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

The 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:

Jeffrey Beall finds a journal that has invented a time machine.
How many scientists does it take to write a paper? Thousands, apparently. Robert Lee Hotz explains.
Meanwhile, Times Higher Education says it won’t count papers with huge author lists toward its rankings of institutions.
“I said, If you’re going to write a paper like that, you should really just name it ‘Fuck Nuance’ instead.” Is nuance overrated? asks Steve Kolowich.
Is aggressive science reporting a human rights violation? asks Janet Stemwedel.
Another take on science and journalism, from Darlena Cunha: “Someone published the wrong information about his work, and when he went to apply for more grant money, his program was rejected based on the article.”
More discussion of freedom of information laws and science: “Tobacco companies should be free to use freedom of information laws even if we don’t like it,” says Nola Ries.
Biomedical institutions are feeling the heat as stars get poached in a battle for supremacy, writes The New York Times.
Recently, we highlighted a paper discussing “unfeasibly prolific authors.” Can novelists be too productive, too? Stephen King raises the question.
We may need a new way to think about conflicts of interest in science, says Austin Frakt.
Frontiers emerges from the latest round of fake peer review revelations unscathed: “Following a thorough cross-check of these names and accounts with our author and editorial board database, it was confirmed that not one of the false reviewers had reviewed for our journals,” says journal manager Gearóid Ó Faoleán.
So, you have your own lab. What’s your plan?
“The vast majority of scientific papers today are published in English,” notes Adam Huttner-Koros. “What gets lost when other languages get left out?”
“From tossing out cross-contaminated cell lines to flagging genomic misnomers, a push is on to tidy up biomedical research,” reports Kerry Grens.
Is the future of social science with private companies?
A new journal, RIO Journal, for Research Ideas and Outcomes, wants to publish your ideas, ScienceInsider reports.
An Onion classic from a decade ago makes the rounds again: “Fifth grade science paper doesn’t stand up to peer review.”
“It is quite clear that the classical peer-review system is reaching the limits of its capacity to ensure the quality of published research,” says a lab head, recommending PubPeer.
“Why is the field fraught with contradictory findings?” asks Helen Tager Flusberg of her field, autism research. “The fundamental problem is that most of the studies are seriously flawed.”
How do you approach a PI when you have misgivings about data? A guide from NatureJobs.
Concerns about reproducibility have been around since at least the 1960s, notes Paul Jump.
Want better reproducibility? Tie good institutional practice to funding, say C. Glenn Begley, Alastair M. Buchan and Ulrich Dirnagl.
Pooling imaging data? Use caution, according to a new study.
“We need to be vigilant to stop biases occurring,” says Jonathan Eisen of gender balance in science.
“To understand the replication crisis, imagine a world in which everything was published,” says Andrew Gelman.
Studies replicated in one country may not replicate in another, notes the German Psychological Society (in German).
Ioana Negru takes a look at integrity and research misconduct in economics.
The U.S. Department of Health and Human Services has proposed “the most significant change to the rules [governing human subjects research] since they were introduced in 1991,” Nature reports.
“The weird and wonderful world of academic Twitter:” Academia Obscura’s Glen Wright explores.
Scientists are hopeless communicators, says Ben Wade, and that needs to change. Some are taking on the challenge.
“When greedy publishers set up shop online, the primary goal is to publish as much as possible, often at the cost of quality.” Kailash Gupta, a former journal editor and NIH program officer, takes on incentives.
“The difference between ‘significant’ and ‘not significant’ is enough to get published in the #1 journal in psychology.” Is that the right title for this Andrew Gelman post?
“The researchers at VroniPlag Wiki have grown tired of documenting plagiarism in medical dissertations,” says Debora Weber-Wulff.
Sarah Morton says science should take a “contributions” approach to measuring impact.
As science thinks about altmetrics, it’s important to learn from the past, says Phill Jones.
Ethics, public relations and author marketing, and China were the big themes at the International Society of Managing and Technical Editors’ annual meeting, writes Ben Hogan.
The idea of being first “feeds into an image of research that just isn’t true,” says Jonathan O’Donnell.
How does rejection cloud the eyes of researchers? Phil Davis explains.
A Norweigian journalist has been caught plagiarizing The New Yorker, Debora Weber-Wulff notes.

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

Jaime A. Teixeira da Silva says:

September 5, 2015 at 1:01 pm

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:
http://www.wsj.com/articles/how-many-scientists-does-it-take-to-write-a-paper-apparently-thousands-1439169200

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
http://www.tandfonline.com/doi/full/10.1080/08989621.2015.1047927#.Va2XY68VjIU
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:
http://www.researchgate.net/publication/280445406_How_authorship_is_defined_by_multiple_publishing_organizations_and_STM_publishers

I wish to spur a deeper discussion on this topic.

Reply
1. Marco says:
  
  September 6, 2015 at 5:09 am
  
  “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.
  
  Reply
  1. Jaime A. Teixeira da Silva says:
    
    September 6, 2015 at 12:57 pm
    
    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.
    
    Reply
Jaime A. Teixeira da Silva says:

September 5, 2015 at 1:05 pm

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.
http://www.mcser.org/journal/index.php/jesr/article/view/7693
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.
http://www.banglajol.info/index.php/BIOETHICS/article/view/24403
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.
http://www.mcser.org/journal/index.php/jesr/article/view/6551
DOI: 10.5901/jesr.2015.v5n2p15

Reply
A query says:

September 7, 2015 at 4:29 am

In January 2015, a figure in an MPMI paper was questioned at PubPeer.
https://pubpeer.com/publications/B239A41839EB9A760B56564F2561AB#fb23251

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.
http://dx.doi.org/10.1094/MPMI-11-11-0281
http://www.apsnet.org/publications/mpmi/2012/April/Pages/25_4_471.aspx
http://www.ncbi.nlm.nih.gov/pubmed/22204645

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:
http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-11-11-0281
The only evidence of the “old” version, at imgur:
http://i.imgur.com/xWt4psf.jpg

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

Reply
1. Another case says:
  
  September 8, 2015 at 12:15 pm
  
  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:
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-23-6-0715
  vs
  the only recorded evidence of the “original” PDF, at imgur:
  http://imgur.com/Ufoza3p
  
  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?
  
  Reply
First retraction? says:

September 8, 2015 at 12:26 pm

This may represent the first retraction of a paper at MPMI (Molecular Plant-Microbe Interactions):
http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-23-6-0771
http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-23-6-0771
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:
https://pubpeer.com/publications/D2549ACBF89B0A7BBF12E9C755CBCD

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

Reply

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

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