Research integrity Uncategorized

Faking Raw Data with an Iron Fist

"you can rest your concerns. As you can see, we have not manipulated any images." - Dr Arati Ramesh

A paper in Nature Chemical Biology was retracted, less than a year after it appeared.

The official reason: the authors lost access to raw data. The real reason: their “raw data” was utterly fake. They even falsified the time stamps on their Photoshopped “original data” images.

This story is a warning to all the institutional investigations worldwide scurrying to close a case and to dismiss the whistleblowers because the accused scientists presented a low-resolution picture of a purported gel, microscopy photo or a spectral analysis as “raw data”.

In our high-technology days, everything can be faked as long as nobody cares to look closer.

This was the paper:

Siladitya Bandyopadhyay, Susmitnarayan Chaudhury, Dolly Mehta , Arati Ramesh Discovery of iron-sensing bacterial riboswitches Nature Chemical Biology (2020) doi: 10.1038/s41589-020-00665-7

The study was published on 5 October 2020, its authors came from the Tata Institute of Fundamental Research in Bangalore, India. They claimed to have found an new iron sensing RNA molecule in bacteria, which they called “Sensei – short for Sense iron“, as an institutional press release celebrated, under the heading:

Sensei RNA: Iron fist in a velvet glove

“[…] the researchers then turned into crafty engineers. They tweaked the sequence of the RNA and identified the parts in the clover leaf-like structure that may bind iron. Then, they went one step further and made a small change in the RNA sequence which shifted the competence of RNA from sensing iron to now detect nickel and cobalt.

“This nanoscale engineering of iron sensing that we demonstrate, will hopefully set the stage for designing iron-biosensors which could be of use to both bacterial biology and biomedicine,” explains Arati.

This story is as much about discovery by serendipity, as it is about what the discovery has taught us – the versatility of RNA, the unbending specificity behind an RNA’s frail structure and its ability to sense something as fundamental as iron. What better way to honour it than by calling it Sensei, meaning teacher?”

There was no discovery, the study was completely fabricated. It was retracted in late June 2021. This was the notice:

The authors are retracting this Article because of issues with data integrity and reproducibility. Specifically, native gel analyses of natural and engineered Sensei RNAs (Figs. 3e and 5c) raised concerns of gel background similarities from different experiments. On learning this, A.R. requested an independent researcher with expertise in RNA research to attempt to replicate the same experiments. We now find that these data are not reproducible. Further, in the in vivo expression analyses, the RpoA control and +J41 western blots (part of Fig 4, Extended Data Fig. 8) raise concerns of gel band duplications. In addition, ITC curves (shown in Fig. 1f and Extended Data Fig. 4b) have raised concerns of inconsistent spacing between successive injections. We no longer have access to the raw data for these experiments and hence are unable to verify the salt-dependent binding affinities of Sensei RNAs.

Given that the key data supporting the iron ion-induced structural changes in Sensei RNAs—a central conclusion of the original paper—are now called into question, we believe that retraction of the work in its entirety is essential. The authors deeply regret this situation and apologize to the scientific community. All authors of the original study have agreed to retract the article and with this retraction text.

A.R. informed the institute about these concerns regarding data integrity, following which an independent inquiry was conducted. The inquiry committee also recommends that the Article be retracted.

The notice didn’t mention the massive Photoshop fraud, probably to speed up the closure of the case on the publisher’s side. Here a sample of bizarrely fake “raw data” which the authors uploaded as supplementary:

Leucanella Acutissima: “Regarding Fig 3E: In addition to some blurring/smudging of background surrounding the bands noted in post #1, the various source data gels contain numerous other irregularities, including extensive sharing and duplication of background features, as well as highly similar gel outlines (e.g., as boxed in red at the bottom of each). One of the gels also contains bands that appear to be duplicated (see bottom right), with horizontal or vertical stretching in some cases.

The Bangalore institute’s press release was issued in January 2021, long after the fraud was uncovered on PubPeer. Maybe this is why it ended with this sentence, as an insider joke:

“The real voyage of discovery consists not in seeking new landscapes, but in having new eyes.”

