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Retraction Watch

Tracking retractions as a window into the scientific process

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

with 33 comments

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one of the key references — a paper in the Journal of Agricultural and Food Chemistry by many of the same authors — had been retracted: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 (ref. 9 in this Letter) was retracted from the scientific literature. The withdrawn paper reported ten compounds exuded by Arabidopsis thaliana roots, which were used in this Letter to monitor the defence response in Arabidopsis seedlings.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.

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33 Responses

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  1. For the record, here is another retraction by the same first and senior author.

    http://www.plantphysiol.org/cgi/content/full/plantphysiol;151/2/967

    In this 2009 retraction of a 2002 paper the first author did not agree to the retraction.

    nameless

    March 2, 2011 at 2:47 pm

  2. And a related question is what should happen to the press releases that went out and all the media reports that followed the original paper: should they also be retracted in some way or another?

    E.g. http://www.nsf.gov/news/news_summ.jsp?org=OLPA&cntn_id=103098&preview=false

    http://www.sciencedaily.com/releases/2005/03/050325154057.htm

    Mico Tatalovic

    March 2, 2011 at 4:59 pm

  3. 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

    Chris B

    March 3, 2011 at 9:17 am

  4. Wasn’t this retraction also embargoed as you noted in one of these examples you posted ?

    Mico Tatalovic

    March 3, 2011 at 2:43 pm

    • 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.

      ivanoransky

      March 3, 2011 at 2:47 pm

  5. 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.”

    SG

    March 4, 2011 at 3:40 pm

  6. 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’?

    0.http://chem-bla-ics.blogspot.com/2011/03/toxbank-data-warehouse-for.html

    Egon Willighagen

    March 12, 2011 at 4:37 am

  7. 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)

    George

    August 19, 2011 at 12:43 pm

  8. 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.

    Jim

    September 30, 2011 at 5:50 pm

  9. 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.

    Pyshnov

    September 30, 2011 at 11:40 pm

  10. 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?

    Pyshnov

    October 1, 2011 at 1:43 am

  11. 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.

    Brett

    December 1, 2011 at 10:29 am

  12. 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!

    Ruth

    November 12, 2012 at 6:07 pm

  13. 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.].

    david

    January 3, 2014 at 12:05 pm

    • 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.

      Ruth

      January 3, 2014 at 1:03 pm

    • Yes, and take a look at figure 5A. The tubulin lanes 1 – 3 look identical. In 5B, the Southern blot should have a different size product for each different enzyme, I believe.

      Steve

      September 5, 2014 at 3:14 pm

      • The retractions from the Jorge Vivanco lab are very disturbing. In fact, Prof. Vivanco was, until this series of retractions, one of the leading experts on Arabidopsis, roots and the rhizosphere, capturing the imagination and hearts of young scientists and breathing inspiration in the 1990s and early 2000s. When I learnt of the first retraction here are RW, that peaked my interest in this topic, which has now made me a staunch activist now and critic of the “establishment” and research elite in plant science, of which Vivanco is one classic example. I am concerned about the list of publications on the Vivanco page, which only lists papers until 2008 (why are the retractions not listed, and where are the 2009-2014 papers?:

        http://lamar.colostate.edu/~jvivanco/publications.htm

        So, if, as Ruth suggests above, that Colorado State University “takes this stuff seriously”, then why doesn’t it start with two issues: accountability and transparency. That means that CSU in fact does not “take this stuff seriously”. Step 1, clean up that publications page and force Vivanco to explain perfectly how so many things are being done rather sloppily in his lab, but still landing (or landed) his group papers in the top plant and science journals. His explanation for this retraction is absolutely pathetic: “The bottom line is that this is a very complicated issue…”. Detecting these 10 compounds is not some arbitrary thing. Isolation and detection of such fairly common secondary metabolites can be achieved with HPLC and GC-MS, among other relatively standard conditions. You don’t just lose such data, you don’t just suddenly not know how those 10 compounds magically appeared then disappeared. And why was Vivanco not supervising this part of the analysis before it was sent to the journal. Where are the compound analyses? Usually such runs can remain on the memory disks of chromatographs for years, unless they are purposefully erased. That is because techniques to detect such compounds, usually against commercial internal standards, are usually very specific (e.g., specific retention times, GC- ass spectra, etc.) so it is impossible, almost, to misidentify, or to claim something that didn’t actually exist. What surprises me the most is how Vivanco is able to retain his position and his lab, without absolutely any repercussions. A scandal, if you ask me. This is the kind of individual who led the international community of root/rhizosphere-related scientists into being so positive about science, and then bitterly let down his peers with this science full of errors. Plant scientists should be revolted more to the core by this case because Vivanco represents a “core” plant science leader with a historical past.

