Weekend reads, part 1: Editor slams PubPeer; scientific fraud pays off

booksThe week at Retraction Watch featured yet another case of fake peer review, and a court sentence for a Danish researcher found to have committed fraud. Here’s what was happening elsewhere (stay tuned for part 2 tomorrow):

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12 thoughts on “Weekend reads, part 1: Editor slams PubPeer; scientific fraud pays off”

  1. Prof. Blatt has taken the time to carefully reflect on my comments at PubPeer, and has provided a response at PubPeer. It is worthwhile reading this reponse. To expand the discussion, I quote the response in its entirety below (also because I am not sure of how safely comments are preserved at PubPeer).

    “Dear all,
    I am cross-posting my response to Dr. da Silva (below) as a courtesy. You will find this post along with Dr. da Silva’s letter on PubMed Commons where I welcome discussion and will engage. One other note, as I received a (pseudonymous) request by email for correction of the typo in Sarkar’s name, the amendment should be online shortly.
    Mike Blatt

    Dear Dr. da Silva,

    Thank you for your comments. I am happy to discuss thoughtfully on the open forum of PubMed Commons. Like you, I reflected long and hard before writing my piece for precisely the reasons we are entering into this discussion: anonymity, fear, and scientific debate. Several of my closest colleagues expressed their anxieties that putting my head ‘above the social media parapet’ could have negative consequences for them. I, too, had my doubts but felt it important to raise concerns expressed to me by colleagues, young and old, which I share. I am therefore writing both in response to your invitation and generally to some of the comments posted to my editorial. I want to thank Philip Moriarty who I have come to know over the past week and who is much more eloquent than I could ever be, and Leonid Schneider who has shown true grace in stepping back from his initial cynicism to participate in the discussion.

    I agree with your point that we should not fear to associate our names with critical opinion and, like Moriarty, I am dismayed by the lack of appetite to engage in open debate (note my emphasis on names and open). I am also deeply disturbed by the attitude of those who think that scientific critique is a license to ride roughshod into any discussion without once considering the possibility of a wider context or background to the questions at hand. At the most trivial level, it is easy – and cheap – to extract a few lines and twist them to the ridiculous; at the most fundamental, it shows an ignorance of social norms that make constructive debate possible. It’s no wonder that my colleagues were anxious and that there is fear within the community. They fear to engage because they do not want to become targets of the vitriol that pervades anonymous social media. To my mind, this is a sign that the “patient is not well” and I agree fully with the assessments of Moriarty, Schneider and others that our current approach to scientific exchange is deeply flawed in many ways.

    So we come to your concerns: journal publication, PPPR, and anonymity. Here I must respectfully disagree with you on several points. Consider your starting premise, that “the final product, i.e. the published paper [is] the product of a failsafe process that is not meant to be challenged.” Surely, this flies in the face of scientific enquiry and one of the first lessons we all learn as students: to challenge ideas in order to progress understanding. Nor is publication a final product; it’s just the most visible at times. The real product of a body of work lies in its capacity to guide subsequent studies and predict their outcomes. As scientists, we subject our own work, and that of others, to scrutiny that either validates, discounts, or refines their outputs. The scientific literature is riddled with misconceptions, false conclusions, and ideas that failed this so-called ‘test of time’. And so it should be. As scientists, we put our work and ideas out into the community and, as a community, we improve and expand on each body of work. In short, publication is only one small step in the scientific process and always has been.

    Second, let me stress that the purpose of editorial review is to assess a body of research, its scientific soundness, and whether it is of sufficient interest to the community – and, most important to the journal readership – to justify publication. Maintaining ethical standards is, of course, part of this task, but only one part of it. Nor is is the editorial process failsafe. No journal editor is able to catch all errors, innocent or otherwise, although on the whole editors are usually pretty good at identifying problems. I agree that there is a place for post-publication critique, including an element of quality control. I stated as much in my editorial.

