UK government gives Brexit science funding guarantee

Philip Hammond, the UK’s chancellor of the exchequer, has promised to underwrite EU research projects after Brexit.

British scientists say they’re relieved by a government promise to guarantee them funding for existing EU research projects, even after the country leaves the European Union. But the reassurance only partly allays concerns about Brexit’s effect on UK science.

The United Kingdom receives billions of euros for research from the European Union, mostly from its €74.8-billion (US$83.6-billion) Horizon 2020 (H2020) programme. June’s referendum vote for the nation to leave the EU left British scientists worried that funding for existing multi-year projects could be yanked away. And the uncertainty led to reports of EU collaborators deciding to drop UK scientists from future grant applications — even though the United Kingdom is still a full member of the EU. Tell Nature: Big or small, we want to hear how Brexit is affecting you

But on 13 August, the government announced that it will step in to pay UK contributions to EU H2020 projects after Brexit, provided that the projects were bid for before the day that the UK leaves the EU (a date which has not yet been fixed). “By underwriting Horizon 2020 funding in this way today, we are again demonstrating the importance we place on maintaining the world leading research that takes place in the UK,” said UK science minister, Jo Johnson.

Other types of EU project were given lesser guarantees. UK recipients of EU ‘structural funds’ (some of which are spent on research infrastructure) are to be assured funding only if they bid for them before an annual address on the nation’s finances known as the ‘Autumn Statement’ — an event that typically takes place in November or December. Still, the promise ensures that, for example, the UK’s University of Manchester can expect to receive £5 million (US$6.4 million) from EU funds for a planned Graphene Engineering Innovation Centre.

“Since the referendum vote, the research community has been struggling with the uncertainty. This provides huge reassurance,” says Sarah Main, director of the Campaign for Science and Engineering (CaSE) in London. The move will also reassure European collaborators, she says.

“This is encouraging news that provides much-needed stability for British universities during the transition period as the UK exits the EU, and provides an important signal to European researchers that they can continue to collaborate with their UK colleagues as they have before,” said Alistair Jarvis, deputy chief executive of the higher-education umbrella group Universities UK in London.

But the campaign group Scientists for EU issued a statement calling the announcement “decidedly underwhelming” and “a confirmation of the bare essentials, but nothing more”. After Brexit, UK scientists may lose the ability to apply for H2020 funding, depending on the terms of the split. And the government has not committed to shoring up those potential lost funds with domestic grants, Scientists for EU pointed out.

“This guarantee alleviates some of the uncertainties about existing and imminent H2020 grants, but does nothing to dispel fears about mobility between the UK and the rest of the EU following Brexit, which is integral to many H2020 schemes, nor does it address longer-term funding issues,” says Paul Crowther, who heads the physics and astronomy department at the University of Sheffield, UK.

Main says that she is still encouraged by the government’s continued support for science. She cites another example of political positive intentions: a letter from UK Prime Minister Theresa May in July to the director of London’s Francis Crick Institute, Paul Nurse, saying that the government was committed to ensuring a positive outcome for UK science. “To be honest, I’m feeling positive,” she says.

Nature doi:10.1038/nature.2016.20434 Nature Original web page at Nature


* Warnings of imminent extinction crisis for largest wild animal species

A team of conservation biologists is calling for a worldwide strategy to prevent the unthinkable: the extinction of the world’s largest mammal species.

In a public declaration published in today’s edition of the journal BioScience, a group of more than 40 conservation scientists and other experts are calling for a coordinated global plan to prevent the world’s “megafauna” from sliding into oblivion.

Among the threats cited by the group as drivers of this mass extinction are illegal hunting, deforestation and habitat loss, the expansion of agriculture and livestock into wildlife areas, and the growth of human populations.

“The more I look at the trends facing the world’s largest terrestrial mammals, the more concerned I am we could lose these animals just as science is discovering how important they are to ecosystems and to the services they provide for people,” said Dr. William Ripple, professor of ecology at Oregon State University and lead author of the study.

Ripple worked with other authors on the study to examine population trends of many species, including many of the most well-known, charismatic species such as elephants, rhinos, gorillas, and big cats that are now threatened with extinction.

Approximately 59 percent of the world’s biggest mammalian carnivore species — including the tiger — and 60 percent of the largest herbivores are now listed on the International Union for Conservation of Nature’s Red List of Threatened Species as threatened with extinction.

“Perhaps the biggest threat for many species is direct hunting driven by a demand for meat, pets, and body parts for traditional medicines and ornaments,” Dr. Elizabeth Bennett, WCS’s Vice President of Species Conservation and a co-author on the study. “Only a massive commitment from the international community will stop this rampant destruction of so many animal populations.”

All of these large species play critical roles in their ecosystems. Species at risk include elephants, that provide a suite of vital ecosystem services as ecological engineers, dispersing seeds and nutrients across vast areas. “The loss of elephants in the forests of Central Africa is increasingly damaging the function of the region’s most important ecosystems,” said WCS Conservation Scientist Dr. Fiona Maisels, one of the study’s co-authors. “We’re only beginning to understand how vital these keystone species are to the health of rainforests and other species that inhabit them.”

Human-wildlife conflict is a serious concurrent threat for many species. “With simultaneous loss of wildlife habitat and expansion of human populations and agriculture, negative interactions between people and wildlife are bound to rise,” said WCS India Scientist Dr. Varun R. Goswami, also a co-author on the study. “For wide-ranging megafauna like elephants and tigers, we need landscape-scale conservation strategies, taking into account the increasing interface between wildlife and people.”

Some megafauna face the threat of obscurity. The loss of elephants worldwide to poachers in pursuit of ivory is well-known and is the focus of extensive efforts to shut down this trade, but the study authors point out that many species are at risk from many similar threats but are so poorly known that effective conservation efforts to save them are difficult.

The paper includes a 13-part declaration that highlights the need to acknowledge the threatened status of many large mammals and the vital ecological roles they play. The declaration also cites the importance of integrating the efforts of scientists and funding agencies in developing countries where many species occur; the need for a new global framework to conserve megafauna; and the moral obligation of saving the world’s biggest mammal species. Science Daily Original web page at Science Daily


Should the gray wolf keep its endangered species protection?

Research by UCLA biologists published today in the journal Science Advances presents strong evidence that the scientific reason advanced by the U.S. Fish and Wildlife Service to remove the gray wolf from protection under the Endangered Species Act is incorrect.

A key justification for protection of the gray wolf under the act was that its geographic range included the Great Lakes region and 29 Eastern states, as well as much of North America. The Fish and Wildlife Service published a document in 2014 which asserted that a newly recognized species called the eastern wolf occupied the Great Lakes region and eastern states, not the gray wolf. Therefore, the original listing under the act was invalid, and the service recommended that the species (except for the Mexican gray wolf, which is the most endangered gray wolf in North America) should be removed from protection under the act.

A decision by the U.S. Fish and Wildlife Service to remove the gray wolf from protection under the Endangered Species Act may be made as early as this fall.

In the new study, biologists analyzed the complete genomes of North American wolves — including the gray wolf, eastern wolf and red wolf — and coyotes. The researchers found that both the red wolf and eastern wolf are not distinct species, but instead are mixes of gray wolf and coyote.

“The recently defined eastern wolf is just a gray wolf and coyote mix, with about 75 percent of its genome assigned to the gray wolf,” said senior author Robert Wayne, a UCLA professor of ecology and evolutionary biology. “We found no evidence for an eastern wolf that has a separate evolutionary legacy. The gray wolf should keep its endangered species status and be preserved because the reason for removing it is incorrect. The gray wolf did live in the Great Lakes area and in the 29 eastern states.”

Once common throughout North America and among the world’s most widespread mammals, the gray wolf is now extinct in much of the United States, Mexico and Western Europe, and lives mostly in wilderness and remote areas. Gray wolves still lives in the Great lakes area, but not in the eastern states.

Apparently, the two species first mixed hundreds of years ago in the American South, resulting in a population that has become more coyote-like as gray wolves were slaughtered, Wayne said. The same process occurred more recently in the Great Lakes area, as wolves became rare and coyotes entered the region in the 1920s.

The researchers analyzed the genomes of 12 pure gray wolves (from areas where there are no coyotes), three coyotes (from areas where there are no gray wolves), six eastern wolves (which the researchers call Great Lakes wolves) and three red wolves.

There has been a substantial controversy over whether red wolves and eastern wolves are genetically distinct species. In their study, the researchers did not find a unique ancestry in either that could not be explained by inter-breeding between gray wolves and coyotes.

“If you did this same experiment with humans — human genomes from Eurasia — you would find that one to four percent of the human genome has what looks like strange genomic elements from another species: Neanderthals,” Wayne said. “In red wolves and eastern wolves, we thought it might be at least 10 to 20 percent of the genome that could not be explained by ancestry from gray wolves and coyotes. However, we found just three to four percent, on average — similar to that found in individuals from the same species when compared to our small reference set.”

Pure eastern wolves were thought to reside in Ontario’s Algonquin Provincial Park. The researchers studied two samples from Algonquin Provincial Park and found they were about 50 percent gray wolf, 50 percent coyote.

Biologists mistakenly classified the offspring of gray wolves and coyotes as red wolves or eastern wolves, but the new genomic data suggest they are hybrids. “These gray wolf-coyote hybrids look distinct and were mistaken as a distinct species,” Wayne said.

Eventually, after the extinction of gray wolves in the American south, the red wolves could mate only with one another and coyotes, and became increasingly coyote-like.

Red wolves turn out to be about 25 percent gray wolf and 75 percent coyote, while the eastern wolf’s ancestry is approximately 75 percent gray wolf and 25 percent coyote, Wayne said. (Wayne’s research team published findings in the journal Nature in 1991 suggesting red wolves were a mixture of gray wolves and coyotes.)

Although the red wolf, listed as an endangered species in 1973, is not a distinct species, Wayne believes it is worth conserving; it is the only repository of the gray wolf genes that existed in the American South, he said.

The researchers analyzed SNPs (single nucleotide polymorphisms) — tiny variations in a genetic sequence, and used sophisticated statistical approaches. In the more than two dozen genomes, they found 5.4 million differences in SNPs, a very large number.

Wayne said the Endangered Species Act has been extremely effective. He adds, however, that when it was formulated in the 1970s, biologists thought species tended not to inter-breed with other species, and that if there were hybrids, they were not as fit. The scientific view has changed substantially since then. Inter-breeding in the wild is common and may even be beneficial, he said. The researchers believe the Endangered Species Act should be applied with more flexibility to allow protection of hybrids in some cases (it currently does not), and scientists have made several suggestions about how this might be done without a change in the law, Wayne said.  Science Daily  Original web page at Science Daily


‘Ransomware’ cyberattack highlights vulnerability of universities

Staff at Canadian university given little guidance on how to mitigate future problems.

These kinds of attacks — holding data hostage — are becoming increasingly common.

The first Patrick Feng knew about a cyberattack on his university was when one of his colleagues told him that her computer had been infected by hackers and rendered unusable.

Feng, who studies technology and sustainability policy at the University of Calgary in Canada, immediately checked the Dropbox folder that he was sharing with that colleague — and found that it, too, had been compromised.

“The hackers had created encrypted copies of all my Dropbox files and deleted the originals,” he says. “And there was a ransom note demanding bitcoin to unlock them.” Bitcoin is an online, anonymous currency, making it an attractive option for cybercriminals.

The attack, which started on 28 May, left many researchers locked out of their data and university e-mail. Most staff and faculty regained access to the school’s networks by 30 May, and e-mail was back up by 6 June.

Feng’s Dropbox folder contained data and draft manuscripts for a research paper that he is writing on innovative ways of teaching research methods to undergraduates, but he wasn’t too concerned. His personal laptop was unaffected, and he asked Dropbox to restore his folder to the last saved version before the attack, which the company was able to do in a couple of days.

Others were not so fortunate. Two of Feng’s colleagues, including the one who had informed him about the hack, had to have the hard drives of their university-issued computers wiped and restored.

A few of the most badly affected faculty and staff have yet to regain full access to their data. But, there is no indication that any personal or school data were released to the public, according to the university. “Research data that was stored on our systems was backed up prior to the attack and remains intact,” says Marina Geronazzo, a university spokesperson.

The university is confident that it will be able to restore all data from those back-ups, she says. But the school did pay a ransom of Can$20,000 (US$15,500) for the decryption keys as a precaution. They say it will be used only as a last resort.