        JATdS

        September 6, 2014 at 4:50 am

        • JATdS – I completely agree that correcting the website would help. Just to clarify, what I wrote is that the U _says_ that it takes this stuff seriously, and continued to say that they do not seem to hold the heads of labs accountable. I do not think that the problem papers are full of errors, I think the root cause is much worse than sloppiness. It is not bad luck that leads to two (known) people in a lab producing papers of this ilk. Bad advising is one component. Lots and lots and lots of pressure on vulnerable postdocs is something that I think likely happens. You say it well, a scandal.

          Ruth

          September 6, 2014 at 1:33 pm

          • Vivanco was a Guggenheim fellow and Fullbright Scholar [1]. He was thus a recipient of funding, grants and possibly even a salary associated with work that is now retracted. If he was awarded money and funding based on research that was expected to be conducted ethically, methodologically and with scientific rigor, but it is now known that several aspects of those studies failed these basic requirements, then why is Dr. Vivanco not expected to return funding? Does the Guggenheim Foundation or the Fullbright Foundation know about this case? He was also awarded a grant by the Pan-American Study Institute program of the National Science Foundation. Surely they would have the responsibilty of demanding more academic and financial justice from Vivanco and CSU? Is ORI investigating this case? The NSU is a US government body, so why is the US Government not looking into this considering that 5 retractions is not a random event? The same web-page [1]: ironically states the following: “Guggenheim fellows are appointed on the basis of distinguished achievement in the past and exceptional promise for future accomplishment.”
            [1] http://www.news.colostate.edu/Release/896

            JATdS

            September 6, 2014 at 4:39 pm

            • The links to the 2009 and 2010 Phytochemistry retractions are not working. Thus a summary is provided here with additional information and links.

              Retraction 1 (2009):
              Frank R. Stermitz, Harsh P. Bais, Tommaso A. Foderaro, Jorge M. Vivanco. 7,8-benzoflavone: a phytotoxin from root exudates of invasive Russian knapweed [Phytochemistry 64 (2003) 493–497] RN = Phytochemistry, Volume 70, Issue 1, January 2009, Page 156

              http://www.sciencedirect.com/science/article/pii/S0031942203002760

              http://www.sciencedirect.com/science/article/pii/S0031942208005876

              http://ac.els-cdn.com/S0031942203002760/1-s2.0-S0031942203002760-main.pdf?_tid=4168e2b4-93f0-11e3-9cd8-00000aab0f6b&acdnat=1392214765_dab753a01f3aee94078ea1d6267c9160

              http://www.ncbi.nlm.nih.gov/pubmed/12943767

              Reason: compound reported (7,8 benzoflavone) non-existent.

              Retraction 2 (2010):
              Harsh Pal Bais, Sang-Wook Park, Frank R. Stermitz, Kathleen M. Halligan, Jorge M. Vivanco. Exudation of fluorescent beta-carbolines from Oxalis tuberosa L. roots. [Phytochemistry 61(5) (2002) 539–543] RN = Phytochemistry, Volume 71, Issue 1, January 2010, Page 123

              http://www.sciencedirect.com/science/article/pii/S0031942209004038

              http://ac.els-cdn.com/S0031942202002352/1-s2.0-S0031942202002352-main.pdf?_tid=2cbc772c-360c-11e4-bbe1-00000aab0f6c&acdnat=1410038844_4e864e38e2d816398a03962418f4069f

              Reason: β-carbolines (harmine and harmaline) from root exudates not confirmed.

              Why was the subsequent paper on Russian knapweed not retracted, and only subjected to an eratum, when the analyses were a diretc follow-through to the retracted 2009 paper?
              Naira Quintana, Tiffany L. Weir, Jiang Du, Corey D. Broeckling, Julie P. Rieder, Frank R. Stermitz, Mark W. Paschke, Jorge M. Vivanco (2008) Phytotoxic polyacetylenes from roots of Russian knapweed (Acroptilon repens (L.) DC.). Phytochemistry Volume 69, Issue 14, October 2008, Pages 2572–2578

              http://www.sciencedirect.com/science/article/pii/S0031942208003580

              http://ac.els-cdn.com/S0031942209000041/1-s2.0-S0031942209000041-main.pdf?_tid=b48bb75c-360d-11e4-b874-00000aab0f27&acdnat=1410039502_95e8b95fc7816a9fb355e1ed32303adc

              RN = retraction notice.