    What I cannot abide is PubPeer’s stance on anonymity, and I am angered by their efforts to masquerade as a site for open discussion that reflects the opinions of the scientific community. Both I consider to be fundamentally deceitful. I outlined my reasons in the editorial and these have been reiterated in several posts in response. Anonymity does not ‘level the playing field’; quite the contrary, it embeds inequality in any debate simply because one side is hidden. Furthermore, anonymity opens the door to all kinds of antisocial and nefarious behaviour. You need only read many of the comments posted in response to my editorial to see the innuendo and vitriol that was unleashed towards me as well as towards others posting on the site. Such verbal abuse belongs … well, let’s just say it does not belong in the public domain outside the schoolyard. Call me old-fashioned if you will, but in my book this is unnecessary, grubby and, what’s worse, counterproductive. For most people, the mob mentality behind this kind of behaviour is quite frightening. And like it or not, mob mentality is the framework of vigilantism. Is it any wonder, then, that so many of my colleagues, young and old, are fearful? Is this the kind of ‘scientific debate’, indeed the kind of society, we want to support? I don’t. It seems to me that anonymity in these circumstances is not the solution, but the problem. It is at the root of much that has gone terribly wrong in scientific exchange today.

    I agree that there are some circumstances in which confidentiality (not anonymity!) is necessary to protect the identities of individuals, especially of whistleblowers (I’ll come to this point in a moment). However, the vast majority of posts on PubPeer do not fall in this category, even those which highlight one or more errors in a figure. I maintain that it is possible for a PhD student or postdoc to approach a colleague, even a senior scientist, in order to point out an error, and to do so in a way that is constructive and non-threatening. This is a vital social skill to learn. I shudder to think that, through ‘social’ media, this skill could be lost to the sound bite of a tweet. Like Julian Stirling (cited on PubPeer in several posts), I have no patience with lazy or conflicted thinking, and I welcome critical analysis when presented thoughtfully. I encourage my students and postdocs to question me, and others, all the time and, no surprise, the ones who have done so have also proven most successful when they leave my lab. I think you and others have vastly overstated the dangers of retribution, in part perhaps by conflating scientific debate and error correction with whistleblowing. They are not the same.

    As for misconduct, of course whistleblowers need protection through confidentiality, but not through anonymity. Again, I have set out my reasoning in the editorial and will not reiterate here. Mechanisms are in place to provide confidentiality, in the first instance through the established channels of most journals. I agree, too, that if these fail, then there must be alternative mechanisms that allow legitimate concerns to be addressed effectively. I, for one, support efforts to ensure such alternatives. However, I do not agree that the answer is through a culture of secrecy and hearsay.

    So how do we encourage thoughtful debate? How do we enable quality control and at the same time protect whistleblowers? I don’t pretend to have all the answers, but it is patently clear to me and many others that the answer is not through a so-called post-publication peer review process that is anonymous and, for all intents and purposes, unmoderated. Again, I point you to my editorial and the three challenges I have laid before PubPeer. I believe Stell and his colleagues have a real opportunity to lead the way in raising the tenor of science in this social media age, but they must address these challenges to do so.

    Finally, to your personal critique, I appreciate that you have included reference to your own pieces, as I am sure other readers will too.

    Thank you.

    Mike Blatt”

  2. Prof. Michael R. Blatt, the editor-in-chief of Plant Physiology, some anonymous queries at PubPeer for your attention.

    MtNramp1 is required for iron uptake by rhizobia-infected Medicago truncatula nodule cells
    Manuel Tejada-Jiménez, Rosario Castro-Rodríguez, Igor Kryvoruchko, M. Mercedes Lucas, Michael Udvardi, Juan Imperial, Manuel González-Guerrero, Plant Physiology (2015)

    Fungal endopolygalacturonases are recognized as MAMPs by the Arabidopsis Receptor-Like Protein RBPG1
    Lisha Zhang, Ilona Kars, Bert Essenstam, Thomas W H Liebrand, Lia Wagemakers, Joyce Elberse, Panagiota Tagkalaki, Devlin Tjoitang, Guido van den Ackerveken, Jan A L van Kan, Plant Physiol. (2013)

