This month in Science Roundup:
Education & Technology
Special Online Collection
An astounding number of students spend their off hours playing technology-based games, either in immersive environments that millions of users share or individually on cell phones and personal computers. As described in a special section of the 2 Jan 2009 issue, opportunities abound for squeezing in a bit of learning along with the game-playing. News, Perspective, and Review articles examined topics ranging from the value of digital libraries and software to aid writing and algebra skills, to efforts to improve large-scale testing using technology and the interface between cognitive science and education. Online, a Science Careers article described a software engineer’s vision of a paperless classroom; a video presentation discussed the opportunities and challenges afforded by using technology in education; and a special edition of the podcast included interviews about computer-assisted military training, immersive interfaces for learning, and a cyber home-learning system in Korea.
Responses to Racism
Research has shown that people are remarkably poor at forecasting how they will feel (and therefore act) in emotionally challenging situations. In a Report in the 9 Jan 2009 Science, Kawakami et al. showed that this behavior extends to responses to racism, which may help explain why racist comments and acts persist even though overt prejudice is publicly condemned. In a series of studies, the researchers investigated how peopled imagined they would feel and behave and how they actually felt and behaved upon hearing a racist comment. As described by lead author Kerry Kawakami in related podcast interview, the team found that witnesses of the racial remark consistently predicted that they would feel worse than they actually did and that they would shun the offender more than they actually did. The findings suggest that racism may persevere in part because people who anticipate feeling upset and believe that they will take action may actually respond with indifference when faced with an act of racism. A Perspective by E. R. Smith and D. M. Mackie highlighted the study.
Pacific Population History
Among the most dramatic of human expansions is the prehistoric colonization of the Pacific islands. According to the pulse-pause theory, the Austronesian people originated in Taiwan around 5000 years ago and spread through the Pacific in a sequence of expansion pulses and settlement pauses. The competing slow-boat scenario posits diffusion from Wallacea (a group of Indonesian islands that lie between Borneo and Australia and New Guinea) 13,000 to 17,000 years ago. In the 23 Jan 2009 Science, genetic data from human gastric bacteria and an independent computational linguistic analysis lent further credence to the pulse-pause theory of Pacific population dispersals. Using lexical data, Gray et al. constructed a family tree of 400 Austronesian languages that places the root of the language family on the island of Taiwan approximately 5230 years ago, followed by languages of the Philippines, Borneo/Sulawesi, Central Malayo-Polynesia, and South Halmahera/West New Guinea. The topology of the tree reveals a series of settlement pauses and expansion pulses linked to technological and social innovations. Moodley et al. performed a genetic analysis of the human gut bacterium Helicobacter pylori, which has spread around the world and diverged genetically alongside its human host resulting in populations of bacterial strains specific for large continental areas. Samples from Pacific human populations revealed two distinct H. pylori strains that indicate that humans spread from Taiwan in two waves. The first wave carrying the Sahul strain split from Asian populations and spread across the exposed land bridges of what is now the Indonesian Archipelago into New Guinea and Australia more than 30,000 years ago. A second wave carrying the Maori strain of the bacterium dispersed from Taiwan about 5,000 years ago, traveling to the Philippines and into Polynesia and New Zealand. C. Renfrew discussed the convergence of the two studies in a related Perspective and podcast interview.
Threats to Land and Sea
Global warming is making growing seasons longer and increasing sea-surface temperatures, which could have serious consequences for marine and terrestrial life. Two Reports in Science this month looked at the effects of climate change on coral reefs and agricultural land.
--De’ath et al. (2 Jan 2009) examined the growth patterns of 320 coral colonies from Australia’s Great Barrier Reef, whose skeletal records show that rates of coral calcification -- an important determinant of reef health -- have declined by nearly 15% since 1990, to values lower than any seen for the past 400 years. Although the main causes of this decline are uncertain, the researchers suggest that increasing water temperatures and ocean acidification -- the declining pH of surface seawater layers caused by the absorption of increasing amounts of atmospheric carbon dioxide -- are likely culprits (see the related News story by E. Pennisi)
--Battisti and Naylor (9 Jan 2009) used observational data and output from 23 global climate models to predict how growing season temperatures will change by the end of the 21st century. Their results suggest that heat stress on crops could cause profound negative impacts on global agriculture and food security unless sufficient investments are made in developing heat-tolerant crops and new irrigations systems (see the related News story by C. Holden).
