New details emerge on retracted STAP papers

Posted by Davide Castelvecchi | Categories: ,

Posted on behalf of David Cyranoski.

New leaked emails from the research editors of Science and Nature provide additional insight into the saga of the STAP papers, which Nature published in January and retracted in July.

The papers had promised new, simpler ways to produce stem cells by applying stress to cells taken from a patient’s tissues. But no other lab was able to reproduce the results, and experts pointed to several problems and inconsistencies in the papers. In April,  first author Haruko Obokata of the RIKEN Center for Developmental Biology in Kobe, Japan, was declared guilty of scientific misconduct; the controversy later took a tragic turn as another co-author, Yoshiki Sasai, committed suicide on 5 August.

An investigative report into the papers, released in May, revealed that a previous version of the work had been rejected by Nature, Cell, and Science in 2012, before being resubmitted and accepted by Nature. (Nature’s news and comment team is editorially independent of its research editorial team.)

That report gave details from the Science referees who pointed out that one figure had been “reconstructed” in a way at odds with normal scientific practice and another one had a “suspiciously sharp” band (see ‘Misconduct verdict stands for Japanese stem-cell researcher‘).

The blog Retraction Watch posted the full comments of three referees who reviewed the paper for Science on 10 September.

The reviews include a modicum of support, but overall the paper is panned by all three. Reviewer number 2 notes, “Unfortunately, the paper presents only a superficial description of many critical aspects of the work,” before launching into 21 points that “need to be addressed”, ranging from seemingly sloppy mistakes to fundamental problems with the data.

Reviewer 3 noted, “If these results are repeatable, a paradigm of developmental biology would be changed.”

The manuscript itself is not available, so it is impossible to know exactly how similar the rejected Science manuscript is to the version that was eventually published in Nature.

When the committee initially brought the problems in the Science paper to her attention, Obokata defended herself by saying that the published Nature paper had main conclusions that differed from those in the rejected Science manuscript, and she refused to show the latter to the investigative committee.

The cells in that manuscript were called stress-altered somatic cells (SAC) cells, whereas those in the paper that was eventually published bore the now-infamous name: stimulus triggered acquisition of pluripotency, or STAP. But judging from the reviewers comments, the STAP cells and SAC cells seem to be quite similar.

Nature‘s research editors do not comment on their correspondence with authors, but on 11 September Science revealed new emails said to have been exchanged between Obokata and a Nature editor in April 2013.  Those emails allegedly quote Nature‘s reviewers as having many reservations, similar to those expressed by Science‘s reviewers, and unanimously recommending that the paper be rejected — which Nature did. The Nature editor did leave open the possibility of publishing the paper if the problems were solved. About nine months later, in December, Nature accepted both papers.

Ozone recovery helped by warming climate

Posted by Matthew Crenson | Categories:

Posted on behalf of Mark Zastrow.

The ozone layer appears to be continuing on the path to recovery, an international panel of 300 scientists reports today. Atmospheric levels of the chemicals that destroy ozone have now declined by 10–15% since peaking in 2000, a sign of improving health.

The current ozone hole over Antarctica is shown here in blue.

The current ozone hole over Antarctica is shown here in blue.

NASA

A report released by a team from the United Nations Environmental Programme (UNEP) and the World Meteorological Organization documents a clear trend of ozone increasing in the upper stratosphere, approximately 42 kilometres high, at a rate of over 3% per decade. The data also suggest that the total amount of ozone in the atmosphere is growing, but they are not yet conclusive.

Models estimate that levels of ozone-depleting chemicals will fall to their 1980 levels by 2030, and the total amount of ozone will rebound soon after, preventing an estimated 2 million cases of skin cancer.

Ozone-destroying industrial chemicals known as chlorofluorocarbons (CFCs), once widespread in air conditioners and aerosol cans, cause the annual ‘hole’ in the ozone layer that forms every year in the Southern Hemisphere’s spring. CFCs were banned worldwide by the Montreal Protocol in 1987, which was ratified by all UN member nations.

However, like CFCs, the chemicals that replaced them — hydrofluorocarbons (HFCs) — are potent greenhouse gases. The report recommends switching to alternatives with less greenhouse potential, such as hydrofluoro-olefins.

In fact, ozone levels are linked tightly to climate. The report finds that half of the ozone recovery is due to greenhouse gases’ changing the temperature structure of the atmosphere. By trapping heat in the troposphere, the gases let less heat escape to the stratosphere — and cooler temperatures enable ozone production, explains Steve Montzka, an atmospheric scientist at the US National Oceanic and Atmospheric Administration in Boulder, Colorado.

