Second Nature paper by researcher found to have violated academic integrity retracted

dhonukshe
Pankaj Dhonukshe

A second Nature paper co-authored by Pankaj Dhonukshe, formerly of Utrecht University and VIB Ghent, has been retracted.

Here’s the notice for “Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions:”

Our Letter reported that PIN transporters for the plant hormone auxin are initially delivered to the plasma membrane in a non-polar manner and that their polar distribution requires endocytosis. Abolishing PIN polarization, such as by inhibiting endocytosis, interferes with local auxin responses in the embryo, leading to transformation of embryonic leaves to the root-like structures.

The data regarding the essential role of endocytosis in the PIN polar localization and the connection between PIN polarity, auxin distribution and cell fate decisions remain reliable, but we have come to realize that the interpretation concerning the initial non-polar delivery of PIN proteins to the plasma membrane is not fully supported by experiments. It concerns the fluorescence recovery after photobleaching (FRAP) experiments presented in Fig. 1a and Supplementary Fig. 2a, which provided the key suggestion for the non-polar delivery model. On the basis of the original data, we confirm that the experiments were performed as published, but despite multiple attempts to reproduce them, the results remain inconclusive. Although in some experiments non-polar recovery can be detected as reported, others yield contrasting outputs that suggest polar recovery. Importantly, in many cases, the cells show signs of severe stress and stop growing following the photobleaching. In light of these findings, we feel that the reported results cannot be used for the conclusion on the initial non-polar PIN delivery and that this question remains open.

Therefore, we prefer to retract this Letter and republish the remaining confirmed findings elsewhere. Author P.D. continues to stand by all the conclusions of the paper, but all the other authors agree with the retraction. We apologise for any adverse consequences that may have resulted from this situation.

The paper has been cited 146 times, according to Thomson Scientific’s Web of Knowledge.

Pankaj Dhonukshe — aka “P.D.” in the notice — tells Retraction Watch:

I do not agree with the retraction because it is not based on any deficiencies in published experiments and results.

‘the interpretation concerning the initial non-polar delivery of PIN proteins to the plasma membrane is not fully supported by experiments. ……. On the basis of the original data, we confirm that the experiments were performed as published’ – these two sequential sentences from the retraction notice contradict each other when (i) the reported results are supported by experiments, and (ii) the experiments are valid and based on the original data.

As clearly written in the abstract of Nature 2008 ‘Real-time PIN tracking showed that after synthesis, PINs are initially delivered to the plasma membrane in a non-polar manner and their polarity is established by subsequent endocytic recycling.’ This real-time PIN tracking has been done by two independent and complementary approaches: (i) Fluorescence recovery after photobleaching (FRAP) and (ii) pulse chase induction (a classical experiment used in many previous published studies). Only FRAP approach is referred in retraction notice and it is questionable that how one of the approaches could be
neglected.

‘FRAP experiments … provided the key suggestion for the non-polar delivery model’ is also not entirely true as the non-polar delivery model is based on two equally important approaches and not on the claimed superiority or inferiority of one of them.

‘Although in some experiments non-polar recovery can be detected as reported, others yield contrasting outputs that suggests polar recovery’ confirms that the replication of the reported findings is possible. Contrasting output could be caused by sensitive experimental situation(s) and therefore, the original findings cannot be subjectively trashed.

‘Importantly, in many cases, the cells show signs of a severe stress and stop growing following the photobleaching’ is not supported by all experiments and in case of pulse chase PIN induction cells do not show this. FRAP approach has been used in many published studies and if FRAP related stress is the basis for the retraction of Nature 2008 then it should also form the basis of retraction of many other publications that utilize FRAP.

‘The data regarding essential role of endocytosis in the PIN polar localization and the connection between PIN polarity, auxin distribution and cell fate decisions remain reliable’ and ‘we prefer to retract this Letter and republish the remaining confirmed findings elsewhere’ raise important issues regarding:

(i) Experimental findings (which are independent of time and scenario) and not interpretation (which may depend on time-related scenarios) should be the basis of science being a source of our knowledge,

(ii) Who will publish this and when, while I (a lead author) have been put in a corner and thus
inhibited from (re)publishing, and

(iii) Credit of original ideas and work cannot be (re)claimed by retracting and republishing
without the involvement of all authors including the lead author.

