“I am deeply saddened and disturbed:” Co-author of retracted Nature paper reveals how problems came to light

Ben Scheres
Ben Scheres

On Wednesday, we reported on a Nature retraction of a paper whose corresponding author had also had a Cell paper retracted, and had been found to have committed a “violation of academic integrity” by Utrecht University. Today, we present the back story of how those retractions came to be, from another co-author of both papers, Ben Scheres, of Wageningen University:

On April 24th 2013 I was alerted to a rumour about anomalies in figures of two papers on which I was an author – Dhonukshe et al., Cell 149:383 2012 and Kakar et al., Nature 495:529 2013. After verifying that figures had been inappropriately manipulated, I contacted the authors and journals involved and the Universities affiliated with the main authors. Shortly after this, an independent investigation of the Kakar et al. paper was initiated based on a complaint filed at Utrecht University by my colleagues Chris Ambrose and Geoff Wasteneys from Canada.

The Kakar et al. Nature 2013 paper contained several duplicated parts of confocal images in Figs. 3a-b, 4d-e, 4g-i, cut-and-pasted RT-PCR images and cut-and-pasted seedling images. The confocal images (see PDF) were particularly worrisome as they were not exact duplicates but shifted in view (3a-b; 4g-i) or both shifted in view and compressed in the vertical dimension (4d-e). These anomalies undermined the credibility of all data in the paper. Once it became clear that the responsible author had no credible explanation and could not retrieve primary data, it was obvious to me that the paper should be retracted. I communicated this opinion to Nature in my role as a co-author.

My colleagues abroad had, in addition, obtained contradictory results on the localization of PIN2 in clasp mutants as described by Kakar et al. This scientific discrepancy caused suspicion and made them scrutinize the entire manuscript. Hence they noted many of the figure anomalies that we independently uncovered, which were included in their official complaint at Utrecht University.

After being informed of the paper discrepancies by myself and the Canadian colleagues, Utrecht and Wageningen Universities installed a joint committee on Scientific Integrity in May to investigate the case. Their report was handed over in August, after which the University Boards circulated a draft decision. Several complaints were raised against this draft, so advice was sought from the National Scientific Integrity Council (LOWI).  The LOWI advice was returned to the Boards and considering this advice a final decision was recently published. The conclusion was that Pankaj Dhonukshe was solely responsible for the figure manipulations. The retraction of the Kakar et al. (2013) paper has just appeared online.

My decision to support retraction of both papers is based on the proven discrepancies in their content and does not rely on scientific questions of reproducibility of experiments. Neither do they depend on a judgement about the intentionality of the figure manipulations. For our scientific field, it is however of utmost importance to find out which conclusions in the retracted papers might still hold. We are currently repeating most experiments described in the Cell (2012) paper and some of those described in the Kakar (2013) paper. As soon as we have clarity on the outcome of these experiments, we will communicate our results. I hope that this will help those that have initiated research efforts based on these papers, to whom I sincerely apologize.

There are ongoing investigations into other papers (co)authored by Dhonukshe. We have meticulously scrutinized all data in the two papers of which I am the corresponding author and Dhonukshe a coauthor: Cruz-Ramirez et al., Cell 150:1002 (2012) and Prasad et al, Current Biology 21:1123 (2011). In the former paper, Dhonukshe contributed a single control experiment (depicted in Fig. 4I-K’) of which we possessed the primary data. The primary and published data matched, but we anyway repeated the experiment and it was reproduced.  In the latter paper, the final version did not contain any data provided by Pankaj Dhonukshe.  In conclusion, we have no reason to suspect data in either paper and thus we fully support their conclusions.

I am deeply saddened and disturbed about all these incidents, but I am confident that with the investigations carried out we will be able to restore the integrity of the scientific literature in our field. Finally, I thank Geoff Wasteneys and Chris Ambrose for uncovering these matters, and I am grateful for the numerous messages of support that i have received from colleagues, which have helped me a lot when dealing with these difficult issues.

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45 thoughts on ““I am deeply saddened and disturbed:” Co-author of retracted Nature paper reveals how problems came to light”

  1. “My decision to support retraction of both papers is based on the proven discrepancies in their content and does not rely on scientific questions of reproducibility of experiments. Neither do they depend on a judgement about the intentionality of the figure manipulations.”

    Something very contradictory in the above statements.

    “Once it became clear that the responsible author had no credible explanation…”

    Something very disconnect between that statement and the ICMJE definitions of authorship, including the responsibilities of authors:

    1. I understand those definitions as recommendations. I guess that is why no one cares about them, because in reality they don`t have any value!

      See the huge difference in that example:
      “It is recommended by the traffic authority not to cross the road when traffic light is red.”
      “It is prohibited by the traffic authority to cross the road when traffic light is red.”

      In my opinion experimental science needs a big change of thinking.

      1. I believe that Elsevier Ltd., specifically through Scientia Horticulturae, and specifically two of the Editors-in-Chief, Dr. Samir Debnath and Prof. Dietmar Schwarz, are questioning whether I am an author using this ICMJE definition. I believe that this is because I am a regular critic of Elsevier. I fully agree with you, Hans. A guideline is not a law, it is a simple recommendation. But you try and explain that to the world’s No. 1 publisher.

    2. I think you may have misunderstood BS…
      “My decision to support… does not rely on scientific questions of reproducibility of experiments. Neither do they depend on intentionality.”
      I think he means that the the images have been shown to be bad AND bad images are sufficient to for him to support retraction,period. There is no contradiction here at all! I would hope that anyone would move for retraction of a paper with bad images like this, independent of intention or reproducibility. He is not claiming that the data are reproducible or making a statement about intention.

      “Once it became clear that the responsible author had no credible explanation…”

      I believe he is referring to the author who specifically contributed these falsified images, PD, in the sense that he was responsible for conducting those experiments. I do not believe that this statement was intended to make the claim that BS is not responsible for the content of a paper that he is an author of.

      “Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
      In addition to being accountable for the parts of the work he or she has done, an author should be able to identify which co-authors are responsible for specific other parts of the work. In addition, authors should have confidence in the integrity of the contributions of their co-authors.”

      In fact, it appears that BS is living up to this rather well. He knew the person responsible for the figures, AND he is ensuring that the integrity of the work is valid by separately attempting to replicate it. Further, he had confidence in PD at the time. Are we to expect that every single author of every paper observes every minute of every experiment? Until we demand that, a few people will lie to their co-authors.

  2. While we welcome the reply, our worry is that none of the images used for any of his papers can be trusted. Only the obvious ‘duplicated parts of confocal images’ can be confirmed as manipulations. But if PD had just used a different WT sample as the basis for the duplications then these problems would not be revealed.

    Honesty is essential because it is simple to manipulate a confocal figure. For example, you could image one genotype and then label it as a completely different genotype. Also, you could change plane of laser, laser levels, or treatment of samples. We are being asked to trust that PD did not perform any of these other easy methods of manipulation.

    Personally, I am treating all the papers with PD as an author as suspect, and until all experiments are repeated, suggest no one use these papers as the basis for their own research.

  3. “…with the investigations carried out we will be able to restore the integrity of the scientific literature in our field”

    Is that Scheres’ only motivation behind his statement?
    His statement didn’t show any evolution in thinking. No concepts or actions which could prevent such occurences in future. The mistake was personified as Pankaj Dhonukshe to satisfy all claims and nothing more. Not very high standards in my opinion.

