Bristlecone "Adjustment" #1

There has been some recent chatline discussion on whether the MBH98 bristlecone pine series were “adjusted” for non-climatic factors. A number of posters seem to think that they were so “adjusted. For example, Tom Rees said on http://www.davidappell.com:

on Monday, January 31st, Tom Rees said

Me again… James: Mann et al 1999 seem to be very clear. They’re not sure what causes the surge in the Bristlecone pines, so they play safe and remove it. So it’s not in the ‘Hockey stick’ at all…

To the extent that one can ever be certain about MBH98 methods, I am completely confident that the “adjustment” discussed in MBH99 was not implemented in MBH98. The archived MBH98 PC series can be replicated almost exactly and do not show any such “adjustment”; an email to Natuurwetenschap by Mann states that the sensitivity on bristlecones was done after MBH98.

This does not totally end the story. Curiously, the archived version of the North American PC1 at NOAA for MBH99 is not the “adjusted” version, but the unadjusted version from the BACKTO_1000 directory. In most walks of life, there would be some check that they did not forget to do the adjustment in their downstream calculations, but I am unaware of any such checks, and, the unavailability of source code or supporting calculations makes direct verification impossible.

Secondly, one of the representations of MBH98 was that the proxies were all linearly related to climatic factors. The discussion of MBH99 states quite clearly that non-climatic factors affect bristlecone pine growth and adjustments are required. (I disagree with the MBH99 adjustment, but will return to that with a full description of the procedure on another occasion in the near future.) If so, then this clearly imposes an obligation on MBH to have promptly notified Nature of the fact that some of the MBH98 proxies did not meet the criteria set out and to publish a Corrigendum, demonstrating the effect on MBH98 calculations.

Shouldn’t MBH “adjust” the bristlecone pines before they do their PC calculations for the 15th century network? Shouldn’t they have done this a long time ago? The bristlecones have already been demoted to the PC4 using correct PC calculations? If they are “adjusted” according to MBH99 methods, do they fall still further? Is there any change to their “significance”? Inquiring minds want to know.

I didn’t mention this issue in my first remarks on the current efforts to salvage MBH98, but it seems it might be an important issue and that MBH have little more homework to do.

8 Comments

  1. Tom Rees
    Posted Feb 8, 2005 at 11:18 AM | Permalink | Reply

    The point is that the ‘Hockey stick’ is from MBH99, not MBH98. Your criticisms of MBH98 may also apply to MBH99, but this has to be shown and not simply assumed (especially given that much of your criticism seems to revolve around the BCPs, which were specifically filtered from MBH99). Inquring minds, as they say, want to know.

    By confusing the two (as you do in your ‘Where’s wald’ post) you do your readers a disservice.

  2. Steve McIntyre
    Posted Feb 8, 2005 at 2:08 PM | Permalink | Reply

    The MBH99 hockey stick is a splice of the MBH98 result for the period 1400-1980 and the 1000-1399 period calculated in MBH99. Thus all the issues that we discuss in respect to MBH98, including the 15th century problems, apply exactly to the MBH99 graphic.

    Leaving aside the question of whether the bristlecone pine adjustment in MBH99 is appropriate (which I don’t think it is), there is no attempt at adjustment in the 15th century step which is common to the two graphics. You’ve misunderstood what MBH are doing here.

    You’ve been wondering what a reconstruction without BCPs would look like: it would look at least as un-hockey stick shaped as our reconstruction in MM05 (E&E). That reconstruction uses a correct PC method, in which the main hockey stick effect of the BCP is demoted to the PC4. In our reconstruction, we used the first 2 PCs of the NOAMER network and hence the BCPs do not dominate, resulting in "warm" early 15th century values. Using the same splicing method as MBH99, these "warm" early 15th century values would carry forward into a 1000-1980 reconstruction. We are not attempting to offer amended MBH calculations as a temperature history and, for our purposes, it was sufficient to show the contradiction arising from 15th century results with MBH claims of 20th century uniqueness. I’m going to post up a more detailed response on the 2 vs 5 PC issues, but the issues briefly are: 1) was the recently reported Preisendorfer method actually used in MBH98 (as opposed to them wishing that they’d used it? does it matter whether it wasn’t used in MBH98, if they can "get" MBH98-type results with it? 2) robustness – is the 5 PC method robust to the presence/absence of BCPs: look at my posting showing the 5 PCs from the CENSORED file – there’s no hockeystick. 3) statistical significance – this is a major focus of MM05 (GRL) and people don’t seem to have paid much attention to this so far, but it’s a really important point.

