[Note: This article is a follow-up of this article that was published on the reporter’s blog. The reporter has been able to access all the correspondence referred to below, except for where the otherwise is explicitly mentioned. This article will be updated as and when new information emerges.]
A high-impact paper published in Nature Chemical Biology (NCB) on iron-sensing riboswitches from a laboratory in the National Centre for Biological Sciences (NCBS), Bengaluru, was retracted after the paper was flagged for data forgery and manipulation. Despite both the NCBS and the principal investigator (PI) having released public statements, independently gathered new information has raised serious questions about integrity of the NCBS investigation process, the lab environment of the PI, and larger questions about ethics and science practice. This report looks at what these questions are, and why concerns about scientific misconduct go beyond this one incident.
On the investigation process
An email from Satyajit Mayor, the centre director of NCBS, sent on July 14 to all NCBS students and researchers, stated:
“…Concerns about manipulation were first raised by readers online, shortly after the article was published on 5 Oct, 2020. The senior author of the paper,…, informed the NCBS Director and Dean of these concerns on 2 Nov, 2020. We then acted as required by our research misconduct policies. Our preliminary evaluation strongly suggested manipulation had occurred. Along with Dr…, we immediately alerted the journal that we were taking these concerns seriously. We simultaneously constituted a committee, chaired by a senior scientist external to and independent of our BLiSc campus, to carry out a full enquiry. The committee were given access to the data trail related to the article in question, and conducted detailed interviews with all its authors as well as with other members of the…laboratory. This investigation concluded on 23 Nov, 2020, and the committee report was submitted to the NCBS Director the following day. Amongst its recommendations, the committee recommended retraction of the manuscript. This was communicated to Dr…who, following further correspondence with the journal, initiated the retraction process on 1 Feb, 2021. The paper was eventually retracted at the end of June, 2021. Throughout this process, the Management Board of NCBS and the agencies that funded the research were kept informed.” [Hyperlinks and redactions of the name of the PI by the reporter]
According to sources who were at NCBS during the time of the investigations, the preliminary evaluation was carried out by a committee of three faculty from NCBS and one from the Institute for Stem Cell Science and Regenerative Medicine (inSTEM). The external investigation committee comprised two faculty from NCBS and one from the Indian Institute of Science (IISc). The Head of Academics at NCBS, Raj Ladher, refused to confirm the composition of the committee saying that the composition and the report of the committee were confidential. A report from The Wire Science indicates that NCBS may not be making the investigation report public anytime soon.
The same email from Satyajit Mayor also says, “Based on this evidence, the committee concluded that the manipulated data were connected to experiments carried out by a single individual.” This also appears in the draft of an email sent by the PI to the chief editor of the journal NCB, where the paper was originally published, as well as the public statement by the PI and NCBS.
However, some new information on NCBS’ investigation process has raised various serious questions.
- As per confidential information from the investigation process made public, the student accused of the misconduct had alerted the committee to manipulation and forgery by another person involved in some experiments of the manuscript. However, the investigation committee seems to have concluded that all the manipulations and forgery were committed by the single student, who is also the first author of the paper. Did the committee overlook the student’s crucial allegation? Why? [TheLifeofScience.com does not have a copy of this communication; however, an anonymous source who was at NCBS has confirmed its correctness]
- In an email to the inquiry committee, the first author mentions how he had received manipulated images from another person. Once again, this points towards the fact that the first author may not have been the only person involved in committing this forgery. Did the investigation committee overlook this serious allegation as well? Why?
- In the same email to the inquiry committee, the first author alleges that data fabrication and manipulation has happened previously in the lab. The question then is whether the committee did engage with this allegation; did it speak to current and previous students of the PI’s lab, and did it investigate the culture of doing science in the lab? The investigation committee is indeed empowered to do this as the NCBS research-misconduct investigation guidelines state: “The committee will have access to laboratory premises and permitted interviews with laboratory personnel, the complainant and the subject.”
- NCBS has a student council. However, there was no student representative in either of the investigation committees. It is important to remember that in an investigation where a student is the primary accused, having a student representative actually benefits the investigation—it may actually make the student feel safer and less intimidated, while also allowing the investigation to deliberate on the concerns that the student has.
