Author Archives: David Reay

Indian universities ordered to cut length of science courses

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Posted on behalf of T. V. Padma

Thousands of students and staff at some of India’s leading universities, including the prestigious Indian Institute of Science (IISc), Bangalore, have been left in turmoil after the institutions were ordered to cut the length of their undergraduate science courses to fall in line with national policy.

The IISc was last week told by Smriti Irani, the new minister for Human Resource Development, that it must immediately shorten all ongoing and planned four-year courses by a year. The decision came just weeks after Delhi University, one of India’s biggest, was told it must cancel its four-year programmes, which were only introduced last year. Several private universities have also been told to roll back their undergraduate course length.

The move has caused significant confusion and upheaval. The IISc attempted to agree a compromise deal with the education authorities that would see it give undergraduates the option of leaving its science courses with a non-honours degree after three years; and rename the four-year course. But this has now caused uproar among students, who accuse the IISc management of bowing to government pressure.

Delhi University is complying with the measure, leaving it struggling to reconfigure courses that have already started while rescheduling those due to begin this year. As many as 25,000 students and staff will be affected.

“Such moves could turn the brightest students of India away from a science career; and threaten innovation in higher education, which is in bad need of an overhaul,” says Vishwesa Guttal, assistant professor at IISc’s Centre for Ecological Sciences.

Traditionally, most Indian universities follow a three-year undergraduate programme for both science and arts, modelled on the UK system. But in 2008, three top science academies, the Indian Academy of Sciences in Bangalore, Indian National Science Academy in Delhi and National Academy of Sciences in Allahabad, prepared a position paper on higher education in science, in which they recommended a four-year programme. Their report highlighted some of the major drawbacks in undergraduate science education in India, including compartmentalised teaching of some sub-disciplines, inefficient admissions systems and repetition of topics at BSc and MSc levels. Other deficiencies included poor laboratory facilities, little exposure to research methodologies and limited options for movement between science and technology streams.

In recent years some institutions, including the Indian Institute of Technology, Kanpur (IIT) and several private universities, have introduced longer courses. The IISc began offering its own four-year undergraduate science programmes in 2011, with a focus-placed on equipping students with research skills in the final year, and building its brand. Some courses at the Indian Institutes of Science Education and Research (IISERs) also adopted four-year programmes.

And in 2013, Dinesh Singh, Delhi University’s vice-chancellor, pushed through a four-year undergraduate programme to replace the three-year one despite strong resistance from teachers and students who were unprepared for the change. It was designed to better prepare students for academic and job market requirements, as well as bring courses more in line with those offered in the United States.

But in June, following the swearing in of a new government under prime minister Narendra Modi, Irani rolled back Delhi University’s four-year programme. The University Grants Commission (UGC) said it “was not in consonance” with the national policy on education. This left thousands of students who enrolled in 2013 in the lurch, and delayed admissions for 2014 as the university struggled to accommodate the changes.

Then, on 6 August, Irani told the Indian Parliament that the government planned to ask the IISc and two private universities to discontinue their four-year undergraduate science programmes. The statement sent shockwaves through the IIS campus, and director Anurag Kumar constituted a committee to look into how the institution could “align our programme with the UGC guidelines”.

Kumar told Nature that the institute would like to retain the four-year programme with its unique strong research component. “The novelty of the IISc four-year programme is that it is creating a small number of researchers trained by some of the top scientists in the country,” he says.

It is understood that the institute has now agreed a compromise deal that would enable students to leave IISc courses after three years with a Bachelor of Science degree, or continue to study for another year and gain a new Bachelor of Science (research) degree. But students and a section of faculty are unhappy at what they see as the institute ‘caving in’ to the UGC’s demands.

There is a sharp divide at Delhi University over the benefits of a four-year programme. Shobhit Mahajan, professor at Delhi University’s faulty of physics, says “there were problems from the word go” with the manner of implementing the change to a four-year system. “It was hare-brained and not based on ground realties of students, teachers and infrastructure.” Besides, adds Mahajan, the main stakeholders – the teachers who were going to teach the new course – were left out of the discussions and decisions.

Tapasya Srivastava, assistant professor at the department of genetics at the University of Delhi, says that while the four-year undergraduate programme may be well established in the US and other countries, “its success in India would require structural changes in not only the Master’s [degrees] but also the preceding school programme. The rudimentary foundation courses seem to make a mockery of the intensive school coursework that a student is put through.”