This kind of “ransomware” attack is becoming increasingly common, says James Scott, a cybersecurity specialist at the Institute for Critical Infrastructure Technology, a think-tank in Washington DC — and universities are hardly immune. In the United States, the education sector is the third most common target for hackers, after healthcare and retail, he says.

In many cases, the ransom money that hackers can extract from their victims is a secondary goal. “Ransomware is the new DDoS,” Scott says, referring to a Distributed Denial of Service attack, in which a network of infected computers overwhelms a target with more connection requests than it can handle. Hackers use these attacks as a distraction while they steal data, he explains.

City of Calgary police are still searching for the perpetrator. Past incidents, Scott says, make him suspect that Chinese sources may have been involved. The country has allegedly targeted Canadian researchers before. In 2014, the Canadian government accused “Chinese state-sponsored actors” of hacking the National Research Council, a federal research agency headquartered in Ottawa.

It’s a matter of Chinese policy to use espionage to bring their country up to speed, technologically, with the West, says Scott, who is not a part of the investigation. “Universities are a huge target for China because of their advanced research.”

Scott says that universities are particularly vulnerable to cyberattacks because they often have multiple overlapping public and private networks, and staff, faculty members or students with infected devices might connect with any number of them. Many labs also have devices “frankensteined” into their networks that were never intended to be there, which opens up new avenues of attack.

Feng says that aside from requiring everyone to change their passwords, the university has provided little guidance on how researchers can better protect themselves against such attacks in the future. He says that it is up to researchers to be aware of the risks, and to take the proper precautions by automatically backing up their data on external hard drives, or to the cloud. “Even though I teach technology policy, and am aware of these kinds of issues, I still thought it was never going to happen to me,” he says.

Nature doi:10.1038/nature.2016.20111 Nature  Original web page at Nature


Federal advisory committee greenlights first CRISPR clinical trial

CRISPR, the genome-editing technology that has taken biomedical science by storm, is finally nearing human trials.

On 21 June, an advisory committee at the US National Institutes of Health (NIH) approved a proposal to use CRISPR/Cas9 to help augment cancer therapies that rely on enlisting a patient’s T cells.

“Cell therapies [for cancer] are so promising but the majority of people who get these therapies have a disease that relapses,” says study leader Edward Stadtmauer, a physician at the University of Pennsylvania in Philadelphia. Gene editing could improve such treatments and eliminate some of their vulnerabilities to cancer and the body’s immune system, he says.

This first trial is small and designed to test whether CRISPR is safe for use in people, rather than whether it cures cancer or not. It will be funded by a US$250 million immunotherapy foundation formed in April by former Facebook president Sean Parker. The trial itself does not yet have a budget. The University of Pennsylvania will manufacture the edited cells, and will recruit and treat patients along with centers in California and Texas.

The researchers will remove T cells from 18 patients with melanoma, sarcoma, or myeloma, and perform three CRISPR edits on them. One edit will insert a gene for a protein engineered to detect cancer cells and instruct the T cells to target them, and a second edit removes a natural T cell protein that could interfere with this process. The third is defensive: removing the gene for a protein that identifies the T cells as immune cells and preventing the cancer cells from disabling them. The researchers will then infuse the edited cells back into the patient.

“Last year’s excitement over CRISPR was in anticipation of this,” says Dean Anthony Lee, an immunologist at MD Anderson Cancer Center in Houston and a member of the NIH’s Recombinant DNA Research Advisory Committee (RAC) that reviewed the proposal. CRISPR, he says, makes genome engineering easy enough that such trials can move forward quickly.

The RAC reviews all proposals for human trials involving modified DNA that are conducted in the United States. Stadtmauer’s team will now have to convince US regulators and review boards at their own institutions to allow the trial. Immunologist Carl June from the University of Pennsylvania, who is a science advisor on the project, says it could begin by the end of the year.

Others may not be far behind. Editas Biotechnologies in Cambridge, Massachusetts, for instance, has said that it wants to use CRISPR in a clinical trial for a rare form of blindness as soon as 2017. However, RAC members say they have not yet been approached about reviewing the trial.

While most attention has focused on CRISPR because of its ease of use, the T-cell trial will not be the first test of the efficacy of using gene editing to fight diseases. In 2014, June led a study using a gene-editing system called zinc-finger nuclease.

His group took blood from 12 people with HIV and removed the gene for a protein on T-cells targeted by the virus in the hopes that this would prevent infection of the cells. The results were encouraging, and the technique is now being used in clinical trials for several other applications.

And last week, researchers at Great Ormond Street Hospital for Children in London began a safety study with 10 children using a similar technique called TALENS. Instead of using a patient’s own cells, this system uses T cells from a donor that have been edited to remove genes that would cause the patient’s body to reject them. The gene editing then directs the T cells to attack the cancer and protects the cells from other immunotherapy drugs.

Although CRISPR is easier to use than these other techniques, and better able to edit multiple genes at once, June says the challenge will be a propensity for “off-target” effects. These are instances in which the system cuts or mutates unintended parts of the genome. And despite precautions, the immune system could still attack the edited cells.

During the RAC meeting, one of the committee’s greatest concerns was a potential conflict-of-interest. Among other financial involvements, June has ties to the pharmaceutical company Novartis, holds patents on T-cell technologies, and could potentially stand to benefit from the success of this trial. June declined to give details as to the exact nature of his conflict of interest, but says that his university is taking steps to manage it, such as preventing him from being involved in selecting patients.

Several RAC reviewers suggested that the University of Pennsylvania not be allowed to recruit patients at all and to leave it to other institutions: this language did not make it into their final approval.

However, the RAC members say they are being extra careful with this study. “Penn has a very extensive conflict and has a history,” says Laurie Zoloth, a bioethicist at Northwestern University in Evanston, Illinois. Looming over the discussion is the name Jesse Gelsinger, who died at age 18 while participating in an early gene therapy trial conducted by researchers at the University of Pennsylvania in 1999.

Subsequent investigation found numerous problems with the study, including unreported animal data on the therapy’s ill-effects and the fact that the investigators had a financial stake in the study’s outcome.

The incident is generally considered to have set gene therapy back by decades. “Any first use in humans we have to be extraordinarily careful,” Zoloth says. So a lot is riding on this trial.

But Mildred Cho, a bioethicist at Stanford University in California and a RAC member, says that safety work in animals for a new therapy will only take researchers so far. “Often we have to take the leap of faith.”

Nature doi:10.1038/nature.2016.20137 Nature  Original web page at Nature


* Plan to fly rhinos to Australia comes under fire

An ambitious project to relocate rhinos from South Africa to Australia has been accused by some conservation researchers of being a waste of money.

The Australian Rhino Project charity, headquartered in Sydney, has attracted huge publicity for its plans to move 80 rhinos to Australia “to establish an insurance population and ensure the survival of the species”. It raised more than Aus$800,000 (US$600,000) in the year to September 2015, and hopes to start by flying out six rhinos later in 2016. The charity says that eventually, rhinos from the Australian herd could be sent back to Africa to re-establish wild populations there, when poaching — which is devastating rhino populations in Africa — becomes less of a threat.

But in a letter published in Nature this week, four researchers warn that the project “is diverting funds and public interest away from the actions necessary to conserve the animals”. The million-dollar cost of moving 80 animals would be better put towards poaching prevention, the researchers say.

“Anyone associated with conservation in Africa is well aware of the massive poaching crisis going on,” says Matt Hayward, a conservation researcher at Bangor University, UK, and lead author of the letter. But he says that moving rhinos to Australia is a bad solution. “I don’t think it can do any harm, but the pot of money is limited. We’re better off focusing in situ.”

But the rhino project’s founder, Ray Dearlove, strongly defends the initiative. A “staggering amount of money” has been put towards anti-poaching initiatives and animals are still being poached, he says, adding that moving rhinos to Australia is “one possible strategy in the complex web of saving the rhino”. (He also criticizes the letter for stating that the rhino-relocation effort will cost US$3.5 million, when the costs are not yet precisely known, and for, before a correction, misstating that 16 rhinos — not 6 — were to be transported in 2016.)

Dearlove adds that he takes exception to the letter-writers’ suggestion that the project “has echoes of colonial times, when African resources were exploited”. “In terms of exploitation, it is completely opposite to that,” he says. “This is an attempt to try and save the species.”

Hayward says that he is not opposed to moving animals for conservation purposes. He himself works on projects to reintroduce European bison (Bison bonasus) to Poland and red squirrels (Sciurus vulgaris) to parts of Wales. And conservationists are increasingly looking to move animals around to establish new or more secure populations, as climate change and activities such as logging or poaching disrupt their habitats.

But Hayward argues that rhinos should not be removed from Africa. A rhino’s value lies not just in the animal itself, but also in its connection to the landscape and environment of its native ecosystem, he says. Hayward and others also criticize the project for moving white rhinos (Ceratotherium simum), which have a global population of 20,170, rather than the much more endangered black rhinos (Diceros bicornis), of which fewer than 4,880 are left.

Mark Stanley Price, a reintroduction specialist at the University of Oxford’s Wildlife Conservation Research Unit, UK, notes that although black rhinos are more threatened, it is not clear whether these animals could be kept wild in Australia. They are browsing feeders — eating leaves, branches and fruit — which makes them less likely to adapt to the local vegetation than the more generalist, grazing white rhinos. “It would be much more difficult to manage black rhinos under those situations. And it is the blacks that need the help,” he says.

Stanley Price adds, “This is an interesting initiative. It’s going to have some particular difficulties. Is it really the right answer?”

But the debate may prove academic: Dearlove says that although not all the permissions required for the relocation effort are yet in place, he still intends to transport the first rhinos this year.

Nature doi:10.1038/nature.2016.20141  Nature  Original web page at Nature


Researchers reeling as UK votes to leave EU

Future of science uncertain after referendum result. It was the result that most scientists didn’t want. The United Kingdom’s vote to leave the European Union has plunged it into political and economic uncertainty — and left researchers worried over the future of their funding and collaborations, the UK’s participation in major European research programmes, and the freedom of movement and employment status of thousands of scientists.

Many researchers in the UK expressed shock and dismay as the result of the 23 June referendum — with 52% of people voting in favour of ‘Brexit’ to 48% against — sank in.

“This is a poor outcome for British science and so is bad for Britain,” Paul Nurse, the head of the Francis Crick Institute in London and a Nobel-prizewinning geneticist, told journalists. “British scientists will have to work hard in the future to counter the isolationism of Brexit if our science is to continue to thrive,” he said.

The messy and protracted process of negotiating a UK departure from the EU means that it may not become clear for years how science is affected. Politicians campaigning for a UK divorced from the EU had pledged before the vote that universities and scientists in the country would not lose out. But immediate concerns for researchers revolve around funding: UK universities currently get around 16% of their research funding, and 15% of their staff, from the EU.

“This is going to be very damaging,” says Jonathan Butterworth, a physicist at University College London who works on the ATLAS experiment at the Large Hadron Collider near Geneva, Switzerland. Another urgent worry, he says, is for students and postdocs from elsewhere in Europe at universities in England, Wales, Scotland and Northern Ireland. “We need strong statements that the level of research and education funding that was coming though the EU will be guaranteed,” he adds.

Jamie Martin, an advocate for the UK’s exit from the EU and a former special adviser to the pro-Brexit politician Michael Gove, said that he would offer “total reassurance” to worried scientists. Although most academic groups had lobbied for the UK to remain in the EU, Martin says that “the good news for them is that the people at the top of the Vote Leave campaign share their instincts on science”. This includes being open to skilled people from outside the UK and understanding the importance of continued funding, he says.

Researchers fear that if the UK leaves the EU, the country could lose access to the bloc’s research programmes, including the Horizon 2020 programme of research grants. The UK currently hosts more EU-funded holders of grants under the European Research Council than any other member state.

Being outside the EU would not automatically rule out the UK’s involvement in EU research programmes. Horizon 2020, for instance, has association agreements with 15 other countries, which gives them equal rights to participation as EU member states in return for a negotiated financial contribution. But associate membership may not be possible for the UK if it moves to restrict the free movement of people.

Swiss scientists, for example, experienced numerous problems when a referendum in that country to restrict the freedom of movement of people from Croatia across its borders led to its researchers being cut out of Horizon 2020 programmes. (A patched-up deal whereby Switzerland’s government is paying for individual Swiss scientists to take part in research programmes is an interim measure that currently holds only until February 2017.)

