Author Archives: Declan Butler

Japan’s nuclear sun to set?

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A week can be a long time in politics, so today’s announcement by the Japanese government that it intends to phase out its 50 remaining nuclear reactors by around the 2030s is perhaps much less of a certainty than it might at first appear. Under the plan, existing reactors would be phased out when they reach 40 years of age so causing a gradual fall in nuclear’s share of electricity generation in Japan, as no new reactors are built to replace them.

Many of Japan’s reactors are relatively young meaning that any phase-out will bite hardest quite a fair bit down the line – see the graph belo,w which gives a snapshot of the age of Japan’s power reactors – leaving potential scope for Japan’s nuclear policy to shift in the future under different administrations, and circumstances. (In passing, several of Japan’s reactors were built in the last decade, and two reactors are under construction, so under the 40-year rule would persist beyond 2040). In contrast, Germany which last year decided to phase out its then 17 nuclear reactors intends to do so by 2022 – see “The knock-on effects of Germany’s nuclear phase-out” (almost all of its reactors were built in the 1970’s and are nearing the end of their lifetimes).

{credit}IAEA{/credit}

Indeed, in the short-term, the pledge to phase-out nuclear energy may provide the Japanese government with political cover to begin restarting reactors, the last of which was shut down in May (see ‘Japan switches off its last nuclear reactor). The reactors, closed for routine maintenance, would usually be reopened immediately after this was completed, but all will need to meet new safety tests and rules to be implemented this autumn before being restarted.

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ArXiv’s funding future boosted by hedge-fund charity

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The financial sustainability of the arXiv preprint server at Cornell University Library in Ithaca, New York, received a boost yesterday with the announcement that the Simons Foundation, based in New York City, would provide the repository with up to US$350,000 a year in funding for the next five years. The sum would include a yearly $50,000 unconditional grant, with the remainder being matched to funds provided by arXiv’s other donors.

ArXiv has been looking to put itself on more solid financial footing since January 2010, when Cornell University Library announced that it would seek outside financial support from the academic institutions that account for most of the usage of the preprint server. The Simons Foundation — which was founded in 1994 by James Simons, a mathematician and founder of the hedge fund Renaissance Technologies, and his wife Marilyn — gave $60,000 to the library in 2011 to help put in place this self-sustaining funding model and a new governance structure.

ArXiv, which turned twenty last year, was founded by Paul Ginsparg in 1991 at the Los Alamos National Laboratory in New Mexico. In 2001, Ginsparg moved to Cornell University, taking the server with him. Last September, Ginsparg gave up his involvement in running the server, which is run entirely by Cornell University Library staff, although he remains on its advisory board.

The arXiv server covers mainly physics, computer science, mathematics and statistics, but has expanded to include papers from other disciplines, including biology. The preprint server’s some 780,000 papers themselves have recently become the object of ‘culturomics’ research.

Correction: An older version of this article mistakenly stated that the Simons Foundation was to donate up to $300,000 per year for the next five years. The correct sum was US$350,000.

French research minister appointed

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Geneviève Fioraso, deputy mayor of Grenoble, and a Socialist member of the National Assembly (the French parliament), representing the Isère constituency, has been appointed minister of higher education and research in the first goverment of French president François Hollande and prime minister Jean-Marc Ayrault. Fioraso is no stranger to research and innovation issues, which has been her speciality both as a member of parliament, and as deputy mayor of Grenoble, while she is also a member of the Parliamentary Office for the Evaluation of Scientific and Technological Choices. Most recently, she was rapporteur of the office’s February report on the challenges of synthetic biology. She was also part of the group of advisers on innovation in François Hollande’s election campaign team.

