IISER Thiruvananthapuram Director: There’s more to it than meets the eye

Keshav-Optimized

In response to the Faulty IISER-Tvm Facebook post that I shared about the lack of action against Prof. V. Ramakrishnan, the Director of IISER Thiruvananthapuram, despite my article pointing out the “copy and paste” content in his papers, Harsh Jog from IISER Pune asked: Can’t the IISER Tvm faculty issue a statement? Why wait for outsiders to clean your home?

Just a few minutes ago Faculty IISER-Tvm  replied saying: “The kind of targeting of individual faculty members that takes place in IISER-TVM under the ‘copycat’ director is enormous. We have had innumerable instances against several faculty members here. In fact, a huge paperwork of fabricated materials was created by this ‘copycat’ director against two of our eminent researchers to remove them from their jobs. The ‘copycat’ director brings his own breed (read: good-for-nothing fellows) from all random places (read: places where research never happens) and takes such decisions as committee-recommended decisions. Research-related purchases are put on hold for several people. Natural pay raises that one should get are denied. The board of governors is aware of certain things. But we don’t know if the board of governors is aware of everything that takes place here.”

It’s sad if it is indeed true.

Prof. A. Jayakrishnan from IIT Madras had cried foul last year right after Prof. Ramakrishnan was appointed as the Director. He said his appointment was “patently wrong”. The faulty members of IISER Thiruvananthapuram had even written a letter to the Prime Minister. 

My experience

But let me share some details that I did not reveal earlier. In an email sent to me on December 4, 2016 he tried persuading me that I was wrong in my assessment saying: “…Your basis of conclusion [of plagiarism] is scientifically baseless and ridiculous.  In view of the same, it is evident that you have deliberately adopted the quantification contrary to the research methodology adopted by the scientific community.

It was then followed by a warning: “If you still persists with your alleged observation of plagiarism being committed by our group on the basis of your own conclusion and publish the so called article of insinuation and defamatory statements which is calculated to injure the reputation of our group or you are acting at the behest of those persons who want to bring disrepute to us and to the institution.

“If you still  write and publish,  it will constitute as a libel and if spoken a slander without any justification, nor a fair comment, nor an absolute privilege, quantified privilege [sic] to justify your illegal acts and  the same will be presumed  to lower our estimation [sic] among the right thinking people generally. It is evident from your conduct that you have deliberately chosen to publish an article not only to defame the institution where I work but also those students who have published the articles.

“If you still publish the article based on your own conclusion which is not all in line with any of the research methodology adopted by the scientific community, you alone will be liable and responsible for all the damages we may suffer on account of your wilful and malicious act and conduct.”

RELATED ARTICLE:

‘Copy and paste’ content spotted in IISER Thiruvananthapuram director’s papers

‘Copy and paste’ content spotted in IISER Thiruvananthapuram director’s papers

IMG_0474

There is 68% similarity in content between this 2014 paper of Prof. Ramakrishnan and other papers.

Over 50 papers published between 1984 and 2014 by Prof. V. Ramakrishnan, formerly with the School of Physics, Madurai Kamaraj University and currently the Director of the Indian Institute of Science Education and Research (IISER) Thiruvananthapuram have varying degrees of content taken verbatim from or have very close similarity with other previously published papers. Large chunks of text have been reproduced verbatim from other papers and the sources have not been cited. In many instances where the sources have been cited, the content has been reproduced verbatim without paraphrasing.

In nearly 15 papers, where Prof. Ramakrishnan is the corresponding author, the extent of text similarity with earlier published papers (technically called similarity index) is as high as 60% and greater. At 68%, a paper published online in May 2014 in the journal Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy has the highest similarity index.

An anonymous person has posted this paper on Pubpeer.com and highlighted the content that has been taken verbatim from other papers.

Most of the papers which have portions that are very similar to other papers have been published in the journal Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy and the Journal of Raman Spectroscopy. Most of the papers have been published from Madurai Kamaraj University, where he was a Professor in Physics before joining IISER Thiruvananthapuram.

The Turnitin software that was used indicates text similarity by stating the percentage of similarity index. For several reasons, the “similarity index cannot be used as an indicator of whether plagiarism has occurred or not” when Turnitin software is used.

