[3dem] 3dem Digest, Vol 92, Issue 22
Marin van Heel
marin.vanheel at googlemail.com
Thu Apr 30 22:38:42 PDT 2015
That is a brilliant idea Matthijn! All those papers that have been
collecting dust in drawers because of %$£*&# referees...
Marin
On 01/05/2015 07:10, Vos, Matthijn wrote:
> Dear all,
>
> I would also like to propose a possible interesting idea, although we can not change the world in a day. Why not change the anonymity around during the review process of both papers and grants and in the cover letter list directly competing groups from which reviewers should preferably not be selected. With the submitter being anonymous and the reviewers known, the work is judged more by scientific value alone. With no possibility of reviewers from competing groups the danger of copying/misusing will be minimized. And with reviewers known the author could confirm that they have not been selected from the indicated pool of competitors working on the same project.
>
> Cheers
>
> Matthijn
>
>> On May 1, 2015, at 1:58, "3dem-request at ncmir.ucsd.edu" <3dem-request at ncmir.ucsd.edu> wrote:
>>
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>> Today's Topics:
>>
>> 1. Re: sharing em maps during peer-review process
>> (Friedrich Foerster)
>> 2. Re: sharing em maps during peer-review process (James Whisstock)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 1 May 2015 00:17:15 +0200
>> From: Friedrich Foerster <frifoe at gmail.com>
>> To: Gabriel Lander <glander at scripps.edu>
>> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>> Subject: Re: [3dem] sharing em maps during peer-review process
>> Message-ID:
>> <CALtyCEh4iDVez_8=5h-77hFcEmPMoertj7dRKCdKrR+0g0nhLg at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> dear all,
>>
>> thank you very much for sharing your experiences. we will then certainly
>> also follow the example of others in the field.
>> just to answer gabe's point about one potential way of misuse: a
>> high-resolution map of course greatly facilitates model building. however,
>> the resulting model will also be the best explanation for lower resolution
>> data, one just would not have found this solution. it may take a pretty
>> good reviewer to figure out that the lower resolution data do not justify
>> the correct biological conclusions.
>> So let us just adhere the ethical principles we should and share the data.
>>
>> cheers
>>
>> friedrich
>>
>>
>>
>>
>>
>> On Thu, Apr 30, 2015 at 11:46 PM, Gabriel Lander <glander at scripps.edu>
>> wrote:
>>
>>> I would like to echo Eva & Ed?s comments (I am also NOT a reviewer).
>>> Given that the EM field hasn?t really settled on a robust methodology to
>>> statistically assess the accuracy & validity of a density (yes we have gold
>>> standard FSC, local resolution plots, tilt-pair validation, etc. but these
>>> are not 100% foolproof, & there are ways to inflate resolution
>>> nonetheless), we generally rely on our eyes to ascertain the quality of map.
>>>
>>> I?m sure your density doesn?t fall into this category of ?inaccurate?
>>> structure determination, so I?m curious what you think a reviewer might do
>>> with your density to misuse it?
>>> I agree with Ed that all densities should be uploaded with a submitted
>>> manuscript, and I am happy to do this for any manuscripts we send out.
>>> -gabe
>>>
>>>
>>> On Apr 30, 2015, at 2:16 PM, Eva Nogales <enogales at lbl.gov> wrote:
>>>
>>> Hi Friedrich,
>>>
>>> We got the same request and we provided the map and model as a Chimera
>>> session to the editor and reviewer. I understand your point, but we have to
>>> trust the system and understand where the reviewers may be coming from. We
>>> do know of more than one example where having had such access may have
>>> precluded publication of some really terrible structures. It will be
>>> interesting to hear what others think (and I have no doubt the reviewer(s)
>>> that asked for your and our maps is/are within the list reading this
>>> email...)
>>>
>>> Eva
>>>
>>> On 4/30/15 1:49 PM, Friedrich Foerster wrote:
>>>
>>> dear colleagues,
>>>
>>> i would be interested in experiences / suggestions / views of others in
>>> the field on the following issue that may be of interest to many of us:
>>> the editor of our manuscript forwarded the request of a peer-reviewer to
>>> access the cryo-em map of our beloved complex. this has never happened to
>>> us, but to our surprise the editor did not consider the request to be
>>> unusual.
