A Nature chain retraction for Arabidopsis paper, and some unanswered questions

courtesy Nature

If a paper is retracted, should papers that cite it get retracted, too? We’ve been on the lookout for this kind of move, which we figure is consistent with cleaning up the scientific record. Today, one appears in Nature.

The original paper, “Mediation of pathogen resistance by exudation of antimicrobials from roots,” purported to show how a particular bug evades the immune system of Arabidopsis, a plant commonly used in the lab. It has been cited 51 times, according to Thomson Scientific’s Web of Knowledge.

The retraction notice says that the paper’s conclusions could no longer be supported because one of the key references — a paper in the Journal of Agricultural and Food Chemistry by many of the same authors — had been retracted:

The authors wish to retract this Letter after a key reference by Walker et al. (ref. 9 in this Letter) was retracted from the scientific literature. The withdrawn paper reported ten compounds exuded by Arabidopsis thaliana roots, which were used in this Letter to monitor the defence response in Arabidopsis seedlings. In this Letter, these ten compounds were shown to have antimicrobial activity against specific pathovars of the bacterial phytopathogen Pseudomonas syringae but not against the pathovar Pseudomonas syringae pv. tomato strain DC3000 that is a highly virulent pathogen of Arabidopsis.

Moreover, wild-type P. syringae DC3000 suppressed the exudation of the ten compounds whereas a DC3000 hrcC mutant did not, leading to the conclusion that DC3000 type III effectors block the exudation or synthesis of the ten compounds. As a consequence of the retraction of the Walker et al. paper, the validity of the use of the ten compounds as markers of the Arabidopsis defence response is now in doubt. Thus, the data in Fig. 3, Table 1, Supplementary Figs 5–8 and Supplementary Table 1 cannot be used to support the conclusions that P. syringae DC3000 is generally resistant to antimicrobial compounds exuded by Arabidopsis or that P. syringae DC3000 type III effectors block the exudation or synthesis of antimicrobial compounds.

Here’s the Journal of Agricultural and Food Chemistry retraction notice:

We have been unable to find experimental data that document the actual isolation of butanoic acid, trans-cinnamic acid, ocoumaric acid, p-coumaric acid, ferulic acid, p-hydroxybenzamide, methyl p-hydroxybenzoate, 3-indolepropanoic acid, syringic acid, and vanillic acid from root exudates of Arabidopsis thaliana Col ecotype. Therefore, the original publication is being retracted, and the authors deeply regret any inconvenience to the scientific readership.

The Nature retraction seems like the right thing to do, and we applaud that step. But we had some questions, key among them what exactly the inability “to find experimental data that document the actual isolation” meant. Was this simply a result that couldn’t be replicated? Were lab notebooks lost? Or was there something more sinister?

We checked with the lead author of both papers, Jorge Vivanco of Colorado State University:

The co-authors and I reached the decision to retract the Nature paper because we were no longer certain about the validity of ten marker compounds used in an assay to prove the point that plants defend themselves more aggressively by means of secreting phytochemicals from the roots against non-pathogens (as compared to the opposite when infected by pathogens).  However, I should mention that the general assertion that plants defend themselves more aggressively against non-pathogens as compared to pathogens has been corroborated widely in the literature. Therefore, it was very hard for all of us to retract this paper because the general assertion was valid but the validity of the particular assay used to reach this conclusion was not too clear.

Those ten marker compounds were originally reported in the J Ag. Food Chemistry paper that you mentioned in your email.  We had a very hard time repeating those studies and it seems that there was an issue with the original identification of those ten compounds.  This paper was retracted from the journal.

Vivanco also asked his co-authors to respond. One of them, the University of Delaware’s Harsh Bais, did so:

Drs. Vivanco’s, Ausubel and my lab are independently working on elucidation of root secretions from Arabidopsis and other plant systems. As indicated in Dr. Vivanco’s email that his lab was not able to replicate the secretion profile in Arabidopsis as retracted in JAFC. My lab also faced similar difficulty in replicating Arabidopsis secretion results. Dr. Ausubel’s lab also tried to replicate the Arabidopsis secretion work and found that the compounds reported as free metabolites in retracted JAFC paper to be conjugates and glucosides.Some of these replication efforts confirm that majority of these compounds (retracted in JAFC paper) are indeed synthesized by Arabidopsis, even though they may not be exuded as free compounds under the conditions of our experiments. In contrast, a different lab has shown the secretion of same compounds in Arabidopsis secretions (Narasimhan et al. 2003.Plant Physiol. 132:146-53). The bottom line is that this is a very complicated issue and even though we have been working on this project for a couple of years, we still do not have a definitive understanding of it.

It certainly does appear to be complicated scientifically, but we still aren’t sure why there were issues with the original data.

We have other questions, after coming across two other retractions by many of the same authors, in Phytochemistry in 2009 and 2010. Many of them were also on a Journal of Agricultural and Food Chemistry paper that was the subject of a correction.

When we asked, Bais told us that the 2009 Phytochemistry retraction and the Journal of Agricultural and Food Chemistry correction had nothing to do with the Nature retraction or the work it was based on.