Five papers scrutinised 

So to ascertain if the similarity in content amounts to plagiarism, five papers, where Prof. Ramakrishnan is the corresponding author, were randomly chosen for closer scrutiny. These papers were published between 2003 and 2015. Three of these papers (here, here and here) were published in the journal Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy and the other two (here and here) were published in the Journal of Raman Spectroscopy.

According to a scientist very familiar with scientific ethics and who cross-checked the five papers for plagiarism, one paper contains substantial verbatim use of material from papers by other authors without citing the sources. And where the sources of have been cited, the content has been reproduced verbatim without paraphrasing. The other papers have substantial verbatim use of material from their earlier published papers, technically called self-plagiarism.

This slideshow requires JavaScript.

Comment in Pubpeer

Responding to the paper posted in Pubpeer.com, an anonymous person says: “I am based in the U.S. and usually look at Pubpeer once a month or so. Out of curiosity had a look at this one, and tried to look at both original papers and found exactly what the submitter has claimed, at least with one section. My comparison is pasted below. There are many highlighted sections, obvious from the rainbow colours. I don’t have time to verify this. May be the ctrl-copy, ctrl-paste business has gone into the results too, then the question is are the experiments really carried out or everything is fake?

The possible way forward are the following:

  1. Notify the sponsoring agency of this research
  2. Notify the University where this work was done
  3. Notify both journals and the senior author of Bilge et al 2009 paper
  4. Put other papers under scrutiny, if this is done once it must be a mistake done by the first author, but if it has happened across many papers, then the corresponding author has to take the responsibility.

Seems to be a major case of scientific fraud, maybe this person is in some obscure university in India, still one has to behave responsibly.”

“Even with citing (attribution), the source text must be used with quotes. Doing otherwise is misconduct as it is not clear that the entire text comes from the cited source. Even paraphrasing extensively even with references is not good practice,” another senior scientist from Delhi says in an email.

Self-plagiarism

Plagiarised content is found in the introduction section in the first paper. Unfortunately, it does not stop here — plagiarism extends to the experimental section and even to the results and discussion sections. The same trend is seen in the papers where self-plagiarism is rampant.

“There are two issues here — plagiarism from other authors’ work and self-plagiarism. Self-plagiarism in the introductory section is somewhat acceptable because scientific background underlying any author’s work is going to be largely similar. However, self-plagiarism in the results and discussion section is not acceptable at all because it is tantamount to cloning one’s own paper again and again ad nauseum so that it appears that the person has authored a very large number of papers. This is exactly what is prevailing in the present case,” a senior chemist from a reputed institute in India, who cross-checked all the five papers against the original papers, says in an email.

Modus operandi

“It is cleverly done and different sections from different papers are stitched together. All the chemical systems in all the papers are very similar. It seems they just repeated the same kind of experiments with another sample, so the story goes the same way. The way in which the problem is formulated, the experimental details, the results, the discussion and the conclusions are identical,” says the chemist.

“Simple ‘copy and paste’ actually worked very well for him because he did not have to write anything new for his paper as his results had nothing new compared to the literature. You can generally expect this when the work in question is of the lowest standard and all the results would give the same conclusions (similar to the literature or his earlier papers). So I think he just had to change the names of the compounds and some other details, but rest is mostly the same from one paper to other of his own or that of literature work,” the senior chemist adds.

Denies wrongdoing

In a couple of emails to me, Prof. Ramakrishnan says: “Most of our experimental research publications include an amount of history and review of earlier research findings in the same area. All our supporting data are duly acknowledged and the source cited in the reference. Therefore, the question of plagiarism does not arise. As you have pointed out that from 1984 they have been in the public domain and so far no reviewer has pointed out that either our group has copied or stolen from others scientific data.”

On his request, two of the five papers (including the paper published online in May 2014 (see slide show) in the journal Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy) and the original papers from where he had plagiarised were sent to him; the plagiarised portions were highlighted in his papers and the original papers. In response, he denies any wrongdoing saying: “The highlighted portion of the attached documents sent by you (markings on reprint of our works) shows the name of journal, author, affiliation, mobile number, email [address] etc as plagiarised one.” He then goes on to say: “Your basis of conclusion is scientifically baseless and ridiculous. In view of the same, it is evident that you have deliberately adopted the quantification contrary to the research methodology adopted by the scientific community.”