But others say the current undergraduate system needed an overhaul. Deepak Pental, former vice-chancellor of Delhi University and one of India’s top genetically modified crop scientists, believes a “radical shift” is required. “We have had a one-track system for the past 30 years and were not creating inter-disciplinary studies,” he says. But with the “mucked up” implementation of a four-year programme in Delhi University, “we have lost an opportunity to improve our undergraduate programme”, he adds.

Student may be jailed for posting scientist’s thesis on web

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Posted on behalf of Michele Catanzaro

A Colombian biology student is facing up to 8 years in jail and a fine for sharing a thesis by another scientist on a social network.

Diego Gómez Hoyos posted the 2006 work, about amphibian taxonomy, on Scribd in 2011. An undergraduate at the time, he had hoped that it would help fellow students with their fieldwork. But two years later, in 2013, he was notified that the author of the thesis was suing him for violating copyright laws. His case has now been taken up by the Karisma Foundation, a human rights organization in Bogotá, which has launched a campaign called “Sharing is not a crime”.

“It is a really awful, disturbing case, for the complete lack of proportionality of the trial,” says Michael Carroll, director of the Program on Information Justice and Intellectual Property at the American University and member of the board of directors of the Public Library of Science. “In copyright systems all over the world we see authors of extreme claims but most other countries would filter out this case,” he adds.

Gómez graduated in biology at the University of Quindío, in Armenia, Colombia, in 2010. His thesis was a study on population ecology of the local Cauca poison frog. “I shared the thesis because it was useful to identify amphibians in the fieldwork I did with my group at the university,” says Gómez.

But according to prosecutors, the move was criminal. Colombian copyright law was reformed in 2006 to meet the stringent copyright protection requirements of a free trade agreement that the country signed with the United States. Yet while the US has few criminal penalties for copyright infringement, Colombia allows only for a few exceptions.

“Lawmakers in developing countries, in their commitments to these kind of agreements, often don’t strike a balance,” says Carolina Botero, a lawyer at Karisma Foundation. “Reproducing a work without permission is not enough to face a criminal trial: it should have been done for profit, which is not the case,” she says.

Gómez says that he deleted the thesis from the social network as soon as he was notified of the legal proceedings. But the case against him is rolling on, with the most recent hearing taking place in Bogotá in May. He faces between 4 and 8 years in jail if found guilty. The next hearing will be in September.

The student, who is currently studying for a master’s degree in conservation of protected areas at the National University of Costa Rica in Heredia, refuses to reveal who is suing him. He says he does not want to “put pressure on this person”. “My lawyer has tried unsuccessfully to establish contacts with the complainant: I am open to negotiate and get to an agreement to move this issue out of the criminal trial,” he told Nature.

The case has left Gómez feeling disappointed. “I thought people did biology for passion, not for making money,” he says. “Now other scientists are much more circumspect [about sharing publications].”

Last remaining support for controversial stem-cell papers collapses

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Posted on behalf of David Cyranoski.

UPDATE: The first sentence of the final paragraph of this story was changed on 5 June to clarify a source.

The retraction of two controversial papers that promised a simple way to create embryonic-like stem cells seems to be imminent today after the lead author unexpectedly gave her full consent. Haruko Obokata, of the RIKEN Center for Developmental Biology in Kobe, Japan, had been the last obstacle to the retraction of both papers.

She agreed to retract the second of the two studies last week, but her agreement yesterday to retract the first one, which detailed the fundamental mechanism behind her claims, paves the way for the unravelling of what was heralded as one of the biggest scientific discoveries of the year.

All co-authors of the papers, which claimed to have created a new type of stem cell, known as stimulus-triggered activation of pluripotency (STAP) cells, now appear to have consented to the retraction. This leaves the papers’ fate in the hands of Nature, the journal that published the two studies in January. Requests for retractions with the unanimous support of the co-authors are usually authorized by the publisher. (Note: Nature’s news and comment team is editorially independent of its research editorial team.)

In the STAP studies, Obokata claimed that when she stressed cells by exposing them to acid or putting pressure on their membranes, they underwent a transformation to an embryonic-like cell. The STAP cells therefore shared the ability of embryonic stem cells and induced pluripotent stem (iPS) cells to convert into any of the body’s cell types, promising a huge advance to biomedical research and clinical applications.

But Obokata’s papers quickly came under fire after various manipulated and duplicated images were found in them. After an investigation into the allegations, RIKEN found Obokata guilty of misconduct on 1 April. Earlier this month, it rejected her appeal of the judgement, and asked her to retract both papers. In the meantime, at least a dozen other research groups reported that they were unable to replicate her findings.

