Yoshinori Watanabe data manipulations: much worse than officially presented

Yoshinori Watanabe data manipulations: much worse than officially presented

Earlier this months, a research misconduct scandal in molecular cell biology broke out in the big news. Yoshinori Watanabe, Japanese researcher of cell division and how cells separate their replicated DNA during mitosis and meiosis, was found guilty of scientific misconduct by his University of Tokyo (read the news here and here). This followed an investigation initiated in the fall of 2016, after anonymous whistleblowers submitted to the university a report accusing 6 Tokyo research groups of data manipulation, first and foremost, Watanabe (I managed to obtain this dossier, and publish it below).

As the outcome of the University of Tokyo investigations, which concluded on May 31st 2017, misconduct was determined in 5 publications from Watanabe’s lab, which appeared between 2008 and 2015 in the elite journals like Science, Nature and Nature Cell Biology. However, the whistleblower dossier lists 7 papers, one of them a paper in Cell from 2015 with duplicated gel images, and a 2011 EMBO Reports paper which contains a western blot which was obviously digitally retouched to remove unwanted bands. Watanabe’s assistant professor Yuji Tanno was also found guilty of misconduct, and indeed his 2015 Science paper with Watanabe looks like a total train wreck of data manipulations.  Yet it seems there is a tendency to present Watanabe’s deeds as mere mistakes (though grossly inappropriate ones) by a great genius scientist, who was confused by the complexity of rules on data acquisition and incidentally broke some while producing outstanding and absolutely reliable top-level research. Some of his peers seem to be calling for leniency or at least some understanding for Watanabe. The selected evidence from the whistleblower dossier which I post below suggests that Watanabe knew perfectly well what he was doing, and he did so in order to produce desirable results which his lab experiments failed to deliver, and which he needed in order to impress the choosy elite journals.

Continue reading “Yoshinori Watanabe data manipulations: much worse than officially presented”

Voinnet’s sidekick Dunoyer welcomed at Nature Plants, despite retractions and admitted misconduct

Voinnet’s sidekick Dunoyer welcomed at Nature Plants, despite retractions and admitted misconduct

The Olivier Voinnet scandal of almost two decades-long research misconduct and data manipulations has reached its logical conclusion. The French plant pathogen researcher, and everyone who helped him manipulating and publishing dishonest (and occasionally retracted) papers was either forgiven or declared as fully reformed. The siRNA-co-discoverer Voinnet who, cynically put, was too big to fail, remained professor at ETH Zürich and kept his ERC funding. He is meanwhile back to publishing in exactly the same elite journals where he had to retract and correct papers for manipulations. Of all his “partners-in-crime”, only his dependent right-hand man (or sidekick) Patrice Dunoyer was ever investigated, and as punishment suspended for an entire month by his French employer CNRS. His lab was about to be dissolved, but the Nature Publishing Group came to rescue and accepted his paper (Incarbone et al 2017) just in the nick of time (it’s not even Dunoyer’s only recent publishing success, another one is Montavon et al 2017 in Nucleic Acids Research). The accompanying editorial in Nature Plants, written by the chief editor Chris Surridge can only be described as bizarre, and is titled: “Giving research a sporting chance“. Surridge, who apparently sees data manipulation as a professional sports in race with doping detectives, wrote:

“Dunoyer has been a long-time colleague and collaborator of Olivier Voinnert, and recently a number of their studies, three with Dunoyer as first author, have been retracted while a number more have had formal corrections published to address problems with presented data. However, these instances were investigated by the CNRS and Dunoyer served a temporary suspension as a result. We therefore treated the study we received as we would any other. It was accepted following two rounds of review, during which it was seen by four reviewers. The published paper contains substantial supplementary information (SI). Along with 10 additional figures, there are a further 12 pages presenting the raw data from which the presented figures have been assembled”.

Continue reading “Voinnet’s sidekick Dunoyer welcomed at Nature Plants, despite retractions and admitted misconduct”

Post-publication peer review of a multimillion-dollar-heavy Nature paper, by Ana Pedro

Post-publication peer review of a multimillion-dollar-heavy Nature paper, by Ana Pedro

The Portuguese cancer researcher Sonia Melo has now achieved the status of a zombie scientist. After an internal investigation which records are kept secret, she was cleared of all suspicions of scientific misconduct and re-installed as group leader at the Instituto de Investigação e Inovação em Saúde (I3S) in Porto (see my report here). This despite an impressive PubPeer record of data integrity concerns, and despite the fact that the European research society EMBO revoked Melo’s Installation Grant funding after having determined problems with her publications. EMBO nevertheless stick to their decision, but Melo’s Portuguese funders like Fundação para a Ciência e a Tecnologia (FCT) apparently see absolutely no need to reconsider their support, certainly not after the I3S whitewashing. Melo previously had to retract a paper (Melo et al, Nature Genetics, 2009) for data manipulations, her other works were however found not problematic by the I3S commission. In two papers in Cancer Cell (Melo et al 2010 and Melo et al 2014), the alleged duplications were apparently proven not to be duplications. As I learned, this was probably because while the top part of the gel images indeed did look suspiciously similar, the lower parts were clearly different. A possibility of digital image splicing was not considered, as it seems. In any case, even if the top bands are indeed the same, it doesn’t really matter. Cell editorial offices made on several occasions perfectly clear that data integrity is not one of their top concerns.

