You have read the public side of the Sensei fraud at the Tata Institute of the National Center For Biological Sciences (NCBS) in Bangalore, India, which resulted in a retraction of a once celebrated paper in Nature Chemical Biology. You may have read the institutional statements, and The Wire article, where we learn how an intrepid principal investigator Dr Arati Ramesh was betrayed by a snake student, who stole and destroyed all her perfectly reproducible discoveries of iron-sensing RNA, then stealthily replaced them with Photoshop fakeries and skedaddled. How the defiant Dr Ramesh uncovered his fraud and heroically retracted her own paper, by her own executive decision, and how her lab grew stronger from this challenge, and how her peers now salute her for her bravery and integrity.

Ah, what a story. There is another version though, told in the emails by Ramesh and by that same accused student, Siladitya Bandyopadhyay. NCBS was asked to comment on the summary of these allegations, but instead warned me that that all these claims are “factually inaccurate, anonymous, and unverified“, and even “quite frankly, can be termed slander“, but refused to say which claims exactly.

Faking Raw Data with an Iron Fist

The emails allege that research misconduct was standard practice in the Ramesh lab, that students were never taught how to do controlled scientific experiments, but instead bullied when they didn’t deliver the pre-defined results. Apparently, one student was assigned as a scapegoat from the very beginning. NCBS was not interested in investigating the main cause of fraud, and tried to bury the affair with a quick retraction, which the journal already decided upon anyway. Ramesh has been misinforming the scientific community, on PubPeer, on her lab page, even in her email to the journal.

“you can rest your concerns“

This was the paper, published on 5 October 2020 and retracted on 30 June 2021:

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 PubPeer comments exposed data manipulations in October 2020, Ramesh insisted “we have not manipulated any images” and provided what she called “original images”, with the expectation “so that you can rest your concerns” and “so that no doubt remains.“. That purported original images proved fake, despite Ramesh’s insistence that they “have TIME STAMPS showing that they were performed on different days”. The principal investigator also wrote:

“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.“

Which is a strange offer, given that her own later official version of events insinuated all these materials were stolen by the rogue student. But then again, Ramesh is one of those PIs who works a lot in a lab herself, she even has her own freezer space. So the above statement doesn’t really fit the official version of all reagents and stocks having been stolen and destroyed.

Click to access personalstatement_retractionncb.pdf

In that statement on NCBS website, Ramesh blames her former student Siladitya alone:

“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).”

Truth is, the student never left “abruptly”, Ramesh is, shall we say, being dishonest here. Or maybe in denial. In reality,upon the completion of a two-week investigation, the student submitted an employment termination request, which was approved, and he also received from NCBS a “No Objection Certificate” (NoC), to help him with a future employment elsewhere. Here an email to the student from NCBS director Satayjit Mayor, dated 4.12.2020:

“I am following up our conversation yesterday regarding the findings of the investigation committee that is as noted below: I am excerpting the Committee report submitted to us on Nov 24, 2020, as discussed with you and now attached for your information. […] I accept your resignation under the conditions that we discussed:
1) You provide us in writing an acceptance of your wrongdoing, and clarify the circumstances and the names of the persons who have helped you committing this fraud.
2) You complete all formalities required for obtaining the NoC as discussed with you.
Failure to comply with either of the above will result in a termination notice to you, with consequences for your record.
I am sorry that your moving on from NCBS could not have been in better circumstances, but i hope that these mishaps and mistakes from your side will not be repeated and you will learn from them and move on.“

How sausages are made

To obtain this NoC letter, the student was asked to reveal all other issues of data manipulation he was aware of. Which he did, and it doesn’t flatter Ramesh’s leadership style at all.

Read yourself what evidence the student provided to the NCBS investigators, I highlight key passages and illustrate the student’s explanations with relevant figures from the retracted Nature Chemical Biology paper.

