Celebrating Diversity
Special Online Collection

Each year, the editors and news staff of Science look back at the big science stories of the past 12 months, and dub one of them the Breakthrough of the Year. In 2007, the top prize went to "human genetic variation" -- a tribute to a number of recent studies that have revealed the extent to which our genomes differ from person to person. As described in a special section of the 21 Dec 2007 issue, understanding the nuances of this variation has important implications for deciphering the genetics of complex diseases and personal traits. Other notable achievements worthy of runners-up commendation included the reprogramming of human skin cells to behave like embryonic stem cells, observation of unusual electron behavior termed the quantum spin Hall effect, insights into the neural mechanisms that underlie memory and imagination, and "solving" the game of checkers. An assessment of last year’s forecast for advances in 2007 and predictions of areas to watch in 2008 rounded out the special section. On Science Online, each article was accompanied by a set of links to selected papers and relevant Web resources; a video presentation highlighted discoveries in human genetic diversity, and a special Breakthrough edition of the podcast looked back at the year’s top science stories.


Reefs in Trouble

Climate change, disease, and human activities such as overfishing and coastal development have destroyed 20% of the world’s 285,000 square kilometers of known reefs, threatening biodiversity hot spots that generate an estimated $30 billion a year in revenue -- mainly from fisheries and tourism. In the 14 Dec 2007 Science, a collection of articles examined the scope of the problems and efforts under way to save these precious ecosystems. In a Review, Hoegh-Guldberg et al. presented future scenarios for coral reefs that predict increasingly serious consequences for reef-associated fisheries, tourism, coastal protection, and people due to continued global warming and ocean acidification. To maintain the status quo requires urgent implementation of conservation measures to reduce stress on corals, but even small further increases in atmospheric carbon dioxide could tip many reef systems into ecological and structural collapse. A special News Focus looked at efforts to jump-start new reefs by fostering coral reproduction in aquaria, molecular clues to how a common coral of Australia’s Great Barrier Reef responds to environmental change, some of the nastiest diseases threatening reef survival, and impacts of intensive fishing on reef predator-prey dynamics (listen to the related podcast interview with News editor R. Stone). An Editorial by D. Kennedy discussed the importance of International Year of the Reef 2008 -- a worldwide campaign to raise awareness about the value and importance of coral reefs and the threats to their sustainability.


Beetle Family Tree

With more than 350,000 species found worldwide, beetles constitute nearly a quarter of all described animal species. In a Report in the 21 Dec 2007 Science, Hunt et al. presented the most comprehensive look yet at the extraordinary diversity of the beetle family tree. The team reconstructed a phylogeny by examining three genes in nearly 1900 species, which represent more than 80% of the world’s recognized beetle families. They identified previously unknown relationships for many groups and also defined basal relationships in the Polyphaga, the biggest group of beetles, and established five families as the earliest branching lineages. Dating of the phylogeny suggests that beetle diversity was not driven by an explosion of flowering plant species or fast diversification rates, as has been suggested. Rather, the researchers surmise that the extreme diversity of beetles reflects a Jurassic origin of numerous modern lineages (which is earlier than previously thought), high lineage survival, and the diversification into a wide range of niches, including the utilization of all parts of plants. A related ScienceNOW story by E. Pennisi highlighted the study.


