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

CSIR: IMTECH scientist sacked for fabricating data

IMTECH

Three papers published by Dr. Swaranjit Singh Cameotra, a scientist at IMTECH, in 2013 in PLOS ONE were retracted in July 2014. – Photo: IMTECH

Swaranjit Singh Cameotra, a senior scientist at the Chandigarh-based Institute of Microbial Technology (IMTECH), a CSIR lab, has been removed from service early this month for fabricating data in three papers published in 2013 (April 17, October 1 and October 8) in a scientific journal PLOS ONE. All the three papers were retracted by the journal in July 2014. Data fabrication was found in four more papers where he was the senior author. This is the first time in recent years that CSIR has taken the extreme step of terminating the service of a senior scientist for scientific misconduct. I wrote about the retraction and the subsequent investigation on July 16, 2014.

In a retraction note published in July 2014, the journal said: “The Council of Scientific and Industrial Research has carried out an investigation about several publications by this group [led by Dr. Cameotra] in order to evaluate concerns raised about the authenticity of the data. The investigation committee… concluded that there are no data available underlying this study and thus that the published results are fabricated. As a result, [CSIR] has requested the retraction of the publication.”

Dr. Cameotra was a senior scientist at the Environmental Biotechnology and Microbial Biochemistry Laboratory at IMTECH.

“It is not easy to issue a removal order of a government employee. There was a thorough enquiry by 2-3 committees and they found hard evidence… every committee gave a clear-cut decision,” said Prof. R.K. Sinha, who is holding additional charge as the Director of IMTECH. “[Data fabrication] is not expected of a scientist.”

According to Prof. Sinha, Dr. Cameotra has submitted an appeal to the Director-General of CSIR to reconsider the decision. Dr. Cameotra will still be eligible to apply for any other government job.

“It is not easy to issue a removal order of a government employee. There was a thorough enquiry by 2-3 committees and they found hard evidence… every committee gave a clear-cut decision,” Prof. Sinha said. “[Data fabrication] is not expected of a scientist.”

Speaking to me, Dr. Cameotra said tersely: “I have no comments.”

According to sources close to the investigation, Dr. Cameotra had admitted that there was no data to substantiate the claims made in the papers. Though he did not fabricate the data himself, as a senior scientist and senior author of the papers he failed to check if the data were correct, a highly reliable source told me. The level of complicity and scientific misconduct had become clear even at an early stage of the investigation.

“In this case, the system was not found wanting,” said Prof. Sinha referring to other cases where Indian scientists have got away with plagiarism, and data falsification and fabrication.

Data fabrication came to light when Georgia Tech, U.S. (where Fazlurrahman Khan, the first author of the papers worked as a post doctoral fellow) found “similarity and overlapping of data presented in the papers and the work Dr. Khan had done while in the U.S.” A committee formed by IMTECH to investigate the matter found that Dr. Khan was responsible for fabricating the data. Dr. Khan has since resigned from IMTECH.


Related story and link:

IMTECH: CSIR scientist used faked data in seven papers

 

Published in The Hindu on July 23, 2016

Editorial: A blot on Indian science

That getting papers published in scientific journals, reputable ones included, using manufactured data is virtually child’s play has been made painfully evident by a team of scientists at the Chandigarh-based Institute of Microbial Technology (IMTECH), which functions under the Council of Scientific and Industrial Research. Three papers that the team published last year in the PLoS ONE journal were retracted on July 9 after an internal investigation by the institute found unequivocal evidence of data fabrication. Four more papers are in the process of being retracted. All the seven papers have the same research associate as the first author and the senior scientist of the institute as the corresponding author. So much was the expertise in data fabrication and “presentation” involved that the reviewers and editors of all the papers failed to spot them. That even with “hindsight” one of the editors was unable to figure out which of the three “similar” but non-identical graphs in the three papers had been fabricated, is proof enough. The same must hold true for the four other papers as well. There is no difference whatsoever in terms of scale or implication between the current case and those involving the South Korean stem cell researcher Hwang Woo-suk and the Japanese stem cell researcher Haruko Obokata. As much as the stem cell researchers shamed their respective countries, the Indian researchers’ unethical practice is a blot on Indian science.