Well said. In October 2020, first criticism was posted on PubPeer by anonymous user Nepenthes Mindanaoensis who used their eyes to make a discovery:

Lanes 3-5 of Figure 3e are surrounded by a square, making it look like they were copy and pasted from somewhere else. I’m not sure how this can happen?

A good question. The three bands are clearly digitally pasted. Also, why was nobody at the publisher Nature Publishing Group checking the accepted manuscripts for such blatant irregularities.

Good thing authors of Nature family journals are required to provide raw data like full-length gel scans in the supplemental material. This is where fraud is often found: Spanish martyr saint Carlos Lopez-Otin and Harvard Medical School dean George Q Daley had to retract a Nature Cell Biology paper because its supplemental gel images were found to be very fishy. And in Lopez-Otin’s case, the raw data was not (visibly) falsified, it just didn’t match the corresponding main figures.

So right away, the prolific PubPeer commenter Leucanella Acutissima chimed in with additional findings from the supplementary records of Bandyopadhyay et al 2020, like the analysis shown above. There was more:

Figs 3E and 5D: The denaturing gels for these two panels show extensive (but not complete) background similarities, despite different band patterns and supposedly different experiments.”

And even more:

Figs 4B/4D: The two gels for Fig 4D show many similar and repeating background features with each other, as well as with the RpoA gel in Fig 4B, which is supposed to be an unrelated experiment. In addition, the RnhB gel in Fig 4B shows unusual background discontinuity suggestive of smudging or blurring.
Fig 4B vs. Extended Data 8C: The band patterns in two blots are unusually similar, despite being different experimental conditions. Also note that the shape of the perimeter (presumably the blot membrane) is identical in the two cases. Finally, adjusting levels shows that they share extensive background features.

Basically, the “raw data” the Bangalore authors uploaded to satisfy the publisher’s requirements, were fake. Fabricated in Photoshop. But this is not where the story ended.

The next day, last author Arati Ramesh commented:

We have uploaded the raw images as obtained from the instrument- so that you can rest your concerns. As you can see, we have not manipulated any images. […]

Original images can be accessed from this link (since original files are large in size we are unable to attach them here): https://drive.google.com/drive/folders/1KBP4DDsVoUeZnf7RDeQA7_kX2xazu8NO?usp=sharing Hope these points answer your concerns. The original images are all attached in this response so that no doubt remains.

This is what the provided “original files” contained:

Compsopogonopsis Leptoclados: “The author hasn’t explained why many blots have perfectly (pixel-by-pixel) repeating background patterns and/or bands

Fake gel bands were cloned and assembled on a fake gel background in Photoshop:

How can these bands and the surrounding background be so similar?

Others found more fakeries in Ramesh’s “original data”, also in the same Denaturing 3e.tif file. Here by L. acutissima:

From the raw image file named “Denaturing 3e.tif” (relating to Fig 3E):
From the raw image file named “Denaturing_Fe2NiCo,NiCo2Fe.tiff” (relating to Fig 5D):”

On 2 November 2020, Cheshire informed the journal. Then, someone had a look at the enzyme chemistry measurements, that being chemical engineering paper after all. Why, yes, these plots were fake also, fabricated also in Photoshop probably.

Pyrgulopsis Thompsoni:: “In Extended Data Fig. 4, the plots look more similar than one would expect. Even the background signal seems to be highly similar. The plots are not exactly similar, but we have to keep in mind that jpg compression of an image can introduce slight distorsions

The last author Ramesh pleaded:

We have submitted all the raw images. These images are procured from the GEL DOC system and have TIME STAMPS showing that they were performed on different days.”

On 11 December 2020, an Editor’s Note was posted by the journal:

“Readers are alerted that the reliability of data presented in this manuscript is currently in question. Appropriate editorial action will be taken once this matter is resolved.”

Ramesh stopped commenting. PubPeer users found more fraud, like this gel picture for Fig 4B, attacked with a smudge tool to remove undesired gel bands:

Had the authors published with another journal, where full-length gels are not required, basically anywhere with Elsevier, nothing would have ever come out. These cheaters may have been too trusting in their digital skills. Their paper was retracted in late June 2021, even if under the pretence of an irreproducibility problem. No reference to PubPeer or Photoshop fraud, the official reason provided by authors:

We no longer have access to the raw data for these experiments and hence are unable to verify the salt-dependent binding affinities of Sensei RNAs.

