Latest Articles Include:
- Credit where credit is due
- Nature 462(7275):825 (2009)
A proposed author ID system is gaining widespread support, and could help lay the foundation for an academic-reward system less heavily tied to publications and citations. - Mind the gap
- Nature 462(7275):825 (2009)
It will take time to assess the value of fresh approaches to science and technology studies. - A class of their own
- Nature 462(7275):826 (2009)
The Japanese winners of Nature's mentoring awards have the universal qualities of outstanding advisers. - Primatology: Monkey talk
- Nature 462(7275):828 (2009)
- Physical chemistry: Dual-aspect particles
- Nature 462(7275):828 (2009)
- Ecology: Reef regulation
- Nature 462(7275):828 (2009)
- Cancer biology: Tumours hate company
- Nature 462(7275):828 (2009)
- Geology: Bubble batholiths
- Nature 462(7275):828 (2009)
- Population genetics: Asia's common origin
- Nature 462(7275):828 (2009)
- Chemistry: One-hit wonder
- Nature 462(7275):829 (2009)
- Palaeontology: Dawn of the anomodonts
- Nature 462(7275):829 (2009)
- Psychology: Personality versus mood
- Nature 462(7275):829 (2009)
- Epidemiology: Malaria's mark
- Nature 462(7275):829 (2009)
- Correction
- Nature 462(7275):829 (2009)
- Journal club
- Nature 462(7275):829 (2009)
- News briefing: 17 December 2009
- Nature 462(7275):830 (2009)
The week in science This article is best viewed as a PDF Policy|Business|Events|Research|Business watch|The week ahead|Number crunch|News maker The British government has announced plans for a national space agency. The agency will replace the British National Space Centre, which was set up by the government in 1985 to coordinate space research. The new agency will consolidate the efforts of six government departments, three science and technology funding bodies and the Met Office. But it is not yet clear whether it will have independent control of funds for space activities. The Consultative Group on International Agricultural Research voted for wide-reaching organizational changes on 8 December. The public–private partnership, which oversees 15 research centres and supports some 8,000 scientists and staff across the world, has established thematic science programmes and set up a trust fund to manage US$500 million in annual donations. Australia has lifted a 5-year ban on clinical trials in which animal cells, tissues or organs are transplanted into humans. The National Health and Medical Research Council said on 10 December that it was satisfied the risks of transmitting animal viruses in this way were low, and that trials could proceed once regulatory and monitoring frameworks have been established. The United States, Russia, European Union and China are among many places that already allow human xenotransplantation trials, the council said. The United States announced on 9 December that it would try to revitalize the Biological Weapons Convention (BWC) that bans the development, production and stockpiling of such weapons. Ellen Tauscher, undersecretary of state for arms control, said that the country would urge all nations to sign the BWC, but rejected efforts to develop a system to verify that the convention was being obeyed. The treaty has foundered since the administration of former president George W. Bush broke with attempts to set up a compliance scheme in 2001 (see Nature 414, 675; 2001). British scientists were rattled by the UK government's 2010 pre-budget report on 9 December, which called for a £600-million (US$975-million) reduction in spending on higher education, science and research for the period 2011–13. Details of the cutbacks were not specified — and the present Labour government may not win next year's general election — but their mention reminded researchers that painful spending cuts almost certainly lie in wait. Five years after the blockbuster painkiller Vioxx was withdrawn after being linked to heart attack and stroke, the US Food and Drug Administration (FDA) is still not taking adequate steps to ensure the safety of marketed drugs, says a report by the Government Accountability Office (GAO). The report, made public on 9 December, checked the agency's progress in enacting recommendations from a 2006 GAO report. It found that the FDA had failed to transfer sufficient authority for post-market drug safety to the Office of Surveillance and Epidemiology and away from the office that approves new drugs. B. STRONG/REUTERS After being derailed by protests from developing countries, the United Nations climate talks in Copenhagen are back to something resembling order. As Nature went to press, government ministers led by conference president Connie Hedegaard and Yvo de Boer, executive secretary of the United Nations Framework Convention on Climate Change (both pictured), were preparing a negotiating text for some 130 heads of state. But the architecture of any possible agreement was still unclear, and a deep divide remained between developed and developing nations. More than 45,000 delegates, journalists and lobbyists had registered to attend — three times the capacity of the Bella Center, where the talks are being held. For daily updates, see "nature.com/roadtocopenhagen":nature.com/roadtocopenhagen. An innovative geothermal project that would drill deep into the Earth to extract energy from hot rocks has been shut down. On 10 December, public authorities in Basel, Switzerland, closed a private geothermal drilling project led by Geopower Basel, after a government study found that the small earthquakes it generated would cause too much economic damage. The project had been on hold since 2006. See page 848 for more. The World Bank announced on 9 December that it planned US$5.6 billion of financing to speed up the deployment of concentrated solar power in North Africa and the Middle East. Its Clean Technology Fund would spend $750 million on 11 projects in Algeria, Egypt, Jordan, Morocco and Tunisia, and $4.85 billion would be mobilized from other sources, including donors and commercial debt. The investment will create around a gigawatt of solar capacity over the next five years, the World Bank says — a sizeable addition to the 6–7 gigawatts of global projects in the pipeline by the end of 2008. Click for larger image Makers of light-emitting diodes (LEDs) are preparing to increase capacity in response to growing demand. LED suppliers were operating at 30% of capacity earlier this year, but are now producing at full stretch, says Emma Ritch, an analyst at business-information firm Cleantech Group in San Francisco, California. Among the companies that have raised hundreds of millions of dollars this year to expand LED facilities are Cree, based in Durham, North Carolina; Seoul Semiconductor, which supplies firms such as Samsung and LG with LEDs for televisions; and Epistar in Hsinchu, Taiwan. Market forecaster Strategies Unlimited in Mountain View, California, says that the market for high-brightness LEDs will almost triple in five years (see graphic). Vrinda Bhandarkar, an analyst there, says demand for LEDs in mobile phones has peaked, but future hot areas include backlights for better-contrast, thinner computer and television displays. General lighting will follow: LEDs are now bright enough to illuminate streets, but still costly (see Nature 459, 312–314; 2009). Capacity may outpace demand by 2011, says Cleantech, when prices could crash and the herd of more than 500 LED-makers could thin out. With a hobbled endowment, Harvard University in Cambridge, Massachusetts, announced