The only consolation in the face of this serious affront to science is that unlike many institutions in India that do not investigate such frauds committed by their scientists, IMTECH has shown the spine and tremendous alacrity to get to the bottom of the issue. While the first author has already paid the price for his commission, the scientist’s role is now under scrutiny. By virtue of being a senior author in all the seven papers, he has much explaining to do to prove his non-involvement in the scandal as some data in the PLoS ONE papers are “not supported by raw data in the lab.” More than the setback suffered by the institute, it would face a barrage of criticism and ridicule and lose all the goodwill it earned as a result of its actions if the probe does not remain unbiased and fails to bring out the truth. There is an important lesson to be learnt from the way South Korea acted without any bias to prove Hwang’s guilt and thereafter withdraw his licence and suspend him. Meanwhile, steps need to be taken immediately to teach research students the ethics of doing and reporting science. For instance, journals have found numerous instances of unacceptable manipulation of images, often arising from researchers’ eagerness to produce perfect pictures.

Published in The Hindu on July 23, 2014

IMTECH: CSIR scientist used faked data in seven papers

IMTECH

Three papers published in the journal PLOS ONE in 2013 by a group of Indian researchers at the Institute of Microbial Technology (IMTECH), Chandigarh, were retracted by the journal on July 9, 2014. Four more papers published  in 2013 by the same group are in the process of being retracted. All the papers contain fabricated data.

IMTECH is a Council of Scientific and Industrial Research (CSIR) institute.

All the three PLOS ONE papers have Dr. Fazlurrahman Khan, Research Associate, as the first author and Dr. Swaranjit Singh Cameotra from the Environmental Biotechnology and Microbial Biochemistry Laboratory as the corresponding author. They were published in online in 2013 on April 17, October 1 and October 8 respectively. Unfortunately, these papers have been cited by five other papers.

The four papers that are in the process of being retracted also have Dr. Khan as the first author and Dr. Cameotra as the corresponding author.

And they were published in the Journal of Hazardous Materials (on June 15, 2013), in Chemosphere (in November 2013) and the other two in the Journal of Petroleum and Environmental Biotechnology (on August 21 and November 29, 2013).

The papers that are being retracted were scrutinised by the institute and necessary action taken to retract them once the fate of PLOS ONE came to light. Dr. Cameotra is a co-author in 15 papers published in 2014 alone.

The only silver lining in the sordid tale is the institute’s keenness to investigate and get to the bottom of the issue. The proof lies in the retraction note published by PLOS ONE: “The Council of Scientific and Industrial Research has carried out an investigation about several publications by this group in order to evaluate concerns raised about the authenticity of the data.

“The investigation committee… concluded that there are no data available underlying this study and thus that the published results are fabricated. As a result, [CSIR] has requested the retraction of the publication.”

“It is very unfortunate. As a director [of IMTECH], I feel bad about it,” Dr. Girish Sahni told this Correspondent. “These papers were retracted based on the findings of the enquiry committee that was formed in January to look into the circumstances. It found that the data accompanying the papers were not supported by raw data in the lab.”

“The current episode is a dark patch, but I, as Director could not foresee it….I have been able to act swiftly only once it came to light,” he said.

Unlike most institutes in India that stonewall journalists seeking information on issues such as this, Dr. Sahni was frank about the case and provided information about the case and its outcome.

According to Dr. Sahni, IMTECH was alerted by Dr. Khan’s boss at Georgia Tech who saw some similarity and overlapping of data presented in the papers and the work Dr. Khan had done while in the U.S. Dr. Khan was a post doctoral fellow at Georgia Tech, U.S. prior to joining IMTECH in 2012. He has since resigned from IMTECH.

Immediate action

“We immediately formed the committee to investigate the basis of the data,” Dr. Sahni said. “We wanted to know if the data were fabricated or whether there was no record-keeping.” The committee found Dr. Khan was responsible for fabricating the data.

