Maria,
"But do "gel"-biologists, also with good criteria of quality, ask for
samples shown in a figure of a gel ? ", if the gel looks 'photoshoped',
then yes!!!
I personally think that in a situation where a referee asks for
coordinates, the responsibility and the accountability lie with the
Journal and its Editor. Aren't Editors themselves were/are
crystallographers? If they see that the referee (after receiving the
coordinates) is being unreasonable and/or goes on to publish similar
data, then the Editors need to name them and shame them.
Trust me, there is lot less trust in the bio-community than in the
xtallography community!!!
Cheers
Ravi
On 19/04/2012 17:14, Maria Sola i Vilarrubias wrote:
Hi all,
With respect to C. Groom,
"The sense I get from the small-molecule community is that they (we)
have a great degree of well placed trust and see real value in
pre-publication review of structures, not just papers - I'm sure this
is true for the overwhelming majority of the macromolecular world too".
Well, it is clear from this comment that in different fields there are
different rules... . In macromolecular Xtallolgraphy, where some
people deal with biologists from biomedical sciences, the impact of
journals is an important aspect during evaluation and, unfortunately,
pre-publication review of structures has no actual value in their
field. For a structural BIO-logist in biomedical sciences, a paper it
is not "just a paper", it is an effort of years reduced to a (or few)
paper(s). The non-structural BIO-people understand what is a Cell
paper, but not at all about what it is a pre-publication of a
structure. My thougts go in the direction of grant applications,
fellowships, promotion, all filtered by the impact factor but not by
pre-publication of structures which, btw, it is neither considered in
the h-index of a researcher.
To find a good solution is difficult. The easiest way is to ask for
coordinates and maps... which is truly uncomfortable considering the
possibility of a reviewer solving its own structure by molecular
replacement. If it is possible to generate false data, it is much more
easy to "invent" the way the structure was solved without telling
which "PDB code" (=reviewed coordinates) was used. This, together with
the trick of saying that the structure is not good enough, please
improve the data quality and, in the meantime, I publish my own one
(this time yes, it's solved by reviewer's means), is not clear to me.
I feel very sorry in being so paranoid! I understand the will of
proper revision. But do "gel"-biologists, also with good criteria of
quality, ask for samples shown in a figure of a gel ?
Best,
Maria
PD. With all this I do not want to say that the reviewer of Marc
Kvansakul's structure is going to do all this type of things, I am
sure it's a good reviewer with the strict intention to do a proper job.
On 19 April 2012 15:55, George M. Sheldrick
<[email protected] <mailto:[email protected]>>
wrote:
Colin,
Speaking as someone who has one foot in small molecule crystallography
and the other in macromolecular, I have to say that attitudes are
completely different, and that there are good reasons for this. A PhD
student or junior postdoc in a macromolecular lab may have spent the
last three (or more) years cloning, expressing. purifying and
crystallizing a protein, and it is very likely that three or more
groups
elsewhere in the world are working on the same target. Even if the
organisms are different, usually only one group will be able to
publish
in a high-profile journal, so being scooped is a major worry and
happens
frequently, even when all concerned are completely honest. A single
small molecule structure is a very much smaller part of the average
chemical PhD which often involves dozens of structures, and a
couple of
duplicated structures will have little influence on the future
career of
the PhD student.
Releasing the PDB hold on a structure just before submitting the paper
has something to be said for it. I would like to do this more
often, but
it is usually vetoed by paranoid biological co-authors. Even if one is
providing the competition with a good MR model, at least they will
have
to cite it.
George
On 04/19/2012 03:09 PM, Colin Groom wrote:
> It has always struck me as something of a surprise that
pre-publication review of structures in protein-land
differs so significantly from small molecule-land. One of the
activities
of the CCDC is to supply pre-release
CSD structures to referees, using a simple, automated system to
establish that the requestors are referees.
This avoids the need for any involvement of the depositor or
journal and
allows a centralised record to be kept
as to who saw which structures and when (although, to my knowledge, we
have never needed to refer to this).
In 2012, requests have averaged at about 5 a day, but the real figure
is probably much higher, as some journals
provide this facility themselves. The sense I get from the
small-molecule community is that they (we) have a
great degree of well placed trust and see real value in
pre-publication
review of structures, not just papers -
I'm sure this is true for the overwhelming majority of the
macromolecular world too.
>
> Colin
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[email protected]
<mailto:[email protected]>] On Behalf Of
[email protected] <mailto:[email protected]>
> Sent: 19 April 2012 13:54
> To: [email protected] <mailto:[email protected]>
> Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
>
> This is off course a valid point. A desperate graduate student
faking a
> structure risks his or hers career and reputation, while an
anonymous
> referee, "borrowing" someone else's results gets away without
any risk
> of being caught. Besides making the name of the reviewer public,
I see
> other options:
>
> 1) submit the coordinates and structure factors to the pdb to get a
> priority date as has been suggested before. Many journals require
> anyways a pdb code before acceptance of the paper. One could even
> publish this priority date in the paper in the footnote where
the pdb
> code is mentioned.
> 2) require from referees a conflict-of-interest-statement that
they, or
> close colleagues are not working on the same or a very similar
> structure. If an author gets the impression that he may have been
> scooped by a less-ethical referee, he could ask the journal to
verify
> that the referees of his rejected paper were not involved in the
> accelerated publication. If it turns out that a referee has made
a false
> statement this would clearly constitute fraud and a reason for
> repercussions.
>
> Herman
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[email protected]
<mailto:[email protected]>] On Behalf Of
> Jobichen Chacko
> Sent: Thursday, April 19, 2012 2:12 PM
> To: [email protected] <mailto:[email protected]>
> Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
>
> Dear All,
> Here comes the problem of blind reveiw, the authors are always
at the
> receving end to share all there data, results and now the full
> cordinates to an unknown person, just trusting the journal
editor. Why
> don't the journals think about making the name of the reviewer also
> public.
>
> Eventhough the persons advocated giving the cordinates, there
were cases
> of holding the paper for reveiw for few months and finally
rejecting it,
> while a very close article appeared as accelerated publn within few
> weeks of rejection of the original paper. Refer to the previous
> discussion on fake structure.
>
> Again it depends on how close you are towards the acceptance. Also
> hesitation to give away your cordiantes without any guarantee of
> publishing it in that journal cannot be considered as a big sin,
> especially if someone's graduation is depend on a single paper.
>
> Jobi
>
>
>
> On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul
> <[email protected] <mailto:[email protected]>>
wrote:
>> Dear CCP4BBlers,
>>
>> I was wondering how common it is that reviewers request to have
a copy
>
>> of the PDB coordinate file for the review purpose. I have just been
>> asked to supply this by an editor after several weeks of
review, after
>
>> one of the reviewers requested a copy.
>>
>> Not having ever been asked to do this before I feel just a tad
>> uncomfortable about handing this over...
>>
>> Your opinions would be greatly appreciated.
>>
>> Best wishes
>>
>> Marc
>>
>> Dr. Marc Kvansakul
>> Laboratory Head, NHMRC CDA Fellow
>> Dept. of Biochemistry| La Trobe University | Bundoora Rm 218,
Phys Sci
>
>> Bld 4, Kingsbury Drive, Melbourne, 3086, Australia
>> T: 03 9479 2263 | F: 03 9479 2467 | E:
[email protected] <mailto:[email protected]> |
>>
>
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