Readers of this site are familiar with our concern over the use of bristlecones/foxtails in MBH98-99 and other multiproxy studies. The NAS Panel found in one place that "strip-bark samples" (which Graybill sought out in his bristlecone collections) should "not be used". They also reported that the MBH results were "strongly dependent" on "Great Basin data" – code for bristlecones and stated, somewhat inconsistently, that this should be reflected in confidence interval calculations. Because bristleconess/foxtails are used in many other studies (Crowley and Lowery 2000, Esper et al 2002, Cook et al 2004, Rutherford et al 2005, Moberg et al 2005, Osborn and Briffa 2006 and Hegerl et al 2006), this policy on bristlecones will have far-reaching consequences on the "other" studies, as I will demonstrate in due course (in a journal submission.)
For now, I’m going to review discusison of the first part of the issue – the validity of bristlecones as a temperature proxy – leading up to the NAS report. I’ll pick up the issue of the impact on MBH in another post.
We arrived at our understanding of the integral role of bristlecones in MBH98 rather indirectly. In Mann’s internet response to MM03, he identified different treatment of 3 series as leading to the different results: the North American PC1, the Stahle SWM PC1 and the Twisted Tree Heartrot Hill series. The latter two series didn’t matter, so the difference between results depended entirely on the North American PC1, which is why this has been such a battleground issue. For people who lack this context, re-read Mann’s 2003 response – see the links at the pdf category at right.
When the debate started, we knew only that we had been unable to replicate Mann’s North American PC1, but did not know about de-centering or bristlecones. In fact, there were a lot of inter-connected issues to disentangle with Mann’s PC series – the PC1 at the original URL was not only de-centered, it was spliced from 4 different steps. Not only that, they had incorrectly collated the data in the splice. After MM03, the MBH98 directory suddenly materialized in the public sector of Mann’s FTP site. We were able to quickly disentangle the splicing. The newly disclosed directory contained unspliced tree ring PCs (I note that no unspliced reconstructed PCs have been made available to this date). Mann condemned us for not replicating the previously undisclosed stepwise PC procedure, but refused to disclose the basis of determining the steps or retaining PCs.
Anyway when we replicated the stepwise procedure on the critical North American network, we still couldn’t replicate his results. It was really quite a puzzle. I started working through Mann’s iste, being thorough about these things, and noticed some Fortran code which proved to be his tree ring PC method. I transliterated the Fortran code into R, working through paragraph by paragraph, to try to reconcile results and, lo and behold, located a difference at the short-segment centering step. Thinking a little about the impact of short-segment centering, it was "obvious" that this would bias towards the weighting of HS-shaped series. We did some simulations (less sophisticated than the later simulations of our GRL article), wrote this up and sent an article to Nature, pointing out that one site (Sheep Mountain) had nearly 400 times the weight of Mayberry slough. At the time, we didn’t know anything very much about Sheep Mountain.
In his reply to our first Nature submission, Mann inadvertently opened up the bristlecone topic. In defence of his method, Mann said that, it wasn’t just Sheep Mountain that was highly weighted, there were 14 other sites that received significant weighting. So what were these sites? I look ed up the heavily weighted sites in Mann’s first eigenvector and then manually looked up the locations corresponding to the site identifications, ca534, ca530, ca529,… now all familiar id’s. The sites looked vaguely familiar – Sheep Mountain, Campito Mountain, Indian Garden, … I’d seen them somewhere before. Of course, it was in the Table from Graybill and Idso 1993 – Mann’s PC1 was, to all intents and purposes, Graybill and Idso’s strip-bark collection.
When the MBH98 directory was made public, there was a very puzzling directory entitled BACKTO_1400-CENSORED, you can imagine how that intrigued me. But there were no identifications to the sites or explanations of it. There were 20 fewer sites in the CENSORED directory (50 versus 70). Elsewhere there was a list of 212 sites and 192 "censored" sites. The 20 excluded sites were virtually all Graybill bristlecone sites. All reached back to 1400 and accounted for the difference between the CENSORED directory and the uncensored directory – Mann had done a sensitivity study on the effect of excluding bristlecones. As we’ve reproted, the PCs from this study did not have a HS-despite the data mining tendency of the MBH algorithm. (This is important to keep in mind – Mannian PCs do not ALWAYS yield a HS.)
