Section 6.4 Responses

6. The scrutiny and re-analysis of data by other scientists is a vital process if hypotheses are to rigorously tested and improved. It is alleged that there has been a failure to make important data available or the procedures used to adjust and analyse that data, thereby subverting a crucial scientific process.   It is alleged that there has been a systematic policy of denying access to data thathas been used in publications, referring to an email from Jones to Mann on 2nd February 2005 which contains the following:  “And don’t leave stuff lying around on ftp sites – you never know who is trawling them. The two MMs have been after the CRU station data for years. If they ever hear there is a Freedom of Information Act now in the UK, I think I’ll delete the file rather than send to anyone. Does your similar act in the US force you to respond to enquiries within 20 days?—our does! The UK works on precedents, so the first request will test it. We also have a data protection act, which I will hide behind”. 

QUESTIONS  TO ADDRESS

  Do you agree that releasing data for others to use and to test hypotheses is an important principle? 

 4. If not, do others have reasonable access to the data at all levels and to the description of processing steps, in order to be able to carry out such a re- analysis?

8 Responses to “Section 6.4 Responses”

  1. Jimchip Says:

    1065785323 22 Sep 2003 (Hughes to Esper):

    Dear Jan – I have recently started to clear up all outstanding business related to the next analysis by Mike Mann, Ray Bradley, et al., and found, to my horror, that I had not replied to your e-mail of last April 8 (copy at end of this message). In response to our request for access to the data on which your 2000 and 2002 papers were based, you indicated that you would need to check with a colleague at WSL. Have you been able to do this, and if so, what is the result? Obviously we are keen to include all important data already in the peer reviewed literature, such as yours, in our analyses. You also requested “the raw measurements of (y)our sequoia data and the western conifer data used in the Mann et al 1998, 1999 papers”. 1) data used in Mann et al 1998 – these are all listed in the Nature on-line >>supplementary materials (attached), and were all from the ITRDB, so they may be downloaded from there. The same list is also attached. We think we can find the raw data (the *.rwl files) and send them to you if you would like – please let me know. 2) The western conifer data used in MBH 99 are a subset of these, as indicated in another set of attached MS-Excel files. These are a little bit repetitive, but contain the following particularly useful information for these 27 longer chronologies: vchron11000 contains, inter alia, the ITRDB ID, species code, first year, last year, collector’s name…

    Dear Jan, You may be familiar with our earlier attempts at very large scale multi-proxy reconstruction of certain aspects of climate, (for example, Mann, Bradley and Hughes, 1998, Nature, 392, 779-787). This work was possible because many colleagues made their data available. We are now assembling an updated and extended dataset for new work along similar lines. We hope to take advantage of data that were not available five years ago, and to use improved methods in our analyses. Would you be willing to permit us to use the (chronologies/reconstruction?) reported in your paper (s) listed below? Esper J. (2000). Long-term tree-ring variations in Juniperus at the upper timber-line in karakorum (Pakistan). Holocene 10 (2), 253-260. Esper J., Schweingruber F.H., Winiger M. (2002). 1300 years of climatic history for western central Asia inferred from tree-rings. >Holocene 12 (3), 267-277. We are particularly interested in (1) the ring-width series of Juniperus excelsa M. Bieb and Juniperus turkestanica Kom. From 6 different sites in the Hunza-karakorrum; (2) 20 individual sites ranging from the lower to upper local timber-lines in the Northwest karakorum of Pakistan and the Southern Tien Shan of Kirghizia.If at all possible, we would prefer to receive tree-ring data as both raw data (individual unmodified measurement series for all samples used) and your final chronologies used in the publication. If you are willing to share your data for the purposes of our analyses, but do not wish them to be passed on to anyone else by us, please tell us, and we will mark the data accordingly in our database. If data have been marked as not being publicly available, we will pass on any requests for them to you.”