    1. What would you propose? It’s always a fear that a coworker could fake or manipulate data. If they do a good job of it then you are unlikely to see any discrepancy. I think we can only deter such actions. We cannot expect to detect them. (But some fakery is so crude that the coauthors are guilty through inattendance.)

      1. Yes I still wonder whether is something more than barefaced, thorough-going fraud here, at least in terms of motivation. There is a line that should not be crossed, and seems to me that PD was too proud, or desperate not to be clear about where it was. As someone pointed out at the beginning of this saga, if you really wanted to fake something why risk the detectable image manipulation? It is almost that the tragedy is in the naivety.

        Reminds me of my time as a teacher and the kind of situation where a group of kids at school doing something wrong in spirit if not in letter – one gets egged on to go a bit further and ends up getting caught, and can’t entirely why he/she got singled out (or how he/she suddenly lost all her friends). Stacks on the stupid one who didn’t quite “get it”. Also just wondering whether there are cultural issues at play here also.

        Of course, wrong is wrong, there are major implications (misleading of scientific community, granting agencies, waste of money) and this needs to be rectified, scientific standards always rigorously policed, and honest colleagues protected. I’d be pretty pissed off about this if I was a co-author!

        But just musing over what leads someone to this point, and how many with similar intent do manage to stay just the right side of the line.

        1. Great point. Since this affair broke I have read papers from both labs in which PD published his papers over the last ten years. It is pretty obvious that these labs produce data to support their ideas rather than trying to disprove a hypothesis. A great example of this approach is this paper:


          1 in 184 is representative. Hmmm, alright. Still waiting for the retraction.

          It is obvious PD thinks he did nothing wrong, as he is sure his idea was right. It is that mindset that makes me think that further manipulations are present in the papers. I imagine him working on the confocal and finding 1 image out of 184 that supports his idea. So he just uses that image.

          And lets not start on the modeling papers. I tried to read the 2012 Cruz-Ramirez Cell paper, but I must be dumb as I find it incomprehensible.

    2. Image manipulations are in part easy to detect, but figures and images are unfortunately only representations of experimental data. They are only a small piece of the whole data set, including negative results and experimental mistakes. It can be concluded that to the public unknown components from the experimental data are even more prone to manipulations than images in a paper which are exposed to the public domain. Therefore it is not known to the public and even not to the authors or co-workers to which extent these representations are based on real and reproducible data. One may assume that it is only by chance a scientist might hold a paper in hands based on valid experimental data. The example mentioned above and many other demonstrate that even in high impact factor journals this fact remains.
      One might have to realise that impact factor and awards are not measurements for quality, and one might start changing criteria for granting funds. Another point is that it might be useful to start implementing systems in scientific groups which lead to the control of all experimental data and documents (e.g. lab-books….) in studies.

      1. I am of the opinion that this is, without a doubt, the most high-profile plant science retraction to date. It thus deserves thorough examination and analysis, criticism and requests for accountability by all parties, including co-authors, not only the spokes-person, Prof. Ben Scheres. This story and these cases, possibly more, has hit the plant science community badly, and hard.

        “it might be useful to start implementing systems in scientific groups which lead to the control of all experimental data and documents (e.g. lab-books….)” This is an argument that has been around for years and years and years. One would think that as long as science has been around that such a basic requirement would exist in every lab, not only in large labs. The fact that in the early 21st century we are still calling for this to happen is a sign of how pathetically useless and powerless controls have become in science and in science publishing. Now, most publishers just request authors to tick a box on the online submission system to support the fact that the data is true and that the submission is valid. And only when the thief has been caught with his finger in the pie does the publisher then use the fact that all “guarantees” have been violated. The robotization of validity to save the publishing company time and investments is one of the reasons why the publishing system has become corrupted: simply because any T, D, or H, can tick a box and feign honesty. Publishing has always been a challenging and somewhat stressful process. But increasingly, I am feeling, at least in plant sciences, it is becoming tortuous. Massively long “peer review” processes, dysfunctional “ethical guidelines”, publishers with contradictory ethical values but who are quick to impose their ethics upon the scientific pool as they see fit for their business model, the lack of real scientifically-based controls, and the increasing reliance on computers and cheap labour in India, at least in the case of Elsevier and Springer, in dealing with quality-related issues.

        I want to focus on the issue of MONEY and the Dhonukshe-Scheres case.

        Related specifically to Scheres’ work, which is amazingly important work related to plant development, and plant sciences more broadly, my comments above do not necessarily call into question his integrity, but what he needs to understand is that when one apple in the cart is rotten, unfortunately, the cart also (usually) becomes rotten and the rot is quite difficult to contain. For a collaborative research group that has undoubtedly received ALOT of money in grants, salaries and travel funding to not have detected the shenanigans of Pankaj Dhonukshe much earlier indicates that the “collaborative” group was dysfunctional. And even though the dishonesty may have originated from a single individual, all co-authors share moral responsibility towards science and society. That is my criticism of Ben Scheres, not about him as a nice guy or about his excellent scientific past, but the fact that he seems to try and wash his hands of collective responsibility. What I am curious to know is how money that was received for funding, salaries and travel grants will be reimbursed for this flawed and/or fraudulent science? I am sure that when it was time to receive grants which had values with many zeroes on it, there were smiles all around. But what I want to know is how some – or all – of those zeroes will be returned back to tax-payers or to funding agencies who have been “ripped off”. While the focus continues to linger on the “morality” of Pankaj Dhonukshe, and the disassociation of any guilt with Ben Scheres, the truth of the matter is that ALL of these researchers have benefitted FINANCIALLY, in one or more forms, and possibly also their research institutes. It is important to understand, in real EURO values, how each research project and researcher has benefitted from these studies, including Ben Scheres, and how the research institutes they are involved with, namely Wageningen University, a premier plant science research institute, and Utrecht University, have also benefitted financially through these projects, either through private funding or through government funding. I noticed that several web-sites have assigned blame squarely on the shoulders of Pankaj Dhonukshe, and also cleared others in the team of blame, totally ignoring the concept of collective responsibility, and thus skirting the issue of FINANCIAL GAIN by all parties involved. While those who are involved in scientific misconduct get some slaps on the wrist and a “mug-shot” on RW, nobody ever asks where did the money come from, how much came in, and where did the money go? This irritates me to no end for many reasons that I will not elaborate on here, or now.

        However, for now, we, the plant science community that is being battered by another scandalous set of high-profile publications, ask Prof. Scheres, an extremely highly respected plant developmental biologist, how he plans to reimburse any or all funding that he, too, has received, in benefit of these publications and the salaries, grants and resources he has benefitted from, over years (?) of research on these projects? One cannot simply take an “ethical” and “moral” stance towards the publishing aspects, to vilify Pankaj Dhonukshe, and to expect a “case closed” stamp on this, because damage has been caused to the global plant science community, and the trust invested by society in plant science with cases like this. Science does not operate on thin air. Prof. Scheres, as well as Wageningen University and Utrecht University, and especially Pankaj Dhonukshe and other co-authors, need to quickly address the issues of MONEY, otherwise trust will rapidly be lost in their accountability and veracity of statements.

        We want to know:
        a) How much money was received by each researcher and/or institute for each project related to these publications.
        b) Who and what funding agencies have funded these projects? What is their public position on these retractions?
        c) How do all parties concerned plan to address morally addressing the issue of money. You received money, you were entrusted with it and that trust was lost. It is time to pay back that which was unfairly received.
        d) How will the authors deal with literature that has already referenced these retracted papers (Cell + Nature)? Will they take on the responsibility of contacting all of those publishers, journals and editors to introduce a correction or erratum to those papers that referenced these papers to indicate that these papers are now retracted? That would be a “morally and ethically” correct thing to do, publishing-wise, Prof. Scheres.