Learning from Mistakes

Human experience is based on learning that our actions have positive or negative outcomes; rewards generally reinforce successful behavior, whereas punishments induce avoidance of erroneous actions. It is clear, however, that some people are slower to learn from negative experiences than others. New results reported by Klein et al. in the 7 Dec 2007 Science suggest that our genetic makeup may have something to do with it. The work relates to the A1 allele (or variant) of the gene encoding the D2 receptor -- a protein on the surface of brain cells that is activated by the neurotransmitter dopamine. This allele is associated with a reduction in D2 receptor density by up to 30%, and this reduction has been linked to multiple addictive and compulsive behaviors. To investigate the possible influence of the A1 variant on learning from errors, the team undertook a neuroimaging study involving a learning task in which participants had to figure out which symbols to choose from displayed pairs of Chinese symbols, based on whether they received positive or negative feedback after each successive choice. The researchers found that carriers of the A1 allele were less successful at learning to avoid choices associated with negative consequences than non-carriers. Moreover, functional magnetic resonance imaging (fMRI) showed that this reduced ability to learn from errors was accompanied by reduced activity in the posterior medial frontal cortex -- a brain area involved in negative feedback monitoring and memory. An accompanying News story by C. Holden highlighted the findings.


Dual-Function MicroRNAs

MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate the function of eurkaryotic messenger RNAs (mRNAs) and have been shown to play important roles in development, cancer, stress responses, and viral infections. More specifically, miRNAs are known to block gene expression by binding to complementary sequences in the 3’ untranslated region (3’ UTR) of target mRNAs and recruiting additional protein factors to help block translation and/or promote mRNA degradation. According to a Report in the 21 Dec 2007 Science (published online 29 Nov) miRNAs are also capable of activating translation, thus revealing a broader effect of these small RNAs on protein expression than previously appreciated. Vasudevan et al. showed that a human miRNA called miR369-3 binds the 3’-UTR of tumor necrosis factor-alpha (TNF-alpha) and is required for the up-regulation of translation seen in nonproliferating cells -- but that miR369-3 represses translation of the same mRNA in proliferating cells. The researchers also showed that two other well-studied microRNAs -- Let-7 and the synthetic miRNA miRcxcr4 -- likewise induced translation up-regulation of target mRNAs upon cell cycle arrest, but repressed translation in proliferating cells. As noted in an accompanying Perspective by J.R. Buchan and R. Parker "this latest twist in function may foreshadow even more faces of these intriguing micromolecules."


Mission to the Sun
Special Online Collection

Aided by spacecrafts, telescopes, computer simulations, and neutrino detectors, researchers have made tremendous progress in the exploration of the Sun. Yet many of the Sun’s mechanisms are still a mystery. In September 2006, the Japan Aerospace Exploration Agency -- in collaboration with partners in the U.S. and U.K. -- launched the Hinode (or "sunrise) solar space telescope mission, aimed at improving our understanding of the Sun’s magnetic fields and the mechanisms that power the solar atmosphere and drive solar eruptions. A special section of the 7 Dec 2007 Science, including a Perspective and nine Reports, presented some of the first results from the 3-year mission. Spectrometers that can view the Sun in optical wavelengths, as well as in extreme-ultraviolet and x-ray wavelengths, imaged structures within the high-energy solar plasma including fine-scale jets related to the magnetic field in the solar corona, or outer atmosphere. New information has also been provided about how magnetic lines may cross and energetically reconnect, causing solar flares. And observations of special magnetic waves known as Alfvén waves offer long-sought clues to the heating of the Sun’s corona, which is much hotter than the solar surface, and the acceleration of the solar wind.


A Cosmic Texture?

After the big bang, the universe began to cool and expand, progressing through a series of phase changes in which various forces and fields became decoupled and particle symmetries were broken. According to theory, these phase changes spread at the speed of light across patches of the universe -- but may have done so irregularly, leaving behind cosmic defects similar to those seen in crystals. In a Report in the 7 Dec 2007 Science, Cruz et al. used Bayesian statistical analysis to argue that an unusual cold spot in the cosmic microwave background -- the afterglow of the Big Bang that pervades the universe-- could be explained by a kind of cosmic defect called a texture. Textures consist of localized, twisted configurations of fields, which collapse and unwind on progressively larger scales. An accompanying Perspective by R. Brandenberger noted that "[I]f confirmed, this result would provide a direct link between observations and physics at energies close to the Planck scale, [an energy] where quantum effects are believed to become important in gravity."