              JATdS

              September 6, 2014 at 5:36 pm

              • A focus on Vivanco’s (et al.) papers in Springer journals and books. I have several concerns about Springer’s books, including the lack of transparency about their content, duplications with articles in Springer journals without cross-referencing each other. Springer book chapters are, in my opinion, one of the greatest uninvestigated black boxes in the scientific literature.

                Subsequent to the Vivanco et al.-related retractions and errata, there is little faith and trust of what is coming out, has come out and will likely continue to come out of that laboratory. In that sense, a deeper analysis of what has been published is required.

                I start with an additional retraction, Vivanco’s sixth (not yet covered by RW):
                Tiffany L. Weir, Harsh Pal Bais, Jorge M. Vivanco Journal of Chemical Ecology November 2003, Volume 29, Issue 11, pp 2397-2412 Date: 22 Dec 2004
                RETRACTED ARTICLE: Intraspecific and interspecific interactions mediated by a phytotoxin, (–)-catechin, secreted by the roots of Centaurea maculosa (spotted knapweed).

                http://link.springer.com/article/10.1023/A%3A1026313031091

                45 citations.
                Reason: After a reevaluation of this work, Tiffany L. Weir and Jorge M. Vivanco no longer have confidence in several key observations and therefore, retract this paper.
                Clicking through a few links will reveal a PDF for the retraction notice elsewhere, as open access:

                http://download.springer.com/static/pdf/350/art%253A10.1007%252Fs10886-009-9671-z.pdf?auth66=1410216045_f28a32abc1607ef357339c31aad0bdb9&ext=.pdf

                That retraction notice lists the reason as follows:
                “After a reevaluation of this work, we no longer have confidence in several key observations and therefore, retract this paper. Specifically, the reported finding in Perry et al. (J of Chemical Ecology 33:2337–2344, 2007) of catechin in experimental blanks, suggest an exogenous source of catechin in our laboratory. The absence of experimental blanks in the current study along with the unreproducibly high levels of catechin reported from in vitro grown C. maculosa plants have led us to believe that the reported catechin may have originated from non-plant sources. In addition, a finding that some of our commercially purchased catechin was contaminated with 2,4-D along with our observation that catechin caused callus formation in some seedlings suggests that at least some of these experiments may have been conducted using a contaminated source. Because we cannot be sure that contaminated catechin was not used, the results of the phytotoxicity and germination inhibition experiments are meaningless.”

                So, how does this wave of errata and retractions affect book chapters that reference these flawed papers? Should such chapters also not be retracted or corrected?

                What about those book chapters that do not include Vivanco et al. as authors or editors, but that reference their papers? What will happen to references of papers that were retracted? Will those papers and chapters issue an erratum? In that respect, Springer S+BM must be held accountable.

                How are up-stream and down-stream publications related to the methodological errors, plants, or other aspects of the retracted papers (or errata), and not only, and thus is there cause for concern here, too?

                Moreover, RW, states about Vivanco’s response to the 2011 blog post: “Vivanco also asked his co-authors to respond. One of them, the University of Delaware’s Harsh Bais, did so:” Can Vivanco show the public the e-mail he sent to his co-authors? Which co-authors exactly did he contact? How can we be sure? This is like asking the fox to guard the chicken-house and to expect an unbiased, frank, open and transparent response and explanation from the same individuals who were responsible for these errors in the literature.

                JATdS

                September 6, 2014 at 8:39 pm

                • Yes, I agree that there is a huge problem with both upstream and downstream papers. As I said above (in January 2014), there is more that should have been retracted, for example 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). It was never retracted but rather was “corrected” by another paper in Plant Signalling and Behavior. That paper (4:1, 9-14; January 2009, Naira Quintana,1,2 Elie G. El Kassis,2 Frank R. Stermitz1 and Jorge M. Vivanco2) is not in web of science. Meanwhile, the initial Vivanco et al. paper continues to be cited as if it is completely valid. And how on earth would someone from the outside know? Even if they searched every paper citing Vivanco et al. 2004 on web of science, they would not encounter the so-called correction. It is so discouraging.