When the fake discovery was published last October, it was celebrated by RSC’s Chemistry World and ACS’ c&en, excited peers were quoted congratulating the authors. The Wire, an Indian online magazine, also reported, but in December added an Editor’s note about the journal’s newly issued notice, and even linked to the PubPeer concerns. The only update c&en ever added was to add a reference to an ACS paper:

to add a reference to a Biochemistry paper about another iron-binding riboswitch and to remove a quote that implied the Nature Chemical Biology paper is the first to describe an iron-binding riboswitch.

Priorities, priorities.

Ramesh has her priorities, too. She is already fighting the COVID-19 pandemic. With biosensors, naturally. Without a PCR machine, but with TIME STAMPS, rest assured. Here is her preprint from January 2021:

Anirudh Chakravarthy, KN Anirudh, Geen George, Shyamsundar Ranganathan, Nishan Shettigar, U Suchitta, Dasaradhi Palakodeti, Akash Gulyani, Arati Ramesh Ultrasensitive RNA biosensors for SARS-CoV-2 detection in a simple color and luminescence assay medRxiv (2021) doi: 10.1101/2021.01.08.21249426

It was already endorsed in PreLights by The Company of Biologists, a very respectable publishing society. Indian newspaper The Print quoted Ramesh, who shared the good news that her colour-change test can detect all SARS-CoV2 strains.

While you are reading this, somewhere in the world some dishonest scientist is presently being absolved and whitewashed by their university or research institution because they showed “raw data” to disprove the allegations of data manipulation. The trick is to not look too closely.


Update 8.07.2021

Ramesh is blaming the first author alone, her former student Siladitya Bandyopadhyay, in a public statement:

“The specific data that were flagged came from one author, who left my lab abruptly within a few days after the investigation (without turning in the correct constructs/strains related to this project and without sharing some of the ITC raw data).”

But now Elisabeth Bik found more, whom shall we blame here?

Dolly Mehta , K. Anjali , Arati Ramesh Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria Journal of Molecular Biology (2020) doi: 10.1016/j.jmb.2020.05.003

These two panels, albeit representing different lacZ reporter assays, appear to look remarkably similar if one of them is rotated differently.”

A commenter purporting to be “someone very close to the NCBS community.” alleges in the comment section below:

Dr Ramesh has a common tendency to pressurize all students in her lab to accomplish experiments in a way that the result matches the bioinformatics prediction. […] Ramesh lab has always been a small lab since most of the students (interns, graduate students or even postdocs) who joined the lab could not tolerate the lunatic environment in the lab for long. There have been several complaints by the departed students for the tremendous mental torture that they faced. But most of the time, the matter remained unresolved for obvious reasons.”

I reached out to Dr Ramesh again.

Update 9.07.2021

Sunil Laxman, group leader at InStem in Bangalore, who also happens to be Arati Ramesh’s husband, explained on Twitter that her paper was never completely fake:

No. Mostly right. But some things happened beyond twitterverse and the senior author was incredibly brave and did the right thing

Somebody now looked at his own papers.

Sunil Laxman, Aaron Riechers , Martin Sadilek , Frank Schwede , Joseph A Beavo Hydrolysis products of cAMP analogs cause transformation of Trypanosoma brucei from slender to stumpy-like forms Proceedings of the National Academy of Sciences of the United States of America (2006) doi: 10.1073/pnas.0608971103

Do. Or do not. There is no try.” – YodaLaxman’s lab website

I suggest to do the right thing and blame the first author here?