Before the vote, a report from Digital Science (a consultancy in London operated by the Holtzbrinck Publishing Group, which also has a share in Nature’s publisher), estimated that the UK could lose £1 billion (US$1.4 billion) in science funding each year if the government did not make up the shortfall in EU-linked research funds.

Researchers have already begun to call for the UK to maintain science funding and to welcome researchers from abroad. “Any failure to maintain the free exchange of people and ideas between the UK and the international community including Europe could seriously harm UK science,” said the head of the Royal Society in London, Venkatraman Ramakrishnan, a Nobel-prizewinning structural biologist.

And Julia Goodfellow, president of the umbrella group Universities UK, which had campaigned against a leave vote, said that her group’s “first priority” would be to try to convince the government that EU staff and students should be allowed to continue studying in the country.

Brexit “creates opportunities for science”, says Martin — such as possible increases in science funding, repealing EU rules that some say hamper research, and the possibility that controlling unskilled migration could in turn mean more scope for increased migration of skilled workers, such as scientists. “Now what it’s about is scientists lobbying to get these changes,” he adds.

In a tweet this morning, science minister Jo Johnson, a supporter of the UK remaining in the EU and the brother of the prominent ‘leave’ campaigner Boris Johnson, simply said: “Big decision. Let’s make it work.”

Nature doi:10.1038/nature.2016.20153 Nature  Original web page at Nature


New vision, model for genomic and clinical data sharing

In today’s Science, the Global Alliance for Genomics and Health (GA4GH) calls for a federated data ecosystem for sharing genomic and clinical data. The authorship, which includes Richard Durbin, Julia Wilson, Stephen Keenan, and David Lloyd of the Wellcome Trust, as well as a diverse team of international leaders in academia, research, medicine, and industry, argues that a common framework of principles, protocols, and interoperable technical systems are necessary to enable responsible and effective data sharing.

GA4GH was established in 2013 to bring the community together to build the tools and establish the standards necessary to achieve that goal. Today, it counts more than 400 organizations and more than 700 individuals in its membership, which spans more than 70 countries. “These stakeholders are working together across traditional boundaries to create the common framework that will allow us to make best use of the millions of genome sequences that currently sit in siloed databases around the globe,” says Peter Goodhand, GA4GH Executive Director and a member of the author group.

“We are at a critical time for genomic data interpretation,” said Richard Durbin of the Wellcome Trust Sanger Institute in the UK, and co-chair of the GA4GH Data Working Group. “We know from the international research that led human genome sequencing that the key to understanding individual genetic differences is to compare them to data from other people. But the scaling up of genomics for clinical use is being carried out by organisations that do not necessarily have the traditions or mechanisms in place to carry out the necessary sharing. We must establish trusted systems to enable safe mutual clinical benefit via effective data exchange.”

To date, GA4GH has created a toolkit of diverse products, including the Genomics API, which allows disparate technology services to exchange genotypic and phenotypic data, as well as the Framework for Responsible Sharing of Genomic and Health Related Data, which outlines the basic principles and core elements for responsible data sharing. GA4GH has also catalyzed the development of three data sharing projects which aim to illustrate the value of sharing data in real world contexts. These consist of (i) an open-ended approach to sharing data across the Internet (the Beacon Project), (ii) an international collaboration among breast cancer genetics experts (the BRCA Challenge), and (iii) a peer-to-peer network of clinicians (Matchmaker Exchange).

In addition to outlining successes, the paper notes a variety of remaining challenges to sharing data across national and institutional boundaries. For example, the membership is currently working on solutions to secure data access while maximizing the scope of information that can be shared, to create tools that are flexible enough to be readily implemented in different knowledge domains, and to establish sustainable funding models that support data curation, hosting, and computation.

“Private funders and national governments will need to be involved on some level to support these activities so that clinicians and scientists may access as much free, curated data as possible,” says Mike Stratton, Director of the Wellcome Trust Sanger Institute, CEO of the Wellcome Genome Campus, and a member of the GA4GH Strategic Advisory Board. “The Sanger Institute has supported the Global Alliance since its inception as we are committed to helping researchers and clinicians access and freely share the genomic and related health data they need to transform human health.”  Science Daily Original web page at Science Daily


Measuring impact of Kenya’s ivory burning ‘urgent’

Gathering evidence on the impact of Kenya’s record-breaking ivory burn on elephant conservation should be an urgent priority according to four University of Queensland scientists.

Dr Duan Biggs from the ARC Centre of Excellence for Environmental Decisions (CEED) said the ivory burns and stockpile destruction had increased by more than 600 per cent since 2011, with Kenya burning a record-breaking 105 tons of ivory on 30 April, valued at up to US$220 million on the black market.

“The historic Kenyan burn aims to send a powerful message against elephant poaching and the illegal ivory trade, yet there is no evidence, so far, that these actions help reduce poaching,” Dr Biggs said.

“More disturbingly, we are unaware of any attempts to track and evaluate the impacts of these burns on the demand for and the price of illegal ivory.”

He said that destroying ivory stockpiles could create a perverse outcome.

“As ivory becomes rarer, the price increases, leading to greater incentives for elephant poachers and illegal stockpilers of ivory,” he said.

Each year more than 30,000 elephants are killed for their ivory by poachers in Africa to satisfy demand in Asia where raw tusks sell for up to $2100 per kilogram. Africa is home to about 500,000 elephants.

Former Kenyan president Daniel Arap Moi began incinerating stockpiles of ivory in 1989 at the same time as the ban on the international trade in ivory came into effect.

CEED Director and co-author Professor Hugh Possingham said it was crucial to track the effects of Kenya’s largest ever ivory burn with data on ivory price and demand.

“The way in which ivory burns affect the attitudes of potential buyers in the markets of East Asia should be assessed,” Professor Possingham said. “Time is short and the stakes are high.”

Track the Impact of Kenya’s Ivory Burn was published in Nature and was also authored by Dr Matthew Holden and Dr Alex Braczcowski.  Science Daily Original web page at Science Daily


Top 10 new species for 2016

A hominid in the same genus as humans and an ape nicknamed “Laia” that might provide clues to the origin of humans are among the discoveries identified by the SUNY College of Environmental Science and Forestry (ESF) as the Top 10 New Species for 2016.

The list also includes a new kind of giant Galapagos tortoise, which could serve as a poster species for conservation and evolution, and two fish — a seadragon in stunning shades of ruby red and pink and, conversely, an anglerfish that would not win an undersea beauty pageant.

Rounding out this year’s Top 10 are three invertebrates — a tiny isopod that builds its own mud shelters, a beetle named after a fictional bear who traveled from Peru to London and a damselfly with a suggestive name, and two plants — a carnivorous sundew that was considered endangered as soon as it was found and a tree that was hiding in plain sight.

Brazil and Gabon each contributed two new additions to the planet’s biodiversity. The others hail from Ecuador, South Africa, the Gulf of Mexico, Australia, Spain and Peru.

The list is compiled annually by ESF’s International Institute for Species Exploration (IISE). The institute’s international committee of taxonomists selects the Top 10 from among the approximately 18,000 new species named during the previous year. The list is made public around May 23 to recognize the birthday of Carolus Linnaeus, an 18th century Swedish botanist who is considered the father of modern taxonomy.

Established in 2008, the list calls attention to discoveries that are made even as species are going extinct faster than they are being identified. “In the past half-century we have come to recognize that species are going extinct at an alarming rate. It is time that we accelerate species exploration, too. Knowledge of what species exist, where they live, and what they do will help mitigate the biodiversity crisis and archive evidence of the life on our planet that does disappear in the wild,” said Dr. Quentin Wheeler, ESF president and founding director of the IISE.

Scientists believe 10 million species await discovery, five times the number that are already known to science. “The rate of description of species is effectively unchanged since before World War II. The result is that species are disappearing at a rate at least equal to that of their discovery. We can only win this race to explore biodiversity if we pick up the pace. In so doing we gather irreplaceable evidence of our origins, discover clues to more efficient and sustainable ways to meet human needs, and arm ourselves with fundamental knowledge essential for wide-scale conservation success,” Wheeler said.

One of the 2016 Top 10 New Species

Giant Tortoise: 185 Years Post-Darwin, a New Species in Galapagos

Chelonoidis donfaustoi

Location: Galapagos, Ecuador

How it made the Top 10: No animals are more immediately associated with evolution or Charles Darwin than the giant tortoises of the Galapagos. Small differences had been noticed between eastern and western populations of giant tortoises on Santa Cruz Island that were assumed to be simply genetic variation within the known species, C. porteri. A careful analysis of both genetic and morphological data, however, shows that the smaller eastern population, with perhaps as few as 250 individuals, is a distinct and new species. This discovery has immediate, important conservation implications. C. porteri has a more limited geographic range than previously believed, restricted to western and southwestern areas of the island, and care must be taken to avoid bridging the natural isolation of the two species. The new species was named in honor of a park ranger known as “Don Fausto,” who worked 43 years to conserve the giant tortoises of Galapagos.  Science Daily  Original web page at Science Daily


Superbug infections tracked across Europe

For the first time, scientists have shown that MRSA (methicillin-resistant Staphylococcus aureus) and other antibiotic-resistant ‘superbug’ infections can be tracked across Europe by combining whole-genome sequencing with a web-based system. In mBio, researchers at Imperial College London and the Wellcome Trust Sanger Institute worked with a European network representing doctors in 450 hospitals in 25 countries to successfully interpret and visualise the spread of drug-resistant MRSA.

MRSA and other superbugs are a life-threatening problem for all hospitals across Europe with an estimated 400,000 cases per year and 25,000 deaths from resistant, hospital-acquired infections.

To enable infection control teams across Europe to easily share information and to form a dynamic picture of the rise and spread of antibiotic-resistant bacteria, the scientists from the newly formed Centre for Genomic Pathogen Surveillance developed, a web-based visualisation and mapping tool.

Dr David Aanensen, head of the Centre for Genomic Pathogen Surveillance and joint lead author on the paper said: “Drug resistance is a growing problem both in Europe and across the world and doctors need fast and accurate information to stop epidemics. Our study demonstrates the potential for combining whole-genome sequencing with internet-based visualisation tools to enable public health workers and doctors to see how an epidemic is spreading and make swift decisions to end it.”

The research team read the whole genomes of S. aureus samples to identify which bugs are related to each other, and which are resistant to antibiotics. Using this approach, the scientists were not only able to show the rise and spread of MRSA across Europe, but also provide a quicker way to identify new hotspots of resistance.

Professor Hajo Grundmann, principal investigator on the study and Head of the Institute of Infection Prevention and Hospital Hygiene at the University Medical Centre Freiburg in Germany said: “One of the problems is that these bacteria not only spread within and between hospitals, but they also change their genetic properties due to evolutionary processes over time. allows us to look at their evolution within the context of how they are spreading across Europe.”

In the paper, the scientists show that combining the drug-resistance profile of a bacteria with its whole-genome DNA sequence allowed them to build up a series of drug-resistance ‘DNA photofits’ for resistance to specific drugs. In the future, such an approach may help doctors decide on the best treatments more quickly and help bring drug-resistant outbreaks to an end.

Professor Ed Feil, joint lead author from the Milner Centre for Evolution, at the University of Bath, said: “We’ve developed user-friendly analysis software that demonstrates how whole genome sequence data can be a powerful tool for pan-European surveillance of MRSA and other important pathogens.

Being able to track the spread of outbreaks across the whole continent allows policymakers to identify potential risks to public health and implement appropriate prevention and control strategies.”  Science Daily Original web page at Science Daily


Human-embryo editing now covered by stem-cell guidelines

The international society that represents stem-cell scientists has updated its research guidelines in the wake of dramatic progress in several fields — in particular in research that involves the manipulation of human embryos. The authors hope that the updated guidelines will allay various ethical concerns, and avoid the need for strict government regulations that could impede the progress of science.

“Self-regulation is the best form of regulation,” says Charles Murry, a member of the committee that updated the guidelines, and a bioengineer at the University of Washington in Seattle. “The biomedical community is best poised to strike the balance between rapid progress and safe, ethical research practice.”

The International Society for Stem Cell Research (ISSCR), which was founded in 2002, has previously released guidelines in 2006 and 2008 on embryonic-stem-cell research and on clinical translation of stem-cell research. The latest guidelines have broader scope, and cover all research on human embryos — including gene-editing of embryos, which has in the past year advanced significantly and generated much controversy.