As the controversy escalated, several co-authors publicly stated their desire for a retraction. But Obokata and a senior co-author on the papers, Charles Vacanti, of the Brigham and Women’s Hospital in Boston, Massachusetts, stood by the papers.

However, in an unexpected move on 28 May, Obokata consented to the retraction of the second paper, which describes how STAP cells can form placental cells as well as embryonic-like and iPS cells. But she remained resolutely behind the main paper, considering the second “just an extension”, her lawyer Hideo Miki said.

Then, out of the blue on 30 May, Vacanti sent a letter to Nature asking for a retraction of the first paper, according to a source in Japan who is close to the story and has seen Vacanti’s letter. This move may have broken Obokata’s resistance. On 3 June she signed an agreement to retract the first paper and handed it to RIKEN, a spokesperson confirmed. The spokesperson says that the authors are now in discussion with Nature with regard to retraction of both papers. Nature does not discuss retractions until final decisions are made.

Confusion as institute releases report on controversial acid-bath stem-cell papers

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Posted on behalf of David Cyranoski.

Beleaguered Japanese researchers are wavering over whether to retract two stunning but controversial papers that detailed a simple acid-bath method of reprogramming mature cells to an embryonic state.

At a marathon press conference held in Tokyo today, officials from RIKEN, Japan’s largest research institute and home to several of the papers’ authors, announced the findings of an interim investigation into alleged inconsistencies in the studies. But despite apologizing for errors in the papers, they gave ambiguous signals about whether retractions will occur and about the veracity of the method.

The investigation followed the publication of the papers in Nature on 30 January. The acid-bath technique described in them by Haruko Obokata and colleagues, which they called stimulus-triggered acquisition of pluripotency (STAP), gained headlines around the world because cells reprogrammed into this state are ideal for studying the development of disease or the effectiveness of drugs, and could also be transplanted to regenerate failing organs. But within weeks of publication, the papers were assailed for using duplicated images and problems with reproducibility, prompting RIKEN to investigate.

The press conference offered a glimpse of just how the papers and the furore over them have mesmerized Japan. A handful of television trucks with satellite dishes lined the street in front of the building in downtown Tokyo. Some 200 journalists packed the meeting room and were flanked by two dozen video cameras and crew at the front. There, Nobel laureate chemist Ryoji Noyori, director of RIKEN, who made a last-minute decision to participate, sat with four other RIKEN staff, including Masatoshi Takeichi, the director of the RIKEN Center for Developmental Biology (CDB) in Kobe. Several dozen more journalists watched the televised broadcast from there.

For almost four hours, reporters peppered the officials with questions about conflicts of interest, compliance, RIKEN’s scientific fraud policy, and the emotional state of Obokata, whose scientific work, from her dissertation to the STAP papers, has been alleged to contain a variety of problems. Noyori and his staff alternated between disappointment, frustration, bemusement and apparent fatigue, and were often at a loss to explain the errors that had been found in the papers.

Most of the errors detailed by the head of the investigative committee, Shunsuke Ishii, were already known to those who have been following the story. Two image duplications were dismissed as regrettable mistakes. Four more serious problems, including the uncited use of long passages from another paper, were still under investigation. Ishii’s committee is looking for signs of deliberate manipulation of data, and said he has so far found none.

At the conference, Takeichi told reporters that after advising the three leading RIKEN CDB co-authors on the papers — Obokata, Yoshiki Sasai and Hitoshi Niwa — to retract, they agreed. But a 14 March statement written by the trio, who were not present, said only that, because of the public uproar over the errors and the questions over reliability of the data, they “were contacting the other co-authors to discuss the possibility of a retraction”.

Takeichi was asked multiple times to expand on the possibility of a retraction, including one reporter trying to pin down the exact wording they used in agreeing to his advice. Takeichi said he could advise but not force the researchers to retract. Asked whether, in the absence of any binding agreement to do so, they might change their minds, he said: “That is up to them.”

Takeichi had previously resisted the need for a retraction until more was known about the papers, but one error — the use of an apparently identical photo in both Obokata’s doctoral thesis and one of the Nature papers — pushed him to call for a retraction of the papers. Obokata has continued to call the problems simple errors that do not affect the findings. Another co-author, Yamanashi University’s Teruhiko Wakayama has also publicly announced his desire that the papers be retracted.

