Section 6.3 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

  …If so, do you agree that this principle has been abused?
 3. If so, should not data be released for use by those with the intention to undermine your case, or is there a distinction you would wish to make between legitimate and illegitimate use?

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6 Responses to “Section 6.3 Responses”

  1. Jimchip Says:

    0938018124 22 Sep 1999 qutoed Jones to Mann: (see also 1.2)

    “Another issue I would like to raise is availability of all the series >>> you use in your reconstructions. That old chestnut again !”

    1057944829 Jul 11 2003 (Osborn to Crowley):

    “The new Mann and Jones 2000-year series I don’t actually have. It appears in Figure 1 of our EOS piece, of course, but Scott Rutherford generated that figure. I generated Figure 2 for EOS and that has the Yamal, Tornetrask, western US and western Greenland O18 stack in it. So I have these data and they are attached in the following files. western US and western Greenland are in file “mann12prox.dat”. I didn’t have time to extract just these two series from the full file, so the file contains 11 others series too. Please do *not* use the others because I’m not sure whether I am free to distribute them or not – I just haven’t time to extract the 2 you want. I’m sure I can trust you not to use anything that I shouldn’t have sent!…I would really strongly suggest that you contact Keith Briffa about exactly what these series are and what the primary reference to them should be. The reason is that there are multiple version of Tornetrask and Yamal series and the differences are certainly not insignificant!”

  2. jimchip Says:

    1228330629.txt

    At 01:17 03/12/2008, Ben Santer wrote:

    Dear Tom,
    I think that the idea of a Commentary in Science or Nature is a good one. Steve Sherwood
    made a similar suggestion. I’d be perfectly happy NOT to be involved in such a
    Commentary. My involvement would look too self-serving.
    One of the problems is that I’m caught in a real Catch-22 situation. At present, I’m
    damned and publicly vilified because I refused to provide McIntyre with the data he
    requested. But had I acceded to McIntyre’s initial request for climate model data, I’m
    convinced (based on the past experiences of Mike Mann, Phil, and Gavin) that I would
    have spent years of my scientific career dealing with demands for further explanations,
    additional data, Fortran code, etc. (Phil has been complying with FOIA requests from
    McIntyre and his cronies for over two years). And if I ever denied a single request for
    further information, McIntyre would have rubbed his hands gleefully and written: “You
    see – he’s guilty as charged!” on his website.
    You and I have spent over a decade of our scientific careers on the MSU issue, Tom.
    During much of that time, we’ve had to do science in “reactive mode”, responding to the
    latest outrageous claims and inept science by John Christy, David Douglass, or S. Fred
    Singer. For the remainder of my scientific career, I’d like to dictate my own research
    agenda. I don’t want that agenda driven by the constant need to respond to Christy,
    Douglass, and Singer. And I certainly don’t want to spend years of my life interacting
    with the likes of Steven McIntyre.
    I hope LLNL management will provide me with their full support. If they do not, I’m
    fully prepared to seek employment elsewhere.
    With best regards,
    Ben
    Tom Wigley wrote:

    Ben,
    Re the idea Michael sent around (to Revkin et al.)
    this is something that Nature or Science might like
    as a Commentary. It might even be possible to include
    some indirect reference to the Mc audit issue. The
    notes I sent could be a starting point. One problem
    is that you could not be first author as this would
    look like garnering publicity for your own work (as
    the 2 key papers are both Santer et al.) Even having
    me as the first author may not work. An ideal person
    would be Tom Karl, who sent me a response saying “nice
    summary”.
    What do you think?
    Tom.


    —————————————————————————-
    Benjamin D. Santer
    Program for Climate Model Diagnosis and Intercomparison
    Lawrence Livermore National Laboratory

  3. Jimchip Says:

    1068652882.txt Osborn to Briffa 11/2003 Mann’s excel files

    From: Tim Osborn
    To: “Keith Briffa” ,”Phil Jones”
    Subject: Fwd: MBH98
    Date: Wed, 12 Nov 2003 11:01:22 +0000

    Keith and Phil,

    you will have seen Stephen McIntyre’s request to us. We need to talk about
    it, though my initial feeling is that we should turn it down (with
    carefully worded/explained reason) as another interrim stage and prefer to
    make our input at the peer-review stage.

    In the meantime, here is an email (copied below) to Mike Mann from
    McIntyre, requesting data and programs (and making other criticisms). I do
    wish Mike had not rushed around sending out preliminary and incorrect early
    responses – the waters are really muddied now. He would have done better
    to have taken things slowly and worked out a final response before
    publicising this stuff. Excel files, other files being created early or
    now deleted is really confusing things!

    Anyway, because McIntyre has now asked Mann directly for his data and
    programs, his request that *we* send McIntyre’s request to Mann has been
    dropped (I would have said “no” anyway).