    One other point, while you’re on the line: the no-dendro calculations in Mann et al [2000] for the period 1730 would have a completely different result in the AD1400 step. Given that Mann had specifically done PC calculations without BCPs in the AD1400 step (the CENSORED directory), he was aware of that a no-BCP claim (and thus a no-dendro claim) would not be true for the 15th century. It’s common ground to all parties that PC4 has a huge effect on 15th century results with centered calculations. What better proof of non-robustness do you need? Steve Mc

  3. Hans Erren
    Posted Feb 9, 2005 at 7:18 AM | Permalink | Reply

    Is it known how the Sheep Mountain hockeystick was constructed in the first place?

    I don’t see much hockeystick in the ring width data.
    ftp://ftp.ngdc.noaa.gov/paleo/treering/measurements/northamerica/usa/ca543.rwl
    compared with the derived chronology
    ftp://ftp.ngdc.noaa.gov/paleo/treering/chronologies/northamerica/usa/ca543.crn

  4. Steve McIntyre
    Posted Feb 9, 2005 at 9:16 AM | Permalink | Reply

    Hans, I presume that you meant ftp://ftp.ngdc.noaa.gov/paleo/treering/measurements/northamerica/usa/ca534.rwl
    and
    ftp://ftp.ngdc.noaa.gov/paleo/treering/measurements/northamerica/usa/ca534.crn.

    There are some very interesting issues on the construction of underlying tree ring chronologies.I’ve spent a lot of time on this matter and have tried to replicate the chronology calculations from first principles. You would think that these calculations would be documented at WDCP, but they aren’t. There are some errors at WDCP e.g. some of the density chronologies used in Briffa et al. [2001] included dates up into the 22nd century.Graybill’s usual practice was to fit smooth curve (negative exponential) to each core to represent an "aging" effect – or alternatively a negatively-sloped line or a flat line; and then calculate the ratio of the ring width measurement to the fitted curve. The available ratios are averaged in each year to make a "chronology" (multiplied by 1000).

    Cook and Peters [1997] (see our E&E) pointed out that this method can lead to upward biases at the end of records if the fitted curves got too low and cited two examples: Campito Mountain , BCP near Sheep Mt, and Gaspe – what a strange combination given our independent isolaiton of these sites. Having said that, even if you simply average the mean ring widths, there is a definite hockey stick at Sheep Mt.

    I spent a lot of time collating the WDCP data into R tables, both rwl and crn. There was quite a bit of very fiddly work fixing formats and if you’re interested in ca534, let me know. Steve

  5. Hans Erren
    Posted Feb 9, 2005 at 9:40 AM | Permalink | Reply

    Sorry for the typo. Indead I meant ca534.
    Another item is clerical errors in individual trees. I could imagine that averaging ringwidths where a few trees have omitted rings (eg caused by diseases, fires, animals) this can totally change the early part of a chronology. Did you consider this?

  6. Hans Erren
    Posted Feb 10, 2005 at 7:50 AM | Permalink | Reply

    Is this new or did I really oversee this one in the past?
    ftp://eclogite.geo.umass.edu/pub/mann/ONLINE-PREPRINTS/Millennium/DATA/PROXIES/pc1-fixed.dat

    linked from

    http://www.people.virginia.edu/~mem6u/mbh99.html

  7. Steve McIntyre
    Posted Feb 10, 2005 at 9:27 AM | Permalink | Reply

    Hans, It’s hard to say whether it’s new or not. The pc1-fixed record is not listed at ftp://ftp.ngdc.noaa.gov/paleo/contributions_by_author/mann1999/proxies, which is the site that I used as a source for MBH99 proxies. It could have been up at eclogite, but not at NOAA. I probably would have done a cross-check for a report on MBH99, but I  didn’t have occastion to  do a cross-check on MBH99 series. It could have been added later, even quite recently; if the series was on the site in a private area, it could be moved to the public location without changing the date stamp. I’ve seen this at Mann’s Virginia site where I know the dates (although I’m blocked unless I go to the university.)

    Before Mann deleted files from his FTP directory in November 2003, I had copied all of the MBH98 directories and can check any changes. But I didn’t copy the MBH99 directories so I can’t say for certain. My guess is that it’s probably been up at eclogite for a while; but then it’s odd that it wasn’t archived at NOAA, which otherwise is a copy of eclogite. You’d think that you’d copy the whole directory rather than piecemeal.  Steve

  8. TCO
    Posted Sep 11, 2005 at 4:17 PM | Permalink | Reply

    I hope you copy everything from now on, given how those guys delete data. I would include WDCP and such within your copying.

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