While the Mannian PC method was biased, it was the interaction with the bristlecones that appeared to make it especially problematic. Also, even if the Mannian method was a lousy method for obtaining a climate signal, it was useful for identifying outliers. The other thing that seemed obvious: if the temperature history of the world supposedly turns on a few groves of bristlecones in the US Southwest, shouldn’t one have encyclopedic information ont hem? This is what engineering-level analysis would require.
Our GRL paper already covered other topics and was too space-constrained to provide a thorough discussion of bristlecones. There, we merely noted that the MBH98 PC1 was dominated by bristlecones and referred to our E&E article for a more extended discussion:
McIntyre and McKitrick [EE 2005] discuss, inter alia, problems relating to the interpretation of bristlecone/foxtail pine growth as a temperature proxy. (MM05a)
Our 2005 E&E article provided a fairly extended survey of different issues pertaining to bristlecone growth — and there were many interesting and intriguing aspects to bristlecones. Again, it’s worth re-reading the relevant section of our E&E article. We pointed out that Graybill had specifically said that he looked for strip-bark samples, which had a different chronology than full-bark samples:
Graybill specifically sought out strip bark samples and reported that strip bark forms had much stronger 20th century growth than entire bark forms at the same site [Graybill and Idso, 1993]. More recently, Bunn et al.  confirmed higher growth in strip bark forms than entire bark forms at sites in Montana…. Brooks et al.  also pointed out the impact of anthropogenic nitrogen on fertilization of high-altitude bristlecone pines, (EE, 81)
We also had a nice quotation from MBH coauthor Hughes, saying that 20th century bristlecone growth was a “mystery”. We missed finding a quote from NAS panelistBiondi in Biondi et al.  (including MBH coauthor Hughes), but presented this in our NAS presentation:
The average of those sites [a network of high-elevation temperature-sensitive tree-ring sites in the Great Basin and Sierra Nevada of Hughes and Funkhouser, unpublished], plotted in Figure 5, is based on many ring-width series, each one being 500 years or longer, without individual growth surges or suppressions and from "strip-bark" five-needle upper forest border pines of great age. Such record is not a reliable temperature proxy for the last 150 years as it shows an increasing trend in about 1850 that has been attributed to atmospheric CO2 fertilization [Graybill and Idso, 1993]
While there has been much blog vituperation directed at us onother topics, there has been surprisingly little realclimate effort to show that bristlecones were a temperature proxy. The best attempt to justify bristlecones has been by Rob Wilson in a posting at climateaudit here . I engaged in a short dialogue with Rasmus, another realclimate coauthor — we’re dealing with an entire Hockey Team — at Roger Pielke’s blog, in which Rasmus said that citing Graybill and Idso was “no more reassuring than blaming the Flying Spaghetti Monster”
Rasmus: Two short comments: (i) The sentence ‘bristlecones, a series known to be potentially contaminated as a temperature proxy’ has been proposed by McKitric and MacIntyre (MM), but this claim has not, to my mind, been backed up by convincing evidence. Is it really known? How certain is this? …
Steve: 1) Rasmus, look at our paper in E&E for a discussion of bristlecones. Graybill and Idso, who published the chronologies which dominate the MBH98 PC1, stated that their 20th century growth pulse was not due to temperature. Even Hughes has said that the growth pulse is a "mystery" – a position hardly consistent with attributing them as a unique detector of world climate history….
Rasmus: Statement: ‘Graybill and Idso, who published the chronologies which dominate the MBH98 PC1, stated that their 20th century growth pulse was not due to temperature.’
Question: what is the evidence for this – in your own words if you please. Why? To just cite Graybill and Idso is not much more reassuring than blaming the Flying Spaghetti Monster…
Rasmus: When I do a Google on ‘Bristlecone temperature’, I get 27500 hits, but when I include ‘flawed’ in the searxch string, I only get 297 (your name keeps cropping up…). Why such a difference if your claim about their quality were true?
I attempted to document my answer. Some of you may be interested in the dialogue, which went on for a while and gives a flavor of realclimate author debating techniques.
realclimate has discussed the issue only slightly. One of their replies was that they had fully discussed the matter in MBH99, carrying out an adjustment which compensated for CO2 fertilization. We’ve pointed out elsewhere (including our NAS presentation) that this “adjustment” was not applied to MBH98 values; that the adjustment petered out at the end of the 19th century and did not affect the 20th century pulse that concerned Lamarche et al 1984 and Graybill and Idso 1993 , and that it remained very unsatisfactory that results should be critically dependent on flawed data about which you did not know whether the adjustment was valid or not.