Sunil Laxman , Ana Rascón , Joseph A. Beavo Trypanosome cyclic nucleotide phosphodiesterase 2B binds cAMP through its GAF-A domain The Journal of biological chemistry (2005) doi: 10.1074/jbc.m408111200

“Around here we don’t look backwards for very long. We keep moving forward, opening up new doors and doing new things, because we’re curious……and curiosity keeps leading us down new paths.” – Walt DisneyLaxman’s lab website

Update 14.07.2021

You know the public version of events. Now how about the behind-the-curtains version, told by internal emails from Arati Ramesh, the rogue student Siladitya Bandyopadhyay, other lab members and the institute’s director? Accompanied by a guest post about Ramesh’s husband Sunil Laxman and his research? Read here.

Update 2.08.2021

Here is my interview with Siladitya Bandyopadhyay:


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119 comments on “Faking Raw Data with an Iron Fist

  1. Kadubu Kadubu

    es schadet mir herr dr Schneider! I am really shocked this is happening in the institute which is directly under the purview of principal scientific advisor of the Prime Minister of India.

    Like

  2. Kadubu Kadubu

    The funding appears to be from India Alliance – DBT Wellcome Trust and HFSP – more international stakeholders…

    Like

  3. Sajeev Akbar

    Already done. See the coauthor of the superconductivity paper criticizing this article

    As one comment said,

    Tell us what to be done Put it under the rug like iisc superconductivity paper?

    Like

    • Pratap Raychaudhuri

      Maybe Arati and NCBS, should go ahead and take a patent for Sensei, and then say…but it has been patented!

      Like

  4. Notsotoxicsap

    As Dr. Ramesh says in her personal statement, the ncb retraction made her group stronger, so the second paper retraction will make her invincible.
    I wonder by getting stronger she means getting better in covering her tracks.

    Like

  5. Acrochordus arafurae

    A new day starts with another image irregularity from one of our beloved PI’s supporters.
    https://pubpeer.com/publications/54AB253C211CF1D6FD61CC5AC3FC07

    This image shares the exact same irregularities (with additions) as the previous paper published in eLife, and also have been flagged on Pubpeer.
    https://pubpeer.com/publications/1A50F332E53A22EF11C50A0E310756

    Dr Laxman, did the same junior author do this?

    Like

  6. Kadubu Kadubu

    @Rahul You mentioned somewhere above that you invited her for seminars at your place. Was this before or after the problems were surfaced on pubpeer?

    Like

  7. Acrochordus arafurae

    I read the Wire article about the NCBS retraction episode and would like to clarify one of the points there:
    “According to sources at the institute familiar with the internal inquiry, she reported the concerns on PubPeer in early November 2020 to the director, Satyajit Mayor. The institute then set up an internal committee, with both internal and external members, that concluded after additional inquiries that the paper would have to be retracted.”

    This is NOT what happened.

    The sequence of events is:

    The NCB paper was flagged on PubPeer with several images being fabricated (visible to the naked eye).

    Dr Ramesh chose to defend the false images with RAW IMAGES so that we can “rest our concerns”.

    The pubpeer community further went ahead to flag almost all manipulated images on this paper. When Actinopolyspora Biskrensis pointed out that the journal had been informed, she chose to defend this with TIMESTAMPS.

    She also mentioned, “Figure 4 shows blots, …….. imaged.” #12, where she claims that there “ARE significant differences between the two gels”. Additionally, she mentioned, “The original images are all attached in this response so that no doubt remains”. (I really cannot remove this epic statement from my mind!!!!)

    She was more than happy to share the “correct constructs/strains related to this project” which surprisingly was stolen by the junior author. “We are more than happy to share all the reagents, constructs and materials and a detailed protocol for ANY of these experiments so that anyone can corroborate the results of the experiments shown in the manuscript.”

    When more concerns started arising, the INSTITUTE CONTACTED DR RAMESH and offered an investigation on this matter. After the first committee meeting, Dr Ramesh was advised to retract the paper straight away, because these concerns couldn’t be explained.

    She went ahead to the NCBS investigation committee with a Western Blot image from “another lab”, which shared similar background duplications, to PROVE that the image duplications in her retracted paper can ACTUALLY come from the “GEL DOC” machine. But the institute refused to take a look at it since it shared no relevance to this project.

    The institute then set up a committee to investigate, with both internal and external members. In the investigation, it was found that the images have indeed been fabricated. But why??