Most of the calcium carbonate production in the oceans has been attributed to marine plankton -- specifically the coccolithophores and foraminifera. In a Report in the 16 Jan 2009 Science, however, Wilson et al. revealed that another important source of marine carbonate has been overlooked: teleost fish. These bony fish excrete large amounts of carbonate precipitates as an osmoregulatory response to the continuous ingestion of calcium- and magnesium-rich seawater. The team modeled the size, composition, and abundance of marine fish across the global ocean and estimated that marine fish contribute 3 to 15% of total oceanic carbonate production. Fish "gut rocks" are richer in magnesium than carbonate produced by plankton, and are therefore more soluble. This may help explain the increased alkalinity in the upper 1000 meters of the ocean -- a controversial phenomenon that has puzzled oceanographers for decades. The researchers further predict that fish carbonate production may rise in response to future environmental changes in carbon dioxide, and thus become an increasingly important component of the inorganic carbon cycle. An accompanying Perspective by B. A. Seibel and H. M. Dierssen noted that "[W]ilson et al.’s important contribution to our knowledge of the inorganic carbon cycle will hopefully infuse a new appreciation for the role of higher trophic levels in ocean dynamics."
Special Online Collection
Beyond laying the foundations for evolutionary biology, Charles Darwin built a home that biology could furnish with the concepts and findings from paleontology, ecology, and population genetics, and more recently molecular biology, developmental biology, and genomics. In the 9 Jan 2009 issue, Science kicked off its yearlong celebration of Darwin’s 200th birthday and the 150th anniversary of the publication of On the Origin of Species. A Review article by P. Bowler examined those aspects of Darwin’s work that led him to develop this revolutionary theory, including his studies of biogeography and animal breeding, and his recognition of the role played by the struggle for existence. The issue also featured an essay by C. Zimmer on how life on Earth might have begun, the first in a monthly series about "origins" that will take a broad look at key developments in evolution and in human culture (listen to a related podcast interview). Other evolution-related content will be added throughout the year.
Serotonin and Swarming
The desert locust Schistocerca gregaria lives a mostly solitary and harmless existence, avoiding others and flying alone at nighttime. Under favorable environmental conditions, however, their numbers surge, triggering a striking transformation to a swarm-forming "gregarious" phase that can cause mass crop devastation. In a Report in the 30 Jan 2009 Science, Anstey et al. revealed a neurochemical mechanism linking the changed behavior of individuals to large-scale changes in population structure and the onset of mass migration. The key to the transformation from mutual avoidance to attraction turns out to be the neurotransmitter serotonin, which is synthesized in response to tactile, olfactory, and visual stimuli as locust numbers and social contacts increase. In forced-crowding experiments, the team found that locusts that behaved the most gregariously had about three times more serotonin in their thoracic nervous systems than solitary insects; serotonin was also sufficient to induce gregarious behavior in the absence of stimuli associated with other locusts (listen to the related podcast interview with corresponding author Stephen Rogers). Other factors may be involved in initiating the full suite of gregarious traits, which includes a change in body color from green to yellow. Although further research on multiple aspects of insect biology is needed, an accompanying Perspective by P.A. Stevenson noted that the new findings "harbor considerable potential" for the development of more effective pest control methods.
Sources of Brown Clouds
During the winter season, a huge plume of air pollution called the Asian atmospheric brown cloud (ABC) hangs over South Asia and the Indian Ocean. It is so large and dense that its cooling effect may balance, or even surpass, the warming effect of greenhouse gases in the region. Biomass burning and fossil fuel combustion both produce black carbon emissions, but the relative contribution of these sources to the Asian ABC has been unclear. In a Report in the 23 Jan 2009 Science, Gustafsson et al. conducted radiocarbon analysis on carbonaceous cloud particles from western India and the Indian Ocean and found that biomass burning accounts for at least one-half of the cloud’s carbon-rich aerosols. Controlling biomass combustion -- namely waste burning in agriculture and forestry, and residential wood and dung combustion for heating and cooking -- will thus be important to mitigate climate effects and to improve air quality in the region. An accompanying Perspective by S. Szidat highlighted the study.
Toward Broadband Invisibility
Transformation optics and metamaterials -- materials in which man-made subwavelength structures generate unusual electromagnetic and optical properties -- allow the manipulation of light with unprecedented control, giving rise to possibilities like invisibility, hyperlensing, and cloaking. Two Reports in Science this month described progress toward achieving "broadband" invisibility, across a large swath of the electromagnetic spectrum.
--Leonhardt and Tyc (2 Jan 2009, published online 20 Nov 2008) sought to overcome the limitations of previous approaches, which typically apply to only one wavelength of light because they are based on mappings of electromagnetic properties onto flat (Euclidean) space (see the related Perspective by A. Nicolet and F. Zolla). The new theoretical approach is instead based on mappings in a curved, or non-Euclidean space (such as the surface of virtual sphere), which may open up applications to a broad range of wavelengths. The team also showed that the physical properties required of materials to achieve invisibility need not be as extreme as in previous approaches.