        As a fellow plant scientist, I am not interested in clear, lacrimal confessions and he-did, she-did accusations and finger pointing. The sadness (and deep disappointment) is not only restricted to the Scheres epicenter, it extends much more widely to the entire plant science community. I want to know how people gained from their dishonesty and how their group members and institutes also gained financially and otherwise, even if they were not “officially” culpable. This has even more importance given that Prof. Scheres is a respected editor of some leading development-related journals (so we expect full accountability not only towards the ethics, the morality, the papers, the research ethos, the quality of the research and all members of the research group, but also the financial aspects):
        http://www.journals.elsevier.com/seminars-in-cell-and-developmental-biology/editorial-board/ (still listed in this Elsevier journal as Utrecht University, making the Elsevier web-site information FALSE and thus also once again reflecting the veracity of information about Elsevier journals).
        http://dev.biologists.org/site/misc/edboard.xhtml (address correct)
        http://dev.biologists.org/content/138/2/181 (interview)
        http://www.nwo.nl/en/research-and-results/programmes/spinoza+prize/spinoza+laureates/overview+in+alphabetical+order/ben+scheres (“With a relatively small research group he has built up an impressive list of publications within a fairly short time span.”)

        1. This post, as well as my other comments, is not intended as a personal or professional bashing in any way. But given the fact that these papers are being used by potentially thousands of plant scientists around the world, given the serious potential that the “guilty” scientist, Pankaj Dhonukshe, has published so many papers on these topics, with so many high profile co-authors from so many countries, the scientific community has the responsibility of conducting its own independent analysis. The words of Scheres, of Dhonukshe, and the PR-manipulated words of the official institutes are hiding something, no doubt, or buffering something which may be much more wide-spread. That is why I have taken the initiative of doing some background searching for those who have the Sherlock Holmesian skills to look in places and ways that our regular eyes cannot see. The skills of individuals like Paul Brookes would be so much appreciated.

          Deeper, independent analysis is now also required of Pankaj Dhonukshe and his collaborators (we cannot only take the official lines spoon-fed to us by the Dutch authorities):
          http://www.uu.nl/EN/Current/Pages/Researchergrowsrootsonupperpartofplant.aspx (“This research was largely carried out in collaboration between Utrecht University (The Netherlands) and Ghent University (Belgium) with help from scientists in Japan, USA and Switzerland.”) referring to, presumably, this paper:
          How do these research ethics violations impact his other studies such as:
          http://www.hindawi.com/journals/tswj/2012/981658/ (2012)
          http://ac.els-cdn.com/S0092867412003479/1-s2.0-S0092867412003479-main.pdf?_tid=f5db03aa-b2c0-11e3-9ece-00000aacb35f&acdnat=1395602938_4e89cb09a4a8e9005cc5b969bda67665 (first, praise to Elsevier for their continued open access policy for retracted papers, although I don’t like how the authors names are covered by the word RETRACTED. Looking at the co-authorship, I would be curious to learn the exact functions of several of those authors, particularly Kakar and Prasad, which stem from multiple countries, and if they fulfill(ed) the requirements of authorship at defined by the ICMJE, which is aggressively imposed upon by Elsevier. This has particular relevance, especially for the two Japanese co-authors, considering that Japan is now starting to uncover more cases of research misconduct.).

          The following papers, all published by Elsevier journals, need very careful analysis, cross-examination and post-publication peer review:

          At Springer:
          http://link.springer.com/chapter/10.1007/978-3-642-35299-7_2 (text and figures need to be thoroughly examined)
          http://link.springer.com/chapter/10.1007/978-3-642-32463-5_16 (text and figures need to be thoroughly examined)
          http://link.springer.com/article/10.1186/1741-7007-3-11 (this one is OA)

          Astonishingly, no papers published in any Taylor and Francis or Wiley-Blackwell journals.

          I also call on public feedback from the British, Swedish, US, Canadian, Czech, Austrian, Spanish, Slovak, German, Dutch, Belgian co-authors who will carry an automatic stain due to the association. We need these opinions because we need to have open conversations about these issues in public forums for plant scientists to feel more comfortable knowing that retractions have the opportunity of serving a positive function, despite their initial negative shock, anger, dismay and sadness.

  4. Surely the glass is mostly full here? You have a straightforward overall admission that the science in this lab was unreliable, which acts as large red flag for work from this group as a whole.

    Re: JW – it’s also interesting that in hindsight people feel more confident about questioning the credibility of other papers from such a group. In my own field I’m astonished by how many times work that has been clearly shown to be unreliable (for example a megacorrection in a Nature journal) continues to be quoted for several years as if nothing was amiss. I used to feel some sympathy for labs that followed false research leads of this form but I have to say now my attitude has changed somewhat and I think to some extent those who cite and build on top of clearly unreliable work are part of the problem. If you don’t practise critical thinking and scrutinise papers carefully then you are not really thinking like a scientist.

    In most case of unreliable science we have to wait years and possibly decades for the ‘invisible boot’ to kick it out – on the grounds that it simply doesn’t ‘work’ and it is impossible to make any further scientific progress in that line of investigation. In this case the answer has come very rapidly – to me a pretty good example of science policing itself. I don’t think we should be overly concerned about getting into the psychopathology of who did what, when and why in such cases – that’s for employers to deal with.

    1. Rational thinking and rational science is becoming a rarity. The concept that the literature is self-correcting is dead. The concept that science will somehow police itself is equally dead. The retractions you are observing, and will continue to observe for some time yet, are pseudo-barometers to deflect a deeper reality of the failure of the publishing world. This is because the external driving factors and forces greatly outweigh the intrinsic value of any content within a scientific paper. 10-20 years ago, I would have agreed that these classical notions of credibility were true, and 100 or even 500 years ago, the power of the scientific message lay within the hands of the scientist himself or herself (most likely the former, indicating that gender-imbalance has most likely been a stay-fast over centuries in science). But that control has been lost. Puppet masters have now become the puppets. Scientists are being treated as a carcasss between a pack of 12 yapping hienas.

      1. I agree to some extent and am also concerned about the future of science. I have personally witnessed the cover-up of scientific fraud on a large scale, and have seen how those who undertook it still continue to pollute science. Retraction Watch reports on many more analogous stories, and of course there is the huge iceberg of fraud that never comes to light. Parasitic journals are proliferating across the globe which operate no peer review, and we know of several citation cartels involving more than 60 journals now black-listed from having an impact factor.