Fioraso, who is 57 years old, has had a diverse career. Starting out as a lecturer in English and economics, she took a post at the Grenoble city hall in 1979, and became a parliamentary assistant in 1983. In 1989, she took on a management role at the high-tech start-up Corys, where she worked on the safety of nuclear and coal-fired power plants. In 1995, she became head of the office of Grenoble’s deputy mayor, Michel Destot, and in the early 2000’s worked as a marketing executive for France Telecom in emerging social and health applications. Elected to parliament in 2007, she is also chief executive officer of Sem Minatec Entreprises, the business incubator wing of Minatec, the renowned Grenoble innovation campus for nanotechnology and electronics, which has some 2400 researchers, 1200 students and 600 industrial staff.

Fioraso is one of 17 women among the 34 ministers nominated to the new government. This parity, promised by Hollande, is a first for France. The new government may undergo a reshuffle after the upcoming parliamentary elections, however, the first round of which will be held on 10 June with the final round being held on 17 June. For the full government line-up see the newspaper Le Monde’s summary.

Other links: Fioraso’s blog and page at the National Assembly.

Nature’s Q&A’s with Nicolas Sarkozy and François Hollande in the run up to the presidential election – “A question of science.”

French physicist jailed for 5 years on dubious intent-of-terrorism charges

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By Declan Butler and Geoff Brumfiel
A French court today sentenced French-Algerian physicist, Adlène Hicheur, to four years in prison with a further one year suspended sentence. He was found guilty of plotting with AQIM, al-Qaeda’s North African branch, to carry out terror attacks on military and economic targets on French soil. The court also ordered the confiscation of €15,000 (US$19,500) that Hicheur had transferred to Algeria for what he said was a property purchase, as well as his computer equipment.

Hicheur’s supporters, including many of his former scientific colleagues, say, however, that Hicheur’s sentencing is a miscarriage of justice, and that he was a victim of excess and overreach by France’s draconian anti-terrorist laws (see ‘The case of Dr Hicheur‘).

The verdict was read out briefly, with little further explanation, at the Fourteenth Chamber of the Palais de Justice in Paris, near the Notre Dame cathedral. At Hicheur’s two-day trial on 29–30 March, prosecutors had called for Hicheur to be sentenced to six years in prison — he could have faced a maximum sentence of ten years.

Hicheur was detained in 2009, when he was then a postdoctoral researcher in high-energy physics at the Swiss Federal Institute of Technology in Lausanne, and has been held in custody in Fresnes Prison near Paris ever since (see ‘Physicist languishes in French prison‘). Given the time he has already spent in prison, combined with various term reductions available under the French judicial system, he is likely to be released almost immediately, possibly within weeks. His lawyers could yet appeal the verdict, but that could result in Hicheur’s spending longer in prison.

Outside the courtroom, Jean-Pierre Lees, a physicist at the Laboratory of Particle Physics in Annecy-le-Vieux, France, who heads a campaign in support of Hicheur’s freedom (see ‘Physicists protest colleague’s terrorism detention‘), was visibly deeply dismayed and stunned by the verdict, and slammed what he alleged was a lack of independence of the judiciary from the political system. “I’m extremely disappointed,” says Lees. “One has the impression that we’re in the Soviet Union and not in France.”

Lees says that online exchanges intercepted by police and presented at Hicheur’s trial, held on 29-30 March, failed to provide any evidence that Hicheur had been involved in planning any terror plot (see ‘Particle physicist ‘falsely accused’, claims brother‘). “He’s been sentenced to five years when there was no tangible evidence of wrongdoing,” says Lees. Hicheur had resigned himself to the likelihood that he would not be acquitted, he adds, and has “lost his faith in the French justice system.”

Lees also complains that whereas a central element of the the prosecution case was that Hicheur had online exchanges with an alleged leader of AQIM, that person, who French authorities say was interrogated by Algerian authorities, was not brought to testify at Hicheur’s trial. “We never even saw his identity card in court, we don’t even know if he really exists,” says Lees.

Hicheur’s trial was held one week after the killing by the RAID, a crack French police squad, of Mohamed Merah, a 24-year-old French citizen of Algerian descent, suspected of killing seven people, including three soldiers in Toulouse and Montauban and four civilians — three of whom were young children — outside a Jewish school in Toulouse. French authorities claimed that Merah had told them he was working with al-Qaeda. Hicheur’s supporters say that this event, which became a key event affecting the French presidential election campaign, did not help him get a fair trial (see ‘French standoff raises fears for incarcerated physicist‘).