- When asked about why there was no student representation, Satyajit Mayor responded that the allegation of misconduct “was not a grievance that was brought to our notice” and that grievance committees at NCBS “have student representatives”. However, during the investigation process, the student did bring grievances related to abuse and harassment in the lab to the notice of the committee, which must have conveyed the same to the Director and the Dean. Then, why did NCBS not initiate an investigation into the grievances with student representatives on board once the student mentioned them during the investigation?
It is clear that there have been lapses in the investigation. It is important to reiterate that the Indian science community will benefit from the investigation report being made public, or the matter be reinvestigated by an independent, external committee. According to a follow-up press release by NCBS, the report is being evaluated by the Tata Institute of Fundamental Research (TIFR) Academic Ethics Committee, which will determine if further investigation into the issue is necessary, TIFR being the parent body of NCBS.
On the “abrupt” departure of the student and the retraction process
The statement released by the PI of the lab where the data manipulation occurred says, “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).”
This contradicts the fact that NCBS did grant the student a No-Objection Certificate (NOC), after clearing all the resignation formalities. While granting the student an NOC is a good move on part of NCBS (it enables the student to move on with their career), it lays doubt on the allegation that the student left “abruptly” without sharing the raw data or constructs crucial to the replication of some experiments. Moreover, when the paper was first flagged on PubPeer, the PI had claimed to upload all the time-stamped raw data, as well as promised constructs (artificially designed nucleic acid fragments carried on a vector) and reagents to anybody who would like to independently replicate the experiment. The raw data and the constructs, then, seem to appear and disappear sporadically.
When asked about how the raw data might have disappeared, Satyajit Mayor said, “Most of the raw data were submitted to the committee. Some of the raw data were missing because it had been erased from the machine on which they were recorded.” However, an ex-member of the PI’s lab who did not want to be identified has alleged that all the raw data pertaining to the study were stored in the lab computer and laptop. Moreover, sources from NCBS confirmed that the PI participates in doing experiments themself, and they have their own freezer space where they store all the constructs required for the current studies going on in the lab. If this is true, then the mystery of the lost data and lost constructs remains unsolved. An email to the PI regarding this did not receive a response.
There are concerns about the events leading to the retraction as well. A draft of the PI’s email to the chief editor of NCB about retracting the paper states that the accused student did not reply to the email from the PI confirming the retraction with all the authors. Interestingly, the email asked for a response only if any of the authors disagreed with the retraction. As per an source who was at NCBS and prefers to remain anonymous, after the first author clarified their intent to retract the paper as well as explained the reason behind their non-response, the PI corrected this statement in the final email to NCB. In fact, in the student’s response to the PI, the first author states that they had communicated their desire to retract the manuscript clearly on many occasions.
On the lab environment
Meanwhile, several concerns about the environment in the concerned PI’s lab have cropped up. Emails from the accused student to the inquiry committee mention how the PI has threatened various students of dire consequences, including not signing registration forms for their PhD or discontinuing their position in the lab, frequently. A source who was at NCBS and prefers to remain anonymous said, “the lab environment is not good and friendly at all. Everyone works under some or the other threat.” The source also mentioned that there have been multiple complaints of misbehaviour against the PI, but the NCBS authorities have remained silent and not taken any appropriate action. Another anonymous source, currently a student at NCBS, concurs. “I think almost everyone knows that the environment in … lab is very tense. There are incidents where … is extremely rude and abusive too,” the source said [Redactions by the reporter]. On the other hand, Arun Sharma, currently a Junior Research Fellow at IISc and an ex-member of the PI’s lab, says, “I did not find the lab to have a toxic environment at all, nor did I observe any malpractice. [The PI] stood beside me teaching me how to do stuff.”
There has also been an allegation against the PI that they have threatened to jeopardise the career of the accused student, even after their departure from NCBS. In an email to the director, the accused student has mentioned that the PI has allegedly threatened to write to their current employers with the intention of “destroying” their career. Emails to the PI requesting a confirmation or denial of these allegations have not received any response at the time of writing this report. The follow-up press release from NCBS mentions, “We are following due process in investigating these allegations.” However, there is no clarity on what this due process is.
Larger questions about ethics and science practice
While the current issue has put NCBS in the spotlight, it is important to remember that the issue extends beyond NCBS, this particular PI and this particular student.