I made a mistake in joining the retraction of Cell 2012 that was forced on me in which ‘at least in one case’ statement that formed the basis of retraction was never specified and clarified to me despite my repeated asking and while I continuously pointed out that in no case the conclusions of Dhonukshe et al. Cell 2012 are in conflict with the raw data and therefore do not allow retraction. I do not want to do that mistake again. I stand with the findings as stated in the titles of the Cell 2012 and Nature 2013.

Dhonukshe now has three retractions. In his note, he is referring to this Cell retraction. The other Nature retraction was the basis of a heartfelt post by one of Dhonukshe’s co-authors, Ben Scheres.

Here’s the summary of the Utrecht University investigation into the matter:

…Utrecht University has decided that a violation of academic integrity has been committed by cell biologist Dr P. Dhonukshe. This finding does not apply to the co-authors of the articles that were the subject of this investigation.

 

12 thoughts on “Second Nature paper by researcher found to have violated academic integrity retracted”

  1. Surely, this will not be the last retraction from this group. On the RW page*, RW readers will find that I posted, in April, several public questions to P.D. and to Ben Scheres (BS) about accountability, authors’ responsibilities (individual and collective), especially considering authorship definitions like those as defined by the ICMJE. At that time, I wrote: ““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 critiques. There is still absolutely no explanation by the authors, including BS, about what happened to the money they received for funding these projects that led to the retraction of now three high-profile faulty papers. In the case of the guilty Taiwanese Minister of Education, the Taiwanese Government has indicated that 100+K of funds related to those papers must be returned if the case holds up, but what about PD and BS? They were all too pleased to receive funding to support their research but when push comes to shove, will they return those funds as gentlemen of the pant science community, or simply wash their hands free of any financial responsibility? The other very serious issue that needs to be urgently addressed are the down-stream references, all 146 of them, that cited this paper. Will PD, BS and their group of authors collectively take responsibility of contacting all 146 journals / editor boards / publishers and request them to issue errata post-publication, to reflect that their retracted paper basically does not exist in the literature? This was my case No. 8 here.**

    * http://retractionwatch.com/2014/03/21/i-am-deeply-saddened-and-disturbed-co-author-of-retracted-nature-paper-reveals-how-problems-came-to-light/#comments
    ** Jaime A. Teixeira da Silva, (2014) Recent retraction cases in plant science that show why post-publication peer review is essential. J. of Advancement in Engineering and Technology. V1I3 DOI: 10.15297/JAET.V1I3.03

    1. “They were all too pleased to receive funding to support their research but when push comes to shove, will they return those funds as gentlemen of the pant science community, or simply wash their hands free of any financial responsibility?”

      I don’t see this happening. I presume the money was received directly by a university. Nothing short of a lawsuit ending in an order to repay would convince a university to part with money (likelihood of gentlemanly sentiment approaches zero). Only if the grant agreement includes a provision to repay is there any chance of such a lawsuit succeeding.

      Then, some of the money was used to pay salaries. I doubt that anyone, except possibly the most senior researcher, holding a full professorship, could possibly have any money to spare at the end of the month, and then being in the position to repay part of his salary. Even for the better-off researchers, I expect that repaying the full salary would requiring selling one’s house, and that would only happen under a forced bankruptcy. That, in turn, could only happen if there were a legal basis for the university to claw back the salary paid, and there isn’t one.

      1. Basically, lar, your excellent analysis paves the perfect path for fraud and miscnduct to proliferate, in fact. Since it is too much trouble to take out lawsuits against scientists or against universities, since there is a mutual benefit-loss balance, scientists accused of misconduct, particularly well paid ones, up until the point at which the fraud and misonduct are detected (aka retraction), are living the high life (or the safe life, at least). If any rage is to be felt, it should be by scientists who struggle to secure a position, those who actually do honest research, and the members of the general public who are struggling with unemployment and increasing government- and university-imposed austerity, only to see their tax euros being shipped off to universities who are, as we know now through several cases at RW, paying generous salaries and grants to individuals like PD and BS. Not to mention that BS and all the other authors apparently get to retain their salaries, positions and grants because Utrecht University and/or VIB Ghent (and universites of all other collaborating authors) have basically assigned the full blame onto PD’s head. Something is really wrong with this whole picture, and if this is the blue-print moving forward, expect fraud and misconduct to increase, even as retractions increase, because the risk of financial consequences are basically null. The situation in the US seems to be initiating an opposite trend, it appears, for reasons I have highlighted elsewhere already.

        1. “Basically, lar, your excellent analysis paves the perfect path for fraud and miscnduct to proliferate, in fact.”