f5krhwn
From Melo et al, Cancer Cell, 2014. Cannot be a duplication, according to I3S. Source: PubPeer

Continue reading “Post-publication peer review of a multimillion-dollar-heavy Nature paper, by Ana Pedro”

Sonia Melo fully exonerated and reinstalled as PI by her Portuguese employer I3S

The Portuguese cancer researcher Sonia Melo has been cleared of all suspicions of scientific misconduct by her employer Instituto de Investigação e Inovação em Saúde (I3S) in Porto. She is now re-installed as research group leader, despite of an earlier EMBO investigation which stripped Melo of her start-up funding and the title of EMBO Young Investigator. Previously, PubPeer users raised strong suspicions of data manipulations as well as concerns about irreproducibility and artefactual results based on questionable reagents. The affected publications were authored by Sonia Melo during her stays in the laboratories of Manel Esteller in the Spanish city Barcelona (see my report here) and Raghu Kalluri at MD Anderson in Texas, USA.

Neither of her former supervisors has been investigated by his respective host institution in connection to PubPeer-posted concerns about their publications with or without Melo. Aside of the EMBO investigation (the findings of which were only made available to Melo’s former and current employers), I3S was the only institution to initiate their own investigation. Unfortunately, its report is not available to the public either. All we now receive is a press release, in which I3S admits to the existence of data manipulations (interpreted as cases of “negligence” which “do not compromise the scientific content”) in 3 of Melo’s papers: the now retracted Melo et al, Nature Genetics, 2009, plus Melo et al, PNAS 2011 and Melo et al, Nature 2015. Both papers will be corrected; the latter was seminal in the fundraising of at least $80 Million for the purpose of developing a commercial cancer diagnostics test. No further Melo publications were investigated, including this one: Continue reading “Sonia Melo fully exonerated and reinstalled as PI by her Portuguese employer I3S”

Pontus Boström: cheater carousel in Sweden

Pontus Boström: cheater carousel in Sweden

Sweden is a tolerant country, which is a very good thing. Unfortunately, sometimes this Swedish tolerance seems ill-advised. Dishonest scientists caught faking data are happily given another chance and fat funding, like the case of the diabetes researcher Pontus Boström shows.

This scientist was found to have fabricated data during his PhD studies with late Sven‐Olof Olofsson at the University of Gothenburg, and went afterwards to publish a seminal paper in Nature with the biggest godfather of the diabetes research field, Bruce Spiegelman. Also this high-impact study turned out to be irreproducible by other researchers and a likely artefact of erroneous antibody use. Yet due to his impressive publishing record and unwavering support of the mighty Spiegelman, Boström was invited to head a group leader position at several Swedish universities, while he settled on the best offer by the Department of Cell and Molecular Biology at the prestigious Karolinska Institutet (KI) in Stockholm, supported by the elite EU funder ERC.  All despite his previous convictions of research misconduct in Gothenburg and ensuing retractions of two meeting abstracts, which were at all times perfectly known to all parties involved. Continue reading “Pontus Boström: cheater carousel in Sweden”

Conspiracy Theory: Is NPG being assimilated by Frontiers???

The post below is a satiric parody, though the general facts and the document I publish are real and true.

On Monday, the 13th of June, Nature Publishing Group (NPG) journals shut down. Instead of high-impact papers, all the bedazzled scientific community could see was: Internal Server Error (500).

The website collapse was first noticed with the NPG journal Scientific Reports, but then spread upwards the impact factor scale to Nature Communications and even Nature itself.

What happened? The NatureNews team, begged to give any insights, remained suspiciously silent. No announcements were made, questions remained unanswered. Continue reading “Conspiracy Theory: Is NPG being assimilated by Frontiers???”

The stem cell faith healers, or magic inside your bone marrow

The stem cell faith healers, or magic inside your bone marrow

Bone marrow stem cells are magic, they can do everything. If you don’t believe it, you are simply a loser scientist and will never get funded.

Prior to his bombastic fall from grace, the celebrity surgeon and professor of regenerative medicine Paolo Macchiarini was considered a genius stem cell wizard and a miracle healer. He not only fully trusted bone marrow cells to generate any kind of tissue inside his patients, nay, he also published his results in highest profile journals like The Lancet (which, by standard academic definition, is proof enough that his theory and methods were valid). Macchiarini did not chase money, neither funding nor salary, it was chasing him. Even after media revealed mass patient deaths and gross inconsistency between Macchiarini’s published reports and the actual medical files of his patients, the Elsevier-run Lancet is reluctant to retract his papers.

Simply put, the faith in the force of the bone marrow stem cells is stronger than their science. These cells are often referred to as mesenchymal stem cells; basically they are those undifferentiated cells from the bone marrow which do not carry the established markers of hematopoietic (blood-generating) stem cells.  What these “mesenchymal stem cells” are actually a mixture of, and which types of cells or tissues they are really able to differentiate into, is still a subject of an ongoing research. Unless you are a stem cell believer, that is, then you don’t bother with such details. Continue reading “The stem cell faith healers, or magic inside your bone marrow”