The other realclimate reply was that the additional use of bristlecones improved the RE statistic (they used the phrase “verification statistics”, but it’s really just the RE statistic) in an MBH98 model. This is their primary position and one expounded in Wahl and Ammann:
Particular concerns with the "bristlecone pine" data were addressed in the followup paper MBH99 but the fact remains that including these data improves the statistical validation over the 19th Century period and they therefore should be included.
Note that the justification is not that the proxies have any physical validity – only that they improve the RE statistic. OK, but so do Dot.com Stock Prices, so this isn’t a good way of determining statistical validity.
Wahl and Ammann 2006
Wahl and Ammann 2006 is more or less an extended version of positions staked out at realclimate. The mention "bristlecones" 36 times. They acknowledge both that the North American PC1 is "a crucial source of information" (i.e. the reconstruction is not robust) and that PC1 is an alter ego for bristlecone/foxtails:
The temporal information captured by PC1 of the North American tree ring network is a crucial source of information in calibration for the 11th-14th century reconstruction (MBH99), and in verification for the early 15th century reconstruction in MBH98, as shown here (cf. section 3.2). A further aspect of this critique is that the single-bladed hockey stick shape in proxy PC summaries for North America is carried disproportionately by a relatively small subset (15) of proxy records derived from bristlecone/foxtail pines in the western United States, which the authors mention as being subject to question in the literature as local/regional temperature proxies after approximately 1850 (cf. MM05a/b; Hughes and Funkhauser, 2003; MBH99; Graybill and Idso, 1993). (p.9)
They point out that MBH methods do not require that bristlecones correlate with gridcell temperature, only that they correlate with a "climate field" somewhere in the world. They argue that because their information is "necessary" to increasing RE scores. See for example:
The failure to verify by scenario 5d, including only two PCs derived from unstandardized data in the MM centering convention, demonstrates that the bristlecone/foxtail pine records are important for the 1400-1449 network–the information they add to PC4 in this way of calculating the PCs is necessary for a meaningful climate reconstruction. Restricting the PCs in MM05a/b to only the first two (5d) indirectly omits the information carried by the bristlecone/foxtail pine records and thereby leads to a non-meaningful reconstruction. (p. 32)
Or again the following:
Given these observations, from a climate reconstruction point of view one can argue that, in general, the bristlecone/foxtail pine records do not introduce spurious noise and their inclusion is justifiable; or said more strongly, their elimination is not objectively justifiable. Their inclusion by standardization of the individual proxy records (independent of the centering convention) or, even if non-standardized series are applied, by using at least four PCs (until the resulting climate reconstructions converge), leads to reconstruction models that demonstrate skill in both calibration and independent verification. (p 34)
Or one more time:
The bristlecone/foxtail pine proxies from the Southwestern United States are shown to add necessary verification skill to the climate reconstructions for 1400-1449 when PC summaries are used and significantly greater verification skill to the reconstructions for 1400-1499 when no PC summaries are used–indicating that in these cases the records carry important climate information at the level of eigenvector patterns in global surface temperatures. These results are valid notwithstanding issues concerning these proxies’ empirical relationship to local/regional surface temperatures after 1850, noted by MBH in previous work (MBH99; cf. MM05a/b; Hughes and Funkhouser, 2003; Graybill and Idso, 1993). These results enhance the validity of the MBH assumption that proxies used in the reconstruction process do not necessarily need to be closely related to local/regional surface temperatures, as long as they register climatic variations that are linked to the empirical patterns of the global temperature field that the MBH method (and other climate field reconstructions) target. (p 36)
Note that none of these arguments rise above saying that they need the bristlecones to improve the RE score; they do not attempt to justify bristlecones as a temperature proxy through direct analysis. I’ll get to RE scores in another post – for now, please note that the RE benchmark that they use is 0.0 – a benchmark that we contest.
M&M NAS Pesentation
In Section 3.6 of our NAS Presentation, we discussed issues relating to bristlecones and it’s worth re-reading. It includes a reference to Biondi et al, 1999, not in our E&E discussion.