RELATED ARTICLE:

IISER Thiruvananthapuram Director: There’s more to it than meets the eye

Lancet gets in touch with Current Science authors on litchi disease ethics issue

img_0446

The paper in Current Science where Dr. Jacob John and others accuse the Lancet paper authors for not crediting their papers published in 2014.

In response to an article I wrote on February 3 about Dr. Jacob John raising ethics issues about the way the authors of the Lancet Global Health paper had failed to properly acknowledge his team’s work on Muzaffarpur mystery disease, the journal has got in touch with Dr. Mukul Das, one of the authors of the Current Science papers, for more details.

Dr. John, Dr. Das and others had published two papers in 2014 (May and August) and another one in December 2015 in Current Science wherein they report clinical similarity between ackee poisoning in Jamaicans and the Muzaffarpur illness. At a time when the Lancet authors were looking for a viral cause, Dr. John’s team had correctly zeroed in on methylenecyclopropylglycine (MCPG) toxin in litchi as the likely reason for illness and reported the findings. The team found consumption of litchi and skipping the evening meal as likely reasons for children exhibiting dangerously low blood glucose level and acute encephalopathy early in the morning leading to death in many cases. They also found the presence of MCPG toxin in litchi through chemical analysis and recommended infusing 10% dextrose within four hours of disease onset to save lives.

While the January 30 paper in the Lancet Global Health has acknowledged and cited all three papers, it does not give due credit to the work done by Dr. John’s team. “They quote our study but don’t honestly say what we have found. They have borrowed all important information connected with the illness from us,” Dr. John had told me.

litchi1“Dr. John and I would jointly be sending our response on Monday or Tuesday [February 6 or 7],” says Dr. Das. “It is very decent of the Lancet to have got in touch with us and seek our clarification on this issue. That shows Lancet is careful of its credibility, careful that any such issue is immediately sorted out. I admire Lancet. This is what we want from every journal publisher, every investigator and every paper. Caesar’s wife must be above suspicion,” says Dr. John. “We never complained to Lancet or the media. It is the media that got in touch with us as they knew about our work. That makes us happy.”

Precedent

The authors from Centres for Disease Control and Prevention (CDC) and Delhi’s National Centre for Disease Control, India (NCDC) have indulged in scientific misconduct in a paper published in January 2015 in the Morbidity and Mortality Weekly Report (MMWR), the authors of the Lancet paper cite the possibility of exposure to MCPG, a toxin in litchi, as a likely cause of acute hypoglycemia and encephalopathy in some children. The paper does not even cite the May and August 2014 papers in Current Science by Dr. John’s team.

Dr. John and Dr. Das had exposed the “scientific misconduct” by the authors in a correspondence published in Current Science. “They were creating a precedent by publishing in MMWR, which is a CDC in-house publication. It gave us a clue to their mind and now it is an extension of that mentality by citing us so we don’t complain but not giving us the credit that we deserve,” says Dr. John.

Published in The Hindu on February 5, 2017

Litchi: Controversy erupts over Muzaffarpur mystery disease study as CMC Vellore scientist cries foul

img_0442

The Lancet Global Health paper published on January 30, 2017.

The scientist who investigated the mystery disease that proved fatal for many 15-year old children in Muzaffarpur, Bihar at the instance of the State government has raised ethics issues about the way the research has been published by the journal Lancet Global Health on January 30.

“Not giving due credit for work done by others is not acceptable in science,” Dr. T. Jacob John, a virologist who was earlier attached to the Christian Medical College, (CMC) Vellore says.

“They quote our study but don’t honestly say what we have found. If they did that then they can’t claim originality. They have done a large case-control study but borrowed all important information connected with the illness from us,” he argues.

Dr. John published in Current Science in May 2014 evidence of a link between a fruit in Jamaica, the ackee, from the same family as litchi, and a disease called acute encephalopathy in Jamaicans. He showed the close clinical similarity between ackee poisioning and the Muzaffarpur illness, where litchi consumption and skipping the evening meal could result in very low blood glucose and acute encephalopathy, leading to seizures and coma, and death in many cases.