Morever, Hicheur’s case was very different — Merah had a criminal record and was heavily armed. He had also travelled to Afghanistan and Pakistan before the attacks, where he had actually been detained by American troops before being returned to France.

The sentencing itself comes just two days away from the final round of France’s presidential election between the incumbent conservative president, Nicolas Sarkozy, and his Socialist challenger François Hollande (polls point to a victory for the latter). Following the Merah killing, Sarkozy called for a crackdown on those who visit extremist websites, pledging that: “From now on, any person who habitually consults web sites that advocate terrorism or that call for hatred and violence will be criminally punished.”

Canada confines mutant flu to maximum-security facilities

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Canada this month announced that any research on mammalian-transmissible strains of the H5N1 avian flu virus in the country’s labs would need to be done at the strictest level of biocontainment, biosafety level 4 (BSL-4). It’s the first country to issue a biosafety rating following the creation of such H5N1 strains in two recent controversial studies (see Nature News Special: Mutant Flu).

The question of which biosafety rating is appropriate for research on the new strains was highlighted as crucial by an expert meeting convened in Geneva last week by the World Health Organization (WHO). The new, modified H5N1 strains are held at Erasmus Medical Center in Rotterdam, the Netherlands, and at the University of Wisconsin-Madison, in two BSL-3-enhanced facilities (the second highest biocontainment level), and the WHO described these as “well-established research facilities with high security and high safety“. But it also recommended that regulators “urgently” review the biosafety and biosecurity conditions under which further research on such strains is conducted, and that until that’s done, the strains should stay where they are and not be shared with other labs.

In biosafety assessment, pathogens are classified in terms of their ‘risk group’ (RG) on a scale of 1–4, where 4 is the highest, on the basis of an assessment of the relative threat they pose to people. They are also classified in terms of the biological containment levels needed, again on a scale of 1–4. What can be a bit confusing is that although required biocontainment levels for various research on a pathogen largely mirror the risk-group rating, they don’t necessarily equate with it. Some types of research may be permitted at a lower biocontainment level than their risk group, if it’s assessed that the research can be done safely with less-restrictive precautions. As the WHO explains, biocontainment level designations are “based on a composite of the design features, construction, containment facilities, equipment, practices and operational procedures required for working with agents from the various risk groups”.

Barry Bloom, a researcher and former dean at the Harvard School of Public Health in Boston, Massachusetts, also emphasizes the importance of training. “Security in handling dangerous pathogens is, in my view, less a function of the physical containment facilities than the training, experience and competence of the scientists working with them,” he says.

Some flu researchers are concerned that work on mammalian-transmissible H5N1 viruses will be severely hampered if it is restricted to BSL-4 laboratories, because BSL-4 conditions are much more constraining than BSL-3 labs, and because there are only a few dozen BSL-4 labs worldwide. Other experts feel that such high containment is essential, given the risk that any escape of the viruses could cause a H5N1 pandemic (see Fears grow over lab-bred flu.)

Whatever biocontainment levels are eventually decided as appropriate by the relevant authorities, many researchers are concerned about the proliferation of such mammalian-transmissible avian flu strains: as more labs work on them, the risk of release — accidental or intentional — goes up. Bloom says that he hopes that the number of labs allowed to work on them “would be limited, transparently identified, and monitored for safety under the aegis of an international body such as WHO”.

Declan Butler asked Sandra Fry, director-general of the Public Health Agency of Canada’s Pathogen Regulation Directorate, and Marianne Heisz, head of the directorate’s Office of Biosafety Programs and Planning, how the agency reached its decision to classify work on the new lab strains as requiring BSL-4 (note that Canada uses the term ‘CL’ in place of BSL) facilities.

Read the Q&A under the fold.
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WHO meeting calls for mutant-flu research to be published ‘in full.’