                  I don’t know who you are, JATdS, but it’s great that someone is asking questions.

                  Ruth

                  September 6, 2014 at 11:08 pm

                  • I mean way back (Nov. 2012) was when I posted including the Ecology Letters paper. It would be great if someone could consolidate all that’s known on all the different issues and publish a summary paper to try to clear the literature a bit and have all that information in one place, all together.

                    Ruth

                    September 6, 2014 at 11:10 pm

                • Another corrigendum:
                  Dayakar V. Badri, Victor M. Loyola-Vargas, Jiang Du, Frank R. Stermitz, Corey D. Broeckling, Lourdes Iglesias-Andreu and Jorge M. Vivanco (2008) Transcriptome analysis of Arabidopsis roots treated with signaling compounds: a focus on signal transduction, metabolic regulation and secretion. New Phytologist Volume 179, Issue 1, 209–223.

                  http://onlinelibrary.wiley.com/doi/10.1111/nph.12660/abstract

                  http://onlinelibrary.wiley.com/doi/10.1111/nph.12660/pdf

                  JATdS

                  September 7, 2014 at 7:01 am

                  • Another retraction, the 7th?:
                    Harsh Pal Bais, Travis S. Walker, Frank R. Stermitz, Ruth A. Hufbauer and Jorge M. Vivanco (2002) Enantiomeric-Dependent Phytotoxic and Antimicrobial Activity of (±)-Catechin. A Rhizosecreted Racemic Mixture from Spotted Knapweed. Plant Physiology April 2002 vol. 128 no. 4 1173-1179
                    Full text (OA): http://www.plantphysiol.org/content/128/4/1173.full.pdf+html
                    Correction: http://www.plantphysiol.org/content/137/4/1485
                    Retraction notice: http://www.plantphysiol.org/content/151/2/967
                    The notice states: “Several aspects of this study were recently found erroneous or nonreproducible (Figs. 1, C and D, and 2, A and B), and therefore it is our responsibility to report that the premise of this study is not correct and therefore this report is formally retracted. For instance, in a recent reinvestigation, the Vivanco laboratory was unable to detect catechin in any form secreted by the roots of Centaurea maculosa plants under in vitro conditions. Whether catechin found in other studies originated from roots, microbes, or other sources is not known. The chirality of this catechin has not been determined. The authors truly regret the inconvenience and difficulties that this action causes Plant Physiology and its readership. Editor’s note: H.P. Bais, the first author of the original study, strongly disagrees with the basis for the retraction.”

                    Why did Dr. Bais, who is also a o-author of several other retracted papers, and now an Associate Professor at the University of Delaware [1], strongly disagree? Why were his disagreements not published?

                    Finally, Ruth (commenting on this page), is that you as the co-author of this retracted paper?

                    [1] http://canr.udel.edu/faculty/harsh-bais/

                    JATdS

                    September 7, 2014 at 7:34 am

        • JATdS:

          http://crb.agsci.colostate.edu/

          It would not be the first time in recorded history that a university creates a new website, but does not remove the old pages. I would not be surprised if the page I linked to above is already the third or fourth version since the link you yourself found.

          Marco

          September 7, 2014 at 3:41 am

          • I am interested in this case, as a plant scientist and science activist. Collating all available information, and with the objective of understanding if there are any other papers published by this group that may be affected by the 7 known retractions and some of the errata, I decided to contact Prof. Jorge M. Vivanco and 12 of the co-authors (Dayakar V. Badri, Jacqueline M. Chaparro, Daniel K. Manter, Enrico Martinoia, Harsh P. Bais, Balakrishnan Prithiviraj, Ajay Kumar Jha, Travis S. Walker, Frank R. Stermitz, Tiffany L. Weir, Corey D. Broeckling, Mark W. Paschke, in no particular order) on retracted papers for which an e-mail could be traced. This is an extremely important case in plant science, and the fact that discussion seemed to have fizzled in 2011-2012 indicates that so many gaps in our understanding remain. The plant science community will no doubt benefit tremendously from this experience, and in order to hold the authors, all of them, accountable for their papers, and the errors they contain(ed) and the effects that they have had on other literature, I have decided to post my e-mail to them publically here at RW. I hpe that the authors will take this opportunity of providing more in-depth analysis of what has been going wrong in that laboratory.