We didn’t see the 2010 Phytochemistry retraction until after we had asked the group about the others. Like the Journal of Agricultural and Food Chemistry retraction that led to the one in Nature, it too refers to missing data:

The authors have been unable to find written experimental data of the isolation of the purported beta-carbolines (harmine and harmaline) from root exudates. The source of the compound in question as originally reported is unclear. While Oxalis tuberosa roots do release fluorescent exudates, the identity of the fluorescient compound(s) awaits actual purification and structural determination.

The authors therefore wish to retract the original publication and deeply regret any inconvenience to the scientific readership.

If we hear back about the circumstances, we’ll update.

22 thoughts on “A Nature chain retraction for Arabidopsis paper, and some unanswered questions”

  1. I don’t necessarily agree that news releases like these should be retracted; rather, it is the responsibility of the news organization that initially felt it important enough to report on, to issue a similar statement reporting the retraction

    1. This is an important issue that we’ve covered elsewhere: http://www.retractionwatch.com/2010/11/04/nature-comes-clean-about-retractions-and-why-theyre-on-the-rise/
      We feel that anyone who sent out a press release about a paper that is eventually retracted should send out another release noting its retraction. That’s the transparent thing to do.

    1. It was, because it was part of Nature’s issue that was embargoed until yesterday when we posted the item. But Nature did not put out a press release, which is consistent with their policy of not press-releasing retractions of papers they didn’t press-release to begin with.

  2. Does Nature usually put the retraction notice in tiny red letters under the title? Other journals print a watermark over the entire article that says “Retracted Article.”

    At least the PDF version has a larger font for the word “Retracted.”

  3. Hi Adam, Ivan, thanx for the great service, and the post on this metabolomics paper in particular!

    I’m sucking up because I am interested in learning how frequent papers are retracted because the original experimental data got lost. This is because I have been and now again am involved in building a platform to preserve raw data (as measured directly from the experiment). I have been advocating keeping data around for years now, but it is hard to convince the bench chemist about the need (“Are you implying I am doing something wrong??”). In fact, I am implying they do, as this retraction story nicely shows why. (I blogged about it in ‘my’ context [0]. My blog post brings up another possible reason for the retraction.)

    So, do you have numbers about the absolute and/or relative number of retractions because data got ‘lost’?


    1. Hi Egon — thanks for the kind words. Nice post, glad to see this story getting some pickup.

      How often lost data is the reason for a retraction is a great question. We don’t have numbers, but here’s one case we covered:

      Another recent one: http://www.anesthesia-analgesia.org/content/104/6/1597.3.full

      We’d love to hear more about what you find out.

  4. Here is another retracted paper from the same lab:

    Intraspecific and Interspecific Interactions Mediated
    by a Phytotoxin, (-)-Catechin, Secreted by the Roots
    of Centaurea maculosa (Spotted Knapweed)

  5. A wonderful point raised here. However pl. note that all the authors along with the corresponding author enjoys the faculty positions (and promotions) which are largely due to those paper (now retracted)..so what is the point in just retracting? what examples they set for future scientists? what guarantee they give that the future work is not faked? A paper in science by the same authors http://www.sciencemag.org/content/301/5638/1377.full is an extension of their study that was among the ones retracted. The scientific community (the University) should consider this as a big red flag and do some thing about it rather than just eating their grant money and saving these people.

  6. What can you do? The paper cited 51 times. The previous one, also retracted, was cited by how many more? It’s very rare that a paper is cited as wrong. So, how many works are now wrong? Retracted paper as a tip of the iceberg? But, wait a minute, not one (well may be one) sci-st saw it being wrong. These icebergs, it appears, in fact change nothing, I mean – with them or without them, sci. stays the same, and that is pretty shocking conclusion. Some explanation may be this:
    It looks likely that this particular paper was written before they did their chemistry. About the two major items they say that their CONCLUSIONS are still good because others had shown the same. So, people are trying not to do anything potentially controversial, the best is to do something that has been proven before. These people here felt secure, and it was very, very nasty and unfortunate that someone went into their private data.

  7. And the whole treatment of the phenomenon… If there were a specific receptor on roots which then triggers the “exudation”, I would call this defence mechanism. But, look, “exuded” are many low molecular weight substances, it doesn’t look like specific defence. But we have Pseudomonas, can it simply change the permeability of cell wall and cause massive leaking? Looks like the action of bacterial toxin. Didn’t understand though, is this a “reaction” to pathogen or vice versa?

  8. This retraction is interesting to me. I worked with the leading author a few years back and back then realized that it was not the theoretical aspects of his work that were not consistent, it was an inability to accurately record basic data collection and protocols that were this authors/researchers main issue. The experimental protocols and notekeeping seemed non-existent back then in this lab. Also, a basic understanding of the separation chemistry was not really understood by some of researchers. How can one expect to repeat anything if you do not understand how it works or what can go wrong? A scientist and researcher must always record everything that is crucial for others to repeat scientific work. One cannot be in such a rush (with enormous egos and agendas) that the ethics and basic notekeeping, repeating of experiments are overlooked or skipped. I am not surprised that this work could not be repeated, it was a matter of time before this happened.