on 10 December that it would halt construction of the US$1-billion science complex on its Allston campus early next year once the foundations are complete. This brings to a standstill the university's ambitious expansion plans (see Nature 454 , 686–689; 2008). Instead, the university said it would shift focus towards improving and leasing vacant Allston properties. It is not clear when building work might begin again; the university is reviewing financing options. The University of Alabama at Birmingham has asked for twelve entries to be removed from the Protein Data Bank. This follows the recommendation of an expert committee that has been looking into allegations of suspect data. The protein structures are cited in hundreds of papers. Last week, The Journal of Biological Chemistry retracted a paper containing one of the structures. A sea-floor observatory in the northeast Pacific Ocean officially went live on 8 December, promising free access via the Internet to its live camera feeds and to data on marine life off British Columbia. The Can$100-million (US$95-million) NEPTUNE Canada project (http://neptunecanada.ca) will study biological, physical and geological processes up to 300 kilometres offshore, using instruments and sensors connected by a cable that runs electricity and fibre-optics in an 800-kilometre undersea loop. A "tremendous increase in funding" for malaria has shown positive results, the World Health Organization (WHO) said on 15 December, as it published its World Malaria Report 2009. US$1.7 billion was committed in 2009, compared with $730 million in 2006, allowing greater distribution of insecticide-treated bed nets and artemisinin-based therapies. From 2000 to 2008, malaria cases have been cut by at least 50% in more than one-third of malarious countries. But the WHO says that $5 billion is still required annually, and resistance to artemisinin remains a threat. Scientists at the Australian Synchrotron in Melbourne voted last week to again work only between 9 a.m. and 5 p.m. in renewed protest at the facility's governing board. The synchrotron is undergoing maintenance over the Christmas break, but if the limited-hours schedule continues in 2010, it will cripple research projects in a facility usually booked around-the-clock. Five members of the synchrotron's scientific advisory committee also resigned last week (see Nature 462, 706–707; 2009). The governing council of CERN meets. Its agenda includes possible expansion of the organization's international membership — Israel and Turkey are among those who have applied to join. → go.nature.com/jk7A9T The United Nations Climate Change Conference in Copenhagen comes to an end. → http://en.cop15.dk South Korea's first icebreaker research ship, ARAON, is scheduled to set sail for the Antarctic on a three-month expedition. → www.kopri.re.kr/index_eng.jsp NASA/Moore, VAFB WISE The Wide-Field Infrared Survey Explorer, a space telescope, was launched by NASA on 14 December. The average investment return in the 2009 financial year from more than 500 US college and university endowments. Source: NACUBO-Commonfund Study of Endowments There are currently no comments. - Budget win for climate probe
- Nature 462(7275):832 (2009)
The US Congress is ratcheting up demands for NASA to launch Earth-monitoring satellites that could help to verify the emissions targets currently being debated in Copenhagen. In a US$447-billion spending bill approved on 13 December (see Table 1), lawmakers told NASA to spend $50 million in fiscal year 2010 on a replacement for the Orbiting Carbon Observatory (OCO), which crashed into the ocean near Antarctica in February after a rocket failure. - Royal Institution faces cash crisis
- Nature 462(7275):833 (2009)
Overspend threatens to curtail science outreach activities. The Royal Institution of Great Britain, once home to historical figures such as Michael Faraday and Lawrence Bragg, has survived since 1799 and is the world's oldest scientific research organization. But it now faces a financial crisis that could bring its 200-year reign to an end. The institute offers a rare blend of research and outreach, says Richard Catlow, who headed its Davy Faraday Research Laboratory from 1998 to 2007. In the United Kingdom, it is well known for its annual Christmas lectures, a series of high-profile lectures aimed at the general public that are televised nationwide. "Discussions about the role of the director of the Royal Institution are currently taking place." But it depends on fundraising and membership for money, and has faced financial difficulties in the past. In 2004 the institution ran up a deficit of £400,000 (US$650,000), according to a 2005 financial statement filed with the Charities Commission, which regulates charities in England and Wales. In 2006, its director, Susan Greenfield, a University of Oxford neuroscientist known for her high media profile, began a £22-million refurbishment of its headquarters in central London, intended to make it a more attractive venue to hire out for conferences and public events. To help pay for the work, the research staff was cut from 60 to just 15, drawing criticism from some scientists (see Nature 453, 568–569; 2008). The project also ran behind schedule and over budget. Fundraising was hampered by the recession, and the institution was forced to dip into its endowment and other 'restricted funds'. By September 2008, it had spent £3.2 million designated for other activities, including the Christmas lecture programme, according to the latest financial statement to the Charities Commission, dated 29 September 2009. Last week, The Guardian newspaper reported that Greenfield was being asked to take a pay cut — and reduce the scope of her role — to help make up for the shortfall. The institution declined to comment to Nature, saying only that "discussions about the role of the director of the Royal Institution are currently taking place between the board of trustees and the current director". Chris Rofe, a former administrator at London's Science Museum and the Millennium Dome, was brought in this April to oversee fundraising and financial accountability. The Charities Commission audit acknowledged that a plan was in place to see the organization through to late 2011 and gradually repay the money spent from restricted funds. But it added: "By their very nature, there is a significant uncertainty as to whether these projections will be achieved." There are currently no comments. - China celebrates panda genome
- Nature 462(7275):833 (2009)
There are currently no comments. - Satellites beam in biomass estimates
- Nature 462(7275):834 (2009)
