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Retraction Watch

Tracking retractions as a window into the scientific process

JBC publisher ASBMB hiring manager of publication ethics — and why Retraction Watch is cheering

with 7 comments

We’re not generally — or ever — in the habit of running job ads here on Retraction Watch. But the purpose of this post is to highlight a new position available at the American Society for Biochemistry & Molecular Biology (ASBMB) that we think is a great opportunity and a step forward for the society.

As regular Retraction Watch readers know, we frequently beat up on one of the ASBMB’s journals, the Journal of Biological Chemistry (JBC), for publishing retraction notices that say simply “This article has been withdrawn by the authors.” We’re not the only ones; Ferric Fang and colleagues name-checked the journal’s policy when they wrote about factors that

…have contributed to the systematic underestimation of the role of misconduct and the overestimation of the role of error in retractions (3, 4), and speak to the need for uniform standards regarding retraction notices (5)

So when we had the chance to talk to ASBMB publications director Nancy Rodnan earlier this month at a Society for Scholarly Publishing workshop at which Ivan was invited to speak, we were very happy to hear about the ASBMB’s plans to add a staffer to do what it can to ensure the scientific record is even more self-correcting.

Rodnan told us that her society, like many publishers, is deluged with allegations of misconduct in its journals, many of which come from the pseudonymous Clare Francis. They want to investigate all of them, but their resources are limited. So they’ve decided to create a new position, a Manager of Publication Ethics:

This person will oversee all correspondence regarding potential misconduct in all ASBMB publications and oversee all decisions in accordance with ASBMB polices. This person will work primarily with the ASBMB Publications Director as well as with journal editors, the ASBMB Publications Committee leadership, and authors to evaluate ethical breaches and make recommendations. This is a new position requiring advanced studies in the biomedical sciences, excellent organizational and writing skills, the ability to conduct thorough investigations, regular coordination with various stakeholders and institutions, sound judgment, and some familiarity with and willingness to become an expert in libel and defamation. The ASBMB will provide training in technical areas such as the use of tools for digital analysis of figures for inappropriate manipulation and plagiarism software.

You can read the whole job description here and apply here. (Full disclosure: Rodnan shared the draft of the job description with us, and asked for feedback. We basically said it looked great, but made a few suggestions.)

In particular, we can’t help but have a glimmer of hope about one particular bullet point:

Write and/or help authors write corrections and retractions

This suggests, of course, that the society is thinking through its process and perhaps willing to consider more information in its retraction notices — a move we would be thrilled to see.

Kudos to the ASBMB, and we hope our readers will consider applying for this position, or at least forwarding the posting to other interested people.

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Written by ivanoransky

November 19, 2012 at 10:55 am

7 Responses

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  1. I agree this is potentially a significant advance. Fear of being sued must be one of the factors that makes journals avoid upsetting their authors, and having someone working specifically to deal with these cases has to put the journal in a stronger position.

    Actually JBC has already shown it is prepared to do more than most journals on this score (by enforcing retraction of the Gopal Kundu paper against the wishes of the authors and the external committee organised by NCCS, Pune). Will the Nature journals do the same? Or will they continue in their state of unconcerned apathy whereby authors can correct any aspect of their paper but still keep it, no matter how fundamental the problems are (see various recent examples of ‘megacorrections’)


    November 19, 2012 at 11:49 am

    • You mean the fact that Nature still has a fraudulent crystal structure on their books (http://www.nature.com/nature/journal/v444/n7116/abs/nature05258.html), with Nature News even publishing the results of the university fraud investigation? Here is the UAB statement on a number of the structures: http://main.uab.edu/Sites/reporter/articles/71570/

      The coordinates for 2HR0 do not form a connected network of molecules in the crystal lattice. The diffraction data do not show the features that should arise from the presence of bulk solvent, whereas the molecular arrangement indicates that large regions are not occupied by protein molecules. The values for ksol and Bsol bulk solvent parameters in 2HR0 are far outside the normally accepted ranges for these parameters. It is also noteworthy that nowhere in the Methods section of his Nature paper is there any mention of non-standard bulk solvent corrections to the Fobs values.

      The B-factors of the model do not vary significantly throughout the molecule, even though long segments of the chain are almost completely exposed to solvent (Janssen et al., Nature 448:E1-E2, 2007; note Figure 2 of their communication). The Rfree and R distributions are exceptionally low at low resolution, and the difference between Rfree and R is unusually small for a structure refined at 2.3 Å resolution with an amplitude-based target function. (Janssen et al Nature 9 Aug 2007; note Figure 1b of their communication). Dr. Murthy provided two responses to this allegation: (1) the Rfree and R distribution would be expected if X-ray terms in a restrained refinement were weighted more heavily than usual, and (2) overweighting the X-ray terms would reduce the R-value at the cost of some geometric distortion. Overweighting the X-ray terms can reduce the R-value at the cost of geometric distortion, however, the reported errors in the bond lengths, bond angles and torsion angles all suggest that the geometry was sufficiently restrained during refinement. Furthermore, many of the unrealistic contacts in this structure are far worse than simple geometric distortion.

      There are 30 chemically impossible, close contacts shorter than 2.2 Å. Despite the large number of physically impossible clashes, the deposited structure factors show remarkably good correspondence in these regions. Inspection of both the Aσ-weighted 2Fo-Fc and the Fo-Fc electron density maps revealed very well-defined electron densities in every region of bad contacts, with no negative peaks present in the Fo-Fc difference electron density map and with B-factors no higher than elsewhere in the structure. This strongly suggests that the deposited structure factors have been calculated from the structure and do not reflect experimental data. Finally, the range of values for σF is orders of magnitude too large, larger even than the range of structure factor amplitudes. Regarding this point, experimental (“real”) σF values are derived from estimates of measurement uncertainties. For this reason, their values are limited and their range is a small fraction of the range of Fo. However, the range of Fo for 2HR0 is 0 < Fo < 14,215, while the range of σ is 0 < σ < 9948. This range for σ is completely unrealistic. No raw crystallographic data, data reduction output, or any other experimental records that would support the correctness of the structure of 2HR0, or demonstrate that this was an experimentally determined structure, were available for examination.

      Pinko Punko

      November 19, 2012 at 12:11 pm

  2. Awesome, we have a blog post coming up soon about fraud in 3 papers, all in 2012, by a member of the JBC editoral board. I wonder if their ethics office will have any teeth? As for their current effectiveness, I would put JBC firmly in the “we’ll look into it, and then you hear nothing” group of journals.


    November 19, 2012 at 9:35 pm

  3. in the advert, what does “This is an exempt position” mean?


    November 20, 2012 at 4:13 am

    • It basically means that it’s a salaried position with no overtime pay. The term comes from American labour law.


      November 20, 2012 at 5:26 pm

  4. Clare Francis for MOPE (Manager of Pub Ethics)! Francis 2012!

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