Lancet author refutes claim

The Lancet authors, however, refute this. “We have acknowledged and cited all three of Dr. John and his colleagues’ papers in Current Science,” Dr. Padmini Srikantiah at CDC Atlanta and the corresponding author said in an email. “There are a few key findings in our study that have not been, to our knowledge, reported previously. First: the evidence of the metabolites of hypoglycin A and methylenecyclopropylglycine (MCPG) in the specimens of affected children, and the demonstrated metabolic abnormalities that resulted due to the effects of these toxins. And, second, a statistically significant epidemiological association between illness and litchi consumption, as well as the modifying effect of the absence of an evening meal.”

Dr. John’s pioneering work 

Dr. John’s team had in the May 2014 paper pointed out that the illness was due to non-infectious encephalopathy and not viral encephalitis as was widely suspected. The absence of inflammatory cell response in cerebrospinal fluid, hypoglycaemia and inconsistent presence of fever were the basis on which he called it as encephalopathy. That it was a form of encephalopathy associated with low blood sugar was again emphasised in an August 2014 paper in Current Science.

litchi1“While in 2013 people from Delhi’s National Centre for Disease Control, India (NCDC) were still searching for more viruses [as the cause], I went to the villages and talked to parents, neighbours and doctors and came up with the hypothesis that it is a biochemical disease and not an infectious disease,” he says.

The May 2014 paper points out a link between the disease and litchi harvest season, the sudden presentation with serious illness, the symptoms of the disease and under nourishment in the affected children.

MCPG and disease link

Besides describing the origin of the disease, the paper mentions MCPG present in litchi, which is similar in action to hypoglycin A found in ackee. “Our hypothesis is that the Muzaffarpur illness is caused by MCPG in litchi,” says the paper. It also mentions about MCPG causing derangement of fatty acid metabolism.

A December 2015 Current Science paper reported presence of MCPG in litchi (both unripe and ripe fruits) based on chemical analysis. It is true that Dr. John did not report MCPG or hypoglycin A in samples of children but the study strongly suggested the role of MCPG.

A May 2016 paper in  Indian Pediatrics again emphasis the link between MCPG toxin found in litchi and the disease and its effect in animals. It says: “Since the part of the fruit consumed by humans contains MCPG, and experimentally it has been shown to cause hypoglycemia in starved animals, the biological plausibility of causality by MCPG is thus confirmed.”

While Dr. John had first raised the suscipion of hypoglycin A in ackee and its similarity to Muzaffarpur disease even in the 2014 paper and followed up on that in the 2015 and 2016 papers, Dr. Srikantiah told me that her team was alerted about the link and its effect on rats by her colleagues at CDC Atlanta.  Dr. Srikantiah’s team makes only a passing mention of Dr. John’s work on the association of litchi and the disease in the Lancet Global Health paper, and clubs its along with other suspected causes such as exposure to pesticides and infectious encephalitis.

Contrary to Dr. Srikantiah’s claim that the modifying effect of the absenc of evening meal in disease causation was their team’s contribution, Dr. John had pointed this out earlier. “Our finding provides the much needed evidence for biological plausibility that litchi consumption by undernourished children, especially after prolonged fasting, triggers the hypoglycaemic encephalopathy early in the morning (4-8 am),” the December 2015 paper says.

The August 2014 paper says: “The hypoglycaemia points to an inhibited gluconeogenesis.” It mentions how well-nourished children are not affected due to glycogen reserve in the body and presumably because a specific metabolic pathway for glucose generation (gluconeogenesis) is not triggered.

Disease prevention and recommendations

During a June 2014 outbreak, Dr. John and another doctor tested blood sugar level immediately after hospitalisation and infused 10% dextrose within four hours of illness onset. This helped save 74% children; six children who died did not receive dextrose infusion on time.

“In view of our observations and conclusions, the Government of Bihar has already introduced some interventions” such as asking parents to restrict litchi consumption by children, making sure no child goes to bed without eating a meal, measuring blood glucose level and infusing 10% dextrose immediately on admission.

Published in The Hindu on February 3, 2017