>>> of course, we share the point that the map would be of great help in
>>> judging the interpretation of the data. however, we also feel very
>>> uncomfortable sending the condensed result of lengthy research to an
>>> anonymous colleague, who could theoretically make considerable misuse of
>>> it. nevertheless, the policy of the journal seems to let us little choice: "Supporting
>>> data must be made available to editors and peer-reviewers at the time of
>>> submission for the purposes of evaluating the manuscript. Peer-reviewers
>>> may be asked to comment on the terms of access to materials, methods
>>> and/or data sets".
>>> in any case we would be curious whether others indeed got similar
>>> requests and how they dealt with it. a good solution for (paranoid?) people
>>> like us could be a good web-based viewer that lets others view our map, but
>>> i would not know of such a tool.
>>>
>>> Thanks
>>>
>>> Friedrich
>>>
>>> --
>>> Dr. Friedrich Foerster
>>> Max-Planck Institut fuer Biochemie
>>> Am Klopferspitz 18
>>> D-82152 Martinsried
>>>
>>> Tel: +49 89 8578 2632
>>> Fax: +49 89 8578 2641
>>>
>>> www.biochem.mpg.de/foerster
>>>
>>>
>>>
>>> _______________________________________________
>>> 3dem mailing list3dem at ncmir.ucsd.eduhttps://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>
>>>
>>> --
>>> __________________________________________________________________
>>>
>>> Eva Nogales
>>> Howard Hughes Medical Institute
>>> Molecular and Cell Biology Department
>>> QB3, Stanley Hall 708C
>>> University of California, Berkeley
>>> Berkeley, CA 94720-3220
>>>
>>> Phone: (510) 642-0557 Fax: (510) 666-3336
>>> URL: cryoem.berkeley.edu(510) 666-3334 Teresa Tucker, Assistant to Eva Nogales
>>>
>>> Professor, UC Berkeley and Lawrence Berkeley Natl. Lab
>>> __________________________________________________________________
>>>
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>
>>>
>>>
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>> --
>> Dr. Friedrich Foerster
>> Max-Planck Institut fuer Biochemie
>> Am Klopferspitz 18
>> D-82152 Martinsried
>>
>> Tel: +49 89 8578 2632
>> Fax: +49 89 8578 2641
>>
>> www.biochem.mpg.de/foerster
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>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 1 May 2015 09:58:10 +1000
>> From: James Whisstock <james.whisstock at monash.edu>
>> To: 3dem at ncmir.ucsd.edu
>> Subject: Re: [3dem] sharing em maps during peer-review process
>> Message-ID:
>> <CAPAkjLnxN9TrKuqQQZx-zKYA4Uis9CsU+1sEWX==Na2YTPh34w at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hiya
>>
>> In crystallography this happens a lot, particularly in the case of lower
>> resolution structures or where the interpretation of a critical point
>> really needs the reviewer to actually review the quality of the structure
>> and look at it - and, in support of what Eva wrote, anecdotally I have
>> heard (from authors of papers who have been the subject of such requests)
>> that some important points have been picked up as a consequence - for
>> example structures in wrong Space Groups, twinning and so on. There is
>> also often a spike of debate around this issue on ccp4bb. For what its
>> worth I've often shared coords with no issue and I guess that one has to
>> trust that most people are decent individuals who will do the right thing.
>>
>> Cheers
>>
>> J
>>
>>> On 1 May 2015 at 07:16, Eva Nogales <enogales at lbl.gov> wrote:
>>>
>>> Hi Friedrich,
>>>
>>> We got the same request and we provided the map and model as a Chimera
>>> session to the editor and reviewer. I understand your point, but we have to
>>> trust the system and understand where the reviewers may be coming from. We
>>> do know of more than one example where having had such access may have
>>> precluded publication of some really terrible structures. It will be
>>> interesting to hear what others think (and I have no doubt the reviewer(s)
>>> that asked for your and our maps is/are within the list reading this
>>> email...)