Additional detail could help bring woodland into a future climate treaty. Click for full image Whatever agreement emerges from the climate meeting in Copenhagen, many expect that it will include a mechanism allowing rich nations to offset their emissions by paying poorer countries to protect their forests — and the carbon they contain. But just how much carbon is at stake? Researchers at the meeting have given their best answer yet: the first satellite-based estimates of the biomass contained in the world's tropical forests. Current biomass estimates for the tropics are based on data gathered by the Food and Agriculture Organization of the United Nations (FAO), and their quality varies greatly from country to country. As a result, baseline figures for biomass are some of the biggest uncertainties in calculating emissions from deforestation and forest degradation, recently estimated to be around 15% of global carbon emissions (G. R. van der Werf et al. Nature Geosci. 2, 737–738; 2009). The latest assessments, presented at Copenhagen, harness data from multiple satellites as well as thousands of ground plots, and should help governments and other scientists to estimate how much carbon is locked within trees, vegetation and soils on a given patch of land — rather than relying on rough averages that are calculated across a forest. Sassan Saatchi, an environmental scientist at NASA's Jet Propulsion Laboratory in Pasadena, California, worked on one study with researchers at the carbon consulting firm Winrock International in Arlington, Virginia. He says that their preliminary calculations (see map) accord well with previous estimates. South America comes in with about 145 gigatonnes of carbon in vegetation and soils, about 26% higher than what has been reported by the Intergovernmental Panel on Climate Change (IPCC). The figures for Africa (51 gigatonnes) and south Asia (46 gigatonnes) are about the same as the IPCC figures. A question of scale But Saatchi says that the study provides additional information about biomass levels at regional and national levels. "You cannot really nail down this problem unless you have the distribution," he says. "You need to know how biomass is distributed and how it's changing over time, almost everywhere, with some resolution and accuracy." Funded in part by the World Bank, the work provides a snapshot at 1-kilometre resolution of tropical forests as they were in 2000, when most of the satellite data were collected, as well as more recent deforestation trends. Also at Copenhagen, researchers at the Woods Hole Research Center in Massachusetts presented another pan-tropical biomass assessment, which had a resolution of 500 metres. Like the Winrock study, it includes spectral data from NASA satellites as well as laser measurements of forest canopy height from an instrument on NASA's Ice, Cloud, and land Elevation Satellite (ICESat) that was designed to study polar ice caps. The two teams have yet to compare results. Richard Houghton, a biomass expert at Woods Hole, says that it is good news that multiple teams are tackling the big-picture question of tropical forest biomass. "We need a couple of independent estimates just to see how well they match," he says. "Anybody can make a map. If they differ, at least it identifies the areas that need further analysis." The next step, says Alexander Lotsch, a geographer at the World Bank in Washington DC, is to produce better estimates for carbon emissions from deforestation. He adds that Saatchi's research is still a "work in progress". ADVERTISEMENT Satellites can reliably track deforestation and, increasingly, small-scale logging. In Copenhagen, Greg Asner of the Carnegie Institution of Science in Stanford, California, and Google.org unveiled an online tool that allows tropical countries, beginning in South America, to map deforestation using an automated system to analyse satellite imagery. Asner has also developed a system for assessing biomass at finer resolution, which will be necessary if forests are going to be linked to international carbon markets. The new pan-tropical biomass maps from Saatchi and Woods Hole won't accomplish that goal, but they can provide scientists and policy-makers with a better understanding of carbon trends. For example, using a similar technique to Saatchi, Asner has found that deforestation in Brazil is moving into higher biomass areas in the interior of the forest. That suggests that emissions will probably rise over time on a per-hectare basis, offsetting some of the reductions in deforestation that Brazil aims to achieve in the coming decade (see Nature doi:10.1038/news.2009.752; 2009). - UK research funding proposal is 'irresponsible'
- Nature 462(7275):834 (2009)
Efforts to judge science on its practical returns often raise hackles, and Britain's latest plan is no exception. Some of the nation's leading universities have condemned a scheme that would assess the economic and social benefits of research to help determine who wins a large fraction of university funding, and more than 12,000 academics have signed a petition opposing the plan. There are currently no comments. - Hope for Japan's key projects
- Nature 462(7275):835 (2009)
Science council recommends funding for research threatened by budget cuts. Scientists are hoping that Japan's prime minister Yukio Hatoyama will avert proposed funding cuts.S. Kambayashi/AP When Japan's government changed hands in September for the first time in five decades, many Japanese people hoped that the newly powerful Democratic Party of Japan would revitalize their country. But the new government has since sent scientists on an emotional rollercoaster. In recent weeks, two cabinet-level bodies, both chaired by Prime Minister Yukio Hatoyama, have recommended drastically different financial futures for major scientific projects. One set of proposals, from the Government Revitalization Unit (GRU) that was set up in September to trim bureaucratic fat, recommends deep cuts for many key projects. These include a proposed next-generation supercomputer, the SPring-8 synchrotron in Harima, and Earth-science research. Scientists protested against those cuts (see Nature 462, 557; 2009). But last week came news of a separate recommendation from the Council for Science and Technology Policy (CSTP), Japan's highest science-policy-making body, proposing continued support for those projects and many others. For instance, the SPring-8 synchrotron and the Global Center of Excellence programmes — meant to strengthen doctoral research programmes — had each been headed for cuts of one-third or more, but the CSTP says they should be "prioritized and given the necessary resources". The next-generation supercomputer, which could have faced outright termination, should also be supported, it says. In Japan, where government decisions are usually made in bureaucratic back rooms and handed out as a harmonious consensus, the apparent contradiction is baffling researchers. "The decision-making process is unclear," says Tadashi Watanabe, project leader for the supercomputer. "It is very unsettling." Final budget decisions will be made later this month, but the prime minister has called the CSTP proposals "valuable opinions", and said that he would "work to ensure they were reflected in the final budget". Many think Hatoyama could be leaning towards accepting the CSTP's recommendations, perhaps because of the outcry over the proposed cuts. "It's too early to tell, but you can safely say that the top leadership did recognize the problem," says Atsushi Sunami, a science-policy expert at the National Graduate Institute for Policy Studies in Tokyo. The GRU was earlier criticized by scientists for recommending cuts without obtaining sufficient external input; projects were usually explained to the decision-making committee in a one-hour session by a bureaucrat. According to the Japanese media last week, the GRU plans to reopen debate on the supercomputer project in a public forum that will involve many scientists. ADVERTISEMENT For researchers, the near demise of beloved projects has been a wake-up call to the need to justify them to the public as well as to bureaucrats and external evaluators. Last week, leaders of the supercomputer project posted on their website a list of frequently asked questions on the project's significance, including: "What is great about the supercomputer?" Watanabe says the team doesn't yet have a long-term strategy for engaging the public, but he wants to emphasize that the supercomputer would have a major role in Japan's main research fields, including nanoscience, life science and environmental science. "We have to get that point across," he says. Sunami agrees that scientists in Japan can't take public support for granted. "Even if the budget for the supercomputer and SPring-8 are saved at a smaller scale," he says, "they have to engage with the public more." - Modellers claim wars are predictable
