Weekend reads: Journal invents time machine; endless author lists; is nuance overrated?

booksThe week at Retraction Watch featured the unmasking of the people behind PubPeer, and an editor doing the right thing following a high-profile retraction. Here’s what was happening elsewhere:

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10 thoughts on “Weekend reads: Journal invents time machine; endless author lists; is nuance overrated?”

  1. Regarding the physics paper with over 5000 authors, and other papers with thousands of authors, I would like the corresponding authors to kindly step forward to explain exactly how all those individuals satisfy the four clauses of the ICMJE definition of authorship that is applied, apparently inconsistently, by some of the top STM publishers.

    I am referring to this article:

    My claims of the inconsistency of the ICMJE authorship definitions are substantiated here:
    Teixeira da Silva, J.A., Dobránszki, J. (2015) How authorship is defined by multiple publishing organizations and STM publishers. Accountability in Research: Policies and Quality Assurance
    DOI: 10.1080/08989621.2015.1047927

    The article has not yet been published in an assigned issue with pages, so I have added the final version to my ResearchGate account:

    I wish to spur a deeper discussion on this topic.

    1. “Physics paper” vs ICMJE – perhaps the acronym is not known enough: International Committee of Medical Journal Editors. I guess the authors of the physics paper have a point when they would ask you why they should conform to guidelines set by Medical Journal Editors.

      Note also that these are guidelines, and thus any journal and any STM publisher has the right to modify those if they want to do so.

      1. Marco, thank you for the feedback. Indeed, I agree with you to some extent. Why do many of the main-stream publishers impose rules regarding authorship created by a group of MEDICAL editors? Please read the article I published carefully to notice that there is a great disconnect between what has been published by such STM publishers as “authorship guidelines” and what is taking place on the ground (i.e., in actual scientific papers). It is these discrepancies that must be analyzed in greater detail, on a subject-by-subject and even journal-by-journal basis to see if they are being applied consistently. However, at least until the recent past, at the publisher level, the ICMJE authorship definitions are inconsistent.

  2. Two small letters of mine published today may be of interest to some. Both are open access.

    Teixeira da Silva, J.A. (2015) The “black swan” phenomenon in science publishing. Journal of Educational and Social Research 5(3): 11-12.
    DOI: 10.5901/jesr.2015.v5n3p11

    Teixeira da Silva, J.A. (2015) Fair use in post-publication peer review. Journal of Educational and Social Research 5(3): 13. http://www.mcser.org/journal/index.php/jesr/article/view/7694
    DOI: 10.5901/jesr.2015.v5n3p13

    The fair-use concept was used in another recent paper of mine where screen-shots of copyrighted web-pages were used to exemplify specific case studies:
    Teixeira da Silva, J.A. (2015) Pay walled retraction notices. Bangladesh Journal of Bioethics 6(1): 27-39.
    DOI: 10.3329/bioethics.v6i1.24403

    The issue of fair-use is also an essential tool for post-publication peer review:
    Teixeira da Silva, J.A. (2015) A PPPR road-map for the plant sciences: cementing a road-worthy action plan. Journal of Educational and Social Research 5(2): 15-21.
    DOI: 10.5901/jesr.2015.v5n2p15

  3. In January 2015, a figure in an MPMI paper was questioned at PubPeer.

    Activation of the Arabidopsis thaliana Mitogen-Activated Protein Kinase MPK11 by the Flagellin-Derived Elicitor Peptide, flg22
    April 2012, Volume 25, Number 4, Pages 471 – 480
    Gerit Bethke,1,2 Pascal Pecher,1 Lennart Eschen-Lippold,1 Kenichi Tsuda,2 Fumiaki Katagiri,2 Jane Glazebrook,2 Dierk Scheel,1 and Justin Lee1
    1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, D-06120 Halle, Germany;
    2Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Avenue, St. Paul 55108, U.S.A.

    The authors, including the editor-in-chief of MPMI, Dr. Jane Glazebrook, recognized the error, and promised to correct it in February 2015.

    I was quite surprised to see that the original PDF file had simply had the incorrect figure replaced with the correct one. The PDF also includes a notice that appears in a text box at the end of the PDF file, stating:
    “In the originally published version, the Western blot panel for the Landsberg-erecta (Ler)
    genotype was erroneously duplicated and depicted as the mpk11 mutant in Figure 1D.
    The figure was changed on February 18, 2015, to present the correct compiled figure
    showing the phosphorylated forms of the MAPKs (mitogen-activated protein kinases).”

    I have some queries related to this process:
    a) Is it common for scientific journals to replace erroneous text, figures, or any other data in files (in this case, a PDF file) of already published papers? I can see that this would be a convenient solution, but is it common?
    b) Most errata or corrigenda I have seen pertaining to the correction of a figure, such as in this case, albeit in other journals and publishers, have always published a separate erratum / corrigendum, with a separate DOI. Those notices tend to be signed and dated. In all cases I have ever seen to date, the original PDF file has NEVER been altered.

    Could anyone comment on this method that appears to be used by MPMI (i.e., alteration of the original PDF files) to correct the literature.

    Those readers who are unable to understand what has been said, please compare Fig. 1D in both sources:
    New corrected PDF:
    The only evidence of the “old” version, at imgur:

    Perhaps Dr. Glazebrook would care to comment publicly on this correction policy at MPMI.

    1. Another case where an error (duplicated photos to represent different treatments) admitted by the corresponding author has simply been corrected in the original PDF file. The alarming aspect is that the original had 6 photos whereas the modified PDF now shows 8.
      Please compare “new” PDF:
      the only recorded evidence of the “original” PDF, at imgur:

      Even though a note appears in a box squashed into the bottom part of the last page of the PDF file, there is absolutely no explanation why two new photos were included, and readers would never know, except for the imgur evidence, that 6 photos existed in the original. This is worrisome. What text was modified in the main body of the manuscript, if any, to reflect these changes in the 6 to 8 photos?

  4. This may represent the first retraction of a paper at MPMI (Molecular Plant-Microbe Interactions):
    MPMI Vol. 23, No. 6, 2010, pp. 771–783. doi:10.1094/MPMI-23-6-0771.
    Evolution of the Eleusine Subgroup of Pyricularia oryzae Inferred from Rearrangement at the Pwl1 Locus
    Masaki Tanaka, Gang-Su Hyon, Toshiki Murata, Hitoshi Nakayashiki, and Yukio Tosa
    Laboratory of Plant Pathology, Graduate School of Agricultural Sciences, Kobe University, Nada, Kobe 657-8501, Japan
    Submitted 22 August 2009. Accepted 15 February 2010.

    The notice states:
    “The authors of Tanaka et al. 23:771-783 (2010) retracted this article because it proved to contain a pair of identical images that were used to represent different treatments in Figure 2A. This article was retracted on 3 June 2015.”

    This figure duplication was documented at PubPeer in May 2015:

    Very unfortunately, MPMI does not appear to follow COPE retraction policies and the whole original PDF file has simply vanished.

    1. Queries involving several MPMI papers remain unresolved.





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