Charles Vacanti, of Harvard University in Cambridge, Massachusetts, who is the senior corresponding author on the more crucial of the two papers, has made clear that he does not plan to retract. He told Nature News: “I believe the questions and concerns raised do not affect the findings or conclusions in our article.”

If the RIKEN researchers do request a retraction, Nature‘s journal editors will have to step in. The journal tries to get all authors to agree before retracting a paper. According to a spokesperson for Nature: “In cases where not all of the authors agree on a retraction, Nature evaluates whether the evidence available supports the main conclusions of the paper. We may decide to retract in cases where the authors cannot provide evidence to support the main conclusions of the paper. In such cases, if some authors still disagree with the retraction, we note the dissenting authors in the retraction notice.”

The investigation has been taking its toll on Obokata, Ishii said. She “coolly” sailed through the first hearing, but she started to seem nervous in the second. For the third, she had been asked to prepare large amounts of data and she seemed more tired and anxious, he added. The investigation will continue, and the committee hopes to report back “soon.”

Nature News is editorially independent of the research publications section of Nature.

EU members protest proposed GM crop approval

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Posted on behalf of Barbara Casassus.

Ministers from 12 European Union (EU) member states have urged the European Commission to reconsider its proposal to approve a new strain of genetically modified maize (corn).

The representatives, from countries including Austria, France and Italy, sent a letter dated 12 February to European Health Commissioner Tonio Borg asking him not to sanction the approval of Pioneer 1507. The move follows a debate at an EU General Affairs Council meeting on 11 February, at which it became clear that the commission is almost certain to sanction cultivation of the crop. This is despite the opposition of 19 of the 28 member countries — and the European Parliament. The letter states that this outcome would not “yield approval under any other decision-making procedure”.

At the meeting, Germany indicated that it would abstain in a vote, a move that would swing the decision in favour of planting the genetically modified organism (GMO), made by DuPont and Dow Chemical. This is because its vote carries more weight than those of smaller nations under the EU voting system. Two other large states — the United Kingdom and Spain — are in favour, but France, Italy and several smaller states are against.

Before the letter was received, commission agriculture spokesperson Roger Waite was quoted by Euractiv as saying: “The commission shall adopt the proposal to approve the GMO. The rules are clear — there is no choice. This is why the commissioner made clear that an abstention is equivalent to a vote in favour.”

But Greek foreign minister Evangelos Venizelos told a press conference after the meeting that a legal technicality could allow the commission to reject the law, as the debate had been about voting intentions and did not produce  a formal vote, according to the European Observer. New scientific evidence against the maize could make the difference.

Many consumers in Europe have long been lukewarm or hostile to GM crops, and Greenpeace and Friends of the Earth Europe claim that Pioneer 1507 releases a toxin that is dangerous for butterflies and moths, the European Observer added.

At the moment, two GM crops are authorized for cultivation in the EU, but only Monsanto’s MON810 maize is being grown, and only in a few countries. Last summer, Monsanto threw in the EU towel, saying that it would withdraw all its applications for authorization in the 28 countries.

That paved the way for Pioneer, which filed its application for 1507 in 2001 and has received approval for food and feed use from the European Food Safety Authority.

IDRC–Nature science journalism award

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Canada’s International Development Research Centre (IDRC) is offering a six-month, full-time science journalism award worth up to CAD$60,000 to an English-speaking Canadian citizen or permanent resident of Canada. The successful applicant will receive training and work as an intern in the London news room of the leading international science journal Nature before spending up to four months reporting science stories from developing countries. He or she will be at an early stage of his or her career, but with at least three years’ experience as a journalist.

Candidates must have a keen interest in science and technology, particularly relating to development, as well as outstanding reporting and writing skills, and strong ideas for news and features suitable for publication in Nature. The internship is expected to begin in April or May 2014.

To apply, please e-mail the following to david.reay@nature.com:

  • A covering letter explaining your suitability for the award
  • A resume
  • Three recent story clips, ideally a mix of news and feature pieces
  • Three brief pitches for stories you think would appeal to Nature’s audience.

Deadline: Wednesday 5 March 2014 (please note that this has been extended from 26 February 2014)

About the IDRC

The IDRC is a Canadian Crown corporation that works closely with researchers from the developing world in their search to build healthier, more equitable and more prosperous societies (see www.idrc.ca).

About Nature

Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology, and is the world’s most highly cited interdisciplinary science journal. It also has an international news team covering the latest science, policy and funding news in both online and print formats (see www.nature.com/nature).