“We must get to the root of the problem. We want to know whether only he [Dr. Khan] was involved or whether Dr. Cameotra was also involved,” Dr. Sahni noted. “Now the matter has been taken up from the vigilance angle to fix responsibility. The process has been initiated.” “We want to confront it and not hide it,” the director said. “Better to throw light and learn from the process… we certainly must retrospect…At the end of the day, we must remember that the end result of such shortcuts is not good.”

Editor’s reaction

Willem van Schaik, associate professor of Medical Microbiology at Utrecht University in the Netherlands who edited one of the retracted papers in PLOS ONE told Retraction Watch blog: “…These three papers were handled by three different editors, which may have made it more difficult to catch any fraud. The papers all follow the same outline: a bacterium was isolated from natural environments and was able to metabolize some unusual chemicals.

“When comparing the three papers, you will see that the graphs are very similar but not identical so even with hindsight, I find it difficult to find which data have been fabricated.

“The manuscript has been reviewed by two reviewers and needed considerable editorial effort. I am very sorry that the reviewers have had to spend their time and effort on a manuscript that ultimately turned out to be a fake.”

Tweets revealing
A torrent of tweets from Prof. Schaik provides a glimpse of his emotions after knowing the true status of the PLOS ONE paper that he edited. “Am incredibly annoyed, and a bit angry, about this: I did not suspect a thing (and neither did reviewers)” was one of his first tweets.

The other three tweets were: “Review process was looooooong (many rounds of revisions for English) but data appeared solid.”

“But I guess when data are completely fabricated, they will look solid (if incredibly uninteresting).”

And the last notable tweet was “Not sure if I now should change how I act as editor. Any thoughts? Have others been in [the] same position as editor?”

Published in The Hindu on July 16, 2014

Now, reversing adult cells to stem cells becomes easy

STAP cells - Haruko Obokata

Photo: Haruko Obokata

If in 2006 Shinya Yamanaka showed to the world that reversing adult cells (differentiated cells) to behave like stem cells — induced pluripotent stem cells (iPS cells) — is indeed possible by introducing four transcription factors, two studies published today (January 30) in Nature have gone a step further.

Haruko Obokata from the Harvard Medical School, Boston and the first author of the papers could reprogram adult mice cells to become pluripotent (the ability to become any of the 256 adult cells) cells without using any of the transcription factors.

Neither did the team resort to cloning (somatic cell nuclear transfer technique), where the nuclear matter from an adult cell is transferred into an egg whose nucleus has been removed.

What the team of researchers did was simple. They exposed the haemopoietic adult cells taken from newborn mice to a mildly (sub-lethal) acidic condition (pH 5.7) for just 25 minutes at 37 degree C.

And behold, the environmental stress did not kill or damage the adult cells but surprisingly reprogrammed the adult cells to behave like pluripotent cells.

Superior attributes

And unlike even embryonic stem cells, the reprogrammed adult cells were found to be capable of contributing to both embryonic and placental tissue formation; embryonic stem cells (ES cells) do not contribute to the formation of the placental tissue. Whether the adult cells reprogrammed by environmental stress could form both tissues or behave just like ES cells (by forming only the embryonic tissue) depends on the medium in which they are cultured.

The studies have shown that adult cells have some hidden plasticity, and when exposed to stress, the plasticity comes into play to convert the adult cells into pluripotent cells.

The stem cells so produced exhibited pluripotency on the seventh day after exposure to stress. But unlike embryonic stem cells or those produced by cloning, the stem cells produced through stressing — stimulus-triggered acquisition of pluripotency (STAP) — “rarely” multiplied or proliferated on their own. Proliferation of stem cells is essential for obtaining a huge mass of cells for therapeutic use.

But the researchers were able to overcome this hurdle. By using a culture medium containing a particular hormone, the STAP cells were enabled to grow into colonies. “These growing colonies looked similar to those of mouse ES [embryonic stem] cells,” they write in one of the papers.

