Tag: biochemistry

The Perennial Northern Blot of Lopez-Otin

The Perennial Northern Blot of Lopez-Otin

On the Iberian peninsula, there seems to be a tradition to give well-connected scientists suspected (or even convinced) of data fudging an award. In Spain, Carlos López-Otín, Professor of Biochemistry and Molecular Biology at the University of Oviedo, was given a Mentoring Award from the elite journal Nature, on recommendation from Spanish academia and despite evidence of data irregularities in his papers. This prompted my readers, in particular the famous pseudonymous data integrity sleuth Clare Francis, to comment on on PubPeer and on my site (as “Zebedee”) with additional evidence, which made Lopez-Otin’s scientific credibility look progressively worse and worse, with each new post.

Eventually, an image of a Northern blot (showing expression of mRNAs which code for proteins) was found to appear recurrently across several papers from that Oviedo lab, where the authors pretended it was a newly produced analysis. In reality, it was a “library” loading control reused so the authors could re-run same RNA gel of human tissue lysates over the years and never check ever again what they have actually loaded on their gels. Eventually Lopez-Otin et al even stopped caring what order of samples that original loading control had.

Clare Francis was soon joined on his quest for the Perennial Northern Blot of Oviedo by Elisabeth Bik, famous microbiology blogger and image duplication detective, and my regular contributor (also pseudonymous) Smut Clyde, who now presents you the findings of no less than 23 appearances of that same northern blot in 23 publications from Lopez-Otin’s lab in the guest post below. It is just as convincing as if the Spanish actor Antonio Banderas appeared in 23 different films still dressed in same costume from his 1995 hit Desperado, carrying same guitar case. Incidentally, also Lopez-Otin’s Perennial Northern Blot made its first appearance at around that year.
 Continue reading “The Perennial Northern Blot of Lopez-Otin” →

Lill space-time-blot anomaly in Marburg

Lill space-time-blot anomaly in Marburg

The biochemistry research lab of professor Roland Lill at the Philipps University Marburg in Germany is a place where space, time and western blot continuum collapses into an anomalous singularity, where paradoxes abound, but only one fact remains certain:  there was never any data manipulation in the lab of this senator of the German Research Council (DFG). Only misunderstandings (here) and solid science, with sometimes unorthodox figure assembly methods (here).

One of those anomalies is the recent correction by Lill and his former PhD student Heike Lange (now tenured CNRS researcher at The Olivier Voinnet Institute for Research Integrity in Plant Sciences (IBMP) in Strasbourg, France, published in the prestigious journal PNAS in March 2018. A western blot was found to contain duplicated, triplicated and mirrored bands, and was replaced with a version of same gel, its irregularities fixed. What exactly the new old figure shows, is not clear. The Ombudsman of Marburg University insists that no digital image versions of the western blot exist, only some almost two decade old thermo-paper printouts which were shared only with PNAS. Neither can those archive documents be scanned or photographed, as it will probably either destroy them, or alter the results they show. A PNAS editor however admitted to me that the correction actually shows a pdf file which the authors Lill and Lange supplied by email, a gel image which again seems to be different from the original thermoprinter records. Yet also this digital pdf file cannot be shared, probably because otherwise the time-space continuum will collapse and our universe, or at least the Marburg lab of DFG Senator Lill might end up teleported back into the year 1999, when the prints were made. And anyway, all two decade old experiments were faithfully reproduced by the Lill lab just now, using exactly same reagents. Those results however are also apparently not for sharing.

Continue reading “Lill space-time-blot anomaly in Marburg” →

Sharma’s bad karma, or is anyone peer reviewing nanotechnology?

Sharma’s bad karma, or is anyone peer reviewing nanotechnology?

Nanotechnology is the way to cure cancer and to save humanity of all its problems in general, often using all possible plants and their parts to create nanoparticles. This is what one learns from certain publications which often appear in chemistry journals, where one can be quite sure no biologist was ever invited to peer review those. In fact, one wonders if anyone at all ever peer reviewed them. That is certainly the impression one gets from the evidence gathered by my now regular pseudonymous guest contributor, “Smut Clyde“. Below, he will tell us a tale of the photoshopping team around the physicist Prashant Sharma at the Indian School of Mines in Dhanbad, India. There are currently two dozens of Sharma papers flagged on PubPeer, several feature a regular coauthor Rashmi Madhuri, who was apparently threatening hers and Sharma’s critics with “an International cyber complaint and formal police complaint” and “a case of defamation of worth 50,000 $ (per author)”.

Besides already available PubPeer evidence of what looks like the most lazy approach to data photoshopping, Smut Clyde lists a case of a single cell culture microscopy image which found its way in no less but (currently) 8 papers by Sharma et al, in different context. There are also examples of some apparently very insolent cloning of nanoparticles and other stuff inside same image, that bad that one feels ashamed for everyone involved. Certainly for the respected journals.

