Representative photo: Julia Koblitz/Unsplash
New Delhi: New allegations have stoked concerns about the NCBS retraction affair, especially with regard to what appear to be unethical practices in the laboratory that biochemist Arati Ramesh leads at the institute.
NCBS stands for ‘National Centre for Biological Sciences’, a premier biological sciences research institute in Bengaluru. It is administered by the Tata Institute of Fundamental Research, Mumbai, under the Department of Atomic Energy.
A clamour broke out in early July when Ramesh and NCBS published separate statements announcing the retraction of a scientific paper written by Ramesh and her colleagues in her lab, from the journal Nature Chemical Biology. Ramesh’s statement became controversial because it threw one of her coauthors – a student in her lab, believed to be Siladitya Bandyopadhyay – under the bus for the paper’s faults.
These faults were predominantly a slew of images in the paper that independent scientists found had been manipulated to fit the conclusion – instead of the other way around, which is usual and ethical practice.
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The new emails, disclosed on For Better Science, a blog run by German science journalist and cartoonist Leonid Schneider, appear to show that contrary to Ramesh’s claims in her statement, she may not have been as blameless for the paper’s manipulation and eventual retraction.
Schneider’s post also calls the terms of the internal inquiry that NCBS conducted into question. Uma Ramakrishnan, who studies mammalian genetic variation at the institute, had told The Wire Science earlier that once the independent scientists’ comments became public knowledge, Ramesh informed the institute’s director, Satyajit Mayor, who then constituted an internal inquiry committee.
Ramakrishnan said she wasn’t at liberty to divulge the identities of the committee members, and only said that it was composed of internal members (outside Ramesh’s lab) and one external member.
The inquiry in November 2020 concluded that the paper, published in the journal Nature Chemical Biology in the previous month, would have to be retracted. Neither Ramesh’s nor NCBS’s statements discussed the committee’s findings.
Sources familiar with the communications told The Wire Science that the emails were real, legitimate and originated from the student in question, where specified. However, they also said that Schneider didn’t have the student’s permission to share the contents of the email verbatim.
An email to Ramesh requesting her comments on the allegations hadn’t elicited a reply at the time of publishing this article.
However, Mayor said that the inquiry committee had been empowered to look into all aspects of the case and to act on their findings, and that its members would have accounted for what the student had shared as well.
“We take all such complaints and allegations very seriously. We have a robust process in place to address these issues when they are happening,” he told The Wire Science over a phone call. “As far as the integrity of our scientific work is concerned, we proactively retracted the paper and set the scientific record straight.”
In a campus-wide email sent this morning, Mayor also wrote, “If you have any concern about any set of data, experiments or writing, you must bring this up at the level of the laboratory head, deans, or director.”
Ramesh had said in her statement that the student in question had “abruptly” left her lab once the manipulation had come to light, taking “some” of the raw data and other materials required to understand the experiments, with him. (Mayor’s email says that “certain raw data could be independently validated on backup servers”.)
But before his departure, Mayor reportedly wrote to the student on December 4, 2020, outlining the terms on which NCBS would give him his no-objection certification, including “completing all formalities”.
One of these formalities appears to have been to “reveal all other issues of data manipulation he was aware of”. Schneider writes that he was able to obtain access to these documents as well, and proceeds to describe some significant allegations against Ramesh.
First, about figure 3e in the (retracted) paper, the note says that Ramesh wasn’t happy with a certain experiment even though it yielded an allegedly disappointing result every time. As a result, according to the student, the figure was modified to fit her expectations. This was one of the first figures that the independent scientists flagged as potentially manipulated: it shows a sharp pattern around a plot suggesting a part of the plot had been copied and pasted from another source.
Second, about figures 3b, c and d, the student wrote that one experiment did not have a loading control at any point. Researchers use loading controls to ensure they have set up certain tests right before they run.
The student continued that he was not aware of the correct way to conduct the experiment he was expected to, that he hadn’t been taught them and that they were not performed in this way in Ramesh’s lab.