- Nature 462(7275):836 (2009)
Insurgent attacks follow a universal pattern of timing and casualties. Seemingly random attacks and a shadowy, mysterious enemy are the hallmarks of insurgent wars, such as those being fought in Afghanistan and Iraq. Many social scientists, as well as the military, hold that, like conventional civil wars, these conflicts can't be understood without considering local factors such as geography and politics. But a mathematical model published today in Nature (see Nature 462, 911–914; 2009) suggests that insurgencies have a common underlying pattern that may allow the timing of attacks and the number of casualties to be predicted. Could a model help to predict the number of casualties in conflicts such as that in Afghanistan?REUTERS "We found that the way in which humans do insurgent wars — that is, the number of casualties and the timing of events — is universal," says team leader Neil Johnson, a physicist at the University of Miami in Florida. "This changes the way we think insurgency works." Johnson and his colleagues argue that the pattern arises because insurgent wars lack a coherent command network and operate more as a "soup of groups", in which cells form and disband when they sense danger, then reform in different sizes and composition. The timing of attacks, the authors say, is driven by competition between insurgent groups for media attention. Johnson, who has presented preliminary versions of the work to the US military, says that the findings allow a glimpse into the heart of insurgency behaviour. "We can get a sense of what is going on and what might happen if we intervened in certain ways," he says. He is now working to predict how the insurgency in Afghanistan might respond to the influx of foreign troops recently announced by US President Barack Obama. Power law The researchers collected data on the timing of attacks and number of casualties from more than 54,000 events across nine insurgent wars, including those fought in Iraq between 2003 and 2008 and in Sierra Leone between 1994 and 2003. By plotting the distribution of the frequency and size of events, the team found that insurgent wars follow an approximate power law, in which the frequency of attacks decreases with increasing attack size to the power of 2.5. That means that for any insurgent war, an attack with 10 casualties is 316 times more likely to occur than one with 100 casualties (316 is 10 to the power of 2.5). "This is surprising because these wars are all fought in different terrains and under different circumstances," says Johnson. "It shows that there is something going on in the way these wars are fought that is common to all." To explain what was driving this common pattern, the researchers created a mathematical model that assumes that insurgent groups form and fragment when they sense danger, and strike in well-timed bursts to maximize their media exposure. The model gave results that resembled the power-law distribution of actual attacks. "They show a nice agreement between the data and their model, which is an important first step," says Aaron Clauset, who researches the mathematics of conflict at the Santa Fe Institute in New Mexico. But he and others question the model's assumptions, such as the number of insurgents in the conflict remaining roughly fixed over time. Clauset says that this idea does not match with other findings. The model also assumes that insurgent groups can freely break up then re-form. But Roy Lindelauf, who models terrorist networks at the Netherlands Defence Academy in Breda, notes that some insurgents in Iraq are battling each other as well as the coalition forces, and would therefore not merge into a single group. Lars-Erik Cederman, a researcher in international conflict at the Swiss Federal Institute of Technology in Zurich, adds that the model "has the potential to improve knowledge about warfare". But, he says, the authors "go too far in claiming they have found a universal underlying pattern" because their work includes only nine wars. Cederman, part of a group that regards insurgency as similar to general warfare, also says that although terrorist attacks can be driven by competition for media attention, it remains far from clear whether insurgencies have the same motive. ADVERTISEMENT "In human social systems, it is usually difficult to nail down what mechanism is behind an observed behavioural pattern," Clauset says. "There are almost always several equally plausible explanations that need to be considered." Johnson agrees that there could be other explanations for the pattern his group has found. But he says, "We have looked for many years for a model, and this is the only one we have found that explains the data." There are currently no comments. - Consent issue dogs stem-cell approval
- Nature 462(7275):837 (2009)
The US expansion of federal funding for human embryonic stem-cell research is being hampered by details in consent forms. Earlier this month, researchers celebrated the government's approval of funding for a broad variety of work on 13 stem-cell lines — the first approved under the policy announced by US President Barack Obama in March. There are currently no comments. - French research wins huge cash boost
- Nature 462(7275):838 (2009)
Universities in France are set to receive an €11-billion (US$16-billion) windfall from a government initiative intended to create an 'Ivy League' of research centres. The cash could help to reverse the decades-long neglect of the country's university system, although the bulk of the funding is likely to be channelled to just a few institutions. - Genetics: Watching science at work
- Nature 462(7275):840 (2009)
There was something of a chill in the air at Cardiff's City Hall in October, and not just because autumn was arriving. Social scientists, and some life scientists, were gathering there for the annual meeting of the Genomics Network, a programme run by Britain's Economic and Social Research Council (ESRC) to stimulate dialogue between the disciplines. There are currently no comments. -
- Nature 462(7275):843 (2009)
From her windowless fifth-floor office at the US National Institutes of Health in Bethesda, Maryland, Deanna Church has few distractions from the job that lies before her. On her computer sit 888 open 'tickets', or outstanding problems with the human genome sequence. There are currently no comments. - World view: Out of service
- Nature 462(7275):846 (2009)
The trappings of our civilization, from flushing the toilet to posting flip comments on Twitter, rely on a set of critical infrastructures. Many of these — water systems, transport links, electricity grids and generating plants — are ageing severely in developed countries. There are currently no comments. - Iran's scientists condemn instances of plagiarism
- Nature 462(7275):847 (2009)
