North American PC calculations are completely different and submitted a figure to Nature (shown below)  showing this. So the blogger argument that short-segment standardization doesn't matter to the PC calculations themselves is not one that was presented by Mann et al. themselves. 

Figure 2. "Comparison of eigenvalue spectrum for the 70 North American ITRDB data based on MBH98 centering convention (blue circles) and MM04 centering convention (red crosses). Shown is the null distribution based on simulations with 70 independent red noise series of the same length with the same lag-one autocorrelation structure as the actual  ITRDB data using the centering convention of MBH98 (blue curve) and MM04 (red curve). In the former case, 2 (or perhaps 3) eigenvalues are distinct from the noise floor. In the latter case, 5 (or perhaps 6) eigenvalues are distinct from the noise floor." Figure and caption from Mann et al. (2004, unpublished)

Mann et al. themselves made a different argument when they realized the effect of their short-segment standardization.  In effect, they acknowledged that our calculations were correct using 2 PC series for the AD1400 network, if the series were standardized over the 1400-1980 period. So instead, they argued that, if they increased the number of PC series in the AD1400 network from 2 to 5, they could still salvage MBH98-like results. They justified this increase by claiming that the number of retained tree ring PC series was determined through application of Preisendorfer's Rule N. We did not have an opportunity to reply to this argument and one of the referees was impressed by this apparent defence and "wavered" in his support for publication. 

However, there are a couple of replies to this argument. First, MBH98 says that the number of retained tree ring PCs was determined through an effort to achieve spatial balance; it does not say that Preisendorfer's Rule N was used to determine the number of retained tree ring PCs (although it does say this in connection with the number of retained temperature PCs.) If you look at the actual pattern of retained PCs in MBH98, it appears impossible to me to actually verify the actual use of the above policy: for example, MBH98 retains 2 PCs for the AD1600 Vaganov network and 9 PCs for the AD1700 Stahle/SWM network. I defy anyone to obtain these selections using a variation of Preisendorfer's Rule N. (Actually, I defy anyone to obtain these selections using any objective method.) Applying the stated MBH98 criterion of spatial balance, the MBH98 reconstruction is already overloaded with American tree ring series; adding 3 more PC series from the North American network (as now proposed as a means of salvaging MBH98) is hardly justified under spatial balance considerations. Second, if the bristlecone pines are now relegated to a PC4, it gets harder to argue that they supply the "dominant low-frequency" signal. Since Mann et al. made very grandiose claims about the "robustness" of their results to the exclusion of all dendroclimatic indicators (especially in Mann et al. (2000)), the isolation of the presence or absence of the PC4 as a factor dramatically affecting early 15th century values directly refutes these grandiose  "robustness" claims, regardless of one's position on whether the PC4 (and the bristlecone pines) should be in or out.

While much attention is being paid to the hockey stick PC1s, no one seems to have picked up on the issues involving bristlecone pines. There are real issues about the validity of these growth rates as temperature proxies. We also recommend that bloggers pay some attention to the BACKTO_1400-CENSORED directory at Professor Mann's FTP site. The PC1 in this directory is virtually identical to our much-criticized PC1 and NH temperatures calculated from the PCs in this directory yield results virtually identical to ours. 

BACKGROUND

The principal focus to date has been on analyzing the reconstruction by Mann et al. in Mann, Bradley and Hughes (1998) and 1999, because this reconstruction was used by the International Panel on Climate Change, especially in its 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. (1998), Crowley and Lowery (2000), Briffa et al. (2001), Esper et al. (2002), Mann and Jones (2003)).   

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. (See here for some comments on replication standards.)   

When we attempted to replicate the results of MBH98, we encountered many data errors and defects in the underlying data set to which we had been directed, which we reported on in McIntyre and McKitrick (October 2003). 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. (See SI.) When we carried out our own re-construction, we obtained quite different results - with high early 15th century values, which prevented the MBH98 claim of 20th century uniqueness, as shown in the diagram below:

FIGURE 2. NH Temperature Reconstructions from MM03.

MM03 occasioned considerable controversy. First, Mann et al. argued that they had sent us the wrong data and this compromised the MM03 calculations. Mann then deleted the "wrong" data from his FTP site. 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. The matter is discussed here, but has little bearing on the scientific outcome of the dispute. Professor Mann did however provide a different 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. 

Second, Mann et al. 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. They asserted that the use of a "stepwise" procedure for tree ring principal components resulted in the use of 159 series, rather than the 112 series referred to in MBH98 and listed in pcproxy.txt. 

FIGURE 3. NH Reconstructions from Mann et al. (2003)

Since the principal components calculations in MBH98 were described as "conventional" and there was no mention of 159 series, we carried out a conventional principal components calculation using the maximum period in which all sites were available. 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). We make no apology for not using obsolete data; 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. The public disclosure record for the studies which supposedly confirm MBH98 (e.g. Crowley and Lowery (2000), Briffa et al (2001) etc.) is actually worse than MBH98. 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.