    Arabidopsis RGLG2, Functioning as a RING E3 Ligase, Interacts with AtERF53 and Negatively Regulates the Plant Drought Stress Response
    M.-C. Cheng, E.-J. Hsieh, J.-H. Chen, H.-Y. Chen, T.-P. Lin, PLANT PHYSIOLOGY (2011)

    Differential Effects of Prenylation and S-Acylation on Type I and II ROPS Membrane Interaction and Function
    N. Sorek, O. Gutman, E. Bar, M. Abu-Abied, X. Feng, M. P. Running, E. Lewinsohn, N. Ori, E. Sadot, Y. I. Henis, S. Yalovsky, PLANT PHYSIOLOGY (2010)

    Hydraulic failure defines the recovery and point of death in water-stressed conifers
    Tim J Brodribb, Hervé Cochard, Plant Physiol., 149 (2009)

    Cytochrome c is released in a reactive oxygen species-dependent manner and is degraded via caspase-like proteases in tobacco Bright-Yellow 2 cells en route to heat shock-induced cell death
    Rosa Anna Vacca, Daniela Valenti, Antonella Bobba, Riccardo Sandro Merafina, Salvatore Passarella, Ersilia Marra, Plant Physiol., 141 (2006)

    A Second Kazal-like protease inhibitor from Phytophthora infestans inhibits and interacts with the apoplastic pathogenesis-related protease P69B of tomato
    Miaoying Tian, Brett Benedetti, Sophien Kamoun, Plant Physiol., 138 (2005)

    Insights into a Key Developmental Switch and Its Importance for Efficient Plant Breeding
    M. Wang, PLANT PHYSIOLOGY (2000)

    Calcium-Mediated Signaling during Sandalwood Somatic Embryogenesis. Role for Exogenous Calcium as Second Messenger
    V. S. Anil, PLANT PHYSIOLOGY (2000)

    1. One of the questioned papers has been corrected.

      Arabidopsis RGLG2, Functioning as a RING E3 Ligase, Interacts with AtERF53 and Negatively Regulates the Plant Drought Stress Response
      M.-C. Cheng, E.-J. Hsieh, J.-H. Chen, H.-Y. Chen, T.-P. Lin, PLANT PHYSIOLOGY (2011)

      “In Figure 3, the wrong insertion was used for 3D. The same image was used for both
      RGLG21-424/AtERF53 Y2H in Figure 3B and RGLG1/AtERF53 Y2H in Figure 3D. The
      corrected figure is shown below. The figure legend is unaltered from the original version.
      Similar results were obtained with each experiment, leading to a substantial number of
      similar figures. The correction does not affect any of the conclusions of the article.”

  3. PubPeer responds to Blatt’s editorial:

    In this piece entitled “Vigilant scientists”, the PubPeer position remains clear right from the first statement and PP rebuttal: “the editor-in-chief of Plant Physiology, Michael Blatt, makes the hyperbolic claim that anonymous post-publication peer review by the PubPeer community represents the most serious threat to the scientific process today. We obviously disagree.”

    It’s an essential read.

  4. Dear Mr Blatt.

    Tough. The landscape has changed. Deal with no longer being the gate-keeper and the final authority.


    Dr Avenger

  5. Actually, one could argue that Blatt is somewhat vigilant himself, especially if one reads his views about image manipulation just 2 years ago. But he is not a vigilante. It’s important to make this distinction.

    Blatt, M., and Martin, C. (2013) Manipulation and misconduct in the handling of image data. Plant Physiology, 163(1), pp. 3-4. (doi:10.1104/pp.113.900471)

    1. At PubMed Commons, I have requested Prof. Blatt to respond to three questions about vigilantism and the anonymous science movement. In order for him to do this, and better appreciate my angle, I have asked him to first view a 2015 movie on vigilantism, Cartel Land. Should he respond, I will report back here.

  6. Philip Moriarty of Nottingham University takes a firm stance at PubPeer in the anonymous debate, and states emphatically and unmistakably where he stands: “And I will continue to call out anonymous commenting when I see it. You’re part of the problem, not the solution.” He goes further. Referring to unspecified anonymous commentators as “spineless” and “grubby”. The Blatt editorial is starting to cause ripples.

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