          You’re giving me a bit too much credit here. 😉

          I don’t agree exactly that lawsuits are too much effort, but I think no lawyer will willingly undertake them because the chances of success are so slim. That’s even assuming a university would not mind calling more attention to cases of misconduct, which is also unlikely.

          At any rate, I agree with your sentiments. Those in receipt of great positions and ample funding are frequently people less deserving of either than others. Nepotism and cheating, I think, are primarily to blame.

  2. Here is what I wrote to the Editor-in-Chief of Nature and now wish to share with pubic:

    A demand for retraction of a Nature publication

    July 17, 2014

    Dear Editor-in-Chief of Nature,

    I sent you an email recently complaining the intentional and repeated removals of my submissions, without (sending me) any decision on the submissions, from Nature’s manuscript tracking system. I have not received your response, as usually the case for my prior communications to you.
    Now I just read a Retraction published in Nature (http://www.nature.com/nature/journal/v511/n7509/full/nature13549.html) which prompts me to write you this demand for retracting another Nature publication.
    A recent research article in Nature [T. M. Norman, N. D. Lord, J. Paulsson, R. Losick, Nature 503, 481 (2013).] made a claim for bacterial differentiation by presenting a so-called “cell fate switching” between a motile unicellular state and a chained multicellular state in bacterium Bacillus subtilis. This study was highlighted as “systems biology: how bacteria choose a lifestyle” [J. W. Locke, Nature 503, 476 (2013)].
    However, after carefully reading this new research paper, I realized that the claim of “cell fate switching” is most likely an illusion derived from using incorrect study approach and making erroneous data manipulation based on some invalid assumptions. Thus, I wrote my first letter to all authors including two corresponding authors, asking 10 initial questions. I told them that their quick response would be very helpful for my further analysis on their paper. Unfortunately, I did not receive any response, even after I sent more letters urging them living up to the corresponding authors’ responsibility.

    Thus, I made my analysis on their claims using information presented in their publication without access to the underlying data. Even so I still could make some solid criticisms on their main conclusion: discovery of an autonomous “cell-fate” switching between a motile unicellular state and a chained multicellular state for bacterium Bacillus subtilis.

    I submitted my analysis as a Communications Arising to Nature. Nature rejected it without requesting a peer review on it. Nature also ignored my plea to it for asking the authors of their publication to give a response.

    The Nature-rejected Communications Arising was published in Logical Biology [13(1): 3-7, 2014] (see attached PDF) and, as part of the evidence for identifying some potential misconduct, was sent to Harvard University’s Research Integrity Officer for Faculty of Arts and Sciences, Dr. Gearoid P. Griffin. My complaint was received by on Feb. 5th, 2014 and also received by the Office of Research Integrity (ORI) on the same time. You and Nature should also received copies of these communications as I usually put you on the CC list.

    Now more than 5 months have passed. I haven’t received any decision from Harvard University with regarding my complaint. But the incorrect interpretation and wrong conclusion made in the Nature publication should not be remained in scientific literature when the so-called “corresponding authors” even do not live up to an intrinsic responsibility of responding to scientific criticism.

    Thus, just as a wrongly interpreted publication not replicated by the authors needs to be retracted as shown in the recent retraction mentioned in the beginning of this email, a mis-interpreted and erroneously concluded publication already solidly challenged by other scientist also needs to be retracted, unless the authors can offer convincing counter-arguments and invalidate the criticisms.

    Nature should learn a real lesson from its heavy spin on the STAP cells. One way to learn a real lesson is to open its door to solid scientific criticisms. This should include stopping unjustified rejection of my submissions criticizing Nature’s flawed and even fraud publications and allowing me to log on to Nature’s website to make timely comment on Nature’s publication.

    If Nature wishes to reduce its chance of publishing too amazing and thus really unbelievable “discovery” /deception in biological field it may be even worthy of sending some “breakthrough” studies to me for a critical review before they break the trust of public to “science”. My service to Nature in this respect will be totally free. But I wish to be identified in real name and thus be held responsible for any of my reviews.