Authorities at NCBS claim to not take ethics training lightly. Raj Ladher clarified, “Every new joinee across campus, be they interns, JRFs, students or faculty must take a lab safety and ethics course to activate their ID card access. The ethics component is an hour long talk (by me) that takes them through why we research with integrity, what constitutes misconduct and what one should do if one finds research misconduct. It’s followed by the lab safety course that is taken by Lab Support, and finishes with a test.” Despite such efforts, why and how a case of forgery and manipulation of such proportions happened at NCBS warrants further investigation. This episode also raises questions about whether a short training program is enough to avoid misconduct, and how institutes like NCBS must tackle the systemic problems that lead to gross ethical violations.
The NCBS incident also calls into question the peer-review process. How is it that the reviewers also missed the overwhelming amount of fraudulent data? Satyajit Mayor calls this “puzzling”, saying that reviewers often do look at raw data. This seems to be one of those times when the peer-review process failed to catch fraudulent data at early stages. He also mentions that collegial interactions at NCBS have reduced owing to the current COVID-19 pandemic, and that collegial interactions and presentations may have helped to catch the fraudulent data at an early stage.
While the current issue has put NCBS in the spotlight, it is important to remember that the issue extends beyond NCBS, this particular PI and this particular student. This is not for the first time that Indian science is meeting the issue of retraction due to forged data; in fact, Retraction Watch, a website that tracks retracted papers, has a special category called ‘India retractions’. Moreover, image forensics expert Elizabeth Bik has pointed out how papers from China and India have a higher chance of having problematic images as compared with publications from other countries. What is, then, at the heart of the problem?
Dwaipayan Bharadwaj, a professor at Jawaharlal Nehru University (JNU), has been documenting flagged and retracted biomedical science papers on his Facebook profile. I asked him what might be the reason for such a high incidence of ethical breaches in papers from Indian biomedical science. He points out two reasons: (a) the award-based evaluation system that dominates the narrative of Indian science academia; and (b) the tenure-track system in some elite institutions adds undue pressure and competition on a scientist’s work. He also mentions that despite journals having opened up to the idea of publishing negative data, scientists are still under systemic pressure to publish positive results in high-impact journals. Bharadwaj also mentions how oftentimes both PIs and students are not very well trained in ethics and philosophy of science, which later translates to ethical misconduct in their science.
Since this case and its proceedings sets precedents and has serious implications for the Indian science ecosystem, an open call on Twitter was issued by the reporter asking Indian academicians what they think would reduce ethical misconduct in Indian science practice. The Tweet and related responses can be found below.
(asking for a report)
— Sayantan Datta (they/them) (@queersprings) July 15, 2021
What is NCBS doing to improve its data storage and ethics training programs? Raj Ladher says, “Since the beginning of the year we have been putting in place improved data storage policies. More recently, we are further evolving our workshops on research integrity that bring in the philosophy of science (falsifying hypotheses rather than proving them), research ethics and integrity, and responsibility. We plan on making annual refreshers mandatory for all academic staff and will tie this to ID card access.” The July 14 email from Satyajit Mayor also says, “This case has revealed weaknesses at multiple levels in our research integrity practices. Since the beginning of the year, we have initiated a full evaluation of our processes and will soon implement more detailed and stringent data integrity policies. A breach of ethics affects all of us, and it is, therefore, our shared responsibility to uphold the highest standards of research. Science can only be done honestly, objectively, and impartially, or it is not Science. We owe this to our colleagues, our funders and the public who put their trust in us. We must all strive to create an atmosphere where research integrity is paramount and can be upheld without fear or favour”. The email goes ahead to encourage students to share their concerns about data with authorities at NCBS.
However, all is not well. Another paper by the same PI has been flagged for unethical image duplication and use. When asked about what the institute is planning to do about this, Satyajit Mayor said, “We will wait for the author’s response. There’s no decision that has been taken.” This response strikes as odd: Why is the institute waiting to start the investigation, given that this is the second time a paper from the same lab has been flagged?
Similarly, some papers from another lab at inSTEM, an institute on the same campus as NCBS, have been flagged. At the moment, there is no information about whether inSTEM is planning to investigate this issue. An email to the inSTEM communication office asking for details did not get a response at the time of writing this report.
[Note: The reporter would like to thank Priyanka Pulla, Shaswati Sarbagna, and Debdutta Paul for their help throughout the process of collecting information and drafting this report.]