The student also wrote that when she was dissatisfied with the outcome of one experiment, Ramesh modified a corresponding image to remove a “repeating pattern”. At the same time, the student wrote, the same experiment was being done wrong because it didn’t have the loading control.
Next, the student wrote about another member of the same lab who had produced the data for image 1g in the paper, labelled: “ITC1 performed on Hdu Sensei ΔP1 RNA shows no heat released with increasing Fe2+ (black) or Co2+ (gray).” But according to the student, as quoted in Schneider’s post, this experiment didn’t use RNA at all.
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Schneider goes on in his post to quote other portions of the student’s email to Mayor in December 2020 pertaining to Ramesh’s leadership of the lab. The student wrote, for example, that he received several emails with manipulated images and that he had seen someone at the lab manipulating data. He also wrote that many people had left the lab after spending shorter than usual amounts of time there, sans explanation.
He also alluded to strong-arming behaviour on the parts of others, including Ramesh – such as when he was pushed, he wrote, to conduct a four-hour long experiment from 8:30 pm and after having spent 12 hours in the lab.
However, he stated that he has accepted that the allegation is against him and that he is ready to accept the consequences.
The subsequent emails in Schneider’s post are about the retraction process. On December 30, 2020, Ramesh reportedly wrote an email addressed to her coauthors – including the student – asking them to speak up in case they had any objections to signing the paper’s retraction statement. Then, in January 2021, Ramesh reportedly wrote to Nature Chemical Biology editor Terry Sheppard saying, among other things, that the student had “not responded” to her email “asking if he would be willing to sign a retraction statement”.
But the student emailed Ramesh on February 2, 2021, saying that he didn’t respond to the December 30 email because he didn’t have objections to signing the statement, and that his silence had been misconstrued. He added that he has always wished to have the paper retracted.
The NCBS inquiry committee has not released the report of its findings into the public domain, although it has been shared with the office of the director of the Tata Institute of Fundamental Research.
Sayantan Datta, a science communicator, journalist and a member of The Life of Science collective, had written on their blog on July 10 asking NCBS to release the report. Doing so would be justified, they wrote, because “scientists are publicly accountable”, and to help ascertain the inquiry’s rigour and contextualise its findings. The latter, they continued, could even set a good precedent for future reports.
Datta also wrote that we don’t “have a good way of reaching out to the accused student or the PI [Ramesh]” to avoid stressing them further, and that the report could stand in for their comments on the issue.
However, Mayor said the committee performed its duties assuming that access to the report would be limited. Ramakrishnan echoed him, that the report was “confidential”, that the committee was protected in order to perform its duties, and that no one outside the committee is privy to its proceedings.
But Ramakrishnan also said that the inquiry was an “internal matter” and that the new “allegations are unverified”. Mayor said that the institute “couldn’t shirk its responsibility to due process”, including the fact that the student’s allegations hadn’t been lodged as a formal complaint.
NCBS communications office head Mahinn Ali Khan said, “I don’t know how the contents of the report are going to settle the questions being raised.”
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Schneider’s last point in his post is that the student had sent an email to “some NCBS researchers” on April 17, 2021. Here, the student alleged that Ramesh had reached out to his new employer – an unnamed bioscience research facility – and issued threats that he said could imperil his career.
The student also referred to another individual, not identified by name in Schneider’s post, who apparently had the same experience and that “she feels horrible”.
On July 7, The Hindu had reported that while NCBS hadn’t named the student in question, two of the paper’s authors – Siladitya Bandyopadhyay and Dolly Mehta – “also list affiliations to the SASTRA University, a private university in Thanjavur, Tamil Nadu.” The newspaper added that according to Mayor, the authorities there had been “informed of the retraction”.
Schneider wrote that “neither Ramesh nor NCBS is not willing to talk” about the issues he flagged in his post.
Isothermal titration calorimetry↩