>>>
>>> Eva
>>>
>>> On 4/30/15 1:49 PM, Friedrich Foerster wrote:
>>>
>>> dear colleagues,
>>>
>>> i would be interested in experiences / suggestions / views of others in
>>> the field on the following issue that may be of interest to many of us:
>>> the editor of our manuscript forwarded the request of a peer-reviewer to
>>> access the cryo-em map of our beloved complex. this has never happened to
>>> us, but to our surprise the editor did not consider the request to be
>>> unusual.
>>> of course, we share the point that the map would be of great help in
>>> judging the interpretation of the data. however, we also feel very
>>> uncomfortable sending the condensed result of lengthy research to an
>>> anonymous colleague, who could theoretically make considerable misuse of
>>> it. nevertheless, the policy of the journal seems to let us little choice: "Supporting
>>> data must be made available to editors and peer-reviewers at the time of
>>> submission for the purposes of evaluating the manuscript. Peer-reviewers
>>> may be asked to comment on the terms of access to materials, methods
>>> and/or data sets".
>>> in any case we would be curious whether others indeed got similar
>>> requests and how they dealt with it. a good solution for (paranoid?) people
>>> like us could be a good web-based viewer that lets others view our map, but
>>> i would not know of such a tool.
>>>
>>> Thanks
>>>
>>> Friedrich
>>>
>>> --
>>> Dr. Friedrich Foerster
>>> Max-Planck Institut fuer Biochemie
>>> Am Klopferspitz 18
>>> D-82152 Martinsried
>>>
>>> Tel: +49 89 8578 2632
>>> Fax: +49 89 8578 2641
>>>
>>> www.biochem.mpg.de/foerster
>>>
>>>
>>>
>>> _______________________________________________
>>> 3dem mailing list3dem at ncmir.ucsd.eduhttps://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>
>>>
>>> --
>>> __________________________________________________________________
>>>
>>> Eva Nogales
>>> Howard Hughes Medical Institute
>>> Molecular and Cell Biology Department
>>> QB3, Stanley Hall 708C
>>> University of California, Berkeley
>>> Berkeley, CA 94720-3220
>>>
>>> Phone: (510) 642-0557 Fax: (510) 666-3336
>>> URL: cryoem.berkeley.edu(510) 666-3334 Teresa Tucker, Assistant to Eva Nogales
>>>
>>> Professor, UC Berkeley and Lawrence Berkeley Natl. Lab
>>> __________________________________________________________________
>>>
>>>
>>> _______________________________________________
>>> 3dem mailing list
>>> 3dem at ncmir.ucsd.edu
>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>> --
>> Professor James Whisstock
>> Director of the ARC Centre of Excellence for Advanced Molecular Imaging
>> NHMRC Senior Principal Research Fellow
>> Department of Biochemistry and Molecular Biology
>> Monash University
>> Clayton Campus
>> Melbourne
>> VIC 3800
>> Australia
>> Phone: +61 418 170 585
>> Website: www.imagingcoe.org
>> Twitter: @imagingCoe <https://twitter.com/ImagingCoE>
>>
>> *Join us at the 3rd Prato conference on Pore Forming Proteins, Prato, Italy
>> - 12th to 15th May, 2015: www.pores2015.org <http://www.pores2015.org/> *
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>>
>> End of 3dem Digest, Vol 92, Issue 22
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--
================================================================
Prof Dr Ir Marin van Heel
Professor of Cryo-EM Data Processing
Leiden University
NeCEN Building Room 05.27
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The Netherlands
Tel. NL: +31(0)715271424 // Mobile NL: +31(0)652736618
Skype: Marin.van.Heel
email: marin.vanheel(A_T)gmail.com
and: mvh.office(A_T)gmail.com
----------------------------------------------
Emeritus Professor of Structural Biology
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email: m.vanheel(A_T)ic.ac.uk
Tel. UK: +44(0)2075945316 //Mobile: +44(0)7941540625
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Brazilian mobile phone +55-19-983189143
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