“I think the great message is that if we act now in understanding the connection between ozone and climate action we can avoid a major problem,” said Achim Steiner, UNEP’s executive director.

Team members hope that the success of the Montreal Protocol will encourage similar action on the reduction of greenhouse gases. “There is tremendous scope for achieving further changes,” Steiner said.

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Economist and lawyer nominated for key science-related EU posts

Posted by alison abbott | Categories:

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Carlos Moedas
Courtesy EC

Portughese economist Carlos Moedas has been nominated as new European Union commissioner for research, science and innovation. Spain’s Miguel Arias Cañete, a lawyer, has been nominated as commissioner for energy and climate change.

Commission president Jean-Claude Junker announced the two nominations, along with those of the 26 other commissioners, on 10 September.

The commission has to be approved by the European Parliament before taking office on 1 November, and this may not be a shoo-in. In 2007 the Parliament exercised this veto right because it disapproved of one proposed commissioner, and the commission president had to submit a new line-up.

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Miguel Arias Cañete
Courtesy EC

Arias Cañete’s appointment in particular could prove controversial. Parliament might ask him to prove that he is not sexist — despite his widely publicized comments during a debate earlier this year in which he expressed his difficulty in politically challenging a woman for fear of “cornering” someone defenceless.

The new research commission will oversee the progress of the European Union’s €80-billion (US$103-billion) Horizon 2020 research programme, which launched this year.

 

Digital mapping uncovers ‘super henge’ that dwarfed Stonehenge

Posted by Ewen Callaway | Categories: ,

Stonehenge_new_monuments_distribution

Ludwig Boltzmann Institute

Every summer solstice, tens of thousands of people throng to Stonehenge, creating a festival-like atmosphere at the 4,400-year-old stone monument. For the 2015 solstice, they will have a bit more room to spread out. A just-completed four-year project to map the vicinity of Stonehenge reveals a sprawling complex that includes 17 newly discovered monuments and signs of a 1.5-kilometre-around ‘super henge’.

The digital map — made from high-resolution radar and magnetic and laser scans that accumulated several terabytes of data — shatters the picture of Stonehenge as a desolate and exclusive site that was visited by few, says Vincent Gaffney, an archaeologist at the University of Birmingham, UK, who co-led the effort.

Take the cursus, a 3-kilometre-long, 100-metre-wide ditch north of Stonehenge that was thought to act as barrier. The team’s mapping uncovered gaps in the cursus leading to Stonehenge, as well as several large pits, one of which would have been perfectly aligned with the setting solstice Sun. New magnetic and radar surveys of the Durrington Walls (which had been excavated before) uncovered more than 60 now-buried holes in which stones would have sat, and a few stones still buried.

“They look as they may have been pushed over. That’s a big prehistoric monument which we never knew anything about,” says Gaffney, who calls the structure a ‘super henge.’ His team will discuss the work at the British Science Festival this week, and they plan to present it to the institutions that manage the site. “I’m sure it will guide future excavations,” Gaffney says.

Arctic archaeologists find Franklin Expedition ship

Posted by Alexandra Witze | Categories: ,

Canadian archaeologists have found one of the Franklin Expedition’s ships — lost since the Arctic explorers famously disappeared in 1846 — off of King William Island in the Canadian Arctic. The ship is either the HMS Erebus or the HMS Terror, Prime Minister Stephen Harper announced on 9 September.

The HMS Terror was lost in the Arctic during the Franklin Expedition.

The HMS Terror was lost in the Arctic during the Franklin Expedition.

National Archives of Canada

The discovery comes in the sixth year of expeditions led by Parks Canada, which has scoured hundreds of square kilometres of ocean bottom in search of the Franklin ships. A remotely operated vehicle (ROV) deployed from Parks Canada’s 10-metre survey vessel Investigator made the discovery on 7 September.

Days earlier, archaeologists working on land reported finding an iron fitting from a Royal Navy ship. It was a major clue that the search team was in the right area, farther south than some had expected but in line with where Inuit had reported seeing a shipwreck in the nineteenth century.

The team found the ship’s remains using underwater sonar, controlled from on board the Canadian Coast Guard icebreaker Sir Wilfred Laurier. A Toronto Star journalist aboard the vessel reported that when archaeologist Ryan Harris saw the sonar feed, he raised two open hands “like a winning sprinter”.

This iron fitting could be a clue to the location of the lost Franklin Expedition.

Government of Nunavut

The ROV, a Saab Seaeye Falcon, carries a high-definition video camera that captured the wreck, resting with its bottom on the sea floor. Parks Canada says it is certain the ship belongs to the Franklin expedition, given its design.