The revised guidelines recommend that all research involving the manipulation of human embryos now undergo a similar review as experiments that use embryos to create stem-cell lines, which has been one of the most divisive research procedures of recent decades. They suggest that such research be added to the remit of existing embryonic stem cell research oversight (ESCRO) committees.

Scientists previously balked at the introduction of ESCRO committees, and there is likely to be resistance to the idea of adding bureaucratic review to other research areas. “No scientist or physician jumps for joy when new regulations are put in place,” says Murry. But he says that the updates are necessary to avoid “a wild-west environment where sensitive research is done without proper regard for community standards”.

At the same time, the new guidelines attempt to clear the way for more research using induced pluripotent stem (iPS) cells, which, like embryonic stem cells, are able to turn into all cell types in the human body but are not taken from embryos. The authors recommend explicitly excluding the generation of iPS cells from regulations on embryonic stem cell research and relying instead on the existing oversight for donor cell recruitment. Some institutions have been confused about how to classify iPS cells, says George Daley, a stem-cell scientist at the Boston Children’s Hospital in Massachusetts and one of the authors of the new guidelines.

Also included in the guidelines is a call for continued observance of a moratorium on growing human embryos in vitro beyond 14 days — a somewhat arbitrary limit that has become the global standard. Two papers published on 4 May reported experiments that showed that it would soon be possible to breach the limit, sparking debate about whether the rule should be reconsidered.

“The ISSCR deserves credit for bringing up and discussing these important issues,” says stem-cell biologist Ali Brivanlou of the Rockefeller University in New York City, who is a lead author on one of the embryo papers. But he adds that further discussion of the issues is needed.  “We need to get together the positives and negatives of moving forward,” he says.

The authors also take the opportunity to reinforce a warning that the ISSCR has long made — that researchers shouldn’t overstate the clinical implications of stem-cell experiments. Hype surrounding such experiments has enabled a worldwide market for unproven, and often ineffective or dangerous, stem-cell therapies, which has been difficult to regulate. “We take a swipe at hyperbole in scientific communication, essentially asking researchers to ‘take it down a notch’ when they speak about the implications of their work,” says Murry.

Nature doi:10.1038/nature.2016.19909  Nature  Original web page at Nature


What are the factors affecting whether women choose a medical research career

Unless exposed to positive research experience and role models during their medical education and training, women are unlikely to consider careers in academic medicine seriously. That’s one conclusion of an Oxford University study published in The Lancet. It asked why, when entry to medical schools is evenly split between men and women, those working in University medical departments are predominantly men.

In the UK, women make up 55% of medical school entrants but just 28% of faculty. In the US, they are 47% of entrants but 38% of faculty. The study reviewed 52 pieces of research evidence from the last thirty years to test eight themes often proffered as reasons for women’s under-representation in the medical academic workforce.

Dr Laurel Edmunds, Senior Systematic Reviewer, said: ‘Despite the focus on encouraging women to pursue an interest in medical sciences, we still lack comprehensive research evidence on what causes them to choose or reject a career in the subject. Most studies we reviewed had methodological limitations and were predominantly from North America. Further methodologically robust research, especially outside North America, is needed to establish the consistency of our review findings.’

The team did find that research evidence consistently pointed to a lack of adequate mentors and role models for women and to the deterrent effect of gender discrimination and unconscious bias experienced while still at medical school. They also found that women who were exposed to medical research while in training were more likely to pursue a research career, and that studies showed that women were more likely to choose a teaching career over a research career.

Professor Alastair Buchan, Head of the Medical Sciences Division and Dean of Medicine at Oxford University initiated and led the research. He said: ‘For four of the themes, we found both supporting and refuting evidence. For example, suggestions that women are less interested in research than men, or that they lose interest in research as education and training progress are not consistently supported by research evidence. We also found that evidence was conflicting on whether financial considerations and work-life balance deter women from a medical research career.’

Professor Trish Greenhalgh, Professor of Primary Care Health Sciences and a practicing GP said: ‘The focus of further research should shift from individuals’ career choices to the societies, organisations, and cultures within which those choices are made. There may be important confounding factors which explain women’s choice or rejection of careers in academic medicine. For example, some of the findings of this review may be explained by the phenomenon of stereotype threat — the idea that we stereotype ourselves as less good because we pick up on society’s stereotypes, and underperform as a result.’

Dr Pavel Ovseiko, Senior Research Fellow in Health Policy and Management, said: ‘What inconsistency of findings across reviewed studies suggests is that there are significant opportunities to overcome barriers by creating a more supportive and inclusive university culture and work environment. Winning the talent war for women in academic medicine requires a combination of practical measures and inspirational leadership from both women and men.’

The research comes as Oxford launches a new website for women interested in careers in medical sciences. The site,, includes interviews with women scientists from Oxford at various stages of their careers, talking frankly about topics a variety of issues including obtaining funding, career progression, mentorship, and parenting.  Science Daily  Original web page at Science Daily


Increase in the number of dog attacks on guide dogs in the UK

Reported dog attacks on guide dogs have risen significantly over a five year period, finds a study published online in the journal Veterinary Record.

A total of 629 attacks were reported between 2010 and 2015, with an increase from an average of three per month in 2010 to eleven attacks per month in 2015. The authors say it is not clear whether this reflects higher levels of reporting or a real trend.

There are around 4,900 working guide dogs in the UK. They provide mobility and support for blind and partially sighted people. Each dog is supported by the charity ‘Guide Dogs’.

Dog attacks on guide dogs are common, and these can have a significant impact on the dog, and the owner’s mobility, independence and social and emotional well-being.

Attacks are treated as an aggravated offence with sentences of up to three years imprisonment for the attacking dog’s owner, under the 2014 Anti-Social Behaviour, Crime and Policing Act.

In this study, a team of researchers from Guide Dogs and the University of Nottingham examined data on all dog attacks on Guide Dogs’ stock between June 2010 and February 2015. They examined the characteristics of the attacks, impact on the dog and owner, as well as the financial implications for the charity.

A dog attack was defined as “when a dog sets upon another dog in a forceful, violent, hostile or aggressive way, involving physical contact.”

They found that a total of 629 attacks were reported during the 56 month period. A total of 97% of attacks occurred in public areas and 55% of victim dogs were working in harness when they were attacked. Owners of the aggressor dogs were present in 77% of attacks.

Attacks were described as being unprovoked in 19% of cases, caused by the aggressor dog in 22% of cases, and caused by a lack of control in 29% of cases.

“The guide dog harness is designed to be visible and should have been apparent to the owners of aggressors who were present,” explain the authors. “It is feasible that a proportion of these attacks could have been avoided if the aggressor was put on a lead when the owner saw the guide dog in harness.”

Guide Dogs’ stock were injured in 43% of attacks and related veterinary costs were estimated to be £34,514.30. Injuries received were most commonly puncture wounds, and veterinary attention was required for 76% of dogs with injuries and a further 5% needed a check up.

Over 40% of qualified guide dogs’ experienced a negative impact on working ability, and less than 20% of qualified guide dogs were unable to work for a period of time.

Twenty dogs were permanently withdrawn from the Guide Dogs’ programme as a result of the attacks. Thirteen were fully qualified and working with guide dog owners, and this resulted in a financial cost of more than £600,000 to the charity.

Dog attacks resulted in physical injuries to 13.8% people, of which 68% were guide dog owners, and 47% required medical attention. The victim dog handlers also reported that their emotional well-being had been affected in 70% of attacks, including 39% feeling anxious, 35% feeling shaken and 30% feeling upset.

The authors say that the overall costs of veterinary treatment and replacement dogs are “estimated to be more than £650,000, but the impacts of the attacks on the guide dog owner are more important.”

They conclude the impact “for the guide dog owners of these dogs are likely to be long-term and complex affecting not only their mobility and physical health, but also their social and emotional well-being.”  Science daily  Original web page at Science Daily


* How the US CRISPR patent probe will play out

There is no shortage of optimism about the scientific potential of CRISPR–Cas9, a technique that can precisely alter the genomes of everything from wheat to elephants. But there is a great deal of confusion over who will benefit financially from its use.

On 10 March, the US Patent and Trademark Office (USPTO) will begin an investigation into who deserves the patent on using CRISPR–Cas9 to edit genes. This ‘patent interference’ could determine who profits from CRISPR in coming years.

Already, companies have sprung up to take advantage of the technique in agriculture, industrial biotechnology and the treatment of human diseases. One firm, Editas Medicine in Cambridge, Massachusetts, raised US$94 million when it went public on 2 February, even though it does not expect to enter clinical trials until 2017.

Nature takes a look at what the interference proceeding entails and what it could mean for the fate of CRISPR–Cas9.

One patent claim comes from a team led by molecular biologist Jennifer Doudna at the University of California, Berkeley, and microbiologist Emmanuelle Charpentier, now at Umeå University in Sweden and the Max Planck Institute for Infection Biology in Berlin. They published a 2012 paper demonstrating that the Cas9 enzyme can be directed to cut specific sites in isolated DNA (M. Jinek et al. Science 337, 816–821; 2012), and initiated their patent application on 25 May 2012.

Another team, led by Feng Zhang at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, published a 2013 paper demonstrating the application of CRISPR–Cas9 in mammalian cells (L. Cong et al. Science 339, 819–823; 2013). Zhang’s team began a patent application on 12 December 2012.

Although the Berkeley team filed first, the Broad team submitted its application to an expedited review programme, and was awarded the patent in April 2014. The Berkeley team then requested a patent interference against the initial Broad patent plus 11 related Broad patents. On 11 January, the USPTO granted Berkeley’s request.

A relic from the past. Until a few years ago, the United States awarded patents to those who could show that they were the first to invent, rather than simply the first to file the patent. Under that system, when competing inventors claimed to have created the same invention first, the USPTO declared an interference proceeding to determine which deserved the patent.

The United States switched to a first-to-file system in March 2013. But several key CRISPR–Cas9 patents were filed before the change.

A panel of three USPTO patent judges will hear evidence from both sides to establish which team invented the application of CRISPR–Cas9 for gene editing. Much of the action will be carried out over the telephone or through written documents. But there will probably be some oral arguments, and these could include testimony from the academic inventors.

Patent interferences can be highly technical, says John Conley, a legal scholar at the University of North Carolina in Chapel Hill. “It’s hard for me to cite anything more convoluted in the law than this,” he says. “It’s mind-boggling.” The USPTO panel will probably try to determine not only which team was the first to use CRISPR–Cas9 for gene editing, but which conceived of the invention first.

The process could be messy. During the era of ‘first-to-invent’ patents, some companies kept ‘inventor’s notebooks’: when someone at the firm thought of a new invention, they were to write it down in the notebook and have the entry notarized in case it came into play during future patent disputes. Few academic labs go to such lengths.

The law that did away with the United States’ first-to-file policy also introduced changes intended to expedite interferences. But a verdict on the CRISPR patents could still be months, or even years, away. And given the high financial stakes, many expect the losing party to appeal against the USPTO interference decision, further dragging out the process.

Not necessarily. In its filings to the Securities and Exchange Commission, Editas Medicine highlighted a potential interference claim by a Seoul company called ToolGen. Having multiple interferences over the same patent is rare, says Conley, but possible.

The Broad and MIT team also fast-tracked several of its applications at the European Patent Office (EPO), and has been awarded several patents so far. Doudna’s single application is pending.

Although the EPO does not have an interference process, outside parties can formally object to a patent. By 11 November 2015, the deadline for objections to the Broad’s first European CRISPR–Cas9 patent, nine parties had come forward — launching an opposition procedure that can take years to resolve.

Once that process is finished, participants can appeal. This adds another four or five years to the clock, says Michael Roberts, a partner at the intellectual-property law firm Reddie & Grose in Cambridge, UK. For this reason, Roberts believes that it will be several years before there is clarity on the earliest CRISPR–Cas9 patents in Europe.

Nature 531, 149 (10 March 2016) doi:10.1038/531149a  Nature  Original web page at Nature


Web tool aims to reduce flaws in animal studies

A free online tool that visualizes the design of animal experiments and gives critical feedback could save scientists from embarking on poorly designed research, the software’s developers hope.

Over the past few years, researchers have picked out numerous flaws in the design and reporting of published animal experiments, which, they warn, could lead to bias. In response, hundreds of journals have agreed to voluntary guidelines for reporting animal studies: checklists of best practice, such as what statistical calculations to use to ward off error.