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A two-day meeting of 22 experts convened in Geneva by the World Health Organization (WHO) has concluded that two controversial flu studies should be published in full. The research — in which ferret-transmissible strains of avian H5N1 flu virus were created — will be published after a delay of probably a few months, which the experts argue is needed to explain better the public-health benefits of the research and allay public concerns over the safety of the work. “There is a preference from a public health perspective for full disclosure of the information in these two studies,” says Keiji Fukuda, assistant director-general of health security and environment at the WHO. “However there are significant public concerns surrounding this research that should first be addressed.”

The panel, largely made up of flu researchers, also concluded that research into creating more transmissible forms of H5N1 and other flu viruses was important and must continue. They agreed to extend a voluntary 60-day moratorium to allow broader discussions on the biosafety aspects of how such work could best be carried out, given the concerns in many quarters as to the potential consequences of an accidental escape of such viruses from the lab. To this end, the WHO intends to hold further meetings with a broader mix of experts over the next few months.

In December, the US government and the US National Science Advisory Board for Biosecurity (NSABB) had requested that  Nature and Science should not publish the two studies. Fukuda said at a press conference today that since then, there has been more time to reflect, and that in particular, it would be far too complex to redact the details of the papers, and to create a mechanism for disseminating the papers only on a need-to-know basis. The meeting reached consensus on all the major issues, he said, but not the recommendation to publish the study in full, given that some of the US experts present, including Paul Keim, the chair of NSABB, adhered to the US administration’s line.

Philip Campbell, the editor-in-chief of Nature, issued a statement: “Discussions at the WHO meeting made it clear how ineffective redaction and restricted distribution would be for the Nature paper. It also underlined how beneficial publication of the full paper could be. So that is how we intend to proceed.”

See my blog post yesterday — ‘Avian flu controversy comes to roost at WHO’ — and Nature‘s News Special on the H5N1 controversy for more background.

Avian flu controversy comes to roost at WHO

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Almost two dozen experts kicked off a two-day international meeting this morning at the World Health Organization (WHO) in Geneva, in a bid to find ways to move forward in the controversy over two studies that have created strains of the H5N1 avian flu virus that are transmissible in ferrets. The meeting may reach some consensus on a few immediate issues, such as what parts of the studies should be published, and who might qualify for access to the full papers on a ‘need-to-know’ basis.

But the narrowness of the expertise of those taking part means that the meeting will not even begin to address the far bigger issue of whether such research should be allowed at all in the future, and if so, how  it should safely proceed. Key to that question is an assessment of the relative public-health benefits, compared to the risks that a proliferation of such research in labs worldwide would increase the risk of an accidental or intentional release of the lab strains. Ferrets are a good proxy for how flu behaves in other mammals, including humans, so any release could itself spark a H5N1 pandemic, with potentially catastrophic consequences given the virus’s likely high mortality rate (see ‘Death-rate row blurs mutant flu debate‘).

The list of experts attending the meeting — which the WHO made public this morning — shows that the panel is overwhelmingly stacked with academic flu researchers, almost all of whom are strongly in favour of such research, and many of whom would like to see it proceed unfettered. By contrast, there are almost no public-health officials of international stature attending, nor experts in risk assessment, biosafety or biosecurity.

The WHO has explained, however,  that the participants were limited to “people who have direct involvement or knowledge about these two studies, their review or oversight, or potential dissemination of results”, and that this meeting has the very limited remit of clarifying “key facts about the two research studies and the most urgent related issues”. 

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Pandemic 2009 H1N1 virus gives wings to avian flu

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Has the 2009 H1N1 flu pandemic increased the risk that the H5N1 avian flu virus could evolve to create a human pandemic?

That’s a possibility raised by the work of Yoshihiro Kawaoka of the University of Wisconsin, Madison, the main conclusions of which — but not the details — are revealed in a Comment article in Nature today. His team created a virus that has the H5 haemagglutinin (HA) surface protein from the H5N1 virus, with all the remaining genes coming from the 2009 pandemic H1N1 virus. The resulting virus proved to be highly transmissible in ferrets, and is therefore likely to have the same behaviour in other mammals, including humans.