    So it’s just the second bit, that we review part 2 of this response, that
    needs to be answered.

    Cheers

    Tim

    >From: “Steve McIntyre”
    >To: “Michael E. Mann”
    >Cc: “Tim Osborn” ,
    > “Ross McKitrick”
    >Subject: MBH98
    >Date: Tue, 11 Nov 2003 23:39:46 -0500
    >
    >November 11, 2003
    >
    >
    >
    >Professor Michael E. Mann
    >
    >School of Earth Sciences
    >
    >University of Virginia
    >
    >
    >
    >
    >
    >
    >
    >Dear Professor Mann,
    >
    >
    >
    >We apologize for not sending you a copy of our recent paper (“MM”) in
    >Energy and Environment for comment, as we understood from your email of
    >September 25, 2003 that time constraints prevented you from considering
    >our material. We notice that you seem to have subsequently changed your
    >mind and hope that you will both be able to clarify some points for us and
    >to rectify the public record on other points.
    >
    >
    >
    >1) You have claimed that we used the wrong data and the wrong
    >computational methodology. We would like to reconcile our results to
    >actual data and methodology used in MBH98. We would therefore appreciate
    >copies of the computer programs you actually used to read in data (the 159
    >data series referred to in your recent comments) and construct the
    >temperature index shown in Nature (1998) (“MBH98”), either through email
    >or, preferably through public FTP or web posting.
    >
    >
    >
    >2) In some recent comments, you are reported as stating that we requested
    >an Excel file and that you instead directed us to an FTP site for the
    >MBH98 data. You are also reported as saying that despite having pointed us
    >to the FTP site, you and your colleague took trouble to prepare an Excel
    >spreadsheet, but inadvertently introduced some collation errors at that
    >time. In fact, as you no doubt recall, we did not request an Excel
    >spreadsheet, but specifically asked for an FTP location, which you were
    >unable or unwilling to provide. Nor was an Excel spreadsheet ever supplied
    >to us; instead we were given a text file, pcproxy.txt. Nor was this file
    >created in April 2003. After we learned on October 29, 2003 that the
    >pertinent data was reported to be located on your FTP site
    >ftp://holocene.evsc.virginia.edu/pub
    >(and that we were being faulted for not getting it from there), we
    >examined this site and found it contains the exact same file (pcproxy.txt)
    >as the one we received, bearing a date of creation of August 8, 2002. On
    >October 29, 2003, your FTP site also contained the file pcproxy.mat, a
    >Matlab file, the header to which read: “MATLAB 5.0 MAT-file, Platform:
    >SOL2, Created on: Thu Aug 8 10:18:19 2002.” Both files contain identical
    >data to the file pcproxy.txt emailed to one of us (McIntyre) in April
    >2003, including all collation errors, fills and other problems identified
    >in MM. It is therefore clear that the file pcproxy.txt as sent to us was
    >not prepared in April 2003 in response to our requests, nor was it
    >prepared as an Excel spreadsheet, but in fact it was prepared many months
    >earlier with Matlab. It is also clear that, had we gone to your FTP site
    >earlier, we would simply have found the same data collation as we received
    >from Scott Rutherford. Would you please forthwith issue a statement
    >withdrawing and correcting your earlier comments.
    >
    >
    >
    >3) In reported comments, you also claimed that we overlooked the collation
    >errors in pcproxy.txt and “slid” the incorrect data into our calculations,
    >a statement which is untrue and made without a reasonable basis. In MM, we
    >described numerous errors including, but not limited to, the collation
    >errors, indicating quite obviously that we noticed the data problems. We
    >then describe how we “firewalled” our data from the errors contained in
    >the data you provided us, by re-collating tree ring proxy data from
    >original sources and carrying out fresh principal component calculations.
    >We request that you forthwith withdraw the claim that we deliberately used
    >data we knew to be in error.
    >
    >
    >
    >4) On November 8, 2003, when we re-visited your FTP site, we noticed the
    >following changes since October 29, 2003: (1) the file pcproxy.mat had
    >been deleted from your FTP site; (2) the file pcproxy.txt no longer was
    >displayed under the /sdr directory, where it had previously been located,
    >although it could still be retrieved through an exact call if one
    >previously knew the exact file name; (3) without any notice, a new file
    >named “mbhfilled.mat” prepared on November 4, 2003 had been inserted into
    >the directory. Obviously, the files pcproxy.mat and pcproxy.txt are
    >pertinent to the comments referred to above and we view the deletion of
    >pcproxy.mat from the archival record under the current circumstances as
    >unjustifiable. Would you please restore these files to your FTP site,
    >together with an annotated text file documenting the dates of their
    >deletion and restoration.
    >
    >
    >
    >5) We note that the new file mbhfilled.mat is an array of dimension
    >381×2016. Could you state whether this file has any connection to MBH98,
    >and, if so, please explain the purpose of this file, why it has been
    >posted now and why it was not previously available at the FTP site.
    >
    >
    >
    >6) Can you advise us whether the directory MBH98 has been a subdirectory
    >within the folder “pub” since July 30, 2002 or whether it was transferred
    >from another (possibly private) directory at a date after July 30, 2002?
    >If the latter, could you advise on the date of such transfer.
    >
    >
    >
    >
    >
    >We have prepared a 3-part response to your reply to MM. The first, which
    >we have released publicly, goes over some of the matters raised in points
    >#2-#5 above. The second is undergoing review. It deals with additional
    >issues of data quality and disclosure, resulting from inspection of your
    >FTP site since October 29, 2003. The third part will consider the points
    >made in your response, both in terms of data and methodology, and will
    >attempt a careful reconciliation of our calculation methods, hence the
    >necessity of our request in point #1. Thank you for your attention.
    >
    >
    >
    >
    >
    >Yours truly,
    >
    >
    >
    >Stephen McIntyre Ross McKitrick