    She was DEAD AGAINST retracting the article in the first place, and NEVER went ahead to inform the institute of these concerns.

    Finally, she couldn’t explain any of the image duplications to the institute, so she was FORCED to retract her paper.

    Her husband, Dr Laxman’s papers have now been flagged as well!

    This is the REAL story so that “no doubt remains”.

    Like

    • Sudrohcorca Earufara

      Alright, you are making some pretty detailed allegations here. I can fully understand your need for anonymity but without giving some information indicating credibility, you run the risk of being a fantasy story teller. Please provide some more information, without of course compromising your identity, that will lend some credibility to the information you are providing.

      Like

      • Acrochordus arafurae

        Dear Sudrohcorca Earufara,

        These are all information, and I STAND BY IT. If you have something better regarding this matter, you are most welcome to enlighten us. Also, for any details on what I mentioned, go and ask the director of the institute. That will clear your thoughts of me being a fantasy storyteller, or your honourable PI being a liar!

        Like

      • She is a FAKE lady and and her entire career is build on fake castles

        Like

    • Kadubu Kadubu

      I will always have my doubts on what they write (wire.in). Since 2020, wire.in has been into science writing from their so called “science communicators”..

      Like

    • I forwarded this comment (and another comment alleging that Dr Ramesh pressuring her students to engage in questionable research practices, and that these students complained and left in protest) to Dr Ramesh and her institute leadership and asked them to oppose these if they disagree.
      I now received this reply from the Communications Office of NCBS:

      “Thank you for your email and for informing us of the latest comments on your site.
      As you know, we have issued an official press statement that addresses this and have no further comment at this time.”

      Like

      • Acrochordus arafurae

        Thank you Dr Schneider for reaching out to them with the comments. No doubt, we received a terrific response from their side. So, what is their response basically? Do they disagree? Do they agree?

        Like

      • Now NCBS clarifies:
        No comment is not a tacit acceptance of false allegation. It simply means we are unwilling to engage with these anonymous commenters on your website, and respond to what, quite frankly, can be termed slander.
        I asked who they say is being slandered here.

        Like

      • New reply:
        The statements and comments are individual opinions. Since some of them are factually inaccurate, anonymous, and unverified, they are not acceptable to us for response or engagement.
        Now, my email to you is a response to your request for comment. It is NOT a comment on the goings on of your website. I would advise you not to misconstrue, misrepresent, or misinterpret what is a response to you in good faith.
        I repeat, we have no comment at this time.

        I pointed out that I am not anonymous and that I understand their last emails as a legal threat against me. I also wrote back that NCBS cannot say that everything published in my comment section is generally a ” false allegation” which they see as “slander” and expect me to remove, or else.
        Law doesn’t work this way, they have to specify exactly which detailed statements they see as false allegations, or to withdraw their claim of slander completely.
        Otherwise, quite frankly, NCBS is slandering me.

        Like

  8. Acrochordus arafurae

    Additionally, she mentioned in her PERSONAL STATEMENT that “The last few months have brought the lab together, more than ever before”.

    NO! THIS CANNOT HAPPEN!

    How can a lab, and most importantly its students, come together under such mental pressure(which didn’t stop even after the student “abruptly left”)?

    Let’s glance at Dr Ramesh’s another friend, an ex faculty at inStem, Dr Akash Gulyani who shared “critical comments on the manuscript” on both of Dr Ramesh’s papers, and is one of the authors on her recent paper:
    Anirudh Chakravarthy, KN Anirudh, Geen George, Shyamsundar Ranganathan, Nishan Shettigar, U Suchitta, Dasaradhi Palakodeti, Akash Gulyani, Arati Ramesh Ultrasensitive RNA biosensors for SARS-CoV-2 detection in a simple color and luminescence assay medRxiv (2021) DOI: 10.1101/2021.01.08.21249426

    Let’s glance at Dr Gulyani’s last published paper, also in eLife.
    https://elifesciences.org/articles/50571

    In this article, Fig 1E depicts an immunoblot showing pull-down of His-tagged Fyn where the starting point is 75, not ZERO, which turns up in the graph (Fig 1F). I wonder why the blot suddenly started at 75!!