The Iran chapter of the Academy of Sciences for the Developing World, speaking for the country's academic community, deplores the recent cases of alleged plagiarism by Iranian scientists (see Nature462, 704–705; 2009).Iran's scientific community is largely free of such unethical behaviour. - Opening dialogue between the recent and the long ago
- Nature 462(7275):847 (2009)
Douglas Erwin's call for palaeontologists to move towards a better understanding of diversity (Nature462, 282–283; 2009) should be extended. Palaeoecologists should move beyond purely descriptive objectives and towards a better understanding of ecosystem evolution. - UK defence group's structure could limit its usefulness
- Nature 462(7275):847 (2009)
You describe a new UK Ministry of Defence programme, in a News story (Nature462, 151; 2009), as being modelled on its US counterpart, the JASONs: this is an independent group of scientific advisers with high-level security clearance who have consulted for the US government on technical problems since the cold war. As a member of the JASONs for more than a decade, I note that several organizational aspects are crucially different. - Geothermal quake risks must be faced
- Nature 462(7275):848 (2009)
Discussion needs to be open about how exploitation of Earth's internal heat can produce earthquakes, says Domenico Giardini, so that the alternative-energy technology can be properly utilized. - A vision of the nanoscale
- Nature 462(7275):850 (2009)
A collaborative effort between a photographer and a chemist could show scientists how to make the small scale more intuitive, says Jeremy Baumberg. - Pop-up physics
- Nature 462(7275):851 (2009)
Finally up and running after a 14-month repair job, the Large Hadron Collider (LHC) at CERN, Europe's particle-physics laboratory near Geneva, Switzerland, is the most complex experiment in the world and took thousands of physicists well over a decade to assemble. So it is perhaps to inspire empathy that an LHC pop-up book asks its readers to spend a few minutes fumbling with pieces of paper that (eventually) fold into a model of the giant ATLAS detector, one of four detectors at the collider. - Trust puts the self on show
- Nature 462(7275):851 (2009)
A maze of corridors winds through featureless partition walls, adorned only by mirrors ranging from the exotic (Etruscan artefacts from the collection of Sigmund Freud) and the surreal (a digital 'time-lapse' mirror in which one's past movements materialize belatedly, like a ghost) to the banal (a cheap, plastic shaving mirror once belonging to actor Michael York). The corridors feed into eight rooms, each exploring an aspect of the knotty question of who we are. - Artistic dispatches on climate
- Nature 462(7275):852 (2009)
Photographs of our blue planet, taken during the 1968 Apollo 8 lunar mission, transformed our grasp of its fragile equilibrium. In 2009, we need similarly defining images to galvanize interventions to mitigate climate change. -
- Nature 462(7275):853 (2009)
The hunt for Earth-like worlds has taken a major step forward with the discovery of a planet only 2.7 times larger than Earth. Its mass and size are just as theorists would expect for a water-rich super-Earth. -
- Nature 462(7275):854 (2009)
When the replication machinery copies DNA, it must unwind the double helix in one direction while synthesis of one of the strands proceeds in the other. Making transient DNA loops may solve this directional dilemma. - 50 & 100 years ago
- Nature 462(7275):855 (2009)
A Survey of Soils in the Kongwa and Nachingwea Districts of Tanganyika. By B. -
- Nature 462(7275):856 (2009)
A merger of data and modelling using a probabilistic approach indicates that sea level was much higher during the last interglacial than it is now, providing telling clues about future ice-sheet responses to warming. -
- Nature 462(7275):857 (2009)
Tagging of DNA-damage-associated proteins by ubiquitin is key to coordinating the DNA-damage response. The ubiquitin-related protein SUMO is revealed as a crucial regulator of ubiquitylation in DNA repair. -
- Nature 462(7275):858 (2009)
Flat microstructures can be designed to spontaneously fold into three-dimensional shapes. Computer simulations of water droplets on sheets of carbon atoms now extend this concept to the nanometre scale. -
- Nature 462(7275):859 (2009)
Imaging of brain structures in living mice reveals that learning new tasks leads to persistent remodelling of synaptic structures, with each new skill associated with a small and unique assembly of new synapses. -
- Nature 462(7275):861 (2009)
An imaging technique has been demonstrated that blends the principles of conventional light and electron microscopy. It renders images with nanometre and femtosecond space-time resolution. -
- Nature 462(7275):862 (2009)
Leading anthropologist of his generation. - Probabilistic assessment of sea level during the last interglacial stage
- Nature 462(7275):863 (2009)
With polar temperatures ~3–5 kyr ago) serves as a partial analogue for 1–2 °C global warming scenarios. Geological records from several sites indicate that local sea levels during the last interglacial were higher than today, but because local sea levels differ from global sea level, accurately reconstructing past global sea level requires an integrated analysis of globally distributed data sets. Here we present an extensive compilation of local sea level indicators and a statistical approach for estimating global sea level, local sea levels, ice sheet volumes and their associated uncertainties. We find a 95% probability that global sea level peaked at least 6.6 m higher than today during the last interglacial; it is likely (67% probability) to have exceeded 8.0 m but is unlikely (33% probability) to have exceeded 9.4 m. When global sea level was close to its current level (≥-10 m), the millennial average rate of global sea level rise is very likel y to have exceeded 5.6 m kyr-1 but is unlikely to have exceeded 9.2 m kyr-1. Our analysis extends previous last interglacial sea level studies by integrating literature observations within a probabilistic framework that accounts for the physics of sea level change. The results highlight the long-term vulnerability of ice sheets to even relatively low levels of sustained global warming. - Parental origin of sequence variants associated with complex diseases
- Nature 462(7275):868 (2009)
Effects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined. For this we used a combination of genealogy and long-range phasing. We then focused on SNPs that associate with diseases and are within 500 kilobases of known imprinted genes. Seven independent SNP associations were examined. Five—one with breast cancer, one with basal-cell carcinoma and three with type 2 diabetes—have parental-origin-specific associations. These variants are located in two genomic regions, 11p15 and 7q32, each harbouring a cluster of imprinted genes. Furthermore, we observed a novel association between the SNP rs2334499 at 11p15 an d type 2 diabetes. Here the allele that confers risk when paternally inherited is protective when maternally transmitted. We identified a differentially methylated CTCF-binding site at 11p15 and demonstrated correlation of rs2334499 with decreased methylation of that site. - Growth landscape formed by perception and import of glucose in yeast
- Nature 462(7275):875 (2009)