  2. jimchip Says:

    Brief note that Steve McIntyre, posted on Sep 26, 2005 at 8:19 AM
    didn’t have access
    http://climateaudit.org/2005/09/26/384/

    Caveats: I’ve used the Esper et al [2002] chronologies as I graphed them up a few days ago; I don’t have all the sites and the Tirol site must differ somehow. For Crowley, I have only the smoothed and transformed version. The transformed version is in [0,1] so I did a qnorm transformation, jittering the 0 and 1 values. The MBH99 data used is the proxy roster from the MWP step.

  3. jimchip Says:

    Compare CRU data transparency to what some others have done. Much of what’s available now could have been available much earlier.

    The source code for some models is now available. Data is now more available. What took so long?
    http://www.esrl.noaa.gov/psd/data/20thC_Rean/
    http://www.ccsm.ucar.edu/models/ccsm3.0/
    http://www.mpimet.mpg.de/en/wissenschaft/modelle/model-distribution.html
    http://forge.ipsl.jussieu.fr/igcmg

  4. jimchip Says:

    1155346370.txt

    From: Hans von Storch
    To: Keith Briffa
    Subject: Re: open data access?
    Date: Fri, 11 Aug 2006 21:32:50 +0200

    > At 11:19 05/08/2006, you wrote:
    > >Dear Keith,
    > >
    > >I read this comment on the prometheus-weblog of Roger Pielke jr:
    > >
    > >”Ask Briffa for site identifications for Briffa
    > >et al 2001? While you’re at it, ask him for the
    > >measurement data for Taimyr, Tornetrask update
    > >and Yamal? Ask Briffa why he didn’t publish the updated Polar Urals results.”
    > >
    > >The background of this inquiry seems to be the
    > >replicability of your studies. I think this is a
    > >reasonable request, but some people claim that
    > >you would “stonewall” any such attempts. (“The
    > >issue of data access was discussed in the dendro
    > >conference in Beijing – some people suggesting
    > >that withholding data was giving the trade a
    > >black eye. Industry leaders, such as presumably
    > >Briffa, said that they were going to continue
    > >stonewalling.”)

  5. jimchip Says:

    1233326033.txt I also find it highly ironic that Santer defends his dataset based on Douglass, et al. Geoff Smith’s polite letters are a good example that almost anything sets Santer off. the whole correspondance is worth reading

    rom: Ben Santer
    To: Smithg
    Subject: Re: data request
    Date: Fri, 30 Jan 2009 09:33:53 -0800
    Reply-to: santer1@llnl.gov

    Dear Mr. Smith,

    Please do not lecture me on “good science and replicability”. Mr.
    McIntyre had access to all of the primary model and observational data
    necessary to replicate our results. Full replication of our results
    would have required Mr. McIntyre to invest time and effort. He was
    unwilling to do that.

    Our results were published in a peer-reviewed publication (the
    International Journal of Climatology). These results were fully
    available for “independent testing and replication by others”. Indeed, I
    note that David Douglass et al. performed such independent testing and
    replication in their 2007 International Journal of Climatology paper.

    Douglass et al. used the same primary climate model data that we
    employed. They did what Mr. McIntyre was unwilling to do – they
    independently calculated estimates of “synthetic” Microwave Sounding
    Unit (MSU) temperatures from climate model data. The Douglass et al.
    “synthetic” MSU temperatures are very similar to our own. The scientific
    differences between the Douglass et al. and Santer et al. results are
    primarily related to the different statistical tests that the two groups
    employed in their comparisons of models and observations.

  6. Jimchip Says:

    http://climateaudit.org/2009/09/26/briffas-yamal-crack-cocaine-for-paleoclimatologists/

    The CRU Archive
    While the Yamal measurement archive is a quantum addition to (indeed, the first useful) information on Yamal, it lacks any sort of metadata as to where the individual samples were obtained.