--Liu et al. (16 Jan 2009) produced a metamaterial cloak for an object placed on a metal surface. It was constructed from thousands of individual nonresonant metamaterial components, each designed and fabricated by an automated process. The new cloak works over a broad bandwith and may therefore be adaptable for visible light.
Chromatin and Mutations
Spatial patterns in the rate of genetic variation are often interpreted as the footprints of natural selection. In a Report in the 16 Jan 2009 Science (published online 11 Dec 2008), Sasaki et al. showed that the packaging of DNA and proteins into chromatin influences the location and rates of mutations across eukaryotic genomes. The principal components of genomic DNA packaging are the nucleosomes, consisting of an octamer of histone proteins around which roughly 150 base pairs of double-stranded DNA can be wound. These nucleosomes are arranged along DNA like beads on a string, with and intervening, variable length of linker DNA between them. The researchers compared the genomes of two closely-related species of Japanese killifish (medaka) and found that mutation rates downstream of transcriptional start sites demonstrated a periodic pattern of peaks and valleys correlating with nucleosome position, with the rate of insertions and deletions peaking at DNA linker regions, where substitution rates (point mutations) were at a minimum. It is likely that transcription-coupled DNA repair contributes to this pattern of mutation. An accompanying Perspective by C. A. M. Semple and M. S. Taylor highlighted the study.
Insights into Membrane Fusion
Membrane fusion is essential for a variety of biological processes, from the compartmental organization of cells to the precise timing of neurotransmission in the brain. Recent studies have revealed the unique and complementary roles of two key components of intracellular membrane fusion machinery: SNARE proteins, which zipper up into a helical bundle that pulls two membranes tightly together to exert the force required for fusion and clasp-shaped SM proteins, which bind to SNARE complexes to direct their fusogenic action. Two Reports in the 23 Jan 2009 Science shed new light on how the protein complexin interacts with these components to exert control on the membrane fusion process. Giraudo et al. discussed how in neurons, complexin clamps otherwise spontaneous membrane fusion by SNARE proteins, allowing neurotransmitters and other mediators to be secreted when and where they are needed as this clamp is released. They showed that a structural motif within complexin appears to act as a molecular switch that directly interacts with SNARE proteins during fusion. Maximov et al. demonstrated that in neuronal systems, complexin can play a negative or positive role in SNARE-mediated membrane fusion during neurotransmitter release, potentially either clamping SNARES to prevent spontaneous fusion, or promoting fusion when appropriate. In a related Review, T. Südhof and J. Rothman offered a unified view of the mechanisms by which SNARE and SM proteins function together as the universal fusion machinery.
Graphene -- the thinnest material known to conduct electricity -- consists of a single layer of carbon atoms arranged in a hexagonal crystal lattice. Its unique physical and electrical properties make it an attractive material for the fabrication of new devices for future carbon-based nanoelectronics. In a Report in the 30 Jan 2009 Science Elias et al. achieved an important advance in expanding graphene’s potential applications: chemically modifying it to create a new material with different physical properties. The team showed that adding atomic hydrogen to graphene transforms the semimetallic material into an electronic insulator (graphane). Graphane is crystalline and retains a hexagonal lattice structure, though it is more compressed. The team also showed that the reaction with hydrogen is reversible; the original metallic state of graphene, including its lattice spacing, can largely be restored by annealing the hydrogenated samples at high temperatures. The study shows that graphene can be used as an atomic-scale scaffold for creating new materials. In a related Perspective, A. Savchenko noted that "it will be interesting to study the effects of incorporating other elements into its structure."
In Science Signaling
Blocking mTOR Signals
The mammalian target of rapamycin (mTOR) is a protein kinase critical to cell growth and proliferation. mTOR functions as part of two distinct multiprotein complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), both of which are involved in the AKT signaling cascade -- a pathway that is reported to be hyperactive in many human cancers. Loss of the tumor suppressor PTEN can hyperactivate mTOR through AKT and represents one of the most frequent events in human prostate cancer. In a Research Article in the 27 Jan 2009 issue, Nardella et al. showed that conditional genetic inactivation of mTOR activity (abrogating signaling through both complexes) has little effect on the adult mouse prostate gland, but suppresses prostate tumorigenesis associated with loss of PTEN. The findings thus support the rationale for developing specific mTOR inhibitors targeting both mTORC1 and mTORC2 for the treatment of tumors triggered by PTEN deficiency and aberrant mTOR signaling.
-- Marshall et al. described an NMR-based assay that enables real-time, quantitative analysis of the activity of Rheb, a conserved small guanosine triphosphatase (27 Jan 2009)
-- P.A. Lochhead discussed how protein kinases are activated by autophosphorylation (20 Jan 2009)
-- E.M. Adler highlighted the signaling breakthroughs of 2008, which extended from protein crystals to cells and subcellular structures to whole genomes (6 Jan 2009)