  9. About a year late, but I just saw Adam give a talk and that inspired me to finally take a look here. Following on the last comment, indeed an unhappy postdoc from that lab once told me that he was informed when found the opposite pattern of that expected that he must have labeled his samples incorrectly. As Brett said, ego and agenda got in the way. As Jim said more than a year ago, the principle scientist involved made their careers (e.g. early tenure, tenure-track job, promotion, raises) based in part on these shoddy (to say the least) works published. Makes one pretty cynical about administrators. Also, there are other papers not necessarily mentioned here such as the Science paper (2003: Vol. 301 no. 5638 pp. 1377-1380, Harsh P. Bais1, Ramarao Vepachedu1, Simon Gilroy2, Ragan M. Callaway3 and Jorge M. Vivanco1) that was _heavily_ corrected, but a letter to the editor suggesting it be retracted was rejected largely because the editors took too long to reply and thus the time surpassed their allowed window for comment), the Ecology Letters paper (Volume 7, Issue 4, April 2004, Pages: 285–292, Jorge M. Vivanco, Harsh P. Bais, Frank R. Stermitz, Giles C. Thelen and Ragan M. Callaway) that was never retracted because it was “corrected” by another paper in Plant Signalling and Behavior (which isn’t in Web of Science; 4:1, 9-14; January 2009, Naira Quintana,1,2 Elie G. El Kassis,2 Frank R. Stermitz1 and Jorge M. Vivanco2). Sigh. I lost two great future colleagues over this mess (former students of mine who dropped out of the research track). But somehow it is those of us who pointed out the problem who are considered the bad guys. Funny thing, if you can see the humor in it, is that one of the authors continues to publish on the same idea, different plant (PLANT PHYSIOLOGY Volume: 151 Issue: 4 Pages: 2145-2151, 2009). All I can say is that with the original plants worked on (Centaureas), I long ago gave every last seed away and washed my hands of them!

  10. A few of the same scientists reported the characterization of the Hyp-1 enzyme from St. John’s wort [Bais HP, et al (2003) J. Biol. Chem. 278(34):32413-32422.]. Since then, other independent groups have not been able to reproduce this catalytic activity [Michalska K, et al (2010) J. Struct. Biol. 169(2):161-171.].

    1. Sadly, I’m not surprised. Another part of the group associated with the Nature retraction and 7+ other retractions or corrections (Vivanco lab) is now retracting work on a completely different topic: http://www.frontiersin.org/Journal/10.3389/fpls.2013.00424/full?utm_source=newsletter&utm_medium=email&utm_campaign=Plant_Science-w43-2013
      The university says that it takes this stuff very seriously, but they do not seem to actually hold the lab leaders accountable.

        1. Thanks for the link, ivanoransky. You should tally the corrections, too! The tally is impressive. IMO, the best case scenario is that the lab puts too much pressure on vulnerable young scientists and they crack. Once broken, unfortunately probably always broken. One lab simply should not have that many problems and that many different study systems.

  11. Erratum published in February 2015, Molecular Plant, Oxford University Press:

    Original paper: Molecular Plant 3(3):491–498; May, 2010; http://dx.doi.org/10.1093/mp/ssq004
    Erratum: http://www.cell.com/molecular-plant/pdf/S1674-2052(15)00096-9.pdf
    Root Secretion of Phytochemicals in Arabidopsis is Predominantly Not Influenced by Diurnal Rhythms
    Dayakar V. Badri 1, Victor M. Loyola-Vargas 1/2, Corey D. Broeckling 1, Jorge M. Vivanco 1
    1 Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523, USA
    2 Unidad de Bioquimica y Biologia Molecular de Plantas, Centro de Investigacion Cientifica de Yucatan, Calle 43 No. 130, Col. Chuburna de Hidalgo, Merida, Yucatan, Mexico

    “In Figure 5, the gel images corresponding to the genes Atpgp1, Atpgp4, Atpdr2, Atpdr6, Atpdr7, Atpdr8, Atmrp2, Atmrp5, Attap2, Atnap5, Atath6, Atath10 and Atgcn3 were misrepresented.”
    “In Figure 6, the gel images corresponding to the genes 4CL-1, 4CL-2, F3H, CYP79B3 and CYP79B15 were misrepresented.”

  12. One more Vivanco paper retracted.
    Perry, L.G., Thelen, G.C., Ridenour, W.M., Weir, T.L., Callaway, R.M., Paschke, M.W. & Vivanco, J.M. (2005) Dual role for an allelochemical: (±)-catechin from Centaurea maculosa root exudates regulates conspecific seedling establishment. Journal of Ecology, 93, 1126–1135. doi:10.1111/j.1365-2745.2005.01044.x.


    “The Executive Editor and Managing Editor of the Journal of Ecology and authors Laura G. Perry, Ragan Callaway and Jorge Vivanco are retracting this article (Perry et al. 2005). A formal investigation by Colorado State University Research Integrity Office has found that (±)-catechin concentrations reported as being found in field soil samples in this article (Fig. 2) (Perry et al. 2005) were intentionally fabricated by a third party. The investigation therefore concluded that the results of this article are not reproducible and its scientific validity has been undermined.”


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