But these lists kick in after scientists submit a paper, says Nathalie Percie du Sert, who specializes in experimental design at the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) in London. “When you get to the reporting stage, that’s a bit too late,” she says. “We want researchers to think about these issues at the design stage.”

Percie du Sert’s solution is a programme called the Experimental Design Assistant (EDA), which launched in October 2015. She hopes that it will help to improve the quality of animal research and perhaps even become an integral part of the conduct of animal studies.

The EDA allows scientists to create a visual representation of an experiment by laying out its key elements — hypothesis, experimental method and planned analysis — in logically connected, coloured boxes. The software then uses a built-in set of rules to spot potential problems, and suggests refinements. These may be simple — the researcher hasn’t specified how to randomize animals to the control or treatment arm — or more complex: there are potential confounding variables in the control and trial arms. The tool can also assist scientists with calculating the sample size needed to ensure a statistically robust result, or with randomization.

There’s nothing fundamentally new in the EDA, says Percie du Sert. It builds on existing knowledge of good experimental design. But it can aid scientists who have little training in the area, she says, and teach them design choices.

Since the EDA’s launch, around 400 accounts have been created to use it, producing between 50 and 100 experimental diagrams in total each month, says Percie du Sert. She does not have access to detailed information about its users; the sensitivities around animal research and the need to protect researchers mean that data on who is using it, and how, are secured.

The Wellcome Trust’s Sanger Institute, a genome-research centre in Cambridge, UK, is rolling out an internal training programme that includes lessons on design and use of the EDA; the agency is encouraging staff to use the software to present experiments to ethical-review committees, says Natasha Karp, a biostatistician at the institute. Karp took part in the working group that oversaw the tool’s development, and says that she uses it to visualize the experiments of the biologists whom she supports.

The EDA is not the only software that aims to improve research quality and reproducibility. Other tools check manuscripts before publication for issues such as errors in formatting or omission of P values. These include Penelope, a paid-for service aimed at journal publishers; another tool called WebCONSORT (which is not yet freely available) is being tested as a way to improve reporting of clinical trials. Protocol Navigator, a free web application created by scientists at Cardiff University, UK, also produces visual experiment maps that can be shared.

But the EDA specifically targets animal research, and as such, is unique in its ability to give a rapid overview of the design and analysis of animal experiments, says Karp. “There isn’t anything else quite like this system.”

Percie du Sert hopes that a visual representation of experiments could become common practice, used in research papers or lab meeting presentations. Eventually, the EDA might even produce time-stamped versions to prove that an experiment was conducted and analysed as designed, she adds, rather than being the product of a scientist searching for meaning in data after the fact — a frowned-upon practice sometimes called HARKing (‘hypothesizing after the results are known’).

The online tool can seem a little complicated, says Jeffrey Mogil, who studies pain at McGill University in Montreal, Canada. “But I actually think that people might get a big kick out of using this,” he says. “It looks like a cool way to break in new grad students or teach the scientific method to undergrads.”

Nature 531, 128 (03 March 2016) doi:10.1038/531128a  Nature  Original web page at Nature


Biotech giant publishes failures to confirm high-profile science

A biotechnology firm is releasing data on three failed efforts to confirm findings in high-profile scientific journals — details that the industry usually keeps secret.

Amgen, headquartered in Thousand Oaks, California, says that it hopes the move will encourage others in industry and academia to describe their own replication attempts, and thus help the scientific community to get to the bottom of work that other labs are having trouble verifying.

The data are posted online at a newly launched channel dedicated to quickly publishing efforts to confirm scientific findings. The ‘Preclinical Reproducibility and Robustness’ channel is hosted by F1000Research, the publishing platform of London-based publishers Faculty of 1000 (F1000). Scientists who are concerned about the irreproducibility of preclinical research say that they welcome the initiative — but are not sure whether it will gain traction.

The idea emerged from discussions at a meeting focused on improving scientific integrity, hosted by the US National Academy of Sciences in 2015. Sasha Kamb, who leads research discovery at Amgen, said that his company’s scientists have in many instances tried and failed to reproduce academic studies, but that it takes too much time and effort to publish these accounts through conventional peer-review procedures.

Bruce Alberts, a former editor-in-chief of Science who sits on F1000Research’s advisory board, suggested that Kamb try the faster F1000 route — an open-science publishing model in which submitted studies are posted online (for a fee that ranges from US$150 to $1000) before undergoing peer review; submissions are subject to checks by F1000 editors to ensure that data are freely available and that methods and reagents are adequately described.

“The idea is to get the data out and get it critically looked at,” Alberts says. The editors then invite open peer review of the studies. If reviewers recommend the work, it is indexed in databases such as PubMed and Scopus.

F1000, in turn, has created a designated channel for these studies in the hope that they will garner attention, give credit to researchers doing careful confirmatory experiments and provide a place where the original researchers of a study and other scientists can discuss reasons behind different outcomes.

In 2012, Amgen researchers made headlines when they declared that they had been unable to reproduce the findings in 47 of 53 ‘landmark’ cancer papers. Those papers were never identified — partly because of confidentiality concerns — and there are no plans to release details now either, says Kamb, who was not involved with that publication. He says that he prefers to focus on more-recent publications.

The three studies that Amgen has posted deliberately do not make a detailed comparison of their results to previous papers, says Kamb. “We don’t want to make strong conclusions that someone else’s work is wrong with a capital W,” he says.

One study adds to existing criticism of a Science paper that suggested that a cancer drug might be a potential treatment for Alzheimer’s disease; a second counters earlier findings (including some by Amgen researchers) connecting a gene to insulin sensitivity in mice, and a third counters a Nature paper reporting that inhibiting one particular protein could enhance degradation of other proteins associated with neurodegenerative diseases.

“We believe that interested scientists can look at our methods and results and draw their own conclusions,” Kamb says. Amgen researchers did not contact the original authors when they conducted their studies, he says, but future postings could be collaborative.

Right now, the main way that the scientific community spreads the word about irreproducible research is through innuendo, which is inefficient and unfair to the original researchers, says Ricardo Dolmetsch, global head of neuroscience at Novartis’s Institutes for Biomedical Research in Cambridge, Massachusetts. “Anything we can do to improve the ratio of signal to noise in the literature is very welcome,” he says.

The F1000 initiative is useful, but previous efforts have tried and failed to encourage the reporting of replications and negative results, cautions John Ioannidis, who studies scientific robustness at California’s Stanford University. That is because, in general, the scientific community undervalues such work, he says.

But Kamb says that he has spoken with several industry leaders who have expressed support, and he hopes that they will contribute eventually. Roger Perlmutter, head of research and development at pharmaceutical giant Merck, says his colleagues can participate in the channel “at their own discretion”. Morgan Sheng, a vice-president at biotechnology company Genentech in South San Francisco, says he can forsee his company’s scientists submitting data to the venture too.

“I believe the main risk of a publication venue like the F1000 channel is that it becomes a place for “bashing” good science, because biological experiments are complex and beset by many variables that are hard to control. Non-replication does not necessarily mean ‘not true’,” Sheng adds. He says the site should be careful to emphasize publication of positive replication data as well.

Academic researchers are unlikely to risk alienating their peers by publishing disconfirming results, predicts Elizabeth Iorns, head of Science Exchange in Palo Alto, California. Her firm provides an online marketplace where scientists can offer to do others’ experiments, which she used to launch a reproducibility initiative in 2012.

But providing industry scientists with a low-barrier way to share their attempts might prove a winning strategy, she says. “Hopefully, the awareness of the reproducibility issue has been raised such that people are no longer afraid to talk about it.”

Nature doi:10.1038/nature.2016.19269  Nature  Original web page at Nature


* Surge in support for animal-research guidelines

Journals throw their weight behind checklist for rigorous animal experiments.

More than 600 research journals have now signed up to voluntary guidelines that are designed to improve the reporting of animal experiments.

Scientists have repeatedly pointed out that many published papers on animal studies suffer from poor study design and sloppy reporting — leaving the research at a substantial risk of bias.

So in 2010, the ARRIVE guidelines (Animals in Research: Reporting In Vivo Experiments) were introduced by a team led by the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs). They provide a detailed checklist of elements that should be included in any reporting of animal research, such as information about animal strain and sex, appropriate statistical calculations and disclosure of adverse events.

More than 150 journals endorsed the ARRIVE guidelines in 2015 alone, according to NC3Rs data — the highest number of signatories in a single year since the checklist’s release in 2010. By the end of January 2016, the total number had passed 600.

Still, endorsement does not mean enforcement: a 2014 study suggested that researchers largely ignore the voluntary guidelines. By comparing some papers published before and after the guidelines were issued, it found that there was little difference in the quality of reporting.

Nature doi:10.1038/nature.2016.  Nature  Original web page at Nature


Public and private investments in Ph.D. research programs pay economic development dividends

Almost 40 percent of these Ph.D. graduates enter industry, where they are disproportionately hired at large and high-wage establishments in technology and professional service industries. They also earn higher-than-average salaries, all of which contribute to economic growth.

The research, published today in Science, is the first to show how federally and non-federally funded research investments may affect the economy by tracing the human dimension of their impact. The study matches administrative records to U.S. Census Bureau data to examine the subsequent employment and earnings outcomes of nearly 3,200 Ph.D. graduates from eight major research universities.

Led by professors Julia Lane (New York University), Bruce Weinberg (Ohio State University), Paula Stephan (Georgia State University) and Jason Owen Smith (University of Michigan), researchers examined an array of outcomes.

The study showed more than 20 percent of these doctoral recipients remain in the state where they trained, about 13 percent within 50 miles of their university.

Only a small percentage of the Ph.D. recipients entered government (4.1 percent) and the majority remained in academia (57.1 percent), many presumably taking a postdoctoral research position. Seventeen percent of the Ph.D. recipients worked in establishments owned by firms with research and development operations versus 10.8 percent of the U.S. workforce. Doctoral recipients employed in pharmaceutical and medicine manufacturing, semiconductors and computer systems design are between four and 19 times the U.S. average.

The authors also found the median U.S. establishment employing these Ph.D. recipients has a higher payroll per worker — more than $90,000 — than the median U.S. establishment owned by a research and development firm (just under $61,000) and the median U.S. establishment (just over $33,000). Fifty-one percent of these doctoral recipients work in establishments where per-worker payrolls exceed $100,000. Although Stephan cautioned the study is descriptive in nature and not causal, she added, “It’s an important first step in providing policymakers the tools they need to assess the broader effects of investments in science.” Science Daily  Original web page at Science Daily


Cancer studies clash over mechanisms of malignicy

The proliferation of blood cells in leukaemia is just one example of unchecked tissue growth associated with cancer — but the extent to which external and internal factors drive this process is open to debate.

Most cases of cancer result from avoidable factors such as toxic chemicals and radiation, contends a study published online in Nature on 16 December (S. Wu et al. Nature; 2015). The paper attempts to rebut an argument that arose early this year, when a report in Science concluded that differences in inherent cellular processes are the chief reason that some tissues become cancerous more frequently than others (C. Tomasetti and B. Vogelstein Science 347, 78–81; 2015).

The work led to assertions that certain forms of cancer are mainly the result of “bad luck”, and suggested that these types would be relatively resistant to prevention efforts. “There’s no question what’s at stake here,” says John Potter of the Fred Hutchinson Cancer Research Center in Seattle, Washington, who studies causes of cancer. “This informs whether or not we expend energy on prevention.”

In their Science paper, mathematician Cristian Tomasetti and cancer researcher Bert Vogelstein at Johns Hopkins University in Baltimore, Maryland, calculated the relationship between the number of stem-cell divisions and the risk of developing cancer in various tissues. Every instance of cell division comes with a risk that DNA will be incorrectly copied, leading to mutations — some of which could contribute to cancer. The duo’s analysis found a correlation: the more stem-cell divisions that occur in a given tissue over a lifetime, the more likely it is to become cancerous.

Tomasetti and Vogelstein then sorted types of cancer according to how much of the variability in risk is due to stem-cell divisions versus to some ‘extrinsic’ factor, such as environmental exposure to carcinogens. The authors argued that although some cancers clearly had strong environmental links — such as liver cancers caused by hepatitis C infection or lung cancer resulting from smoking — there were others for which the variation was explained mainly by defects in stem-cell division. In those cases, they argued, early detection and treatment would be more effective than prevention.