An important challenge in systems biology is to quantitatively describe microbial growth using a few measurable parameters that capture the essence of this complex phenomenon. Two key events at the cell membrane—extracellular glucose sensing and uptake—initiate the budding yeast's growth on glucose. However, conventional growth models focus almost exclusively on glucose uptake. Here we present results from growth-rate experiments that cannot be explained by focusing on glucose uptake alone. By imposing a glucose uptake rate independent of the sensed extracellular glucose level, we show that despite increasing both the sensed glucose concentration and uptake rate, the cell's growth rate can decrease or even approach zero. We resolve this puzzle by showing that the interaction between glucose perception and import, not their individual actions, determines the central features of growth, and characterize this interaction using a quantitative model. Disrupting this interaction by knocking out two key glucose sensors significantly changes the cell's growth rate, yet uptake rates are unchanged. This is due to a decrease in burden that glucose perception places on the cells. Our work shows that glucose perception and import are separate and pivotal modules of yeast growth, the interaction of which can be precisely tuned and measured. - Transport mechanism of a bacterial homologue of glutamate transporters
- Nature 462(7275):880 (2009)
Glutamate transporters are integral membrane proteins that catalyse a thermodynamically uphill uptake of the neurotransmitter glutamate from the synaptic cleft into the cytoplasm of glia and neuronal cells by harnessing the energy of pre-existing electrochemical gradients of ions. Crucial to the reaction is the conformational transition of the transporters between outward and inward facing states, in which the substrate binding sites are accessible from the extracellular space and the cytoplasm, respectively. Here we describe the crystal structure of a double cysteine mutant of a glutamate transporter homologue from Pyrococcus horikoshii, GltPh, which is trapped in the inward facing state by cysteine crosslinking. Together with the previously determined crystal structures of GltPh in the outward facing state, the structure of the crosslinked mutant allows us to propose a molecular mechanism by which GltPh and, by analogy, mammalian glutamate transporters mediate sodium- coupled substrate uptake. - The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress
- Nature 462(7275):886 (2009)
Mutations in BRCA1 are associated with a high risk of breast and ovarian cancer. BRCA1 participates in the DNA damage response and acts as a ubiquitin ligase. However, its regulation remains poorly understood. Here we report that BRCA1 is modified by small ubiquitin-like modifier (SUMO) in response to genotoxic stress, and co-localizes at sites of DNA damage with SUMO1, SUMO2/3 and the SUMO-conjugating enzyme Ubc9. PIAS SUMO E3 ligases co-localize with and modulate SUMO modification of BRCA1, and are required for BRCA1 ubiquitin ligase activity in cells. In vitro SUMO modification of the BRCA1/BARD1 heterodimer greatly increases its ligase activity, identifying it as a SUMO-regulated ubiquitin ligase (SRUbL). Further, PIAS SUMO ligases are required for complete accumulation of double-stranded DNA (dsDNA) damage-repair proteins subsequent to RNF8 accrual, and for proficient double-strand break repair. These data demonstrate that the SUMOylation pathway plays a significan t role in mammalian DNA damage response. - A super-Earth transiting a nearby low-mass star
- Nature 462(7275):891 (2009)
A decade ago, the detection of the first1, 2 transiting extrasolar planet provided a direct constraint on its composition and opened the door to spectroscopic investigations of extrasolar planetary atmospheres3. Because such characterization studies are feasible only for transiting systems that are both nearby and for which the planet-to-star radius ratio is relatively large, nearby small stars have been surveyed intensively. Doppler studies4, 5, 6 and microlensing7 have uncovered a population of planets with minimum masses of 1.9–10 times the Earth's mass (M⊕), called super-Earths. The first constraint on the bulk composition of this novel class of planets was afforded by CoRoT-7b (refs 8, 9), but the distance and size of its star preclude atmospheric studies in the foreseeable future. Here we report observations of the transiting planet GJ 1214b, which has a mass of 6.55M⊕ and a radius 2.68 times Earth's radius (R⊕), indicating that it is intermediate in stature between Earth and the ice giants of the Solar System. We find that the planetary mass and radius are consistent with a composition of primarily water enshrouded by a hydrogen–helium envelope that is only 0.05% of the mass of the planet. The atmosphere is probably escaping hydrodynamically, indicating that it has undergone significant evolution during its history. The star is small and only 13 parsecs away, so the planetary atmosphere is amenable to study with current observatories. - A single sub-kilometre Kuiper belt object from a stellar occultation in archival data
- Nature 462(7275):895 (2009)
The Kuiper belt is a remnant of the primordial Solar System. Measurements of its size distribution constrain its accretion and collisional history, and the importance of material strength of Kuiper belt objects1, 2, 3, 4. Small, sub-kilometre-sized, Kuiper belt objects elude direct detection, but the signature of their occultations of background stars should be detectable5, 6, 7, 8, 9. Observations at both optical10 and X-ray11 wavelengths claim to have detected such occultations, but their implied abundances are inconsistent with each other and far exceed theoretical expectations. Here we report an analysis of archival data that reveals an occultation by a body with an approximately 500-metre radius at a distance of 45 astronomical units. The probability of this event arising from random statistical fluctuations within our data set is about two per cent. Our survey yields a surface density of Kuiper belt objects with radii exceeding 250 metres of , ruling out inferred surface densities from previous claimed detections by more than 5σ. The detection of only one event reveals a deficit of sub-kilometre-sized Kuiper belt objects compared to a population extrapolated from objects with radii exceeding 50 kilometres. This implies that sub-kilometre-sized objects are undergoing collisional erosion, just like debris disks observed around other stars. - Photon-by-photon feedback control of a single-atom trajectory
- Nature 462(7275):898 (2009)
Feedback is one of the most powerful techniques for the control of classical systems. An extension into the quantum domain is desirable as it could allow the production of non-trivial quantum states1, 2, 3, 4 and protection against decoherence5, 6. The difficulties associated with quantum, as opposed to classical, feedback arise from the quantum measurement process—in particular the quantum projection noise and the limited measurement rate—as well as from quantum fluctuations perturbing the evolution in a driven open system. Here we demonstrate real-time feedback control7, 8, 9, 10, 11, 12 of the motion of a single atom trapped in an optical cavity. Individual probe photons carrying information about the atomic position13, 14 activate a dipole laser that steers the atom on timescales 70 times shorter than the atom's oscillation period in the trap. Depending on the specific implementation, the trapping time is increased by a factor of more than four owing to feedba ck cooling, which can remove almost all the kinetic energy of the atom in a quarter of an oscillation period12. Our results show that the detected photon flux reflects the atomic motion, and thus mark a step towards the exploration of the quantum trajectory15, 16 of a single atom at the standard quantum limit. - Photon-induced near-field electron microscopy