Sir John Franklin left England in May 1845 with 128 other men in the Erebus and Terror, aiming to find and explore a Northwest Passage. Both ships vanished. In 1859, searchers found a message in a cairn on King William Island reporting that Franklin and some of the crew had died while the ships were trapped in ice. The remaining men eventually abandoned ship and began walking south. Studies of bodies of various crew members, found in graves scattered across several islands, suggest that lead poisoning may have contributed to their deaths. Cut marks on some bones suggest cannibalism, again supporting Inuit accounts.

The Canadian government funded the bulk of the search along with several private partners. In recent years, oceanographers from Arctic nations have been mapping assiduously in the far north to help establish sovereignty over possible future oil and gas exploration in the region.

Even today, ships can run into trouble in the area. On 3 September, the Arctic Research Foundation’s  vessel Martin Bergmann, which was taking part in the search, hit a previously unknown shoal and became grounded for about two-and-a-half hours.

Rise in greenhouse-gas concentrations continues at alarming rate

Posted by Quirin Schiermeier | Categories: ,

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A US atmospheric observatory in Barrow, Alaska, is part of a global network that monitors carbon-dioxide concentrations.
Credit: NOAA

The carbon dioxide concentration in the atmosphere increased in 2013 at the fastest rate in almost 30 years, spurring concerns about global warming ahead of a United Nations climate summit later this month.

According to the annual Greenhouse Gas Bulletin of the World Meteorological Organization (WMO), released on 9 September, the average amount of CO2 in the atmosphere reached 396.0 parts per million in 2013 — 2.9 parts per million above the 2012 level. This is the largest annual increase since 1984. Averaged over an entire year, the global annual CO2 concentration is now expected to pass the symbolic threshold of 400 parts per million in 2015 or 2016.

The report is based on observations from the WMO’s Global Atmosphere Watch network. Preliminary data suggest that reduced CO2 uptake by plants and soils might add to the worrying increase in atmospheric CO2 concentrations resulting from fossil fuel burning.

Atmospheric methane, the second most important long-lived greenhouse gas, also reached a new high of about 1,824 parts per billion last year, mostly due to increased emissions from cattle breeding, rice farming, fossil fuel mining, landfills and biomass burning.

Between 1990 and 2013, radiative forcing by long-lived greenhouse gases — the main cause of global warming — has increased by 34%, according to the WMO report.

The question remains, however, of why the rise in global mean temperatures near the surface has apparently slowed, after a series of exceptionally warm years in the 1990s. Scientists have suggested a number of possible explanations for the global warming pause. According to the latest hypothesis, regularly occurring changes in circulation patterns in the Atlantic and Southern Ocean may have caused an increased volume of relatively warm water to sink to the depth of the ocean, thus reducing the amount of ocean heat escaping to the atmosphere.

The world’s oceans take up one-fourth or so of CO2 emitted into the atmosphere. As emissions have been steadily rising for decades, the corresponding changes in ocean chemistry are dramatic: the current rate of ocean acidification seems to have been unprecedented in at least over the last 300 million years, according to an analysis included in the WMO report.

World leaders are set to discuss steps to reduce greenhouse gas emission at the United Nations climate summit on 23 September in New York.

Balzan prizes honour plant ecologist and mathematician

Posted by alison abbott | Categories: , ,

Plant ecologist G. David Tilman of the University of Minnesota in Saint Paul and mathematician Dennis Sullivan of the City University of New York are among the four winners of this year’s prestigious Balzan Prize. The announcement was made on 8 September.

The prize is awarded by the International Balzan Prize Foundation, based in Milan, Italy, and Zurich, Switzerland. Each year, the jury selects four different categories for the award. Each winner receives 750,000 Swiss francs (US$800,000) and must spend half of it on research projects carried out, preferably, by young scholars or scientists.

Tilman was recognized for contributions to theoretical and experimental plant ecology that have illuminated how plant communities are structured and interact with their environment.

Sullivan was recognized for his work in topology and the theory of dynamical systems, as well other fields of maths, including geometry, the theory of Kleinian groups, analysis and number theory.

The other 2014 winners were Mario Torelli of the University of Perugia, Italy, for classical archaeology, and Ian Hacking of the University of Toronto, Canada, for epistemology and philosophy of mind.

The categories for the 2015 prizes will be oceanography, astroparticle physics including neutrino and γ-ray observation, history of European art (1300–1700) and economic history.

Lasker Award goes to breast-cancer researcher

Posted by Lauren Morello | Categories: , ,

Posted on behalf of Mark Zastrow. 