Something about that did not sit right with Yusuf Hannun, a cancer researcher at Stony Brook University in New York. “What they did was interesting, but I was startled by the conclusion,” he says.

The original work, Hannun and his colleagues argue, assumed that the two variables — intrinsic stem-cell division rates and extrinsic factors — were entirely independent. But what if environmental exposures affect stem-cell division rates, as radiation is known to do?

Hannun and his team also used other lines of evidence to try to pinpoint the contribution of environmental factors to cancer risk. They looked at epidemiological data showing that, for example, people who migrate from regions of lower cancer risk to those with higher risk soon develop disease at rates consistent with their new homes. The authors also examined patterns in the mutations associated with certain cancers; ultraviolet light, for example, tends to create a tell-tale signature of mutations in DNA. And they used other mathematical models, expanding the data set used in the earlier work to include prostate and breast cancer — two of the most common cancers. “There’s no question what’s at stake. This informs whether or not we expend energy on prevention.”

The models suggested that mutations during cell division rarely build up to the point of producing cancer, even in tissues with relatively high rates of cell division. In almost all cases, the team found that some exposure to carcinogens or other environmental factors would be needed to trigger disease.

Tomasetti counters that he never intended to explain why cancers develop. His analysis, he says, was based on normal stem-cell division in healthy tissue and was meant to explain only why some cancers are more prevalent than others. He also argues that the models created by Hannun and his colleagues make too many assumptions and fail to incorporate some features of tumour growth.

Some specialists in cancer prevention welcome the Nature paper because of fears that the public — and possibly also funders of scientific research — might conclude that prevention efforts are not worthwhile, says Edward Giovannucci, who studies cancer prevention at the Harvard T. H. Chan School of Public Health in Boston, Massachusetts. “By not smoking, your lifetime risk of lung adenocarcinoma drops dramatically,” he says. “The fact that your risk of pelvic sarcoma is even lower because there’s less stem-cell division — so what?”

Nature 528, 317 (17 December 2015) doi:10.1038/528317a  Nature  Original web page at Nature


* Risks associated with the use of antimicrobials in animals worldwide

The World Organisation for Animal Health (OIE) has evaluated the quality of national animal health systems, including Veterinary Services, in more than 130 countries.

More than 110 of the countries evaluated – mainly developing and emerging countries – do not yet have relevant legislation concerning appropriate conditions for the importation, manufacture, distribution and use of veterinary products, including antimicrobials. In some cases, legislation is totally non-existent. Where it does exist it is very often not properly applied because of lack of public funds for the implementation of controls.

In such countries, antimicrobials are usually freely available to anyone, directly or indirectly, without restriction. Worse still, they circulate as normal goods and are often adulterated (dosage less than that mentioned on the packaging, different molecule or complete placebo). Thousands of tonnes of adulterated antimicrobials destined for use in animals are circulating worldwide (and the same is true of antimicrobials for human use).

Unfortunately, the use of antimicrobials in animals by untrained personnel is not confined to developing and emerging countries. In a significant number of Member Countries of the Organisation for Economic Co-operation and Development (OECD), it is easy to acquire antimicrobials, particularly via the internet, and many farmers do so. Some of these countries still allow the use of some antimicrobials on fruit trees to control certain bacterial diseases, as well as the incorporation of some antimicrobials into animal feed as growth promoters or for other non-therapeutic purposes. Political action, for example by the G8 countries or the World Trade Organization, could hope to persuade countries in this category to change these practices, estimated by many credible scientists as risky.

In the area of preventing antimicrobial resistance in animals (and its potential benefits for public health), although some countries and regions are already very cautious, the adoption of effective provisions by the rest of the world is likely to be long, difficult and controversial, not to say illusory.

Unfortunately, globalisation of the food trade, coupled with traditional and medical tourism, enable (and will continue to enable) existing or future resistant bacteria to colonise the entire planet with ease, regardless of any preventive measures implemented locally.

How can we face this important challenge?

The OIE trains national Focal Points appointed by its Member Countries and forms networks to enable them to develop and modernise legislation on the production, importation, distribution and use of veterinary products, as well as to carry out such tasks as monitoring the consumption of antimicrobials, because very little is yet known about actual volumes used in the 180 Member Countries involved in the OIE veterinary legislation support programme.

OIE Member Countries adopt international standards on the prudent use of antimicrobial agents and on the harmonisation of the risk assessments that they undertake to implement. International cooperation in the form of development aid is crucial to helping developing countries, and even emerging countries, to apply these standards, especially since, in the short term, animal production is expected to grow by more than 50% owing to increasing use of intensive production systems in these countries.

The OIE also recommends policies to introduce minimum geographical coverage by veterinarians so as to ensure animal health surveillance, using this network to guarantee the early detection of potential epizootics (including zoonoses such as animal influenza) and a rapid response to contain outbreaks at source. Such a network can also improve the general health of animals by allowing the judicious and proper limited use of antimicrobials. The network’s existence and sustainability is partly dependent on revenues from services provided by veterinarians, many to mainly poor customers in the isolated or deprived areas where they work, which are home to the numerous animals to be monitored. These revenues come mainly from the delivery of products, including antimicrobials, which veterinarians administer directly to the animals. This can raise a potential conflict of interest that needs to be addressed. It is why our organisation provides

Standards and programmes to improve the quality of veterinary education worldwide, including in the fields of microbiology, pharmacology and ethics. A standard on the design and functioning of national and regional Veterinary Statutory Bodies empowered by the law and by State delegation of the necessary powers to oversee qualifications, ethical standards and professional excellence, as well as to expel anyone whose conduct is improper.

While some countries have decoupled prescription from delivery for certain veterinary drugs, including antimicrobials, this may pose logistical problems of responsiveness to diseases, particularly at the farm level, and may facilitate illegal practices (direct and uncontrolled self-supply and intervention of unscrupulous and ignorant individuals, mainly via the internet). The risks associated with these practices may have consequences that are much more serious than any irregularities in drug prescription or delivery by veterinarians, which are much easier to control and prevent. Several countries that have implemented decoupling have seen an increase in the general consumption of antimicrobials (according to those in a position to assess such consumption). It is worth noting that the human consumption of antimicrobials continues to grow despite the fact that decoupling of drug prescription and delivery is widespread in human medicine.

It appears that measures to limit the emergence of resistance in animals, including managing and limiting globally what are deemed to be the riskiest practices, (including the use of antimicrobial agents in plant production), should be made a global priority, including in developed countries.  OIE  Original web page at OIE


UK government proposes scrapping major universities funder

An organization that distributes a large slice of the national science budget to English universities each year will face the axe, if a UK government proposal gains political support.

In a consultation document which may presage a wider shake-up to the way science is funded in the UK, the government suggests scrapping the Higher Education Funding Council for England (HEFCE), which doles out around £1.6 billion ($2.4 billion) for research annually to universities.

The document, published by the department for Business, Innovation, and Skills (BIS) on 6 November, makes it clear that other organizations would take up HEFCE’s responsibilities, although exactly how remains an open question.

Even if the idea never comes to pass, it suggests the government is not shy of suggesting radical changes to the British science funding landscape.

That is likely to heighten the concerns of UK scientists who are already braced for a government-wide spending review, scheduled for 25 November, which it is feared may lead to cuts to the science budget.

And the proposal comes as researchers await the results of a separate review into the future of the seven UK agencies who distribute the rest of the nation’s science budget: the research councils.

The UK science budget is distributed in two ways. HEFCE hands out a grant to universities each year for both research and teaching (allocated on the basis of an audit of university research quality), while the research councils invite researchers to compete for grants.

The consultation document emphasizes that if HEFCE were scrapped, this would not mean an end to this ‘dual support’ system. But it suggests that a single body might in future encompass the functions of both HEFCE and the research councils, with assurances that the two types of funding remain separate.

It is unclear how that would affect the status of the research councils, which are currently independent entities but might not be if they fell under a new umbrella body. Asked whether such a move might constitute a merger of the research councils, a spokeswoman for BIS told Nature that the design of the future research system remains “all up for consultation”. Impact of UK research revealed in 7,000 case studies.

Moving HEFCE’s research functions into the research councils “sounds like a stupid idea to me,” says Kieron Flanagan, a science-policy researcher at Manchester Business School. “If you’ve accepted the principle that we maintain the dual support system, it doesn’t make sense to put both aspects of that in the same hands”.

Ultimately, the BIS document says, any decision would be guided by responses to the consultation – which can be received until January 2016 – and by the results of the review into the research councils, which is being led by Nobel-prizewinning geneticist Paul Nurse, the president of London’s Royal Society. Given HEFCE’s legal status, scrapping it would also require the approval of Parliament.

In the light of Nurse’s review, and a perceived drive by BIS secretary Sajid Javid to reduce the numbers of the department’s partner agencies, researchers had already been speculating before today’s consultation document whether the research councils might be merged.

But Flanagan also thinks that merging the research councils to create a giant agency would be a mistake. The agencies already share some back-office functions, and any further merging would bring marginal gains but sizeable risks, he adds. “I don’t think there’s any example of a large, successful research system that has a single, science funding body.

These are not the only ideas explored in the BIS proposal. Another option is to create a new body to replace the research-related functions of HEFCE (whose teaching-related and regulatory responsibilities would be taken up by a different organisation, the Office for Students). Flanagan and others wonder whether BIS might itself hand out research money, although this is not an option flagged in the consultation document.

The proposal is clear that scrapping HEFCE would not mean scrapping the UK’s university research audit, known as the Research Excellence Framework. However, in the future the government will look to reduce the burden of the audit, potentially by making greater use of metrics, it says. A future audit might also try to limit costs by discouraging the “industries” which it says some institutions create around the exercise, such as carrying out multiple mock assessments and bringing in external consultants.

More widely, the BIS consultation is designed to refocus the UK university system on teaching. The Office for Students would, for example, take responsibility of a new Teaching Excellence Framework, which will judge university’s teaching performance against measures such as student satisfaction and graduate job prospects. In the future, universities’ ability to increase the tuition fees they charge in line with inflation will be tied to “high quality teaching”, the document adds.

Nature doi:10.1038/nature.2015.18743  Nature   Original web page at Nature


Ocean’s wildlife populations down by half

A new WWF report reveals an alarming decline in marine biodiversity over the last few decades. According to WWF’s Living Blue Planet Report, populations of marine vertebrates have declined by 49% between 1970 and 2012, with some fish species declining by almost 75%. In addition to fish, the report shows steep declines in coral reefs, mangroves and seagrasses that support marine food webs and provide valuable services to people. With over 25% of all marine species living in coral reefs and about 850 million people directly benefiting from their economic, social and cultural services, the loss of coral reefs would be a catastrophic extinction with dramatic consequences on communities.

According to the report, the biggest drivers of these declining trends are from human actions — mainly overfishing, habitat destruction, and climate change. Although the report paints a dim picture of ocean health, it also provides solutions and opportunities to turn the tide. It highlights the need to protect critical marine habitats, manage fish stocks more sustainably, improve fishing practices, and redirect financial flows to support these needed initiatives.

“The good news is there are abundant opportunities to reverse these trends,” said Brad Ack, senior vice president for oceans at WWF. “Stopping black market fishing, protecting coral reefs, mangroves and other critical ocean habitats, and striking a deal in Paris to slash carbon pollution are all good for the ocean, the economy, and people. Now is the time for the US and other world players to lead on these important opportunities.”

One immediate opportunity for international action happens later this month when world leaders meet in New York to discuss the UN’s Sustainable Development Goals. At the meeting, it’s essential that political leaders support the goals with significant investment and meaningful implementation plans to address the habitat destruction, illegal fishing, overharvest, and marine pollution driving the degradation of our oceans.

“The ocean is a renewable resource that can provide for all future generations if the pressures are dealt with effectively,” said Marco Lambertini, Director General of WWF International. “If we live within sustainable limits, the ocean will contribute to food security, livelihoods, economies and our natural systems.”

Report is available for download at Science Daily  Original web page at Science Daily


Could more intensive farming practices benefit tropical birds?

The world is facing an extinction crisis as more and more forests are converted into farmland. But does it help when farms share the land with birds and other animals? The short answer is “no,” according to new evidence based on the diversity of bird species reported in the Cell Press journal Current Biology on September 3. If the goal is to preserve more bird species, representing a greater span of evolutionary history, then it’s better to farm more intensively in some areas while leaving more blocks of land entirely alone. In other words, land-sparing wins out over land-sharing.