    I think that some information can be gleaned from the nomenclature of the ID numbers. There are 252 distinct series in the CRU archive. There are 12 IDs consisting of a 3-letter prefix, a 2-digit tree # and 1-digit core#. All 12 end in 1988 or later and presumably come from the living tree samples. The nomenclature of these core IDs url (POR01…POR11; YAD04…YAD12; JAH14…JAH16 – excluding the last digit of the ID here as it is a core #) suggests to me that there were at least 11 POR cores, 12 YAD cores and 16 JAH cores. The JAH and POR cores (7 in total) were over 200 years, while all of the YAD cores were under 200 years – so there may be some difference between the Briffa selection and the Hantemirov selection.) YAD presumably stands for Yadayakhodyyakha River (see map and Figure 3); POR for Porzayakha River (see Figure 3); JAH for one of the unlabelled tributaries in Figure 3.

    There are 235 IDs consisting of a 1-digit alphanumeric followed by a 4-digit tree number and a 1-digit core #. The tree numbers appear to be unique within this group – the lowest is 0008 and the highest is 2258. There are three different prefixes: L, P and _, with L having by far the most. Perhaps these prefixes correspond to three different subfossil provenances: alluvial, peat and surface. (I don’t rely on this; they might relate to something geographic.)

    There are 5 IDs that are 4-5 digits (X13, X02S,M021,M022,M331): these in 1963, 1978 and 1982 and look like they are results from previous coring of living trees. Perhaps these 5 cores plus the 12 cores from living trees (with 6-digit IDs) are the same as the 17 cores from living trees selected in the H and S chronology. But maybe this is a coincidence. One never knows – it’s climate science.

  7. Jimchip Says:

    1076083097.txt we’re separating ‘providing the code’ from ‘running the code’

    From: Phil Jones
    To: “Peter H. Gleick” , Mearns Linda O
    Subject: Re: MBH Submission (fwd)
    Date: Fri Feb 6 10:58:17 2004
    Cc: Stephen H Schneider , N.W.Arnell@soton.ac.uk, frtca@fy.chalmers.se, d.camuffo@isac.cnr.it, scohen@sdri.ubc.ca, pmfearn@inpa.gov.br, jfoley@facstaff.wisc.edu, harvey@geog.utoronto.ca, ahssec@ansto.gov.au, Thomas.R.Karl@noaa.gov, rwk@ucar.edu, rik.leemans@wur.nl, diana.liverman@eci.ox.ac.uk, mccarl@tamu.edu, lindam@atd.ucar.edu, rmoss@usgcrp.gov, ogilvie@spot.colorado.edu, pfister@hist.unibe.ch, barrie.pittock@csiro.au, pollard@essc.psu.edu, nj.rosenberg@pnl.gov, crosenzweig@giss.nasa.gov, j.salinger@niwa.co.nz, santer1@llnl.gov, h.j.schellnhuber@uea.ac.uk, dgvictor@stanford.edu, F.I.Woodward@sheffield.ac.uk, gyohe@wesleyan.edu, yurganov@hotmail.com

    Dear All,
    So now it seems that we’re separating ‘providing the code’ from ‘running the code’. I
    can’t
    see the purpose of one without the other. Even if Mike complies I suspect there will need
    to be several sessions of interaction, which neither side will be very keen on. As I said
    before
    I know the code will involve lots of combinations (for different periods with different
    proxies).
    Also I would expect, knowing the nature of the PC-type regression approach, that there
    will
    be library routines. If the code is sent, there needs to be conditions. We don’t want
    McIntyre
    (MM) to come out and say he can’t get it to work after a few days.
    So, it is far some simple. I’m still against the code being given out. Mike has made
    the
    data available. That is all they should need. The method is detailed in the original
    paper –
    in the online (methods) and also in several other papers Mike has written.
    As an aside, Mike is now using a different method from MBH98. Also, as an aside,
    whilst we’ve been deliberating, MM have submitted another comment on MBH98 to another
    journal. In this they say they have a program that replicates MBH98 (although it isn’t
    very convincing that they have it exactly right, as they never show a like for like
    comparison) , but
    most of the comment goes on about the results being different due to different
    combinations of
    proxies. The latter isn’t surprising.
    It might appear they want the code to check whether their version works properly. If
    this
    is the case, then there are issues of IPR. So, if they get the code, how do we stop them
    using it for anything other than this review.
    Cheers
    Phil
    At 11:40 04/02/2004 -0800, Peter H. Gleick wrote:

    Yes, excellent point. This should be what we do. Further, we can point out that we’ve
    bent over backward here and provided more than typically necessary in order to satisfy
    persistent but inappropriate demands.
    Peter
    At 08:46 PM 2/4/04 +0100, Mearns Linda O wrote:

    Peter et al.,
    Thanks for reminding me about the new email list.
    My point about the code is still that ‘providing the code’ can be
    interpreted alot of ways. I have thought about this, and imagined if in
    one of my larger and more complex projects, I was asked to provide all
    code. I could do that just by sending the pieces with a summary file
    explaining what each piece was used for. It still theoretically allows
    someone to see how coding was done. And I do think that is a far sight
    easier than providing stuff that can be run, etc. I am suggesting that
    one could do the minimum. Then the point is, one isn’t faced with garish
    headlines about ‘refusal to provide code’. I think it is harder to come
    up with a garish headline about ‘refusal to provide completely documented
    code with appropriate readme files and handholding for running it’.
    Linda

    Dr. Peter H. Gleick

  8. Jimchip Says:

    1076359809.txt “Steve’s going to find it very hard to ask you to send the code.”

    From: Phil Jones
    To: “Michael E. Mann”
    Subject: Re: Fw: Law Dome O18
    Date: Mon Feb 9 15:50:09 2004

    Mike,
    These were two simple ones to provide. Also Tas told him I had one of them. I guess
    these
    are the ones that aren’t available on web sites.
    Anyway, it is done now. If he starts asking for them in dribs and drabs, I’ll baulk at
    that.
    Ben waded in with very positive comments re the CC issue. Steve’s going to find it
    very
    hard to ask you to send the code. Those that say on the CC board that you should send the
    code, have little idea what is involved. Most are on the social science side.
    Cheers
    Phil
    At 10:19 09/02/2004 -0500, you wrote:

    HI Phil,
    Personally, I wouldn’t send him anything. I have no idea what he’s up to, but you can be
    sure it falls into the “no good” category.
    There are a few series from our ’03 paper that he won’t have–these include the latest
    Jacoby and D’Arrigo, which I digitized from their publication (they haven’t made it
    publicly available) and the extended western North American series, which they wouldn’t
    be able to reproduce without following exactly the procedure described in our ’99 GRL
    paper to remove the estimated non-climatic component.
    I would not give them *anything*. I would not respond or even acknowledge receipt of
    their emails. There is no reason to give them any data, in my opinion, and I think we do
    so at our own peril!
    talk to you later,
    mike
    At 02:46 PM 2/9/2004 +0000, Phil Jones wrote:

    Mike,
    FYI. Sent him the two series – the as received versions. Wonder what he’s up to?
    Why these two series ? Used a lot more in the 1998 paper. Didn’t want the Alerce
    series.
    Must already have the Tassy series from Ed. I know Ed has a more recent series than we
    used in 1998. Got this for the 2003 work.
    Cheers
    Phil

    From: “Steve McIntyre”
    To: “Phil Jones”
    Subject: Fw: Law Dome O18
    Date: Mon, 9 Feb 2004 08:05:23 -0500
    X-Mailer: Microsoft Outlook Express 6.00.2800.1158
    X-Authentication-Info: Submitted using SMTP AUTH LOGIN at
    fep04-mail.bloor.is.net.cable.rogers.com from [65.49.25.138] using ID
    at Mon, 9 Feb 2004 08:02:13 -0500
    Dear Phil,
    Tas van Ommen has refered me to you for the version of his dataset that you used in
    Jones et al Holocene 1998 and I would appreicate a copy. I would also appreciate a copy
    of the Lenca series used in this study. Regards, Steve McIntyre

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