- Nature 462(7275):902 (2009)
In materials science and biology, optical near-field microscopies enable spatial resolutions beyond the diffraction limit1, 2, but they cannot provide the atomic-scale imaging capabilities of electron microscopy3. Given the nature of interactions4, 5, 6, 7, 8 between electrons and photons, and considering their connections9, 10 through nanostructures, it should be possible to achieve imaging of evanescent electromagnetic fields with electron pulses when such fields are resolved in both space (nanometre and below) and time (femtosecond)11, 12, 13. Here we report the development of photon-induced near-field electron microscopy (PINEM), and the associated phenomena. We show that the precise spatiotemporal overlap of femtosecond single-electron packets with intense optical pulses at a nanostructure (individual carbon nanotube or silver nanowire in this instance) results in the direct absorption of integer multiples of photon quanta (nħω) by the relativistic electrons acce lerated to 200 keV. By energy-filtering only those electrons resulting from this absorption, it is possible to image directly in space the near-field electric field distribution, obtain the temporal behaviour of the field on the femtosecond timescale, and map its spatial polarization dependence. We believe that the observation of the photon-induced near-field effect in ultrafast electron microscopy demonstrates the potential for many applications, including those of direct space-time imaging of localized fields at interfaces and visualization of phenomena related to photonics, plasmonics and nanostructures. - Fault zone fabric and fault weakness
- Nature 462(7275):907 (2009)
Geological and geophysical evidence suggests that some crustal faults are weak1, 2, 3, 4, 5, 6 compared to laboratory measurements of frictional strength7. Explanations for fault weakness include the presence of weak minerals4, high fluid pressures within the fault core8, 9 and dynamic processes such as normal stress reduction10, acoustic fluidization11 or extreme weakening at high slip velocity12, 13, 14. Dynamic weakening mechanisms can explain some observations; however, creep and aseismic slip are thought to occur on weak faults, and quasi-static weakening mechanisms are required to initiate frictional slip on mis-oriented faults, at high angles to the tectonic stress field. Moreover, the maintenance of high fluid pressures requires specialized conditions15 and weak mineral phases are not present in sufficient abundance to satisfy weak fault models16, so weak faults remain largely unexplained. Here we provide laboratory evidence for a brittle, frictional weakening m echanism based on common fault zone fabrics. We report on the frictional strength of intact fault rocks sheared in their in situ geometry. Samples with well-developed foliation are extremely weak compared to their powdered equivalents. Micro- and nano-structural studies show that frictional sliding occurs along very fine-grained foliations composed of phyllosilicates (talc and smectite). When the same rocks are powdered, frictional strength is high, consistent with cataclastic processes. Our data show that fault weakness can occur in cases where weak mineral phases constitute only a small percentage of the total fault rock and that low friction results from slip on a network of weak phyllosilicate-rich surfaces that define the rock fabric. The widespread documentation of foliated fault rocks along mature faults in different tectonic settings and from many different protoliths4, 17, 18, 19 suggests that this mechanism could be a viable explanation for fault weakening in the b rittle crust. - Common ecology quantifies human insurgency
- Nature 462(7275):911 (2009)
Many collective human activities, including violence, have been shown to exhibit universal patterns1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19. The size distributions of casualties both in whole wars from 1816 to 1980 and terrorist attacks have separately been shown to follow approximate power-law distributions6, 7, 9, 10. However, the possibility of universal patterns ranging across wars in the size distribution or timing of within-conflict events has barely been explored. Here we show that the sizes and timing of violent events within different insurgent conflicts exhibit remarkable similarities. We propose a unified model of human insurgency that reproduces these commonalities, and explains conflict-specific variations quantitatively in terms of underlying rules of engagement. Our model treats each insurgent population as an ecology of dynamically evolving, self-organized groups following common decision-making processes. Our model is consistent with several recent hypotheses about modern insurgency18, 19, 20, is robust to many generalizations21, and establishes a quantitative connection between human insurgency, global terrorism10 and ecology13, 14, 15, 16, 17, 22, 23. Its similarity to financial market models24, 25, 26 provides a surprising link between violent and non-violent forms of human behaviour. - Rapid formation and selective stabilization of synapses for enduring motor memories
- Nature 462(7275):915 (2009)
Novel motor skills are learned through repetitive practice and, once acquired, persist long after training stops1, 2. Earlier studies have shown that such learning induces an increase in the efficacy of synapses in the primary motor cortex, the persistence of which is associated with retention of the task3, 4, 5. However, how motor learning affects neuronal circuitry at the level of individual synapses and how long-lasting memory is structurally encoded in the intact brain remain unknown. Here we show that synaptic connections in the living mouse brain rapidly respond to motor-skill learning and permanently rewire. Training in a forelimb reaching task leads to rapid (within an hour) formation of postsynaptic dendritic spines on the output pyramidal neurons in the contralateral motor cortex. Although selective elimination of spines that existed before training gradually returns the overall spine density back to the original level, the new spines induced during learning a re preferentially stabilized during subsequent training and endure long after training stops. Furthermore, we show that different motor skills are encoded by different sets of synapses. Practice of novel, but not previously learned, tasks further promotes dendritic spine formation in adulthood. Our findings reveal that rapid, but long-lasting, synaptic reorganization is closely associated with motor learning. The data also suggest that stabilized neuronal connections are the foundation of durable motor memory. - Stably maintained dendritic spines are associated with lifelong memories
- Nature 462(7275):920 (2009)