  4. Jimchip Says:

    1074277559.txt Confidential Delete after reading…

    From: Phil Jones
    To: mann@virginia.edu
    Subject: CLIMATIC CHANGE needs your advice – YOUR EYES ONLY !!!!!
    Date: Fri Jan 16 13:25:59 2004

    Mike,
    This is for YOURS EYES ONLY. Delete after reading – please ! I’m trying to redress the
    balance. One reply from Pfister said you should make all available !! Pot calling the
    kettle
    black – Christian doesn’t make his methods available. I replied to the wrong Christian
    message
    so you don’t get to see what he said. Probably best. Told Steve separately and to get
    more
    advice from a few others as well as Kluwer and legal.
    PLEASE DELETE – just for you, not even Ray and Malcolm

    Cheers
    Phil

    Date: Fri, 16 Jan 2004 12:37:29 +0000
    To: Christian Azar , christian.pfister@hist.unibe.ch
    From: Phil Jones
    Subject: Re: AW: CLIMATIC CHANGE needs your advice
    Cc: “‘David G. VICTOR'” , ‘Katarina Kivel’ ,
    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, pgleick@pipeline.com,
    harvey@geog.utoronto.ca, ahs@ansto.gov.au, Thomas.R.Karl@noaa.gov, rwk@ucar.edu,
    rik.leemans@rivm.nl, diana.liverman@eci.ox.ac.uk, mccarl@tamu.edu, lindam@atd.ucar.edu,
    rmoss@usgcrp.gov, ogilvie@spot.colorado.edu, barrie.pittock@dar.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,
    F.I.Woodward@sheffield.ac.uk, gyohe@wesleyan.edu, leonid@atmosp.physics.utoronto.ca,
    shs@stanford.edu
    Dear Steve et al,
    I’ve been away this week until today. Although the responses so far all make valid
    points, I
    will add my thoughts. I should say I have been more involved in all the exchanges
    between
    Mike and MM so I’m probably biased in Mike’s favour. I will try and be impartial,
    though, but
    I did write a paper with Mike (which came out in GRL in Aug 2003) and we currently have
    a long paper tentatively accepted by Reviews of Geophysics. With the latter all 4
    reviewers
    think the paper is fine, but the sections referring to MM and papers by Soon and
    Baliunas
    are not and our language is strong. We need to work on this.
    Back to the question in hand:
    1. The papers that MM refer came out in Nature in 1998 and to a lesser extent in GRL
    in
    1999. These reviewers did not request the data (all the proxy series) and the code. So,
    acceding to the request for this to do the review is setting a VERY dangerous
    precedent.
    Mike has made all the data series and this is all anyone should need. Making model
    code available is something else.
    2. The code is basically irrelevant in this whole issue. In the GRL paper (in 2003 Mann
    and Jones), we simply average all the series we use together. The result is pretty much
    the same as MBH in 1998, Nature and MBH in 1999 in GRL.
    3. As many of you know I calculate gridded and global/hemispheric temperature time
    series
    each month. Groups at NCDC and NASA/GISS do this as well. We don’t exchange codes
    – we do occasionally though for the data. The code here is trivial as it is in the
    paleo work.
    MBH get spatial patterns but the bottom line (the 1000 year series of global temps) is
    almost the same if you simply average. The patterns give more, though, when it comes to
    trying to understand what has caused the changes – eg by comparison with models. MM
    are only interested in the NH/Global 1000-year time series – in fact only in the MBH
    work
    from 1400.
    4. What has always intrigued me in this whole debate, is why the skeptics (for want of
    a better term) always pick on Mike. There are several other series that I’ve produced,
    Keith Briffa has and Tom Crowley. Jan Esper’s work has produced a slightly different
    series
    but we don’t get bombarded by MM. Mike’s paper wasn’t the first. It was in Nature and
    is well-used by IPCC. I suspect the skeptics wish to concentrate their effort onto one
    person as they did with Ben Santer after the second IPCC report.
    5. Mike may respond too strongly to MM, but don’t we all decide not to work with or
    co-operate with people we do not get on with or do not like their views. Mike will say
    that MM are disingenuous, but I’m not sure how many of you realise how vicious the
    attack on him has been. I will give you an example.
    When MM came out, we had several press calls (I don’t normally get press calls about
    my papers unless I really work at it – I very rarely do). This was about a paper in
    E&E, which when we eventually got it several days later was appalling. I found out
    later that the authors were in contact with the reviewers up to a week before the
    article
    appeared. So there is peer review and peer review !! Here the peer review was done by
    like-minded colleagues. Anyway, I’m straying from the point. Tim Osborn, Keith Briffa
    and I felt we should put something on our web site about the paper and directs people
    to Mike’s site and also to E&E and the MM’s site. MM have hounded us about this for
    the last four months. In the MM article, they have a diagram which says ‘corrected
    version’ when comparing with MBH. We have seen people refer to this paper (MM)
    as an alternative reconstruction – yet when we said this is our paragraph MM claim they
    are not putting forward a new reconstruction but criticizing MBH 1998 !! We have
    decided to remove the sentence on our web page just to stop these emails. But if a
    corrected version isn’t a new or alternative reconstruction I don’t know what is.
    So, in conclusion, I would side with Mike in this regard. In trying to be
    scrupulously
    fair, Steve, you’ve opened up a whole can of worms. If you do decide to put the Mann
    response into CC then I suspect you will need an editorial. MM will want to respond
    also.
    I know you’ve had open and frank exchanges in CC before, but your email clearly shows
    that you think this is in a different league. MM and E&E didn’t give Mann the chance
    to
    respond when they put their paper in, but this is a too simplistic. It needs to be
    pointed
    out in an editorial though – I’m not offering by the way.
    I could go on and on ….
    Cheers
    Phil
    At 10:36 15/01/2004 +0100, Christian Azar wrote:

    Dear all,
    I agree with most of what has been said so far. Reproducibility is the key word. If the
    Mann el al material (to be) posted on the website is sufficient to ensure
    reproducibility, then there is no compelling need to force them to hand it out. If not,
    then the source code is warranted. Also, even if there is no compelling need to make the
    source code public, doing it anyway would clearly be beneficial for the entire debate.
    Yours,
    Christian
    ——————————————————————–
    Christian Azar

  5. Jimchip Says:

    1075403821.txt IPR Legal Advice re McKittrick says it is standard practice in Econometrics journals to give all the data and codes !!

    From: Phil Jones
    To: mann@virginia.edu
    Subject: Fwd: John L. Daly dead
    Date: Thu Jan 29 14:17:01 2004

    From: Timo Hämeranta
    To:
    Subject: John L. Daly dead
    Date: Thu, 29 Jan 2004 12:04:28 +0200
    X-Mailer: Microsoft Outlook, Build 10.0.4510
    Importance: Normal

    Mike,
    In an odd way this is cheering news ! One other thing about the CC paper – just found
    another email – is that McKittrick says it is standard practice in Econometrics journals
    to give all the data and codes !! According to legal advice IPR overrides this.

    Cheers
    Phil

    “It is with deep sadness that the Daly Family have to announce the sudden death of John
    Daly.Condolences may be sent to John’s email account (daly@john-daly.com)

    Reported with great sadness

    Timo Hämeranta

  6. Jimchip Says:

    1083962601.txt “Mike and I are not sending anything, partly because we don’t have some of the series he wants, also partly as we’ve got the data
    through contacts like you, but mostly because he’ll distort and misuse them.”

    From: Phil Jones
    To: “Tas van Ommen” , Caspar Ammann ,
    Subject: RoG paper
    Date: Fri May 7 16:43:21 2004

    Dear Tas and Caspar,

    Attached is the proof version of the RoG paper with Mike Mann. This is about 99.99%
    the final one. Mike and I sent back a few small changes to AGU a month or so ago. Keep
    this to yourself for a while yet – I would expect the paper out sometime in the
    July/August
    period.
    Many of us in the paleo field get requests from skeptics (mainly a guy called
    Steve McIntyre in Canada) asking us for series. Mike and I are not sending anything,
    partly because we don’t have some of the series he wants, also partly as we’ve got the
    data
    through contacts like you, but mostly because he’ll distort and misuse them.
    Despite this, Mike and I would like to make as many of the series we’ve used in the
    RoG
    plots available from the CRU web page. Can we do this with the series we’ve got from
    you? You don’t have to do anything, except to reply yes or no !
    Cheers
    Phil

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