            “Dear Prof. Jorge M. Vivanco,
            (in fact, I encourage as many co-authors in CC as possible to comment)

            I recently became aware of your 7 recorded retracted papers (and several errata/corrigenda) through blog entries at Retraction Watch:

            http://retractionwatch.com/2013/10/30/image-manipulation-leads-to-fifth-retraction-for-plant-research-group/

            http://retractionwatch.com/2011/03/02/a-nature-chain-retraction-for-arabidopsis-paper-and-some-unanswered-questions/

            I have also noticed that you (or any of your co-authors who share communal public responsibility if considering the new authorship guidelines of the ICMJE) have not provided a very satisfactory or detailed response to these public notices at Retraction Watch, which is the reason why I am also CC’ing your co-authors* (for whom an e-mail could be traced) in a bid to have maximum open discussion and accountability, factors that are quintessential to science.

            I am planning to write a small case study on your retractions and errata, and their implications in plant science, given your extremely high profile in the history of plant science over the past 2-3 decades or so, because they represent an important impact on plant science, I believe. When the draft is ready, I will send it to you and your co-authors for counter-critique and to give you an opportunity of correcting any factual errors.

            In the meantime, I have four queries:
            a) What is your personal or official position and interpretation of these 7 retractions?
            b) Are there more than 7 retracted papers? If yes, could you please indicate which cases are missing at Retraction Watch.
            c) Why are your 2009-2014 publications not listed on your CSU web-page (http://lamar.colostate.edu/~jvivanco/publications.htm), including the retracted papers? It appears as if you have more than one web-page with different, contrasting and inaccurate/incomplete lists of publications. Why is that and Colorado State University approve of this?
            d) Would you be willing to make the PDF files all of your papers (including dozens of book chapters and journal papers) available for post-publication peer review by specialists?

            I warmly and openly invite you and all of your co-authors to provide comment at Retraction Watch and to give deep and complete insight as the public debate expands. Consequently, this e-mail will be posted there in a bid to ensure public (particularly to the plant science community) accountability.

            I look forward to your response and to having your fullest collaboration as this case study gets developed, and published. This forms part of a wider effort to understand the issues that underlie retractions in the plant sciences within the context of post-publication peer review [1]. There are also follow-up queries and even some concerns about the ensuing careers and/or papers of some of the co-authors of the retracted papers, but these will be natural follow-ups to the core story. For example, why is Dr. Bais’ web-page outdated, and without a list of his publications, including the retractions (http://maint.academicwebpages.com/bais/people/bais.html), why did Dr. Bais object to at least one retraction, but did not have the opportunity of explaining himself in detail?

            These are all issues that remain unclear and that need to be resolved, as I see it, before trust can be regained about papers that you (and your co-authors) have published, are publishing and will undoubtedly continue to publish from now on.

            Sincerely,

            Jaime A. Teixeira da Silva

            Reference:
            [1] http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00485/full

            * PS (regarding the CC list)
            Dayakar V. Badri (CSU), Jacqueline M. Chaparro (CSU), Daniel K. Manter (USDA), Enrico Martinoia (Univ. Zurich), Harsh P. Bais (now Delaware Biotechnology Institute), all from retracted FPS paper;
            Balakrishnan Prithiviraj (now at Dalhousie University, Canada), Ajay Kumar Jha (CSU), Frederick M. Ausubel (Harvard Medical School), all from the retracted Nature Letters paper;
            Travis S. Walker (CSU), Frank R. Stermitz (CSU), all from the retracted JAFC paper (incl. Dr. Pais);
            Tiffany L. Weir (CSU), Corey D. Broeckling (CSU), Mark W. Paschke (CSU), all from the 2008 Phytochemistry paper with an erratum.
            The e-mails of Kathleen M. Halligan, Sang-Wook Park, Ravikanth Veluri, and Tommaso A. Foderaro (Roche Colorado Corporation) of the retracted Phytochemistry papers could not be identified for comment. Nor could the e-mails of Naira Quintana, Jiang Du, Julie P. Rieder (formerly CSU) from the 2008 Phytochemistry paper with an erratum.
            No additional co-authors of papers subjected to an erratum, corrigendum or expression of concern have been contacted.”

            Jaime A. Teixeira da Silva

            September 7, 2014 at 9:21 am


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