        But science has always been prone to such dark forces or ‘hyenas’. The problems one hundred years ago facing science were quite different; for example, Darwin’s evolutionary ideas were misinterpreted by many and converted into valueless prejudiced accounts of ‘races’ (published in Science and other ‘journals’) and eugenic practises lasting until the 1960s in Europe. Ethics was almost non-existent – prisoners used to provide most of the ‘volunteers’ for experimental work undertaken at Johns Hopkins. Are things really so much worse now? We still have many rocks of good science – universities and funding bodies which do support good science, journal editors and reviewers who can rank and support good science, and societies and organisations which maintain standards. It isn’t time to pack up our tools quite yet…

    1. The confocal is not a problem by itself but when is the only technique used in a paper the possibilities of data misinterpretation are high. It is really easy to open the microscope pinhole to go far and out of the laser resolution to obtain the image needed for a figure. I mean, I only know one group that do this type of experiments as blind interpretations about samples without labels (using only a random code) and with different persons in different times, indeed in different microscopes. Also when a protein-protein interaction is described in a paper, is almost always demonstrated in many ways (Y2H, CoIP, pulldown etc) and not only with the confocal (FRET, BIFC). In my opinion the huge productivity in these groups relies at some extent in their extremely specialization in only one technique and in only one plant tissue (roots) that gives always “nice pics for covers”. As JW commented this pubpeer entry is the perfect example of how these groups do their research: https://pubpeer.com/publications/B5B747042EF3AA0864621F6033F6F1.

      1. A tool or a technique is nothing, it is useless, without an operator. Do not blame the tool. Blame the operator. Operators use tools to seek answers to hypotheses, to prove or disprove them. Even in cases such as modeling where millions of cycles are performed by equations within a machine, both of which are (hu)man-made, it is the operator (i.e., scientist) who makes the final interpretations. This has been a standard truth of science, independent of the level of perfection of the tool, or even the existence of technology. Corn or wheat (sensu lacto) most likely could have been classified as such by farmers 1000 or 2000 years ago without the need for fancy tools, deep science, or hi-tech techniques. The fact that Dhonukshe et al. used confocal microscopy, despite its weaknesses (and pre-supposed strengths), and other hi-tech techniques, is not an excuse to have abused the technology for a stated (or unstated) purpose. The real danger behind this story, and these two retractions in particular, is that the pool of experts available to detect the misconduct or errors is becoming increasingly smaller as the pool of specialized techniques expands. That si why the publishers, Elsevier (Cell) and Nature Publishing Group / MacMillan (Nature) have the responsibility of releasing the peer reviewers’ reports, so that we, the scientific community, can better understand why these errors were not detected by apparent “specialists” and “peers” during the apparent quality control step, i.e., peer review. The only reason why such peer reports will most likely never be released, even by such high IF journals, is to avoid further embarassment and public damage to their images. Who were the peer reviewers? Was the peer review process blind, or double blind? Which editors were in charge of oversight and quality control? Which was the confocal microscope expert that was in charge of these two papers? Post-publication peer review in plant science needs, very urgently, the increasing input of more and more specialists, as I have indicated before here (http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00485/full), not only to address the complexities at the higher levels of science publishing, such as in these cases, but also to deal with the great injustices taking place among lower and medium ranked journals. The saddest part is that many members of the plant science community consider exploring the already published literature, through PPPR, not only as a waste of time, but as some sort of a treasonous act, either against their peers, their colleagues, the publishers, or even science. The culture of “nonsense” in thought patterns is slowly encroaching upon the culture of “logic”. Fear based on ignorance and short-sightedness is what is limiting, right now, the correction of masses of problematic papers in the plant science literature. As long as I have air passing into and out of my lungs, and the vision to see my PC screen, I will continue to openly criticize the plant science community for not doing more, collectively, to assist in this project to re-examine, and correct, the entire plant science literature.

  5. After I published my statement about the Nature 2013 retraction last Wednesday, 19th March 2014, Ben Scheres published a piece on Retraction Watch on Friday March 21, where he gives his statements. However, his statements contain several incorrect formulations which I want to explain by providing the facts and commenting on each of his statements. Please see the two PDFS- (i) ‘Pankaj Dhonukshe responds to Ben Scheres’s published statements on Retraction Watch‘ in which I comment on each of Ben Scheres’s statements and (ii) ‘Attachments mentioned in the text‘ where all facts incorporated in the comments are shown.

    1. I am following this story very carefully because there are many lessons to be learnt by plant scientists, whether senior lab PIs, or lower-level post-docs or even undergrads who are co-authors due to their contributions to a paper. I have read quite thoroughly the defense letter that Dhonukshe has posted on another blog, with a comment-by-comment rebuttal to Scheres’ comments. This is highly commendable as it provides the public valuable clues, though e-mails, and the rebuttals themselves, that there are conflicts, contradictions and problems that underlie some cleverly crafted statements made by Utrecht University (UU) and Ben Scheres. IT also exposes increasing number of gaps and unresolved issues that make the background of this saga far from understood, and extremely far from being resolved.

      I have concluded, from what you have stated, the following, and also have extended queries which are at the moment the “black box” of this case:

      a) Prof. Scheres is skirting his inherent responsibility as a co-author of these papers, and thus the ICMJE definitions of authorship.

      b) You were in fact not responsible for the assembly of figure plates, and that a team at UU was involved: “experts from biology department of Utrecht University in a multistep-multipersonal process.” Please list the EXACT individuals who were involved.

      c) You claim that you missed the “duplications” and/or “manipulations” to figures, which seems fair considering that you did not assemble the plates. In that sense, all co-authors, including Zhang, Kakar, Scheres, Ambrose and Wastenys, Friml all to come public and respond and give their interpretations, too?

      d) Kakar seems to be a key linking person, yet I have yet to see any public statements by this individual. What was their exact role in the research of all of the papers you have co-authored, including other non-retracted papers? Perhaps you, Dhonukshe, could also provide much more detailed insight about ALL of your papers, including your recent review(s) exclusively with Kakar, which did not include Scheres, Ambrose, or Westenys. Were those reviews written as a form of “personal and professional revenge”, suggested by the dates of publication and the dates of the story listed in your documents?

      e) Could the exclusion by Scheres’ in the repeating experiments be to prove/disprove that the repeatability of the methodology was related exclusively to you, Kakar, or Zhang (assuming that the latter two have also been excluded from the repetition trials)?

      f) Assuming that none of the documents, statements, or e-mails contents have been tampered with, indeed, one could surmise that Scheres might be making a number of incorrect, inconsistent, contradictory, and even false statements. What is the personal interpretation (Dhonukshe) given to these cases? Why do you think or believe such contradictions exist, or were made? We would also need Scheres to stand by his statements, or correct them, if he feels that they did not reflect what he really thought at the time.

      g) It appears as if Scheres has maintained his position at Wageningen University, but you (Dhonukshe) have none at the moment. Is this a fair and correct assessment? What about Kakar and Zhang?

      h) As for the retracted Cell paper, what do all the other co-authors, who also share in the collective responsibility of this paper, and all its content (including its good points and faults), think? Specifically I mean: Daan A. Weits, Alfredo Cruz-Ramirez, Eva E. Deinum, Simon H. Tindemans, Klementina Kakar, Kalika Prasad, Ari Pekka Mähönen, Chris Ambrose, Michiko Sasabe,Guy Wachsmann, Marijn Luijten, Tom Bennett, Yasunori Machida, Renze Heidstra, Geoffrey Wasteneys, Bela M. Mulder. If one tracks these names in common science data-bases, it will reveal that some of these individuals are amongst the top-tier of plant developmental scientists and molecular biologists. Their silence will not advance the plant science’s understanding of how such small errors can lead to such massive consequences. I encourage you to contact them all individually, and request them to come out in the public, so we can have more discussion. I suspect that because you are publically publishing private communications (e-mails and others) that your co-authors, some of whom it seems you never met ever, will be reluctant to comment, respond, or provide comment, much less publically. But you never know until you try. I think a sincere plea at transparency, rather than a plea for understanding and forgiveness, would yield some interesting results.