What’s intriguing is that before the 2009 pandemic, several research groups had tried the same experiment, using the garden-variety seasonal H1N1 flu, but without success. The difference is that the 2009 pandemic H1N1 virus, which is a triple reassortant of pig, avian and human viruses, contains the triple reassortant gene (TRIG) cassette, which is believed to make it far easier for a flu virus to swap genes with those from other species. This suggests that H5N1 may find it much easier to reassort with pandemic 2009 H1N1 virus circulating in the wild to create a pandemic virus, whereas it had coexisted with seasonal flu since 1997 without evolving into a pandemic strain, explains Bruno Lina, a virologist and flu researcher at the CNRS, France’s basic-research agency, who works at the University of Claude Bernard Lyon-1.

The study by Kawaoka’s team, which has been accepted for publication by Nature, is one of two studies that have succeeded in creating H5N1 strains capable of transmitting between ferrets. The other, by a team led by Ron Fouchier of Erasmus Medical Center in Rotterdam, the Netherlands, has been submitted to Science. The papers have been at the centre of controversy since 20 December, when the United States government — acting on advice from the US National Science Advisory Board for Biosecurity (NSABB) — asked both journals to publish only the main conclusions of the two flu studies, but not to reveal details. Insights from the research might help to improve pandemic preparedness in the future, but some are concerned that the publication of such work would amplify the risk of an accidental, or intentional, release of the virus that could spark a human pandemic. Flu researchers working on such studies last week declared a 60-day voluntary pause to allow governments and other bodies “time to find the best solutions for opportunities and challenges that stem from the work” (see ‘Pause on avian flu transmission studies‘).

Kawaoka and Fouchier succeeded in creating the transmissible virus in completely different ways. Fouchier used mutation, taking a H5N1 virus and then mutating it until it became transmissible. He initially introduced three mutations, using a technique called reverse genetics, but the resulting virus was not transmissible, so he then took that virus and passaged it through multiple ferrets, a procedure that is known to allow viruses to adapt to their host. The result was a virus with just five mutations, which were enough to make it highly transmissible.

Kawaoka instead used reassortment. He took an HA protein from H5N1 and inserted it into a virus made of up genes from the pandemic 2009 H1N1. The flu virus has eight genes. Two code for the surface proteins HA and neuraminidase (NA), and six code for internal proteins. The eight genes are on separate segments, which means that when two different flu viruses infect the same host, they can swap genes and create new viruses in a process known as reassortment. An H1N1 human and H5N1 avian virus, for example, could generate a new virus that has most of the genes from the human virus, making it transmissible in humans, but an avian haemagglutinin and/or neuraminidase. A largely human virus carrying an H5, to which humans have no previous exposure of immunity, could cause a pandemic if it retained the transmissibility of the human virus, and the lethality of H5N1.

Fouchier’s virus was lethal in ferrets, whereas Kawaoka’s was “no more pathogenic than the pandemic 2009 virus”, and killed none of the animals. A reassortant that occurred in the the wild might have different pathogenicities. But two independent groups have now shown that H5N1 can transmit in ferrets, and so such human-transmissible viruses could potentially arise naturally in avian and other animal populations. What controls the exchange of genes between viruses is poorly understood, says Lina, who himself failed in the past to create highly transmissible reassortants of H5N1 and seasonal H1N1. Triple-reassortant viruses that have this TRIG cassette, of six highly conserved internal genes, seem capable of capturing various HA and NA genes from multiple species, he says. “The pandemic 2009 H1N1 virus has a flexibility of function which makes it capable of associating at the molecular level with virus and gene segments from pig, bird and humans.”

The 2009 pandemic H1N1 is circulating in humans in countries such as Indonesia, China and Egypt, where H5N1 cases in human continue to occur. Co-infection of a person with both viruses would give them opportunities to reassort. Pandemic H1N1 also infects pigs, from which it originally emerged, which could provide further opportunities for reassortment. This emphasizes the need for better surveillance to detect human cases of H5N1 infection.

