A second Nature paper co-authored by Pankaj Dhonukshe, formerly of Utrecht University and VIB Ghent, has been retracted.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