NAS considered bristlecones in Chapter 4 — Tree Rings and Chapter 11 — Multiproxy Reconstructions and, while their recommendations were not entirely consistent, both have important implications for MBH and other reconstructions. In Chapter 4, they did not cite our E&E article (in fact, the article was strangely not cited at all by NAS), but their citations correspond to the citations in our E&E 2005 article and our NAS presentation. They stated
The possibility that increasing tree ring widths in modern times might be driven by increasing atmospheric carbon dioxide (CO2) concentrations, rather than increasing temperatures, was first proposed by LaMarche et al. (1984) for bristlecone pines (Pinus longaeva) in the White Mountains of California. In old age, these trees can assume a “stripbark” form, characterized by a band of trunk that remains alive and continues to grow after the rest of the stem has died. Such trees are sensitive to higher atmospheric CO2 concentrations (Graybill and Idso 1993), possibly because of greater water-use efficiency (Knapp et al. 2001, Bunn et al. 2003) or different carbon partitioning among tree parts (Tang et al. 1999)”Åstrip-bark’ samples should be avoided for temperature reconstructions, attention should also be paid to the confounding effects of anthropogenic nitrogen deposition (Vitousek et al. 1997), since the nutrient conditions of the soil determine wood growth response to increased atmospheric CO2 (Kostiainen et al. 2004).
While the publicity has attached to their use in MBH, they are also used in Crowley and Lowery 2000, Esper et al 2002, Cook et al 2004, Rutherford et al 2005, Moberg et al 2005, Osborn and Briffa 2006 and Hegerl et al 2006. Implementation of the above policy on bristlecones will have an impact past MBH.
In Chapter 11, the NAS Panel did refer to our mention of bristlecones as follows:
A second area of criticism focuses on statistical validation and robustness. McIntyre and McKitrick (2003, 2005a,b) question the choice and application of statistical methods, notably principal component analysis; the metric used in the validation step of the reconstruction exercise; and the selection of proxies, especially the bristlecone pine data used in some of the original temperature reconstruction studies. These and other criticisms, explored briefly in the remainder of this chapter, raised concerns that led to new research and ongoing efforts to improve how surface temperature reconstructions are performed. (106)
In chapter 11, the NAS Panel acknowledges the "strong dependence" of MBH on "data from the Great Basin region" and, somewhat inconsistently, merely says that this needs to be considered in the calculation of statistical uncertainties, although the Statistics chapter, again inconsistently, does not include a discussion of how these calculations should be implemented.
The more important aspect of this criticism [about principal components] is the issue of robustness with respect to the choice of proxies used in the reconstruction. For periods prior to the 16th century, the Mann et al. (1999) reconstruction that uses this particular principal component analysis technique is strongly dependent on data from the Great Basin region in the western United States. Such issues of robustness need to be taken into account in estimates of statistical uncertainties (106)
Ironically, they even cite Wahl and Ammann 2006 as authority for the fact that exclusion of subsets can have an impact on results. This is entirely in keeping with our interpretation of Wahl and Ammann under the rhetoric – that they confirm the non-robustness that we had previously reported (as they had confirmed the failed verification statistics that we previously reported). Are our feelings hurt that the NAS panel attributed these damaging claims about MBh to Wahl and Ammann as opposed to us? I guess we will manage to bear the pain.
While they accept Wahl and Ammann as authority for non-robustness, they squarely turn away from the argument of Wahl and Ammann 2006 – that the use of the proxies is justified by the increase of RE scores. In Chapter 4, they recommend not using the proxies altogether. In Chapter 11, they say that this would increase uncertainties. One of the impacts is that you get high 15th century results without bristlecones. In the discussion of this topic, the NAS Panel palced wieght on the fact that one could "get" a HS without using PCs, but, in my opinion, did not fully turn their minds to the role of bristlecones and a couple of other problematic series, to which I’ll return in another post.
I can see nothing about our position on bristlecones with which the NAS Panel disagreed and I see a repudiation of the Wahl and Ammann/realclimate justification for their inclusion as being the “correct” reconstruction on the one hand, and even for including them at all. Their findings here (as in the Statistics chapter which I’ll discuss on another occasion) are fundamental to considering the “other” studies.