Monitoring of human cases could also help to prevent flu viruses acquiring human transmissibility. There has been some evidence of limited human-to-human transmission of H5N1 in clusters of human cases, and a virus that passes along even a small chain of human hosts has opportunities to adapt to its host, just as H5N1 did in Fouchier’s ferrets.

But as a news article in this week’s edition of Nature shows (see ‘Caution urged for mutant flu work‘), surveillance of H5N1 in birds worldwide is patchy, particularly in poorer countries, where the virus is prevalent. It is also largely geared towards simply detecting and monitoring outbreaks, and few of the viral samples collected are ever sequenced, with just 160 H5N1 isolates submitted to the GenBank database last year. Moreover, if H5N1 surveillance in birds is poor, the situation is far worse in pigs, where there is virtually no systematic surveillance, even in richer countries. H5N1 infections in pigs are uncommon and cause only mild illness, creating little economic incentive to monitor them — GenBank contains partial sequences from just 24 pig H5N1 isolates in total.

Read all Nature‘s coverage of the issue at the mutant flu special.

After Fukushima, emergency back-up equipment recommended for US nuclear reactors

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The United States may follow France in recommending that nuclear power plants build new equipment dedicated to containing a serious accident, in the wake of the Fukushima meltdowns.

The US Nuclear Regulatory Commission (NRC) said on 11 January that  it considered as “a reasonable starting point” a plan put forward by the Washington DC-based Nuclear Energy Institute, a body representing the nuclear industry, to reinforce safety at US power plants.

The plan would involve placing portable pumps, generators, batteries and other emergency equipment at various locations around power plants — a mobile system that could be brought into play in the event of a serious accident providing extra resources to try to prevent a degeneration into a meltdown. The NRC is now reviewing what measures are needed to learn the lessons of Fukushima, and is expected to announce new rules before the 11 March anniversary of the accident.

This new focus on also having equipment dedicated to containing an accident is similar to that of sweeping French rules announced earlier this month, requiring all reactors to build a set of safety systems of last resort. But the French plan goes further, requiring the systems to be contained in bunkers that will be hardened to withstand more extreme earthquakes, floods and other threats than the plants themselves are designed to cope with.

“Simply buying some additional emergency equipment will do little to enhance safety unless it is protected against more severe events than plants are currently able to withstand and it is rugged and highly reliable. Otherwise, a severe event may render the new equipment as unusable as the existing equipment, says Ed Lyman, a nuclear expert with the Union of Concerned Scientists in Washington DC. “The French plan appears to address this. However, in the US the standards for the reliability of the new equipment have yet to be determined, and industry is unlikely to support requirements that the equipment meets the highest standards for protection against extreme events.”

Iranian chemical engineer assassinated

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Iranian press has reported that a chemical engineer, who is allegedly an official at the country’s Natantz uranium-enrichment facility, was assassinated this morning in the north of Tehran. Two men on a motorcycle are reported to have attached a magnetic bomb to his car.

Almost all international media reports have described the man as a “nuclear scientist”, but so far his expertise and affiliation remain unclear. Iran’s Fars news agency named the man as Mostafa Ahmadi Roshan Behdast, aged 32, and reported that he was “a professor at Tehran’s technical university” and “a graduate of oil industry university and a deputy director of Natanz uranium enrichment facility for commercial affairs”.  Iran’s Press TV described the man as “Mostafa Ahmadi Roshan… who was a chemical engineering graduate of Iran’s prominent Sharif University of Technology and served as marketing deputy of Iran’s Natanz nuclear installation”. Mehr news agency gave a similar description.

A statement on Sharif University’s Persian website (translated using Google Translate) confirmed that the victim, whom they name as Mostafa Ahmadi, graduated in chemical engineering from the university, and that as a student had done research on polymeric membranes to separate gases. But it is not yet clear whether he held an academic position or whether his work might have been relevant to any aspects of Iran’s nuclear programme.

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