About the award

Nature will manage the selection process and the IDRC will award up to CAD$60,000 to the successful applicant. This will cover travel costs, living expenses, research expenses, visa or other related costs, in London and in other countries visited during the six-month period. The award will also cover the cost of participating in a conference relevant to the award winner’s professional development as a journalist. For more information click here.

Millions of TB cases going undetected, says WHO

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Posted on behalf of Meera Senthilingam.

Around 3 million people who were infected with tuberculosis (TB) in 2012 were not picked up by global health systems, the World Health Organization (WHO) has revealed. In addition, the testing and treatment of patients with drug-resistant forms of the disease are inadequate, according to the body’s 2013 Global Tuberculosis Report, published today.

The report states that in 2012 an estimated 8.6 million people developed TB, and that 1.3 million died from it. This is a decrease from previous years, but the rate of decline in disease incidence is slow, at only 2% per year, and when broken down to the regional and country level, outcomes are not as positive. Overall however, the 2015 United Nations Millennium Development Goals (MDG) of cutting TB incidence rates from the global baseline of 147 per 100,000  in 1990 and the target of reducing TB mortality rates by half from 25 per 100,000 worldwide in 1990, are on track. Mortality rates have already fallen by 45%.

The majority of TB cases in 2012 were in Southeast Asia (29%), Africa (27%) and the western Pacific region (19%). About 80% of those with TB live in one of 22 high-burden countries, only half of which have already met or are on track to meet the 2015 targets. The remaining 11 countries have faced challenges such as resource constraints, conflict and instability and HIV epidemics, which have constrained their control of tuberculosis.

Progress towards improving the diagnosis and treatment of multidrug-resistant TB (MDR-TB) is well below target level, with 450,000 estimated MDR-TB cases in 2012, three quarters of MDR-TB cases remaining undiagnosed and many diagnosed but unable to receive treatment.

“The debt toll of tuberculosis, a disease that is preventable and curable, is far too high,” said Mario Raviglione, director of the WHO Global TB programme, before announcing the five priority actions recommended in the report. These are to (i) reach the 3 million missed TB cases, (ii) address the MDR-TB crisis, (iii) intensify and build on TB-HIV successes, as less than 60 percent of TB patients living with HIV were found to be receiving antiretroviral drugs, (iv) increase domestic and international financing to close resource gaps, and (v) accelerate the rapid uptake of new tools, including diagnostics for resistance such as GeneXpert and the newly available drug for resistance, bedaquiline.

“There is finally momentum to break the TB epidemic, but if we don’t pursue these five actions, then our gains in the past few years are at risk,” concluded Raviglione.

Non-governmental organizations gave a mixed response to the WHO report. “[Médecins Sans Frontières] is finding alarming numbers of cases of DR-TB in many countries where we treat TB, in large part thanks to a breakthrough in diagnostic technology, but we are still very far away from making real progress against this killer disease,” said Grania Brigden, TB adviser for Médecins Sans Frontières’ Access Campaign.

“Funding has increased in recent years but there is still a huge funding gap,” says Osamu Kunii from the Global Fund to Fight AIDS, TB and Malaria. “We need data and information and this global report is critical to make decisions on country allocation of resources and monitoring and measuring progress.”

Minister halts Italian stem-cell therapy trial

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Posted on behalf of Alison Abbott

The clinical trial of a controversial stem-cell therapy supported by the Italian government has been stopped before recruiting any patients – to the relief of scientists who have been fighting the trial for months.

On 10 October, health minister Beatrice Lorenzin announced that she would follow the advice of a special panel of scientific advisors and disallow the trial. In their stinging report, the advisors described the clinical protocol submitted by the Brescia-based Stamina Foundation as scientifically unfounded and potentially dangerous.

“This is the end of the matter,” says Luca Pani, president of the Italian Medicines Agency. “And we are very happy.”

The Stamina affair had been polarising Italian society for more than a year. Stamina had been treating seriously ill patients since 2007 before its laboratory was closed down for safety reasons in August last year. Patient groups lobbied passionately for access to the therapy, but experts warned that the approach had no scientific base and could be dangerous.

The government decided in March to finance a €3million trial to put the clinical protocol to the test (see ‘Stem-cell ruling riles researchers‘). But when Nature revealed that the protocol itself was fraudulent, the scientists called for the trial to be abandoned (see ‘Italian stem-cell trial based on flawed data‘).

Davide Vannoni, Stamina’s president, immediately announced plans to move the trial abroad. The Turin-based pharmaceutical company Medestea which finances the Stamina Foundation says it will take the therapy to China.