      i) It is clear that your career is at a cross-road. Unlike Scheres, who has an established career and who has a long track record to defend his “relative innocence”, most of your own published work is related almost exclusively to Scheres, indicating that you have more to lose. While the “institutional” frame-work is clearly in place to defend Scheres, or at least to exclude him from any misconduct (thus ignoring his collective responsibility as a co-author), in the absence of any clear evidence of direct misconduct by him, or others, it is obvious that all blame will fall squarely on your shoulders.

      j) This statement is massively disconcerting: “Significant differences in methodology (Wasteneys-Ambrose used ‘cut roots’ and we used ‘roots intact to plants’) can lead to scientific discrepancy.” If such a tiny difference is calling into the scientific integrity of the paper, then I would say that 99% of published plant science is subject to “questionable” scientific discrepancy. I do admit that tissues in planta and tissues excised from the plant could result in quite different results, depending on the analysis, methodology, etc.

      k) Money. How exactly were the funds used? In addition to those “research grants”, were you also receiving scholarships, salaries by UU or any other source? Were these results, with or without figures, the subject of any presentations at national or international meetings, and if so, which? In those cases, would you be willing to indicate who funded the travel expenses, accommodation and daily expenses? Considering that two retractions have taken place, that this has been declared as misconduct by official investigating bodies at UU and LOWI, by Scheres, your co-author, by the editor boards of Cell and Nature, and thus by the wider scientific community, do you think it is right, and fair, to return part of your research grants and benefits to the European tax-payers? If retractions are supposedly about doing the right thing and correcting the academic record, then surely this must also be accompanies by an equivalent correction of the financial record, considering that research does not take place from fresh air.

      l) In your opinion, or from your knowledge, how has Scheres or any other co-author benefitted, financially, or otherwise, from the publication of the Cell and Nature papers, apart from their high-profile nature? For example, was the job at Wageningen University, and change from UU, which I assume to have been the equivalent of a job promotion, with better salary and perks, linked in any way to these two papers? Are you aware of a pay-for-impact factor scheme at UU or any university of any co-author? In other words, is there a specific financial remuneration based on an IF score? If yes, please provide details. Do you believe, at base, that Scheres’ sudden interest in becoming the corresponding author on May 9, 2013, may have been related in any way to a “gaming of the system” for personal or professional interests?

      m) Your statement about Scheres’ previous publications is really disconcerting, and worrisome: “similar anomalies found in some of Ben Scheres’ other papers (please see pages 12-19 of ‘Attachments mentioned in the text’) where I am not a coauthor or a first or last author should come into question and investigation”. The proof you provide in pages 12-19 of your Annex are pretty consistent with apparent figure manipulations, at least at the same level as those which led to the retractions in your Cell and Nature papers. What does Scheres and his co-authors say about the claims you make about the following papers?:
      Cruz-Ramírez et al. Cell. 2012 Aug 31;150(5):1002-15
      Cruz-Ramírez et al. PLoS Biol. 2013 Nov;11(11):e1001724
      ten Hove CA et al. Curr Biol. 2010 Mar 9;20(5):452-7
      Willemsen et al. Dev Cell. 2008 Dec;15(6):913-22
      Laskowski et al. PLoS Biol. 2008 Dec 16;6(12):e307.
      Wildwater et al. Cell. 2005 Dec 29;123(7):1337-49.

      n) Ben Scheres states: “After being informed of the paper discrepancies by myself and the Canadian colleagues [Ambrose, Wastenys], Utrecht and Wageningen Universities installed a joint committee on Scientific Integrity in May to investigate the case.” Can you please indicate the EXACT individuals who formed this “committee”. If the individuals are known, which they should be for transparency, do you believe, or do you have concrete proof, of any conflicts of interest that such individuals may have with Scheres, Wastenys, Ambrose, any other co-author, or official Belgian or Dutch authorities? Is that committee the same as the “Utrecht University’s Technical Committee”?

      It is obvious that mistakes were made, and while some co-authors are willing to take responsibility, others are not. A paper is not the creation of a single individual, unless some others lied about approving the paper and taking public responsibility for the data* and all its content, upon submission to a journal, which in itself would be a serious ethical faux-pas. It seems as if Dhonukshe has been quite sincere and forthcoming in his self-defense in response to what he claims is misinformation by Scheres. Yet, what Dhonukshe needs to understand, as do all of the co-authors, that this case is not just about their positions, their self-centric reputations or salaries, it is about science’s integrity and the honesty and transparency of the entire process leading from the lab, up until publication and, in unfortunate cases, up to a retraction. Considering that Dhonukshe has been quite revealing in his statements and documents, it would be important to go the extra mile to comment on the a)-n) statements above. The plant science community is (or should be) watching this case extremely carefully. How all players (not only Dhonukshe, but also Scheres, Ambrose, Wastenys, their universities, the publishers, ethics committees) proceed and respond, privately and in public, openly, or secretly, will have massive repercussions for the plant sciences and publishing, particularly at high levels. If we, for one second, feel that there is lack of transparency, lying, falsification of statements, manipulation of positions for personal or professional gain, or any other marginal or tangential misconduct-like actions, then faith in the whole system will be lost. From that day on, the system will be gamed and manipulated as never before in the history of plant science. Guaranteed. The ball is in your (collective) court.

      *From http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html:
      “The ICMJE recommends that authorship be based on the following 4 criteria:
      • Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
      • Drafting the work or revising it critically for important intellectual content; AND
      • Final approval of the version to be published; AND
      • Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.”

    2. Your response to Dr. Scheres indicates that you believe that he should share equally in responsibility for these retractions/botched images/questioned data. Your response also admits that, on at least some level there was something wrong with these papers, and that you, as an authors are responsible. Therefore, some folks might appreciate it if you, rather than simply rebutting Dr. Scheres, actually told your story, explained explicitly how these bad images came to be, possibly provided repeated versions of the data that was lost, and accepted explicit, personal responsibility for the errors. Further, it might be worthwhile to discuss the exact process that Dr. Scheres would have had to go through to discover that the images were in fact bad. While all authors are responsible for a paper to some degree, it is, quite literally, impossible for every author to absolutely guarantee that another author doesn’t cheat. In the simplest manner, if I take a picture of a XX1 mutant and label it as YY2, unless someone physically observed me doing this, they would never know. As science presently operates, this is pretty much impossible; we don’t incarcerate a classroom when one student steals another’s lunch money.

      1. QAQ, I am not against your logic, or your critique, at least to some extent. Dhonukshe made mistakes, he has admitted these, openly and in public, to committees and to co-authors, so let’s fairly listen to what he has to say because all stories and cases have multiple valid voices and opinions. He (and his colleagues) still has several important questions to answer, in my opinion, and amends to make, before this case can be considered closed. The retraction, in my view, is only the start, not the closure. I also believe, quite strongly, and I do not know this individual in any capacity, and thus share no COIs, is that, compared to many who have been accused of misconduct on RW, through a retraction, Dhonukshe has actually been quite forthcoming and open. He has not threatened RW with a law suit, he has provided responses (thus far) quickly and in a timely way, and he has simply rebutted what he has perceived as being wrong. I think there is no need to flog a dead horse, so what the scientific community and society should now do is to guide Dhonukshe out of this difficult situation, using his ability to answer to the truth, and apparent desire to get all the facts out as truthfully as possible. Either this, or face having a highly enraged and embittered scientist among the ranks of jobless, which has the potential to be dangerous (at many levels). I think some of the psychologists on this blog should provide their interpretation of the risks, please. Therefore, may I suggest that we lend some credence to Dhonukshe, at least initially, and, for a second, actually believe that some of his claims might be true. This means that Scheres, all Dhonukshe’s other co-authors, UU, and all other parties that have been involved in these two papers and in Dhonukshe’s scientific career to date have the responsibility of coming forth and providing their opinions and a balanced, open and transparent discussion. Answering questions a) to n) above, fully, and not selectively, would be the first test that amends are being made in the name of science and correction of the scientific record, and not in the name of their own personal interests. Of course, this might not happen, but this is what should happen. If this could actually (hypothetically) happen, then there could be a truth and reconciliation phase, mistakes could be corrected, unfairly received money could be returned, even if proportionally, and maybe, just maybe, something positive could emerge from these battle-scarred players, namely greater caution, better ethics, stronger rules, more check-points, greater accountability.