“Fig 3e: This figure shows that the Sensei RNA changes its structure with response to a ligand. This experiment was repeated multiple times, but every time the shift was much higher than it is shown in the figure. In spite of repeating the experiment multiple times, Arati was not happy with the shift that we obtained each time, so the band shift was moved a bit lower as was required.“

“Fig 4bcd, Ext fig 8c: All the blots in question correspond to the Fe Biosensor which shows that in the presence of iron, the protein expression increases by around 8 fold. This experiment has been repeated by multiple students in the lab including [….] and we all concluded that the protein expression does increase in the presence of iron. Initially when we started with the experiment and when it was concluded that the expression is increased, we did not run a loading control ever. More recently, when we decided to publish this data, we started running the loading control (RpoA) in a separate blot alongside the overexpression blot. Since our protein size matches that of RpoA, we ran the loading control on a separate blot, and this is the standard practice in the lab.“

“Just a few days back after talking to my friends in other labs, I started to realize what loading control actually means and that a blot can be stripped and reprobed with another antibody to obtain a blot and this is the only correct way of doing it. This was never taught to me or is practised in the lab. Due to this, every time when someone repeated this experiment, the overexpression pattern used to change (sometimes it was 8 fold, sometimes it was 5 fold etc).“

“The original blots for the multiple attempts are attached in my lab notebook. I did a densitometry analysis on the two bands in ImageJ which showed that the expression is 4-5 fold and this was obtained a majority of the times the experiment was repeated, but Arati felt after looking at the blot that the overexpression was 8 fold so we will have to bring the pattern as 8 fold even after using a separate blot for loading control. If you see earlier experiments repeating this blot in my notebook, you can see that the overexpression pattern is really not 8 fold and there is a degradation band below the original band.”

“We also repeated this experiment multiple times and every time the degradation band was visible. Arati wanted the blot to be clean under any circumstances and so she suggested that we use Bead beating (a method used to lyse yeast cells, or any cells with an intact cell membrane) instead of Sonication (that is a standard practice of lysing cells like bacteria). Even after repeating the experiment with bead beating multiple times, the same pattern was visible as earlier and Arati was not convinced about it. So, the lower bands in the original blot were removed and just the overexpression band was kept. Also, I have recently realized that we cannot conclude anything from an overexpression blot if the loading control is not used, so what I understand now is that the entire experimental setup was wrong.“

“Fig 1g: This data was generated by […] and you can find this in his lab notebook copy number 2. This data shows that the mutant RNA does not bind to cobalt and iron. I just came to know a few days back that RNA was not even used in this experiment at all. EDTA has been used instead of RNA, and Calcium chloride was used instead of iron and cobalt. I still do not know how this reaction really works, but this is what happened.  Also, if you check […]’s box labelled “RNA and metal solutions for ITC” in the -20 RNA freezer in our lab, the tube labelled as “RNA for ITC” is not even RNA. You can understand this if you take this sample and measure the concentration on Nanodrop or even run on a gel. This is for one mutant of RNA. He also did this ITC for another mutant, where the same set of chemicals were used and this will also be there in his lab notebook.“

NCBS did not care. They gave the student the No Objection Certificate, then blamed him for everything, retracted the paper and declared Ramesh to be his innocent victim. The case is closed. Scientists have been congratulated their friend Arati on slaying the snake and arising victorious.

As one computational biology colleague in Chennai, who once hosted Ramesh’s seminar, commented under my earlier article:

“In short, this was handled exactly as it should be, by the PI, the institution and the journal (and also the pubpeer community). […] I know the PI a little (and have visited NCBS often and can vouch for the leadership’s uprightness). I do not believe the PI would have pressurised the student to fake data. […] As for Schneider, he has an agenda. Previously he has posted toxic and borderline racist tweets on Indian science.“

Faking Raw Data with an Iron Fist

Bullying in an Elite Lab

This was Siladitya’s experience of working in Ramesh’s lab, told in an email from 23 November 2020 to NCBS internal investigators (highlights mine):

“When I joined the lab in 2017, I didn’t even know how to cast an agarose gel or how to even do a simple PCR. I was told that I have to replicate the data that was generated by someone in the lab and if that does not happen, I will never get to stay in the lab. I was told to replicate a fluorescence data and before that I have never known how to even do fluorescence. I have several emails giving me manipulated images, but I really do not want to use anything now since the allegation is against me and I am ready to accept whatever action is taken against me. Since the first day I stepped into the lab in Dec 2017, I have seen someone manipulating data, for example, the NiCo story [possibly related to Furukawa et al Molecular Cell 2015, -LS] But again, I do not want to take the person’s name here solely because he taught me a lot of techniques that I have mastered over the past 3 years and I am grateful for that.

Numerous people left the lab in the past years in literally two months of joining. I can think of two interns, […] who simply left the lab without informing anyone. […] literally left the lab in a week and we never got to know why he left.