    Kd was calculated from the pulldown experiment. I am not a chemist, but as far as my knowledge goes, a pulldown is a very debatable method to determine Kd from any experiment, and this wasn’t checked by SPR or ITC, which are the most robust methods for checking interaction. Also, the blot Src (in Fig 1E) is absolutely clean and doesn’t include any blot as a loading control. I went to check the RAW DATA, and to my HORROR, I discovered that the journal didn’t care enough to include the full blot image in the source data. The blot is so fantastically clear, that even a molecular marker is not visible.

    Finally, let’s have an insight into the authors of Dr Ramesh’s paper from JMB.
    Dolly Mehta, Anjali Koottathazhath, Arati Ramesh. Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria. J Mol Biol. 2020 Jun 26;432(14):4032-4048

    All other authors have left the lab long back except Ms Dolly Mehta. The names of most of these students who appeared in the acknowledgement or author section of this paper never went on the HALL OF FAME- the lab webpage (owing to most of their duration in the lab being extremely SHORT).

    No wonder, Dr Ramesh isn’t replying to Dr Schneider’s emails. I am guessing she and her team have been very busy lately with ground-breaking discoveries.

    Like

    • Kadubu Kadubu

      eLife charges APC. eLife is an elite journal and civilians like me have hard time in publishing in it…You are shaking establishments like NCBS, inStem and eLife…..

      Like

  9. acrochordus arafurae

    ” some of them are factually inaccurate, anonymous, and unverified, they are not acceptable to us for response or engagement. ”

    “SOME OF THEM”? So the rest are MOSTLY RIGHT? AGAIN??

    Like

  10. https://www.theguardian.com/commentisfree/2018/sep/13/scientific-publishing-rip-off-taxpayers-fund-research
    George Monbiot on Elsevier.

    If you have Robert Maxwell called his discovery “a perpetual financing machine”.. This man according to GMonbiot owns Elseiver. Scientific publishing is in wrong hands.

    Academic publishers make Murdoch look like a socialist.
    https://www.theguardian.com/commentisfree/2011/aug/29/academic-publishers-murdoch-socialist

    Scientific publishing has to be in ethical hands and not with underbellies of a society. Elsevier is with UB

    Then the article recently by Ian Birell Beijings useful idiots.

    https://unherd.com/2021/06/beijings-useful-idiots/?tl_inbound=1&tl_groups%5B0%5D=18743&tl_period_type=3&mc_cid=7539bd6e01&mc_eid=0b675aa60d

    Birrells intreview below
    https://disinformationchronicle.substack.com/p/ian-birrell-explains-the-science

    Moderna vaccine founder says this.
    https://disinformationchronicle.substack.com/p/i-am-convinced-that-the-virus-came

    Like

  11. Pingback: Student, Meet Bus – For Better Science

  12. Uncanny_resemblance

    https://www.thehindu.com/news/national/after-recall-of-paper-over-data-manipulation-ncbs-storm-over-charges-of-harassment/article35384752.ece

    Harrasment charges on arati ramesh and also a email conversation between the first author of the paper and NCBS’ director

    Like

    • Kadubu Kadubu

      Has there been any cases of where scientists who committed scientific misconduct or other types of violations of ethics (including harassment) penalised in India so far? i am highlighting the one which are publicised on media or social media. I request the “science journalists” to post this somewhere. @Jacob Koshy. I could not find any, as the contrary, some of them even kept their position or even promoted to director of the institute, vice chancellor etc. Correct me if I am wrong.

      Like

  13. Pingback: “On no condition can the prediction be wrong” – NCBS Scapegoat Student in Interview – For Better Science

  14. Arvind Samy

    Arti Ramesh and her husband Sunil seems to be doing scientific fraud for a very long time, right from their own PhD days , until now it came to lime light. Its shame they are allowed to work in the same institute and still maintain their lab web page. They need to be immediately terminated and kicked out. They enjoyed enough(job , promotions, grants, media coverage) from their fake manipulated garbage science .The funding agencies should also legally recover all the tax payers money wasted for doing sloppy fake science.

    Like

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