Changes in synaptic connections are considered essential for learning and memory formation1, 2, 3, 4, 5, 6. However, it is unknown how neural circuits undergo continuous synaptic changes during learning while maintaining lifelong memories. Here we show, by following postsynaptic dendritic spines over time in the mouse cortex7, 8, that learning and novel sensory experience lead to spine formation and elimination by a protracted process. The extent of spine remodelling correlates with behavioural improvement after learning, suggesting a crucial role of synaptic structural plasticity in memory formation. Importantly, a small fraction of new spines induced by novel experience, together with most spines formed early during development and surviving experience-dependent elimination, are preserved and provide a structural basis for memory retention throughout the entire life of an animal. These studies indicate that learning and daily sensory experience leave minute but perman ent marks on cortical connections and suggest that lifelong memories are stored in largely stably connected synaptic networks. - Division and apoptosis of E2f-deficient retinal progenitors
- Nature 462(7275):925 (2009)
The activating E2f transcription factors (E2f1, E2f2 and E2f3) induce transcription and are widely viewed as essential positive cell cycle regulators. Indeed, they drive cells out of quiescence, and the 'cancer cell cycle' in Rb1 null cells is E2f-dependent1, 2. Absence of activating E2fs in flies or mammalian fibroblasts causes cell cycle arrest3, 4, but this block is alleviated by removing repressive E2f or the tumour suppressor p53, respectively5, 6, 7. Thus, whether activating E2fs are indispensable for normal division is an area of debate1. Activating E2fs are also well known pro-apoptotic factors, providing a defence against oncogenesis8, yet E2f1 can limit irradiation-induced apoptosis9, 10. In flies this occurs through repression of hid (also called Wrinkled; Smac/Diablo in mammals). However, in mammals the mechanism is unclear because Smac/Diablo is induced, not repressed, by E2f111, and in keratinocytes survival is promoted indirectly through induction of DNA repair targets12. Thus, a direct pro-survival function for E2f1–3 and/or its relevance beyond irradiation has not been established. To address E2f1–3 function in normal cells in vivo we focused on the mouse retina, which is a relatively simple central nervous system component that can be manipulated genetically without compromising viability and has provided considerable insight into development and cancer2, 13. Here we show that unlike fibroblasts, E2f1–3in vivo. Thus, activating E2fs are not universally required for normal mammalian cell division, but have an unexpected pro-survival role in development. - E2f1–3 switch from activators in progenitor cells to repressors in differentiating cells
- Nature 462(7275):930 (2009)
In the established model of mammalian cell cycle control, the retinoblastoma protein (Rb) functions to restrict cells from entering S phase by binding and sequestering E2f activators (E2f1, E2f2 and E2f3), which are invariably portrayed as the ultimate effectors of a transcriptional program that commit cells to enter and progress through S phase1, 2. Using a panel of tissue-specific cre-transgenic mice and conditional E2f alleles we examined the effects of E2f1, E2f2 and E2f3 triple deficiency in murine embryonic stem cells, embryos and small intestines. We show that in normal dividing progenitor cells E2f1–3 function as transcriptional activators, but contrary to the current view, are dispensable for cell division and instead are necessary for cell survival. In differentiating cells E2f1–3 function in a complex with Rb as repressors to silence E2f targets and facilitate exit from the cell cycle. The inactivation of Rb in differentiating cells resulted in a switch o f E2f1–3 from repressors to activators, leading to the superactivation of E2f responsive targets and ectopic cell divisions. Loss of E2f1–3 completely suppressed these phenotypes caused by Rb deficiency. This work contextualizes the activator versus repressor functions of E2f1–3 in vivo, revealing distinct roles in dividing versus differentiating cells and in normal versus cancer-like cell cycles. - Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks
- Nature 462(7275):935 (2009)
DNA double-strand breaks (DSBs) are highly cytotoxic lesions that are generated by ionizing radiation and various DNA-damaging chemicals. Following DSB formation, cells activate the DNA-damage response (DDR) protein kinases ATM, ATR and DNA-PK (also known as PRKDC). These then trigger histone H2AX (also known as H2AFX) phosphorylation and the accumulation of proteins such as MDC1, 53BP1 (also known as TP53BP1), BRCA1, CtIP (also known as RBBP8), RNF8 and RNF168/RIDDLIN into ionizing radiation-induced foci (IRIF) that amplify DSB signalling and promote DSB repair1, 2. Attachment of small ubiquitin-related modifier (SUMO) to target proteins controls diverse cellular functions3, 4, 5, 6. Here, we show that SUMO1, SUMO2 and SUMO3 accumulate at DSB sites in mammalian cells, with SUMO1 and SUMO2/3 accrual requiring the E3 ligase enzymes PIAS4 and PIAS1. We also establish that PIAS1 and PIAS4 are recruited to damage sites via mechanisms requiring their SAP domains, and are nee ded for the productive association of 53BP1, BRCA1 and RNF168 with such regions. Furthermore, we show that PIAS1 and PIAS4 promote DSB repair and confer ionizing radiation resistance. Finally, we establish that PIAS1 and PIAS4 are required for effective ubiquitin-adduct formation mediated by RNF8, RNF168 and BRCA1 at sites of DNA damage7, 8, 9, 10, 11. These findings thus identify PIAS1 and PIAS4 as components of the DDR and reveal how protein recruitment to DSB sites is controlled by coordinated SUMOylation and ubiquitylation. - Coordinating DNA replication by means of priming loop and differential synthesis rate
- Nature 462(7275):940 (2009)
Genomic DNA is replicated by two DNA polymerase molecules, one of which works in close association with the helicase to copy the leading-strand template in a continuous manner while the second copies the already unwound lagging-strand template in a discontinuous manner through the synthesis of Okazaki fragments1, 2. Considering that the lagging-strand polymerase has to recycle after the completion of every Okazaki fragment through the slow steps of primer synthesis and hand-off to the polymerase3, 4, 5, it is not understood how the two strands are synthesized with the same net rate6, 7, 8, 9. Here we show, using the T7 replication proteins10, 11, that RNA primers are made 'on the fly' during ongoing DNA synthesis and that the leading-strand T7 replisome does not pause during primer synthesis, contrary to previous reports12, 13. Instead, the leading-strand polymerase remains limited by the speed of the helicase14; it therefore synthesizes DNA more slowly than the lag ging-strand polymerase. We show that the primase–helicase T7 gp4 maintains contact with the priming sequence during ongoing DNA synthesis; the nascent lagging-strand template therefore organizes into a priming loop that keeps the primer in physical proximity to the replication complex. Our findings provide three synergistic mechanisms of coordination: first, primers are made concomitantly with DNA synthesis; second, the priming loop ensures efficient primer use and hand-off to the polymerase; and third, the lagging-strand polymerase copies DNA faster, which allows it to keep up with leading-strand DNA synthesis overall. - SSB protein diffusion on single-stranded DNA stimulates RecA filament formation
- Nature 462(7275):944 (2009)
Nature461, 1092–1097 (2009) In this Article, Figure 3 was printed incorrectly with missing labels. The correct figure is shown below. - Rejuvenation
- Nature 462(7275):950 (2009)
The chase is on.
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