[…]

One time there was a girl named […]. She made glycerol stocks at the final concentration of 25% Glycerol which is generally used all over and mentioned in almost all protocols on the web. Arati threw away all her stocks because she wanted the amount of glycerol in the stocks to be 30%. This has happened in front of me.

I honestly want to tell you that I have really never learned how to actually do science, let alone manipulate data. I know that after this incident I will probably be expelled out of NCBS and I know this is what should happen to me but if I ever get a chance to do research in life, I really want to learn how science is actually done and how it works. I really want to get the whole idea of how troubleshooting is done, that all my friends in other labs talk about. I know it’s hard and takes a lot of time and effort, but I really want to learn that someday if I ever get a chance. I was reproducing all experiments in front of […] and Arati in the lab.

So, one day when my native gel was not getting reproduced by other members in the lab, […] told me to start another set of experiments at 8.30 PM which would take another 4-5 hours to complete, I refused to do it that day. They started forcing me to do the experiment that day, and I was working from 8.30 in the morning, so this was too much for me. So, I myself told Arati and […] in our lab that I want to retract the paper and I do not want to work any further in this lab. I honestly do not even know how this whole system works and I have never had a publication before, nor have I ever worked in a lab. “

The Fortnight Investigation

According to my information, the investigation started also on 7 November 2020, a Zoom meeting was set up on that day. That was after Ramesh told everyone on PubPeer to “rest your concerns” with her fake raw data, and after the journal was informed. There, as a source revealed by sharing a relevant email from a lab member to Ramesh:

“during a zoom meeting, you had mentioned that you will communicate the iron riboswitch work into another journal if the NCB retraction takes place.”

Ramesh never replied to me when asked to oppose this or any other allegations against her. In the emails from early July 2021 which I was privy to, she was at least not in a hurry to re-publish the retracted paper, but she certainly did not exclude this option. The investigation ended, as the email from the director above explains, on 24 November. See how quickly the NCBS experts solved this whodunit mystery and closed the case? TWO WEEKS. Ruthless efficiency!

On 30 December 2020, after the published editorial note from 11.12.2020 promising “Appropriate editorial action“, Ramesh wrote to her lab members:

“Dear Susmit, Siladitya and Dolly,

You are all aware of the concerns raised regarding the NCB paper. In light of the concerns and the investigation that followed, I have been advised by the institute and the journal to retract the paper. I also share the same concerns about some of the work shown in the paper and hence agree that the retraction is the only course of action. 

If you have any objections to the retraction, please let me know ASAP. Also, you will be asked to sign the retraction statement. If for any reason you are unwilling to sign the statement, please let me know ASAP. 
-Arati”

Wait, were we not educated that it was Arati’s own independent decision to retract the paper? Didn’t she explain to us, on her lab’s website:

“We found that the native gels were not reproducible. Given that the Fe-induced structural change in Sensei RNAs, as shown by the gels, was an important finding reported in this paper, we felt that retraction of the work in its entirety was essential.“

Turns out she only felt that after both Nature Chemical Biology and NCSB informed Ramesh that they decided to retract her paper?

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Sunil Laxman did the right thing, too

By “Paul Jones”

A rogue student hoodwinked the National Center For Biological Sciences, one of the country’s most prestigious institutions. As the victimised PI stated, the villain fled with the RAW DATA, the correct constructs/strains, and perhaps the instrument too.

In the aftermath of the incident, many respected scientists came to Dr Ramesh’s defence, quite irrationally. A few even went so far as to accept responsibility for any subsequent incident. But, alas, a second strike did come. As opposed to the previous case, the image here wasn’t altered in any way, just the data, we suppose.

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

Leucanella Acutissima further illuminated our understanding on PubPeer by saying,

“It is one thing to realize a mistake and relabel. It is quite another thing to take a photo first, then relabel afterward, then take a second photo, and then use BOTH photos in the paper and portray them as different experiments.”

The corresponding author is likely to be defended by many who say that the data is MOSTLY RIGHT. Unfortunately, this time the accused on the first paper was nowhere to be seen on the second. What are our options here? Should we blame the junior first author again here? Maybe also this data has already been stolen, or perhaps this student also left abruptly? 

Without mentioning his tiny conflict of interest, the husband of the corresponding author, Dr Sunil Laxman offered to provide an explanation on Twitter. Dr Laxman is quite an influential faculty at the Institute For Stem Cell Science and Regenerative Medicine, and also happens to share critical comments on all Ramesh manuscripts. 