“I think the most surprising result is that species richness within communities does not explain the loss of phylogenetic diversity under land-sharing,” says David Edwards of The University of Sheffield. “So even if farming at low intensity over a larger area retains the number of species present, those species are less evolutionarily distinct and thus preserve less phylogenetic diversity.”

Edwards and his colleagues examined this question of farming practices in the Chocó-Andes of Colombia, a global hotspot for birds, including many species that can’t be found anywhere else. It’s also a place where tropical cloudforest landscapes are threatened by widespread pastures for cattle.

“The Chocó-Andes are a hotspot of endemism and have been widely impacted by low-intensity farming, making this one of the most threatened faunas on Earth,” Edwards says. “It is vital to consider how best to farm here, but also to use this region as a model for how best to farm in other locations.”

The researchers sampled birds in three study areas, each containing contiguous forest and cattle farms. While they found many bird species living within low-intensity farmland communities, those areas showed a loss of more than 650 million years of evolutionary history in comparison to the forest.

Edwards and his colleagues then used landscape simulations to examine the outcomes of land-sharing versus land-sparing practices. Their analyses show that land-sharing becomes increasingly inferior to land-sparing as the distance from intact forest grows. Isolation from forest also leads to the loss of more evolutionarily distinct species from communities within land-sharing landscapes, which can be avoided with effective land-sparing.

Edwards’s team concludes that “land-sharing policies that promote the integration of small-scale wildlife-friendly habitats might be of limited benefit without the simultaneous protection of larger blocks of natural habitat, which is most likely to be achieved via land-sparing measures.”

There’s plenty of work to do in order to simultaneously protect natural habitats and boost farm yields. Sustainability initiatives for oil palm, soy, and other crops now take a land-sharing approach by requiring the protection of biodiversity within tropical farmland. “My feeling is that land-sparing-type approaches–such as biodiversity offsets, which can protect larger tracts of natural habitat–are gaining traction, but there is a long way to go for expansion of such policies writ large,” Edwards says.  Science Daily  Original web page at Science Daily


* China announces stem-cell rules

Scientists hope new rules could spur stem cell research in China. Chinese stem-cell scientists have welcomed long-awaited measures that, state media claim, will rein in rogue use of stem cells in clinics while allowing research.

The measures — announced on 21 August by China’s National Health and Family Planning Commission through state media — offer a straightforward path towards clinical studies, researchers told Nature. But some also warn that the measures do not have the teeth needed to stop clinics offering unproven and unapproved treatments.

For years, clinics around China have been ignoring government regulations and warnings from the scientific community, offering desperate patients costly and, according to experts, probably ineffective treatments. These were often labelled as clinical trials as a cover to charge patients. Other countries have experienced similar problems.

In January 2012, the government took stock of the situation. It implemented a ban on unapproved stem-cell therapies and a temporary moratorium on new clinical trials, promising to establish a clear framework for future trials. Since then, however, many rogue stem-cell clinics have continued to operate, while stem-cell scientists with valid research agendas have waited for a way to move forward

Qi Zhou, a stem-cell and cloning scientist at the Chinese Academy of Sciences (CAS) Institute of Zoology in Beijing, has been waiting for the guidelines so he can move his research from animal models to humans. In unpublished work, his team has already implanted dopamine-producing neurons derived from stem cells into monkeys that have been chemically induced to show symptoms similar to those of Parkinson’s disease. The monkeys have shown some improvement, and he now hopes to try the treatment on humans. “I think it’s time, time to start doing some clinical research,” he says

Jianwu Dai, a regenerative-medicine specialist at the CAS Institute of Genetics and Developmental Biology in Beijing, hopes to implant a small collagen scaffold seeded with stem cells into humans to try to repair spinal-cord injuries. His team has treated some 25 people using the scaffold seeded with mononuclear cells, a type of blood cell taken from bone marrow, and Dai says he has seen some improvements. But he thinks that neural stem cells derived from embryonic stem cells will deliver better results

The new measures outline requirements for such studies, including obtaining patients’ informed consent and using clinical-grade stem cells that have been approved by an independent body. They say that stem-cell clinical studies can be carried out only at authorized hospitals, and they forbid the hospitals from charging recipients or advertising. Researchers who want to do pilot studies, such as Zhou and Dai, will need to register with the health ministry with documentation showing that there are sufficient animal studies to support trials in humans and that they are using certified cell lines verified by independent evaluation

The penalties for breaking the rules are not yet clear, although a senior health-ministry official has pledged to use them to clean up the stem-cell field in China

Zhou does worry that rogue clinics will continue to offer completely untested treatments. “Some hospitals, some companies won’t care. They do what they want,” he says.

Douglas Sipp, who researches stem-cell policy at the RIKEN Center for Developmental Biology in Kobe, Japan, says that the mechanism laid out for clinical studies looks pretty similar to those in other countries, and more rigorous than some. But he worries that the measures might not apply to military hospitals, or to private clinics affiliated with military hospitals, which have in the past fallen outside health-ministry jurisdiction in China.

“In principle, I applaud any efforts to rein in practice of predatory clinics that take advantage of patients. But the fact that these new rules do not appear to have penalties leaves open the question of how effective they will be,” says Sipp. “I have seen China crack down on stem-cell clinics at least twice in the past, and the results were inconclusive.”

Nature doi:10.1038/nature.2015.18252  Natur  Original web page at Nature


Human activities are jeopardizing Earth’s natural systems, health of future generations

A new report released by The Rockefeller Foundation-Lancet Commission on Planetary Health, calls for immediate, global action to protect the health of human civilization and the natural systems on which it depends. The report, Safeguarding Human Health in the Anthropocene Epoch, provides the first ever comprehensive examination of evidence showing how the health and well-being of future generations is being jeopardised by the unprecedented degradation of the planet’s natural resources and ecological systems.

“This Commission aims to put the health of human civilizations, and their special relationship with the larger biosphere, at the centre of concerns for future planetary sustainability. Our civilization may seem strong and resilient, but history tells us that our societies are fragile and vulnerable. We hope to show how we can protect and strengthen all that we hold dear about our world,” says Dr Richard Horton, Editor-in-Chief of The Lancet and one of the report authors.

The report was written by a Commission of 15 leading academics and policymakers from institutions in 8 countries, and was chaired by Professor Sir Andy Haines of the London School of Hygiene & Tropical Medicine, UK. It demonstrates how human activity and development have pushed to near breaking point the boundaries of the natural systems that support and sustain human civilizations

“The Rockefeller Foundation-Lancet Planetary Health Commission has issued a dire warning: Human action is undermining the resilience of Earth’s natural systems, and in so doing we are compromising our own resilience, along with our health and, frankly, our future,” said Dr Judith Rodin, President of The Rockefeller Foundation. “We are in a symbiotic relationship with our planet, and we must start to value that in very real ways. Just as Foundation leaders 100 years ago took a holistic view and launched the field of public health, the Commission’s report marks a paradigm shift for a new era of global public health, one that must be integrated with broader policy decisions.”

The Commission warns that a rising population, unsustainable consumption and the over-use of natural resources will exacerbate these health challenges in the future. The world’s poorest communities will be among those at greatest risk, as they live in areas that are most strongly affected and have greater sensitivity to disease and poor health.

“We are on the verge of triggering irreversible, global effects, ranging from ocean acidification to biodiversity loss,” says Professor Haines. “These environmental changes — which include, but extend far beyond climate change — threaten the gains in health that have been achieved over recent decades and increase the risks to health arising from major challenges as diverse as under-nutrition and food insecurity, freshwater shortages, emerging infectious diseases, and extreme weather events.”

Concerns that global environmental change represents a growing threat to human health are underlined by two new research articles being published in conjunction with the report. One article, published in The Lancet, quantifies for the first time the human health implications of declines in animal pollinators (such as bees and other insects). The study, led by one of the report Commissioners, Dr Samuel Myers, from Harvard T. H. Chan School of Public Health, USA, shows that global declines in animal pollinators could lead to up to 1.4 million excess deaths annually (an increase in global mortality of 2.7%) from a combination of increased vitamin A and folate deficiency and increased incidence of non-communicable diseases like heart disease, stroke, and certain cancers. The research shows that these health effects would be experienced in both developed and developing countries.

The second study, also led by Dr Myers, and published in The Lancet Global Health, quantifies for the first time a major global health threat associated with anthropogenic carbon dioxide (CO2) emissions. The study shows that reductions in the zinc content of important food crops as a response to rising concentrations of CO2 in the atmosphere will place between 132-180 million people at new risk for zinc deficiency globally by around 2050. In addition, these nutrient reductions will exacerbate existing zinc deficiency for billions around the world. Zinc deficiency leads to hundreds of thousands of premature deaths from infectious disease because of reduced immune function.

Solutions to these clear and potent dangers are within reach, say the Commission authors, but the world needs to take decisive, coordinated action to protect the environment and secure the health of future generations

The Commission outlines a range of beneficial policies and actions that can be taken by governments, international organisations, researchers, health professionals and citizens that are good for both health and the environment. Examples include benefits from reduced air pollution, healthy diets with more fruit and vegetables, active transport (walking and cycling), reduced urban heat stress from green spaces, and increased resilience to coastal flooding from intact wetlands and mangroves. In addition, the report identifies some major gaps in evidence and the research that is needed. Some of the recommendations include:

  • Integrated social, economic and environmental policies: Policies and initiatives need to be designed to promote more efficient use of current resources to allow for the replenishment of natural systems. They should also spur innovation and make sustainable practices more mainstream, such as reducing waste and developing resilient cities.
  • Better governance: Leaders need to take initiatives to reduce the risks to health and vital ecosystems, and implement policies to reduce subsidies that block sustainable practices, encourage behavioral change, incentivize the private sector, support research, and promote public discourse. To help ensure that Planetary Health is at the center of national policy, governments should give responsibility for monitoring trends and developing policies to a body that answers directly to the Head of State.
  • Improved health systems: Environmental health needs must be integrated into health budgeting and purchasing. In addition, as environmental threats will be characterised by surprise and uncertainty, health systems must be designed for resilience, planning for potential risks and adapting quickly to meet challenges and restore services.
  • A reorganisation and expansion of our knowledge on Planetary Health: There are substantial gaps in knowledge that can be closed with the expansion of trans disciplinary research, improved understanding of the links between health and environmental change and potential adaptation strategies, building integrated surveillance systems and reporting on progress nationally and international.  Science Daily  Original web page at Science Daily


Fears for bees as UK lifts insecticide ban

A UK government agency has used emergency rules to make controversial neonicotinoid insecticides available to some farmers, despite a European ban.

These chemicals have been linked to declines in bee populations in numerous scientific studies, and the European Union (EU) imposed a temporary ban on much of their use in 2013. But the UK’s Department for Environment, Food and Rural Affairs (Defra) has now said that some farmers should be able to use them anyway under EU rules that permit the “emergency” use of banned chemicals to protect crops .

In a statement, the department said it had “fully applied the precautionary ban on the use of neonicotinoids introduced by the EU”. But it also said: “Based on the evidence, we have followed the advice of the UK Expert Committee on Pesticides and our Chief Scientist that a limited emergency authorisation of two pesticides requested by farmers should be granted in areas where oil rape crops are at greatest risk of pest damage.”

The National Farmers Union, which applied for the authorisation, says it is needed to protect around 300 square kilometres of oilseed rape in England from cabbage stem flea beetles. The union says that amounts to around 5% of the total oilseed rape crop in England.

The risk neonicotinoids pose to bees is disputed and the EU ban has been controversial. Manufacturers of the chemicals and some scientists say that the evidence that use can harm bees is limited, and that laboratory studies showing harm do not reflect the true situation in the field.

But researchers who worry about the chemicals say that there is now enough evidence – including from real-world trials – to say that use should be restricted. Earlier this year Nature published work by Maj Rundlöf, an ecologist at Lund University in Sweden, and her colleagues that showed wild-bee density in fields treated with neonicotinoids was around half the bee density in untreated, control fields.

Lynn Dicks, a pollinator researcher at the University of Cambridge, says that in the light of the Rundlöf work, “I find this [Defra] decision extraordinary”. Based on that research, she says, “areas with 5% of the UK’s rape crop might expect to lose two-thirds of their wild bumblebee queens going into the winter of 2016/17 because of this decision”.

