Melo and Kalluri defend discredited Nature paper with preprint, where they admit data “adjustments”

Melo and Kalluri defend discredited Nature paper with preprint, where they admit data “adjustments”

Sonia Melo, the Portuguese cheater scientist and her former US-boss Raghu Kalluri issued some days ago a biorxive preprint, which sole purpose is to defend their discredited Nature paper from 2015. There, they originally claimed to have found a unique biomarker for early pancreatic cancer, a much hailed promise to save lives of many cancer patients. However, soon it was found out that the results were not reproducible, the Nature paper Melo et al, 2015 contained evidence of data manipulation (just like other Melo publications with Kalluri and her PhD boss Manel Esteller). The antibody, on which the central evidence for the allegedly unique pancreatic cancer biomarker glypican 1 (GPC1) was based, proved to be delivering staining artefacts; the vendor Thermo Scientific soon discontinued it. Even Kalluri seemingly distanced himself from his results.

Now in their new preprint, Melo and Kalluri claimed to have perfectly reproduced their original 2015 GPC1 results with a new antibody, which however proved to be likely exactly the same as the old one, but sold by a different vendor.  As soon as this became known, the authors issued a new preprint version just two days later, featuring yet another entirely new GPC1 antibody, with an utterly new set of results to complement the 6 day older ones.  However, also these results are most likely useless. The authors namely freely admit in their preprint method description to have intentionally manipulated their flow cytometry (FACS) data to obtain a positive signal specifically where needed. It seems that one full professor and three research group leaders have absolutely no understanding about data integrity in flow cytometry (or maybe even in research in general). Obviously, they simply adjust the FACS settings for each sample in an analytic row any way it pleases them until they see a result they like. As they don’t even hide it, they seem to think this is the proper way to do science. Continue reading “Melo and Kalluri defend discredited Nature paper with preprint, where they admit data “adjustments””

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.

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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”

Manel Esteller, the Schrödinger cat of Barcelona

Manel Esteller, the Schrödinger cat of Barcelona
This text was first published on September 30th as Spanish translation on Hipertextual.

The Spanish Institut d’Investigació Biomèdica de Bellvitge (IDIBELL) in Barcelona has discovered a new application of the famous Schrödinger uncertainty theory, by extending quantum mechanics from single atoms to entire scientific publications and its authors. The traditional Schrödinger cat inside a box with a poison-releasing radioactivity detector can be simultaneously dead and alive, and you never know which until you open the box. According to IDIBELL, a senior scientific research group leader can be also simultaneously 100% responsible and utterly not responsible for any given scientific publication of his, depending on the nature of observation. Such a “Schrödinger cat”-scientist is Manel Esteller, cancer researcher and director of strategic projects at IDIBELL. On the one side Esteller is being hailed and awarded with highest prizes for his publications on cancer genetics (most recently the Gold Medal of Honour by the Catalan Parliament), from the other side he is being declared as entirely not responsible for these same research papers, as soon as any evidence for data manipulations in them surfaces. Esteller’s quantum state of responsibility for his own research oscillates between yes and no depending on whether you open his IDIBELL box in order to give him a prize or to report suspected research misconduct.

This is how the Barcelona Theory of Quantum Irresponsibility developed.

Continue reading “Manel Esteller, the Schrödinger cat of Barcelona”

The mysterious public career execution of Robert Ryan

The mysterious public career execution of Robert Ryan

On August 24th I received an anonymous email over my website from a „Concerned Microbiologist”:

“I would like to bring the following to your attention on Robert P Ryan at the University of Dundee. https://pubpeer.com/search?q=Robert+P.+Ryan
He holds several high profile research grants and has won several awards. He is under investigation at the University of Dundee.
He has also featured in articles signing his praises in terms of his research achievements.
http://www.scotsman.com/news/university-of-dundee-s-rising-science-stars-1-3932042

Only days after, on August 28th, big news broke out in Scottish and Irish media. The Scotsman brought the headline: “Leading scientist suspended amid ‘research misconduct’ investigation”.  The newspaper then indicated that Ryan has to answer for suspected image manipulations in his papers:

“It is alleged he used identical images across multiple papers, claiming they were different strains. In some cases, it is alleged the evidence was flipped or rotated, which could indicate an “intent to deceive”, according to one source. The extent of the alleged misconduct is unclear, but the source indicated it is alleged to have spanned “a number of years” and involved numerous prestigious journals”.

Similar reports appeared on the same day in The Irish Times, The Courier and Herald Scotland, the latter also wrote:

“It is understood his research group at the university has been dissolved, with PhD students and staff scientists reallocated elsewhere while a formal investigation takes place”.

Continue reading “The mysterious public career execution of Robert Ryan”

Sonia Melo loses EMBO YIP Funding, suspended as PI

Sonia Melo, the Portuguese scientist accused of data manipulation and misconduct, now loses her EMBO Installation Grant funding by the European research agency EMBO. The EMBO funding was of ”50,000 Euros annually for three to five years” for her research lab at the Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup) in Portugal, as well as “benefits similar to those of the EMBO Young Investigator Programme“.  EMBO has began their investigation into Melo’s publications in January 2016  after they were made aware of the accusations of data manipulation raised against Melo on PubPeer (see details here).

As I was informed by Tilmann Kiessling, Head of Communications at EMBO:

“as a follow up to your reporting on Sonia Melo, this is to confirm that EMBO has withdrawn the installation grant awarded to her. After EMBO had become aware of the allegations against papers authored by her we set up a committee to investigate these allegations. After a thorough analysis of all papers that had formed the basis for her application for the grant, the committee concluded that the body of work upon which the selection for an installation grant was made contained evidence of a level of negligence in handling and presenting data that would have precluded a recommendation for an award. The committee therefore decided that Sonia Melo should not become a member of the EMBO network of Young Investigators and Installation Grantees, and that the installation grant will be revoked. This has been communicated to Sonia Melo and her home institution on February 29.”.

As I previously reported, Melo’s former PhD advisor, Manel Esteller was intended to be investigated by his host institution, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL) in Barcelona (which for now is not going to happen, see update below). Melo and Esteller already had to retract a paper (Melo et al, Nature Genetics 41, 365–370, 2009) due to image duplications. Continue reading “Sonia Melo loses EMBO YIP Funding, suspended as PI”

Sonia Melo case: PhD advisor Esteller sham-investigated, postdoc PI Kalluri with $ 80Mio COI

Sonia Melo, Portuguese cancer researcher and recipient of the prestigious EMBO Installation Grant, now has her publications investigated by EMBO for suspected image manipulations. Her current and former research institutions are apparently actively avoiding any attempts to scrutinise her papers, some due to very heavy financial conflicts of interest. Yet my information suggests that Melo’s former PhD advisor and co-author, Manel Esteller, is being presently investigated by his research centre in Barcelona.

Melo already had to retract a first-author publication from her PhD period with Esteller from the journal Nature Genetics. The retraction notice admits image duplications:

“We have recently become aware of the presence of duplicated images in the Figures 3 and 4 and Supplementary Figures 5 and 6 in our publication Nat. Genet. 41, 365–370, 2009, that were assembled according to the specified author contributions. We therefore retract the publication for the sake of the high standards we expect for research and scientific journals. All the authors have signed this statement”.

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Continue reading “Sonia Melo case: PhD advisor Esteller sham-investigated, postdoc PI Kalluri with $ 80Mio COI”