    Sincerely,

    Shi V. Liu MD PhD

    LB2014V13N1A2_CellFate.pdf
    46K

      1. It is the first time for me to see Shi V. Liu’s comments on RW, but what a vocal scientific activist he is! So, bravo, for standing up for your values and for what you believe in. One of the reasons, I believe why Nature will not respond to your queries is because they might perceive you as having serious conflicts of interest. So, for example, as your Twitter account states “A pioneer in scientific research and publishing, running Eagle Institute of Molecular Medicine, Truthfinding Cyberpress, Logical Biology, Scientific Ethics, etc”. I did a quick Googe and found literally dozens of your papers, which I assume are opinion papers, published in Logical Biology, whose publisher is Truthfinding Cyberpress, which appears to be your own company. People will then naturally ask, did any peer review take place for your journal and papers, or did you simply self-publish your opinions because no respectable or established leading journals would? Good or bad, your protest model is attractive, at least for me, because it allows for the bottle-neck of frustrations ot be publically recorded. For exmaple:
        A Public Robbery of Science in the Public Library of Science http://im1.biz/albums/userpics/10001/V5_I1_A18_Robbery.pdf
        Shi V. Liu’s Collection of Rejections by Mainstream Journals: 2008-2009
        http://im1.biz/albums/userpics/10001/LB2009V9N2A13_Rejection2008_2009.pdf

        So, bravo, good to see another aggressively vocal critic out there who is not afraid to put his name in the defense of science before plitics and all else.

        1. Logical Biology was launched in 1999 (perhaps as the world-first Open Review and Open Access) for “debating controversial issues and promoting logic as a tool for scrutinizing long-held conventional views in biology” (see “Debating controversies can enhance creativity”; Nature 403, 592 (10 February 2000) | doi:10.1038/35001232; http://www.nature.com/nature/journal/v403/n6770/full/403592a0.html ). Later, other double-open journals such as Scientific Ethics, Top Watch, Pioneer, and International Medicine were also launched by Truthfinding Cyberpress (TFCP) which I serve as the president. All publications in these journals were editorially reviewed and were usually sent to the authors whose papers (published in other peer-reviewed journals such as Cell, Nature, and Science) were directly criticized before their publication in a TFCP journal. Most time, the published papers were also sent to the corresponding authors of the criticized paper and invitations for rebuttal were issued by the journal. Thus, it does not matter whether the publications in TFCP journals have been peer-reviewed or not. But it does matter when the original journals which published the flawed and even fraud papers all consistently reject criticisms on their publications and the “corresponding authors” all failed to respond to criticism.
          By the way, TFCP journals have a tradition to publish any criticism towards their publications and, as a matter of fact, invited an author to change his casual comment on Logical Biology’s editor’s article into a formal criticism for publication in Logical Biology.
          To see aim and scope of TFCP publication, please read “A True Revolution in Scientific Publishing” (Pioneer 2(1): 4-6, 2007; http://im1.biz/albums/userpics/10001/P2007V2N1A2_Statement.htm) and the “4P White Paper of TFCP (http://im1.biz/albums/userpics/10001/TFCP_statement_20070315.pdf).
          As I stated in 2000 in the above mentioned Nature Correspondence, “With the emergence of electronic publications, which do not have to rely on a fixed format, the reviewing/citation components can now be integrated into publications. Supplemental information and hyperlinks can be added to electronically published papers to connect them with related information — a review or a follow-up research article, say. In this way, the value of the published work is automatically revealed through the reading of linked literature. Ultimately, pre-publication review might even be eliminated and replaced with continuous post-publication review, creating a free atmosphere for expressing creative ideas.” Thus, those who still trust pre-publication peer review as the ONLY way to safeguard science and despise other formats of publication should re-think their attitude towards science.

          1. Dr. Liu, I have a 180-page post-publication peer review critique, including screen-shots of the errors, of the chrysanthemum biotechnology literature. I have, very frustratingly, seen that paper rejected by almost every top plant science journal from main-stream publishers. So, would Logical Biology be interested in taking on this “burden”? How would you handle others’ papers if your own papers didn’t pass through traditional peer review?

          2. You can submit the manuscript to Logical Biology by emailing me directly at SVL8EPA@gmail.com. I will invite authors whose publications are criticized by your paper for responses. Your paper, as well as any response coming back from the authors of other papers, will be published in an appropriate way which, if you will, can include its history of rejections by other journals.

          3. I like the idea, but I am already in the process of sending the full paper to ALL of the authors of papers I criticize. I am not sure how many will answer, of course, but that data will also be included, because it is essential to start documenting also the lack of accountability by scentists. In a way, this is a blue-print for PPPR methodology in the future. As soon as I am complete with my preparations, I will be in touch. I look forward to an open, frank, transparent and fruitful process. I dn’t care about the IF of journals. I only care that the management and editors feel as passionately about the mission as hand as I do.

          4. I wish you good luck for your effort. Just remember that there is a place for you to communicate true science when all pseudo-scientific journals will refuse your true science.

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