        QAQ, I disagree with two statements you have made. Firstly, there is absolutely no evidence that suggests that Dhonukshe expects Scheres to share EQUAL responsibility, although, theoretically, he should, since he is the senior advisor, so if his control of his student wasn’t rigorous enough, then this shows, to some extent, the weakness of the supervisor, or PI. Although it is true that it might be difficult to stop (or detect) someone who purposefully wants to be dishonest, there are several clues dropped by Dhonukshe that suggest that this is NOT the case, including the fact that the misconduct-related, manipulated figures were in fact NOT assembled by Dhonukshe, but rather by a UU technical team, which would imply that, post assembly of those plates, that ALL co-authors in fact, from that point on, shared EQUAL responsibility, 25% for each author (as there were four in the Nature paper). The comparison with lunch money is inappropriate: “we don’t incarcerate a classroom when one student steals another’s lunch money.” Firstly, this was not theft, so the comparison is incorrect. Dhonukshe is not a thief. Secondly, these are not students or children. They are adults, so the responses between them will be clearly quite different because the high-stake consequences would be quite apparent to all players. A key question is, did Dhonukshe willfully manipulate the images when he seems to have proved that in fact it was not he who manipulated the figure plates? Would Dhonukshe be so stupid, to be blunt, to do that, knowing the high-level risks? And actually, where I came from, when one child in the classroom was really naughty, the entire classroom would be punished. What this then did was inculcate a sense of common classroom responsibility, as well as personal responsibility. Seems like the school system may have changed (for the worse)…

        In summary, let’s give all players more time and a fair chance to fill in all the gaps.

        1. I would caution against using the argument “he seems to have proved that in fact it was not he who manipulated the figure plates” as a basis for a defence of PD. Please show this proof.

        2. Dhonukshe said that all authors should “jointly” share responsibility… I imprecisely paraphrased this as equally… apologies.

          As far as the lunch money, yes, it wasn’t the perfect analogy. I’m sorry that you had mean teachers.

          I think we both want generally the same thing: to give all players more time and a fair chance. I was concerned because the way I personally read the statement from Dhonukshe, it was more of an indictment of the coauthors and a rebuttal to accusations than a direct account of what happened. I think that all would be well served by an account of what happened from his point of view in narrative rather than a rebuttal. I was trying to make the case that a scenario that’s mostly his fault is possible, as well as one that’s really a group fault. With more explanation, perhaps we’d all be better off…

          1. QAQ, please don’t take the issue too personally. I am neither defending nor attacking PD, or you. I am simply trying to induce as much information from him, and all other parties involved, as possible. I think you and I sit on the exact same page when it comes to what we are demanding from all players in this case, i.e. full transparency and all the facts. Once again, without appearing to defend PD, I imagine that being in his situation, a calm narrative would be almost impossible. Probably all fangs are bared and he clearly wants to show the cold, contradictory facts and bring some shame to the other side of the fence, i.e., basically all other players in this saga. I imagine that trying to report the contradictions made by senior plant scientists must be an extremely frustrating thing when one is under the dissecting miscroscope…

    3. Bravo, Dhonukshe! You are posting those emails on a public site. Is it allowed? Some of those emails are confidential, right? Is it legally allowed?
      Interesting to read Nature’s response (Deepa Nath?) to Dhonukshe’s email – this is a serious issue and the response appears to be immature.

      1. The examples of alleged data manipulation in earlier papers by Scheres (papers where Dhonukshe was not an author) provided in the document by Dhonukshe need further investigation.

      2. I can’t comment on laws outside of the US, but within the US, and I would assume in most other cases, very few communications are truly privileged. In the US, that would generally be limited to medical records/patient data, legal counsel and government classified or court sealed information.

        If you communicate with someone, via e-mail, voice or written word, no matter what you tell them, they are free to share it with whomever they please (except in the previously mentioned circumstances). Private communication is only private in so far as both parties choose to keep it private. Sending someone an e-mail is like giving them a letter. You can’t expect them to not show their friends. (At least in the US for non-privileged information,) disclaimers at the end of e-mails saying that it’s only for the intended recipient are entirely meaningless (except perhaps to make it explicit that a conversation was occurring between an attorney and client).

        1. QAQ, for non-US citizens, this is a really fascinating piece of evidence. I have been ripped apart for sharing e-mails, even when the e-mails are carefully edited out (on select occasions). Can you please provide some web-links to the actual laws that support your claims that it is NOT illegal to share “private” e-mails, i.e., between two individuals or two parties. What if the disclaimer requests not to share? This is really important because several of the “ivory tower” editors and publishers I am now wrangling with about numerous issues are from the US, so I need this law in defense of my exposure of their shenanigans. In addition, if any other RW commenter could provide the links to the laws that indicate that publically sharing an e-mail between, very broadly, “two parties”, in countries in the developing world, particularly Japan, the EU, Australia, and then also big players such as China, India, or Brazil, this could be extremely beneficial to many who are whistle-blowers. The problem right now is that most science whistle-blowers don’t know the legal limits of their actions, so this uncertainty limits how far they are willing to push their limit. When providing this information, it would also be important to indicate the limit between sharing e-mails publically, as you allude to, as being free, and fair play, or being libelous, and exposing, as what I think KK was alluding to? In other words, was PD’s public posting of the e-mails meant to publically embarass Scheres, or simply to show his contradictions? It would be useful to get a pro-bono lawyer’s opinions here, too.

          1. To clarify… If you have signed a condientiality agreement, you could be civilly liable as well. I was talking about a situation in which either 1) the sender asks the receiver to keep the communication confidential but the receiver had not agreed to this explicitly 2) a formal agreement was not reached.

            Also, I think that contracts to break the law aren’t enforceable, so if we have a confidentiality agreement and I send you an email telling you how I’m going to defraud the government, you can publish that.

          2. QAQ: I applauded PD’s courage to publicize the email communications he had (including the one with Nature). Usually some emails are confidential. people can take legal actions. Thanks JATdS – we need to know where to get legal clarifications on this.

  6. I have also been following this with interest for its broader implications, and add/reiterate a few points that emerge from the Dhonukshe explanation and rebuttal.

    1. The “self refining nature of science” may well be something we can all have faith in, but Dhonukshe seems to be invoking this as a reason for not being particularly concerned with the quality of what is published. Oh well, it was wrong, science will correct itself, seems to be the fundamental attitude. Dangerous in someone with aspirations to be a scientific leader.