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

— Sunil Laxman (@sunillaxman) July 5, 2021

Another concerned biologist from NCBS, Dr Deepa Agashe declared on Twitter to “feel comfortable speaking up” because she happened to “know something about this case” when she came across “unfair questions” where her “colleague at NCBS” was concerned. Do you know something about the second case too, Dr Agashe? 

I don't see how this is relevant, but ok. The fraud is indeed major; the retraction and statements speak for themselves. I happen to know something about this case so I feel comfortable speaking up when I see unfair questions; that it is my colleague at NCBS is irrelevant.

— Deepa Agashe (@DeepaAgashe) July 8, 2021

In addition, this incident polarized the student community. Not only eminent faculties, but also eminent ex-graduate students (who happened to share the adjacent lab) expressed concerns regarding the ethics courses being issued at the institute. A well-known ex-graduate student of NCBS was concerned about external graduate students not getting enough “compulsory orientation of scientific ethics” anymore. Like, things like these didn’t happen in mine and Arati’s days, the rotten youth of today [head shaking].

Being in the NCBS graduate program about 10 years ago, I can say that we did have compulsory orientation of scientific ethics. I don't know if it still exists. Also many students work at NCBS while being registered externally for PhD. Do they go through the same training? I doubt

— Prabahan Chakraborty (@PrabahanChakra) July 11, 2021

I ask here, do faculties go through the same ethics course that enables them to publish fraudulent research, not once, but twice, Dr Chakraborty? If a former Science Slam winner 2018 and FameLab India Finalist like you could irrationally support this student-blaming exercise, even though the evidence of PI misconduct was quite plain to see from the start, can we really trust your own science now? As you yourself said, “Fighting Fire with Fire”.

What we have learned from this story is that, when it comes to eminent scientists with a long list of publications under their belts, there is only one belief:

The Principal Investigator is infallible and innocent. The student did it.

As Dr Laxman perfectly objectively said, his wife’s retracted paper was never completely fake, but:

“Mostly right. But some things happened beyond twitterverse and the senior author was incredibly brave and did the right thing.“

But to our HORROR, several science integrity sleuths at PubPeer pointed out similar image duplications at two of Dr Laxman’s own papers from 2005 and 2006. The flagged papers are likely to have been part of Dr Laxman’s PhD thesis, and were written under the same corresponding author. I regret to inform you, Dr Laxman is the junior author here.

We weren’t finished yet. More fabrications were on their way.  Identical authors shared two more articles flagged on PubPeer, Dr Laxman merely being the corresponding author here. In the first paper flagged from eLife, the first author Sriram Varahan boldly remarked that there were differences between the flagged images, and stated “We would like to reconfirm that the colonies used in Fig 2F of the manuscript are all unique colonies” which may simply “look very similar, but with minor differences”. Unknown circumstances led to a Correction being issued for this article, where the image was replaced anyway, with “no change to the conclusions made in our paper“.

However, the second article from the same group, with exactly same authors, has yet to receive any responses from the authors.

Sriram Varahan, Vaibhhav Sinha , Adhish Walvekar , Sandeep Krishna , Sunil Laxman Resource plasticity-driven carbon-nitrogen budgeting enables specialization and division of labor in a clonal community eLife (2020) doi: 10.7554/elife.57609 

I cannot “rest my concerns” because the authors are not replying anymore. Are they probably still searching for the data, maybe it has been stolen also? Are the images just similar? Are the conclusions affected?

It is important to note that the NCBS retraction by Dr Laxman’s wife was merely a follow-up of a similar problem on several Indian authored papers. In addition, this fiasco sheds light on the documentation process and publication of research. A naked eye could already see the manipulations in one of the first images flagged on PubPeer. The fact that it was so strongly defended to “rest our concerns” makes me wonder if in the academic world, the pressure to publish has eroded our integrity towards the whole purpose of research? 

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Update 14.07.2021

Look what Aneurus Inconstans found, featuring Dr Laxman.

Last year, in December 2020, Laxman was awarded a prestigious EMBO Global Investigator grant. Because like his wife Arati, who was given a HFSP grant the year before, Sunil is that talented.

Update 2.08.2021

Here is my interview with Siladitya Bandyopadhyay:

https://forbetterscience.com/2021/08/02/on-no-condition-can-the-prediction-be-wrong-ncbs-scapegoat-student-in-interview/

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