What is indeed interesting is that the researchers achieved the same measure of success when they repeated the experiment using various adult mice cells — brain, muscle, fat, bone marrow, lung and liver muscle.

The question is whether such reversal could be seen or achieved when adult cells are subjected to other stresses like physical damage, heat shock etc. Also, the study raises an important question — why do adult cells retain latent plasticity that gets expressed when subjected to stress?

While mammalian cells are “more resistant” to conversion, except in certain cancers, conversion of adult cells into pluripotent cells occurs in plants when subjected to “drastic environmental changes.”

Similarly, adult cells of amphibians, reptiles, and birds exhibit similar ability to reverse their status to become pluripotent cells or switch identity.

Common in nature

In an accompanying news piece, Austin Smith from the University of Cambridge highlights external factors in developmental biology. For instance, sex determination in crocodiles is dependent on temperature and frog cells destined to form skin cells go on to become brain tissue if exposed to acidic conditions.

It remains to be seen if cells taken from adult mice would respond the same way. The adult cells used for these experiments were from newborn mice. Finally, it is too early to say with confidence if the results can be replicated in humans.

Published in The Hindu on January 29, 2014

Expert committee report plagiarised

Published in The Hindu on August 30, 2012

Mobile tower. - Photo R. Prasad-Optimized

Large-scale investigation into harmful effects of radiofrequency fields from mobile phone towers is lacking. – Photo: R. Prasad

 

The “Report on possible impacts of communication towers on wildlife including birds and bees,” is a textbook example of how not to write scientific reports.

An expert committee, also comprising a few scientists from reputed institutions, was constituted in August 2010 by the Ministry of Environment and Forests to study the issue. It was on the basis of their recommendation that the Central Department of Telecommunications was recently directed to ensure that new mobile towers do not come up within a one-kilometre radius of existing towers.

The report begins by emphatically stating that “adverse effects… from mobile phones and communication towers on health of human beings are well documented today!” Nothing can be more incorrect than this. Brain cancer is one of the most feared adverse effects of extended duration of usage of mobile phones over a long period of time. However, many large-scale studies, including the Dutch and Denmark study and WHO’s INTERPHONE study have not found any significant risk.

Shortly after the WHO labelled electromagnetic fields as “possibly carcinogenic to humans (Group 2B),” it clearly communicated in June 2011 that “no consistent evidence of adverse health effects” has been found in humans from radiofrequency fields.

Large-scale investigation into harmful effects of radiofrequency fields from mobile phone towers is lacking.

But despite several studies not finding any significant or “consistent” effects, it is prudent to adopt a precautionary approach and reduce the duration of usage and number of times mobile phones are used. Most importantly, children, especially younger children, should be discouraged from using mobile phones.

In the same vein, steps to reduce exposure to electromagnetic radiation from mobile towers should be taken.

Contradiction

The report contradicts itself in some instances. After stating that wildlife “appear to be at high risk” from electromagnetic field, it retracts by stating that not much information is available on the “biological impact on wild species!”

There is also willful misrepresentation of facts when they chose not to include details from the cited work that would in any way weaken their argument. For instance, one paper does indicate that other variables in addition to mobile tower radiation might be causing some adverse effects. By not mentioning the co-founding factors, the committee report conveys a completely different message.

Plagiarism

The egregious part is the rampant plagiarism found in the literature survey section. Some sentences have been reproduced verbatim from published papers without any attribution. While some parts of the report on the effects of electromagnetic radiation on birds/house sparrows and honey bees have been attributed, they still fall under the gambit of plagiarism.

This is for the simple reason that the sentences or chunks of material have been reproduced verbatim without quotation marks. According to the IEEE guidelines, “the absence of quotation marks [that] does not clearly reference or identify the specific, copied material” amounts to plagiarism even when the source is cited.

Some of the papers referred to have been published in less credible journals. The report also suffers from a lapse that is commonly encountered at the student level — references cited in the text missing in the bibliography.

What ails science education is that people who are in a position to guide students on the correct ways of science writing are found wanting.