PLoS ONE GMO cassava paper retracted after data “could not be found”
The authors of a paper suggesting that cassava, a starchy vegetable that’s a major food source in much of the developing world, could one day be turned into a food staple “capable of supplying inexpensive, plant-based proteins for food, feed and industrial applications” have retracted it, following an institutional investigation that failed to find critical supporting data.
Here’s the notice for the PLoS ONE study, “Transgenic Biofortification of the Starchy Staple Cassava (Manihot esculenta) Generates a Novel Sink for Protein:”
Following the publication of this article, the authors have been unable to confirm the presence of the zeolin gene within the transgenic cassava plants in several subsequent studies. This raises concerns about the validity of the results reported in the article.
Additionally, the Committee on Research Integrity at Donald Danforth Plant Science Center has carried out an institutional investigation which revealed that significant amounts of data and supporting documentation that were claimed to be produced by the first author could not be found. Given that the validity of the results could not be verified, and in line with the recommendation issued by the corresponding author’s institution, the authors retract the article.
The authors apologize to the readers.
The paper’s first author is Mohammad Abhary, who left the Danforth Center in mid-2011, and the corresponding author is Claude Fauquet.
The study has been cited five times, according to Thomson Scientific’s Web of Knowledge. It was funded by the Gates Foundation through its BioCassava Plus program, and cassava research is an important part of The Danforth Center’s portfolio. We know that because Ivan visited their ever-expanding greenhouse earlier this year, after being invited to give a talk on responsible conduct of research. (The Danforth Center offered to pay Ivan’s travel and an honorarium, but we declined.)
Danforth president James Carrington tells Retraction Watch that Fauquet brought the problems to his attention earlier this year, after members of Fauquet’s lab were unable to replicate the work. Questions arose shortly after the paper was published, in January 2011, when researchers tried to extend the findings. A more systematic analysis, Carrington said:
indicated that the materials that were published in the paper were not as they were described, or that the materials that were described could not be found.
By the time the issues reached Carrington’s desk, members of Fauquet’s lab had done “a fair bit of experimentation” and “additional re-analysis of the materials.” The key finding was that panel C of Figure 1 in the paper, which purported to show the presence of two proteins — p35S zeolin and pPatatin zeolin — could not be replicated. Carrington:
The transgenic plants that were supposed to contain those transgenes, plants labeled as such, did not contain what those plasmids were supposed to contain. In the re-analysis, both the plasmids and the transgenic materials were found to be lacking the key genes.
That disclosure — equivalent to an allegation of scientific misconduct, said Carrington — triggered the formation of a Research Integrity Panel, as described in Danforth’s Research Integrity Policy.
We asked Carrington what investigators thought was actually in panel C, if it was not what it seemed to be:
We could not come to conclusive proof about how the data were generated. As referenced in the retraction, however, the original data on which these figures were based, and original data on which other figures in paper were based, most of that original data could not be found. The specific route by which these were produced we could not determine.
The samples that should have contained the answer were the ones stored in the lab.
However, the materials in the tubes, and other plant material, those materials lacked what they should have had. They did not contain the zeolin genes, as indicated in the retraction. Instead they had what was essentially an empty vector. Recombinant plasmids were supposed to have a gene called zeolin, which as the paper explains was intended to increase the protein content in cassava tubers. However, when the plasmids and transgenic materials were re-analyzed during the course of in-lab investigation and the committee on research integrity investigation, indeed there were plasmids, and indeed the plants were transgenic, but they did not include the zeolin.
The results of the investigation mean that
the data do not stand, they cannot be repeated, and therefore the paper is being retracted and therefore none of the results can be validated.
However, Carrington noted, the retraction does not invalidate other work on cassava.
Indeed, it is possible to increase the nutritional content of cassava. There’s at least one other nutrient we know we can increase, a vitamin, not published yet. We can increase the resistance to viruses, all done quite reliably and reproducibly. The principle of changing the nutritional value and resistance to viruses, that principle has been established quite well…It doesn’t condemn the approach, nor some of the other work done with cassava.
The Fauquet lab has not gone back to redo the study properly, Carrington said, because the Gates grant that funded the project ended a few years ago. And the Danforth notified the Gates Foundation — which continues to fund other Center work — early in the process, sometime earlier this year, as per their research integrity policy. The disclosure — the Foundation was kept up to date throughout the investigation — has had no effect on funding from Gates, Carrington said.
Abhary, meanwhile, left the Danforth — and the U.S. — in mid-2011. He had been at the Center since early 2006, carrying out his graduate school research. Carrington notes that he did not learn of the questions about the work until Abhary had already left the Center.
The PLoS ONE paper was the only one by Abhary while he worked at the Danforth, Carrington said:
But we’re looking very carefully at secondary and tertiary instances of science that was done that might have used things that were provided. I cannot say there will never be any revelations in the future related to things during his time in the Fauquet lab.
The case is the first such investigation since the Danforth instituted its research integrity policy in 2011. It’s also the first that Toni Kutchan, who served as the center’s research integrity officer until she became director of research, has ever dealt with. About two years ago, notes Kutchan, the Danforth put additional procedures into place in response to NSF Responsible Conduct of Research requirements. That included speakers, other sessions, and
a new policy to make people more aware of requirements for the retention of data, storage of samples, so it is ultimately transparent so you can show your materials. We stepped that up more this year. We’re also discussing now, although products are not quite there, going to electronic notebook keeping.
Original documents could not be found, and proper documentation of the experiments were not found, for example, the types of things you would normally put in a notebook to explain how the experiment was done, the results and experimentation.
This really shined a bright light on the need to document research through processes that were well-known through training, and that could be tracked, whereby data were preserved for periods of time that met national standards.
The case will be the subject of a session designed to limit the likelihood of similar incidents, Kutchan said.
Carrington tells Retraction Watch:
We’ve taken this really seriously.
We have to agree, both based on the details he was willing to share, and the fact that he and Kutchan spent 45 minutes on the phone with us on short notice. If only every institution were the same.