In those cases, the expert nanotechnology editors and reviewers do not have an excuse to have missed the evidence of gross data manipulation due to being dazzled by heavy biology they are not really experts in. Here, it was obviously duplicated electron microscopy, spectra analyses and chemical reaction kinetics which did not at all look like they represented original experimental data. Maybe they are supposed to stand in as illustration, and the authors promised to send their real research data afterwards, and then forgot.

Except that in one case, Sharma et al did have to fix a publication with a Corrigendum, which apparently shows the same photoshopped collage, but slightly zoomed out. For the esteemed editor-in-chief of ACS Biomaterials and professor at Tufts University School of Engineering, David Kaplan, this was apparently good enough. The irony: this was only caught because the original manuscript version is available on the “pirate” site Sci-Hub, which hosts almost all paywalled scholarly publications. The same site, which ACS (American Chemical Society) just now successfully sued in US court and had several of its internet domains removed, to prevent nosy people from accessing ACS property without paying. All, as ACS declares: “for the benefit of Earth and its people”.

After the evidence against Sharma et al papers began to pop up on PubPeer, a strange thing happened. Massive wave of comments targeting many papers from Sharma’s institutional colleague at Indian School of Mines, Sagar Pal, appeared on PubPeer, which were basically randomly picked figures from Pal’s papers combined with a comment declaring those to be fake. The tone occasionally tried to emulate the jovial descriptions of irregularities found in Sharma et al papers. Yet those accusations were all without exception ridiculously empty and utterly unfounded, and indeed PubPeer removed them soon (possibly after my tweets).  Continue reading “Sharma’s bad karma, or is anyone peer reviewing nanotechnology?” →

DFG Senator Roland Lill explains how to do science properly

DFG Senator Roland Lill explains how to do science properly

My earlier article about strange image irregularities in the publications of the German mitochondria researcher Roland Lill seem to have motivated this pre-emeritus biochemistry professor of the University of Marburg to come to PubPeer and address the issues. While in his earlier statements he simply waved off all concerns of western blot band duplications, this time and with other papers he admitted those, while presenting the original Western Blot scans. Together with the first author on two such papers, Janneke Balk, Lill explained why copy-pasting western blot bands, sometimes on top of other gel images, had nothing at all sinister in it, but used to be somewhat of a normal research practice 10-15 years ago. And in some cases, gel bands can naturally duplicate themselves.

Any advice on research integrity from the side of a Senator of the German Research Foundation (DFG) and of the German Academy of Sciences Leopoldina is certainly most valuable, this is why I will present here his explanations, so the younger generation of scientists can learn about correct figure preparation, including the proper use of gel band copy-paste function. The past evidence was forwarded to me by a reader of my site.  I will also offer Professor Lill and you for debate another example from his past publication, where a western blot was duplicated in different context. This was forwarded me from yet another reader of my site.  Continue reading “DFG Senator Roland Lill explains how to do science properly” →

Data integrity conspiracy against German research senator Roland Lill?

Data integrity conspiracy against German research senator Roland Lill?

Roland Lill is the quiet star of German molecular biology. The 63-year old professor works at the University of Marburg, on mitochondria, using yeast as a model organism. Lill is also since 2014 member of the Senate at the German Research Foundation (DFG), re-elected just recently, where he represents the interests of German molecular biologists and decides on federal funding distribution and research policies. Since 2016, the Marburg professor is also Senator for Biochemistry and Biophysics at the Leopoldina, which is the German Academy of Sciences. Furthermore, Lill is EMBO member since 2013 and he also used to be Fellow of the Max Planck Society.

Lill’s research focus is on iron-sulfur biogenesis, and his achievements for German science are indeed strong as iron, as evident by his awards and medals (including the Leibniz Prize of €1.55 Mn in 2003), his impressive funding acquisition success and publication record. Recently however, a sulfuric smell of rotten eggs emitted from the whistleblowing platform PubPeer, tainting his legacy. Currently 9 Lill papers are affected, the evidence looks worrisome, and might indicate possible data manipulations. Mostly it is about apparently duplicated gel bands. Luckily however, most papers are 13 and more years old, nobody would expect Professor Lill to have stored the original data for so long, even if it was ever available. The despicable attack on Professor’s Lill research record will be surely thwarted by the journals’ reluctance of dealing with problems in old papers, and of course by the tremendous respect and influence this Senator enjoys in German academia. In fact, both DFG and the two research integrity Ombudspersons of the University of Marburg refused to comment on the PubPeer evidence. Leopoldina announced to me to have the “accusations” addressed by their Ombudsman; DFG mentioned to have had the PubPeer information “forwarded inside the house”.

Continue reading “Data integrity conspiracy against German research senator Roland Lill?” →