Nature doi:10.1038/nature.2015.18052 Nature Original web page at Nature


Universities highlight gender-equality policies after sexism row

Nobel laureate Tim Hunt, who ignited a debate over sexism in science with his comments about women at a conference last month, will not be reinstated as an honorary professor at University College London (UCL), the university has confirmed.

Meanwhile, other UK universities have told Nature that  that the affair has not prompted changes to their diversity policies, or guidelines on work behaviour. But, they say, gender equality is an issue that they are striving to address, sometimes in creative ways, and with positive results.

Hunt, a biologist who won the Nobel Prize for Physiology or Medicine in 2001, resigned from his UCL position on 10 June in the wake of comments made two days previously at the World Conference of Science Journalists in Seoul. “Let me tell you about my trouble with girls. Three things happen when they are in the lab … you fall in love with them, they fall in love with you, and when you criticize them they cry,” he told delegates – remarks that he said were intended to be light-hearted.

Hunt faced a barrage of condemnation and he also resigned from the Royal Society’s Biological Science Awards Committee. But some high-profile scientists and some who knew him personally said that his treatment had been disproportionate, and petitions to have him reinstated emerged. Hunt’s critics also subsequently faced a vehement backlash online.

In a short statement on 9 July, the university’s governing body, UCL Council, wrote that it “unanimously supports the decision taken by UCL’s executive to accept the resignation”. The council said that the extent of media interest was unprecedented and that it recognized the distress caused to Hunt and his wife Mary Collins, an immunologist at UCL. But it also said that “all parties agree that reinstatement would be inappropriate”.

Hunt declined to comment on the UCL statement but wrote in an email to Nature: “I’ll just point out that my ‘contract’ was due to expire early in 2016, and I’d already given my last lecture, so there really didn’t seem much point in reinstatement from my point of view.”

UCL also said that it had “requested that the executive undertake a review of its communications strategy”. The controversy has shone a spotlight on the broader issue of sexism in science but has not yet led to specific changes at other UK universities, say academics.

“His comments will from now on make it far easier for everyone in academia to comprehend that what we say and the way it is interpreted by others, not how we wanted it to be interpreted, are paramount,” says Alastair Edge, who chairs the physics department’s diversity and equality committee at the University of Durham, UK. Existing staff guidelines at UCL highlight this point and would have contributed to the decisions the university made, he adds. “In my personal opinion, had a Durham scientist said equally unreconstructed nonsense then I hope he or she would have been treated similarly.”

Michèle Clarke at the University of Nottingham, UK, who is chair of its staff equality and diversity advisory group, says that although the Tim Hunt affair was unfortunate, it hasn’t changed the group’s views or procedures. These already include training and awareness-raising, she notes

Discussion at a training event for senior women seeking career progression, which happened around the time of Hunt’s remarks, “elicited some amused and amazed comments” but no calls for direct action, Clarke says. “I think we all hope those attitudes are beginning to die out with the ‘old guard’.”

Hunt’s comments have highlighted the issue of the underrepresentation of women in science in the mainstream media, says Jane Norman, who is vice-principal of equality and diversity at the University of Edinburgh, UK, and a researcher in maternal and foetal health. But the university was already working hard in this area with a vareity of measures, she says. These include targeting funds to stimulate research by women returning from maternity leave, and by training senior staff and selection panel members about ‘unconscious bias’ — a well-documented psychological effect exhibited by most people. Over the past two years, the university has seen a reduction in stereotyping and unconscious bias among those attending the training, says Norman.

Durham University engineer Karen Johnson says that she has faced “great difficulty” in engaging students with issues of gender inequality, “maybe because they haven’t experienced any sexism in their lives yet”.

Johnson plans to introduce a new kind of equality training for the department’s next intake of undergraduates and PhD students. Each will receive a copy of the book Lean In, by Facebook chief operating officer Sheryl Sandberg, and write an essay based on it. Johnson explains: “We don’t have the resources to train all our students in awareness of issues like unconscious bias, and the fact that we’re all sexist – male and female – a little bit.”

Though she recognizes the criticism that the book downplays systematic gender bias in favour of encouraging women to self-promote, Johnson was personally inspired by the book. “It points at something that’s contentious but a real issue, that [a lack of] confidence can stop women from putting themselves forward.”

Nature doi:10.1038/nature.2015.17956  Science Daily  Original web page at Science Daily


More transparency needed in science research, experts say

While transparency, openness and reproducibility are readily recognized as vital features of science and embraced by scientists as a norm and value in their work, a growing body of evidence suggests that those qualities are not necessarily evident today. Scientists have now announced guidelines to further strengthen transparency and reproducibility practices in science research reporting.

An international group of academic leaders, journal editors and funding-agency representatives and disciplinary leaders, including Rick Wilson, the Herbert S. Autrey Chair of Political Science and professor of statistics and psychology at Rice University, has announced guidelines to further strengthen transparency and reproducibility practices in science research reporting. The group, the Transparency and Openness Promotion (TOP) Committee at the Center for Open Science in Charlottesville, Va., outlined its new guidelines in a story published in this week’s edition of the journal Science.

While transparency, openness and reproducibility are readily recognized as vital features of science and embraced by scientists as a norm and value in their work, a growing body of evidence suggests that those qualities are not necessarily evident today.

“A likely culprit for this disconnect is an academic reward system that insufficiently incentivizes open practices,” Wilson said. “In the present reward system, the emphasis on innovation undermines practices that support openness. Too often, publication requirements — whether actual or perceived — fail to encourage transparent, open and reproducible science.”

TOP’s objective is to translate scientific norms and values into concrete actions and change the current incentive structures to drive researchers’ behavior toward more openness. “We know the disciplines differ in what is emphasized, so we sought to produce guidelines that focus on what is shared across disciplines,” Wilson said.

Each of eight standards has three levels of adoption in the TOP guidelines; each moves scientific communication toward greater openness, according to the article in Science. These standards are modular, facilitating adoption in whole or in part. However, they also complement each other; commitment to one standard may facilitate adoption of others.

The standards include citation standards for journals, data transparency, analytic methods (code) transparency, research materials transparency, design and analysis transparency, preregistration of studies, preregistration of analysis plans and replication.

Two standards reward researchers for the time and effort they have spent engaging in open practices. Citation standards extend current article citation norms to data, code and research materials. Regular and rigorous citation of these materials credits them as original intellectual contributions. Replication standards recognize the value of replication for independent verification of research results and identify the conditions under which replication studies will be published in the journal.

Four of the standards describe what openness means across the scientific process so that research can be reproduced and evaluated. Reproducibility increases confidence in findings and also allows scholars to learn more about what results mean. Design standards increase transparency about the research process and reduce vague or incomplete reporting of the methodology. Standards for research materials encourage the provision of all elements of that methodology, and data-sharing standards give authors an incentive to make data available in trusted repositories.

The final two standards address the values resulting from preregistration. Standards for preregistration of studies facilitate the discovery of research, even unpublished research, by ensuring that the existence of the study is recorded in a public registry. Preregistrations of analysis plans certify the distinction between confirmatory and exploratory research, or what is also called hypothesis-testing versus hypothesis-generating research. Making the distinction between confirmatory and exploratory methods transparent can enhance reproducibility.

“The guidelines are sensitive to concerns by both journals and researchers,” Wilson said. “For example, we encourage journals to state exceptions to sharing because of ethical issues, intellectual property concerns or availability of necessary resources. We encourage journals to pick and choose among the different levels and standards in order to define what they expect of the researchers.

“We acknowledge the variation in evolving norms about research transparency. Depending on the discipline or publishing format, some of the standards may not be relevant for a journal. Journal and publisher decisions can be based on many factors — including their readiness to adopt modest to stronger transparency standards for authors, internal journal operations and disciplinary norms and expectations,” Wilson said.

The present version of the guidelines is not the last word on standards for openness in science, according to the report. “As with any research enterprise, the available empirical evidence will expand with application and use of these guidelines,” the TOP Committee wrote. “To reflect this evolutionary process, the guidelines are accompanied by a version number and will be improved as experience with them accumulates.”  Science Daily  Original web page at Science Daily


US Congress moves to block human-embryo editing

The US House of Representatives is wading into the debate over whether human embryos should be modified to have heritable changes. Its fiscal year 2016 spending bill for the US Food and Drug Administration (FDA) would prohibit the agency from spending money to evaluate research or clinical applications for such products.

In an unusual twist, the bill — which was introduced on 17 June — would also direct the FDA to create a committee that includes religious experts to review a forthcoming report from the US Institute of Medicine (IOM). That IOM analysis, on the ethics of creating embryos with three genetic parents, was commissioned by the FDA.

The House legislation comes at a time of intense debate on such matters, sparked by the announcement in April that researchers in China had edited the genomes of human embryos. The US National Institutes of Health (NIH) moved quickly to remind the public that a 1996 law prevents the federal government from funding work that destroys human embryos or creates them for research purposes.

Privately funded research to edit the human germline remains legal in the United States. But the pending House bill seeks to make it harder to test embryo-editing in clinical trials. A provision in the legislation would prevent the FDA from using federal funds to evaluate or permit treatments that involve viable embryos with heritable genetic modifications, or sperm or eggs that could be used to create such an embryo.

“This step seems dumb — or ill-advised,” says Hank Greely, a bioethicist at Stanford University in California. It may also be premature, since the FDA has not shown any indication that it would approve such research. And such a ban would not apply to the type of research that the Chinese scientists performed, because it did not involve viable embryos.

Moreover, the provision — as it stands — could backfire. Applications to the FDA to investigate a new drug are approved automatically unless the agency moves to block them. But Patricia Zettler, a law professor at Georgia State University in Atlanta and a former FDA attorney, says that blocking an application would require the use of public funds — which the House bill would prohibit.

Greely suspects that the Republican majority in Congress “is trying to throw a (cheap) bone to some of its supporters; regrettable (to me) but not important”. The House Appropriations Committee, which drafted the FDA spending bill, did not respond to requests for comment.

Although the House bill has been approved by a subcommittee, it would need to win approval from the full House, the US Senate and US President Barack Obama to become law. The provisions that would affect the FDA are contained in a report that accompanies the bill and has not yet been publicly released.

The FDA has been considering the implications of modifying human embryos for some time, and last year, it commissioned an IOM report on the ethical and social implications of “three-parent embryos”. Such embryos could help women to avoid passing genetic diseases to their offspring, by replacing faulty mitochondria in a mother’s eggs with healthy mitochondria from another woman.

The FDA appears to be waiting for the IOM’s peer-reviewed analysis, due later this year, before deciding whether to permit clinical trials on mitochondrial replacement.

The House legislation calls for an additional layer of review. It would direct the FDA to establish “an independent panel of experts, including those from faith-based institutions with expertise on bioethics and faith-based medical associations” to review the IOM report once it is released. The panel would have 30 days to evaluate the report and provide its own recommendations to the House Appropriations Committee.

William Kearney, a spokesman for the IOM’s parent organization, the US National Academy of Sciences (NAS), declines to comment on the House bill. But he says that the NAS has occasionally included religious experts on its committees when appropriate.  “We always strive to balance our committees with the expertise necessarily to carry out the study in a scientific manner in order to produce an evidence-based report,” he says.

In fact, the IOM committee evaluating mitochondrial transfer includes a professor of religious studies, James Childress, from the University of Virginia in Charlottesville. But experts who have served on committees convened by the IOM or its parent organization, the US National Academy of Sciences, say that the House bill’s provisions are highly unusual.

“It’s hard for me to understand what Congress thinks can be added by another layer of taxpayer-supported ethics reflection,” says Jonathan Moreno, a bioethicist at the University of Pennsylvania in Philadelphia. “You don’t have to be a faith-based bioethicist to recognize that there’s some global responsibility for modifying the human germline.”

Zettler says that Congress  frequently orders the agency to include certain types of experts on independent advisory committees. But Zettler is not aware of any previous situations where lawmakers mandated the participation of religious experts, and she says the purpose of such a requirement is unclear.

The FDA is charged with evaluating the safety and efficacy of medical products, but it is not allowed to take ethical and social implications of research into account — except to ensure that human subjects are protected in clinical trials.

Moreno worries that if the House bill becomes law, it could set a precedent for Congress to require other agencies to second-guess the National Academy of Sciences. “It is a signal that the culture wars aren’t dead,” he says.

Nature doi:10.1038/nature.2015.17858  Nature  Original web page at Nature