    2. “2 out of 180 images” it is clear that there is a large amount of information crammed into these big papers, and I am sure it all gets quite complex. However, I do not think it appropriate to use this as an excuse of reason for why mistakes have been made. IMO once you enter such a high-profile forum the onus is on you to conform to those standards. Yes it might demand more than the usual degree of care, but that is (a) the nature of your field and (b) the arena that you enter when you aspire to publish these massive high-profile papers . In fact (at least from my more lowly perspective, it would seem that the elite nature of these journals is all the more reason that we should all be able to hold those who publish in them to the highest possible standard. It seems to me very much like a politician seeking to downplay their corrupt or criminal behaviour as resulting from the stress of their job.

    3. “multiperson and multistep” It is easy to see how mistakes can be made in complex processes. But this is not good enough as an explanation, and I think my argument from (2) above also applies here. Everything is based on the images in these papers, and yet the authors delegate the responsibility of compiling/editing/assembling figures to a non-scientific team? Something rings hollow to me about this. If Dhonukshe values transparency and honesty the way he claims to, then he needs to dig a bit deeper and come clean on where the real, actual responsibility for this problem lies. Maybe what is claimed about other Scheres papers is true, and Scheres himself needs to be held to account for other anomalies, but that is a separate issue and should not be used as a distraction or smokescreen or justification for these specific problems.

    4. “copied and mislabeled” ” the responsible author” Following from above, I think it is significant that the claim here is that two separate mistakes were made. It is claimed that the image was copied incorrectly (portrait to landscape) but also mislabelled. This is plausible – although the change in dimensions is not exactly as predicted so cropping and alignment must also have been done. Did the image processing staff make both mistakes? If there is any question that mistakes may be made during this process (as Dhonukshe is aware by invoking the “thousands” of images), do the authors check to see whether the correct versions of their own images are returned to them in the processed, assembled images? PResumably the image processing staff are not having scientific input not credited as authors themselves. At least one of the authors must have looked closely at these figures after processing/assembly, because it was presumably at that point that the arrows and labels were added. In other words, EVEN IF the image processing facility made the two mistakes asserted by Dhonukshe, is there not still the implicit admission that the authors have lost track of their own data such that they do not even recognize whether the appropriate image (i.e. the one that they selected out of hundreds, intended to have shown in the figure and presumably communicated in an original powerpoint or PDF document to the image processing facility) was even shown in the final product? This is almost as concerning as deliberate manipulation.

    5. “to eliminate another member of scientific community” “selective, forced removal” Dhonukshe seems to feel that he is being victimized, by the fact that other authors went to Scheres behind his back. True this is not quite the standard protocol if you are simply questioning unrepeatable results, and suggests that Wasteneys and Ambrose may have had some other/prior reason to doubt Dhonushke’s veracity, such that they believed that there was no point in their dealing directly with him. I could imagine that this might relate to direct experiences/observations of Dhonukshe’s standards and practices. In that case, it seems reasonable to approach first or at least inform the (other) senior author on the paper. However, the fact that they did not, still does not mean it is the conspiracy Dhonukshe suggests it to be. Co-authors will talk to co-authors, that is natural. As JATdS also observed earlier, it would be interesting to hear from all other authors on this – why did Scheres and Wasteneys close ranks and submit an official complaint, rather than discussing the matter with Dhonukshe first? Scheres and Wasteneys should provide a justification for this, because without it, the charge of victimization has some validity, and if it is indeed victimization, it is shameful.

    6. “not being familiar with guidelines about presenting gel data” in 2012 this is not an excuse for anyone trained in and publishing in molecular biology. I am curious as to whether Dhonukshe did the splicing himself, did not notice these were spliced, or noticed and did not think it was wrong, or noticed and did not think it was significant that it was wrong. Not clear from his statements.

    7. “shows that similar mistakes can occur in case of other researchers” A detailed account of who was responsible for what should be provided, and given the way this has unfolded, I suggest this should come from Scheres.

    1. Girasol, excellent points. I guess the main point, as you so succinctly wrote, was “once you enter such a high-profile forum the onus is on you to conform to those standards”. This sort of reminds me of the arguments made by a certain Dr. Vinoo Cameron, MD, on Beall’s latest story: http://scholarlyoa.com/2014/03/27/new-oa-publisher-the-council-for-innovative-research/#comments
      Does the fact that this individual, who has quite radical ideas about the prime number 19, who is described as a ”Christian Physician Mathematician” (http://americanloons.blogspot.jp/2013/05/554-vinoo-cameron.html), and who publishes also in “predatory” OA journals (http://www.sciencepub.net/nature/ns1102/009_15631ns1102_51_52.pdf) make him less subject to scrutiny than Scheres or PD? I think not.

      As I have expressed elsewhere, just because a paper was published in a low level journal does not mean that it should avoid scrutiny. If anything, it should attract greater scrutiny, or at least encourage equally meticulous scrutiny at higher and lower levels. Overall, alot of pertinent questions have been posted publically above. It is not like Scheres et al. or PD et al. are not aware of RW and this blog story, so they are now under even greater pressure to provide responses. This story cannot afford to fall into the deep RW archives. We need to keep tabs on all players in this story and keep up the pressure for answers.

      If we don’t get answers, the risk is very practically real. Basically any person in plant science, at least, in the future, can simply turn around and say, to any critic in academia, as a defense of their misconduct, “well, if a plant scientist who published in Nature or Cell didn’t have to answer to public queries, then neither do I”, or “if Scheres, Ambrose, Wastenys, Dhonukshe or others, who published with the best publishers, namely NPG/MacMillan and Elsevier, did not have to be held accountable to scientists’ queries, then why should I?” Extremely irritating, but perfectly valid excuses if we don’t get responses to ALL of our queries. And hence, the endangerment of plant science’s integrity.

      Apart from the “ethics”-related issues, I am particularly curious about the financial issues as these projects have been extremely well funded. And, so far, I have seen ZERO transparency about this issue which ALL co-authors benefitted from.

    2. “Scheres and Wasteneys should provide a justification for this, because without it, the charge of victimization has
      some validity, and if it is indeed victimization, it is shameful.”

      There is a point beyond which all this should stop. There might be many issues upon which
      Scheres and Wasteneys should provide justification, but is is nonsensical to question them on endless issues. Dhonukhse cannot insinuate ad-infinitum that some scientists are less questionable than others.
      Scientific community is a highly competitive environment, scientists fight each other for academic credit and
      funding. Therefore it their best interest to question and scrutinize each other
      published work, and Scheres and Wasteneys cannot be excepted from this rule. According to Scheres this is exactly
      what happened in the case of Dhonushke : he did published a scientific result which was not reproducible but other
      group of scientists, and they did their best to understand
      what could explain the difference by focusing on what Dhonushke published. And this is, accordingly to Scheres, how
      fraud was discovered.

      Lets have a sample on how Mr. Dhonukshe understands to answer Sheres:

      Ben Scheres: “My colleagues abroad had, in addition, obtained contradictory results on the localization
      of PIN2 in clasp mutants as described by Kakar et al. This scientific discrepancy caused suspicion and
      made them scrutinize the entire manuscript.”

      To which PD answers:
      “Now here is a key point: As he mentions, as supported by extensive rebuttal from Kakar and Dhonukshe
      submitted to Utrecht University and as evaluated by plant biology experts consulted by Utrecht
      University this is a ‘scientific discrepancy’. Significant differences in methodology (Wasteneys-Ambrose
      used ‘cut roots’ and we used ‘roots intact to plants’) can lead to scientific discrepancy and, therefore,
      scientific discrepancy can never be a reason for an official complaint and blaming of violation of integrity.
      Scientific differences or competitions should not promote science as a game arena for selective and
      forced removal of individuals.”