The 2014 Albert Lasker Special Achievement Award has been awarded to the geneticist Mary-Claire King. King, of the University of Washington in Seattle, is the leader of the team that discovered the BRCA genes, mutations in which are linked to breast cancer. King’s team found that the 10% of women affected by such mutations have nearly an 80% chance of developing breast cancer. The rush to develop tests for the mutations triggered a legal dispute in the United States that ended with a US Supreme Court ruling prohibiting the patenting of naturally occurring genes.

King was also recognized for her contributions to human rights in developing DNA analysis to prove genetic relationships. These have have been used to find the ‘lost children’ of Argentina — who were kidnapped and separated from their biological families as infants — and to identify the remains of soldiers missing in action and of disaster victims.

Other winners of this year’s Lasker awards, often referred to as ‘the American Nobels’, include molecular biologists Kazutoshi Mori of Kyoto University in Japan and Peter Walter of the University of California in San Francisco, in the category of basic medical research. They independently uncovered how cells correct proteins that are improperly folded by activating the transcription of certain genes.

The winners for clinical medical research were neurologists Alim Louis Benabid of Joseph Fourier University in Grenoble, France, and Mahlon R. DeLong of the Emory University School of Medicine in Atlanta, Georgia, for their work in high-frequency deep-brain stimulation. By targeting an area of the brain involved in motor functions called the subthalamic nucleus, they found the technique could be used to treat those with Parkinson’s disease to alleviate tremors and motor problems.

NIH finds forgotten ricin during lab sweep

Posted by Lauren Morello | Categories: , ,

A laboratory sweep at the US National Institutes of Health (NIH) has turned up forgotten stores of the toxin ricin and four pathogens, according to a 5 September agency memo.

The agency undertook the search after discovering improperly stored vials of deadly smallpox virus in a refrigerator at its Bethesda, Maryland, campus in July. That news came just weeks after the US Centers for Disease Control and Prevention (CDC) said that employees at one of its labs in Atlanta, Georgia, were potentially exposed to anthrax because they did not follow established safety guidelines. And in March, CDC employees shipped samples of the dangerous H5N1 influenza virus to another government laboratory without taking proper precautions.

The NIH says that its lab-safety sweeps revealed small amounts of improperly stored ricin and pathogens that cause tularemia, plague, botulism and the tropical disease melioidosis. All five substances are classified as ‘select agents’ — pathogens and toxins that the US government considers to pose a severe threat to public health and safety.

The ricin was discovered in a historical sample collection dating from 1914 and may be 85–100 years old, the agency memo says.

“All of the agents were found in sealed and intact containers and there were no personnel exposures associated with the storage or discovery of these vials or samples,” NIH director Francis Collins said in the memo. Collins added that the agents were reported to the CDC and destroyed.

Meanwhile, the US Food and Drug Administration said on 5 September that it had found improperly stored samples of Staphylococcus enterotoxin, a pathogen that can cause food poisoning. The discovery was first reported by the Associated Press.

 

Australian gene-patent case dismissed

Posted by Heidi Ledford | Categories: , ,

An Australian federal court has thrown out a lawsuit challenging a patent on the cancer-associated gene BRCA1. The decision, issued 5 September, is the latest setback for patient advocates who argue that the patent limits genetic-testing options for Australian cancer patients.

The patent, held by Myriad Genetics of Salt Lake City, Utah, is used to protect a genetic test for mutations in BRCA1 that may enhance the risk of cancer, particularly breast and ovarian cancer.

The Australian case is an echo of a previous legal challenge to patents on BRCA1 and BRCA2 in the United States. That case culminated last year in a unanimous, landmark Supreme Court decision that overturned decades of practice by the US Patent and Trademark Office, invalidating all patents on naturally occurring human genes. The implications of that decision for other US patents on natural products are still being worked out.

The Australian case began in 2010, and was brought by breast-cancer survivor Yvonne D’Arcy and a patient advocacy group, Cancer Voices Australia. But a federal judge dismissed the case on 15 February 2013, arguing that the patent’s reference to isolated DNA was enough to establish that it claimed a “manner of manufacture”, rendering the patent valid under Australian patent law. D’Arcy filed an appeal, which culminated in a second dismissal yesterday.

But that action may not spell the end of the patent challenge. In the wake of the decision, the non-governmental organization Cancer Council Australia called for legislative changes to prevent monopolies on diagnostic tests.

And D’Arcy may yet appeal today’s ruling.  “The judgment has significance for access to genetic testing, research and the development of treatments for diseases,” wrote Rebecca Gilsenan, principal lawyer at the firm Maurice Blackburn, which represented D’Arcy, in a statement. “We will look at appealing the decision once we have considered the judgment in detail.”