      So he is taking the statement of Scheres out of the context and give it an interpretation which suits PD
      conveniently: different results should be a matter of scientific debate and not an issue of complaint. What PD is
      missing now is a very simple: you cannot have a scientific debate on data which is doctored! There is no point to
      debate anything unless the data is valid and published correctly as it came out from observations.
      What PD is doing here is a logical fallacy known and classified as red herring. It is a typical rhetorical technique
      with the only purpose of diverting attention away from the main point and create confusion.
      All his rebuttal to Scheres is written like this. In choosing to make such public statements, who did PD think that
      his readers/listeners are: a bunch of pokemons? Is this his best way to make his voice heard and being credible in
      the same time?

      The public statements of PD do not seem to make him any good: he seems to shoot himself in the foot with
      any statement he makes. An example that I found outrageous is his statement given with ‘candid’ innocence that he
      did not understood so far how important is the quality of a presentation, and for him it mattered only the message of
      his research. How come a grown up, in the position of professorship, with millions of euros entrusted to his hands
      could be so naive: did he never learned during all his academic career that is is his best interest
      to publish his results as clear as possible by leaving minimal room for interpretation in order to avoid confusion?

      Enough to say, his understanding in making public statements for his defense pertains to a disgusting
      rhetoric that only a cheap politician retorts to, NOT a scientist. Every single statement he makes does nothing but
      undermines his credibility further.

      So please stay away Mr Dhonukshe: you wasted resources and public money by choosing to publish bogus data, create
      confusion in scientific community, and now you keep some scientists busy in cleaning up the mess. You accused Scheres
      of stealing your research: wrong! Nobody is stealing anything from you. You research was done on public money, so
      you do not own your research. An neither Scheres. You are still confused, aren’t you?
      All that you could own is academic credibility, and for that you have to earn it by complying with an elementary code
      of conduct and integrity.

      After all the damage you have done it will be outrageous if you will ever get appointed back in the academia. You
      admitted of doing mistakes, but neither know you did not understand what your mistake was: your choice of becoming
      scientist and belief that you are able to trick the scientific community
      by earning undeserved credit!

      1. Red herring is right. Take case of cut-and-paste DNA gel blots. In Nature paper bands are placed next to other with no lane distinction, a misrepresentation of gel but not fabrication of data. In Cell paper gel images are manufactured by pasting same band multiple times in same image. Very different. Dhonukshe calls attention to only Nature gel images as mistakes, to take attention away from Cell images which are clearly fabrication.

  7. To my best knowledge Utrecht University technical team is responsible for minor data processing i.e: contrast improvement. NOT for cutting / pasting / aligning anything. This is and always had beed authors responsibility.

    1. “I am deeply saddened and disturbed” that members of the academic community, such as Scheres and Dhonukshe, do not step out into the public domain to respond to questions and critques. Is it because I asked about the money that one month after this story broke at RW, the plant science community is still scratching their heads about what happened, why it happened and who is going to take responsibility for this? Each and every scientist represents a fundamental chain, even if small, in the integrity of the whole publishing process. When important members of that chain believe that they are too superior to other members of the chain to resond to public criticisms, then the chain will disintegrate and lose its strength. Welcome to the real world of plant science publishing, where dozens upon dozens of scientists fail to address the critics. Those who follow my posts at RW will notice that increasingly I post questions that need to be answered, or report cases of potential duplications, to show that one factor is now beginning to characterize the plant science literature, authors, editors and publishers: the lack of public accountability.

  8. A mega-correction has appeared for another Ben Scheres paper. This case is extremely important because Dhonukshe is not a co-author.

    Original information
    A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer
    Alfredo Cruz-Ramírez, Sara Díaz-Triviño, Guy Wachsman, Yujuan Du, Mario Arteága-Vázquez, Hongtao Zhang, Ikram Blilou, Anne B. Neef, Vicki Chandler, Ben Scheres
    Published: November 26, 2013
    DOI: 10.1371/journal.pbio.1001724

    20 Oct 2014: The PLOS Biology Staff (2014) Correction: A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer. PLoS Biol 12(10): e1001997. doi: 10.1371/journal.pbio.1001997

    http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001724 (original paper)
    http://www.plosbiology.org/article/fetchObject.action? uri=info:doi/10.1371/journal.pbio.1001724&representation=PDF (original PDF)
    http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001997 (the massive correction)

    There is an archived Tweet at the paper’s PLOS page written by the first author: “3,000 views in 2 weeks, that pays the effort invested !”

    Prof. Mark Estelle (University of California, San Diego) was the academic editor in charge of this paper. Marke Estelle was also the editor of another Scheres PNAS paper:
    …and another PLOS paper:

    An interesting list of speakers at a 2009 conference:
    Mark Estelle, Ben Scheres, Olivier Voinnet, among others.

    1. RW readers may ask, why the emphasis on Mark Estelle? Perhaps this retraction of a Mark Estelle might be more explanatory:
      AFB4 Auxin Receptor Is a Negative Regulator of Auxin Signaling in Seedlings
      Katie Greenham 1, Aaron Santner 2, Cristina Castillejo 1, Sutton Mooney 3, Ilkka Sairanen 4, Karin Ljung 4, Mark Estelle 1
      1 Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
      2 Cook Inc., Bloomington, IN 47402, USA
      3 School of Biological Science, Washington State University, Pullman, WA 66224, USA
      4 Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden

      The notice states: “In this article, we reported that the AFB4 protein is a negative regulator of auxin response based on the auxin hypersensitivity of the afb4-2 mutant line. Recently we obtained a second afb4 allele and confirmed that it is an RNA null. This mutant is not auxin hypersensitive, indicating our conclusion that AFB4 is a negative regulator of auxin response is incorrect. For this reason, we wish to retract the article. Other conclusions from the study, including the demonstration that AFB4 and AFB5 are auxin receptors and are the major targets of the synthetic auxin picloram, remain valid. The corresponding author wishes to apologize to the scientific community for any confusion that might have arisen from the study.”

    2. One of the Olivier Voinnet papers being questioned at PubPeer lists Mark Estelle as a co-author:
      Science 21 April 2006: Vol. 312 no. 5772 pp. 436-439
      DOI: 10.1126/science.1126088
      A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling
      Lionel Navarro 1,2, Patrice Dunoyer 2, Florence Jay 2, Benedict Arnold 3, Nihal Dharmasiri 4, Mark Estelle 4, Olivier Voinnet 2,*,†, Jonathan D. G. Jones 1,*,†
      1 The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
      2 Institut de Biologie Molèculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France.
      3 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
      4 Department of Biology, Indiana University, Bloomington, IN 47405, USA.
      http://www.sciencemag.org/content/312/5772/436.full.pdf (open access)

  9. Noortje Kornet and Ben Scheres
    Members of the GCN5 Histone Acetyltransferase Complex Regulate PLETHORA-Mediated Root Stem Cell Niche Maintenance and Transit Amplifying Cell Proliferation in Arabidopsis
    Plant Cell April 2009 21: 1070-1079. First Published on April 17, 2009; doi:10.1105/tpc.108.065300

    There are supposed to be 5 supplemental figures and 4 supplemental tables.
    Yet, on the supplemental page, the following message appears:
    “Not Found. Content not found.”
    Where are the 9 supplemental files?

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