Atmospheric Oscillation Insights

The Madden-Julian Oscillation (MJO) is a massive (1000-kilometer-wide) atmospheric disturbance that propagates slowly eastward through the tropics from the Indian Ocean to the western Pacific over a course of 30 to 60 days. Despite its extensive influence on weather events and climate variability worldwide, key aspects of the MJO are still unclear, in part because the range of scales of the processes it involves have been difficult to simulate with existing climate models. Now, two Reports in the 14 Dec 2007 Science describe new data and modeling insights that advance our understanding of this important climate force. Using data obtained from the Argo floats -- a global array of 3,000 free-drifting instruments that measures the temperature and salinity of the upper 2000 meters of the ocean -- Matthews et al. measured the deep-ocean response to wind surges associated with the MJO. Their analysis shows that surface wind stress can force eastward-propagating oceanic equatorial Kelvin waves as deep as 1500 meters -- much deeper than ocean models have predicted -- with amplitudes up to six times that of the annual cycle. Miura et al. used a model that allows direct coupling of the atmospheric circulation and clouds -- a shortcoming of current models -- to successfully simulate the migration of an MJO event that occurred between December 2006 and January 2007. Their results demonstrate the potential for making month-long MJO predictions when appropriate global cloud-resolving models are used. An accompanying Perspective by D. L. Hartmann and H.H. Hendon highlighted the studies.


Storing Light in Optic Fiber

Many of the world’s information networks are linked by fiber optic cables, which can quickly convey pulses of light to transmit data. However, storing that information for later processing requires converting the light to electrical signals, using standard computer memory to store the information, and then converting it back to light for transmission -- a process that costs time and can generate a lot of heat. Now, in a study in the 14 Dec 2007 Science Zhu et al. report that multiple optical pulses can be stored directly in an optical telecommunication fiber -- by coherently transferring their information content to an acoustic vibration, or sound wave -- and then retrieved later (see the related News story by A. Cho. A stream of data pulses are sent through the fiber in one direction, while a "write" pulse is simultaneously sent in the opposite direction. As the pulses pass through each other, they interfere, leaving behind an acoustic wave that contains the information content of the data pulses. At a later time, a "read" pulse is passed through the fiber in the same direction as the write pulse, depleting the sound wave and releasing the data pulses from the fiber. In the reported experiment, 2-nanosecond-long pulses were stored for up to 12 nanoseconds with good readout efficiency. Corresponding author of the study, Dr. D.J. Gauthier, discussed the achievement in a related podcast segment.


Understanding Glass Dynamics

The hallmark of any glass is a very low atomic or molecular mobility within a disordered solid. Structural rearrangements are an essential property of these materials and may explain why glasses are resistant to flow even though they are structurally similar to liquids. However, understanding the dynamics of these rearrangements has been difficult because they typically occur at length scales that are too small and time scales that are too short for direct observation. In a Report in the 21 Dec 2007 Science, Schall et al. used confocal microscopy to obtain three-dimensional images of thermally induced structural rearrangements in a colloidal glass in the presence of an applied shear. The researchers identified localized zones where the colloidal particles undergo irreversible, thermally activated shear transformations. Elasticity of the glass results in coupling between the transformation zones, which, upon increasing strain, leads to a network of transformation zones that extends across the sample. As noted in an accompanying Perspective by M.L. Falk, insights from this type of study can help "pave the way for new materials that take advantage of the disorder inherent in glasses, which may in the years ahead provide as rich a source of new materials advances as crystals have to date."

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In Science’s STKE

Common Regulator of Danger Responses?

Toll-interleukin-1 receptor (TIR) domain-containing proteins are important players in vertebrate immune defense against pathogens. Four of the five members of this family of so-called adaptor proteins are required for the activation of immune cells downstream of the recognition of microbial molecules by Toll-like receptors (TLRs). However, the physiological function of the fifth mammalian protein, sterile alpha and TIR motif-containing 1 (SARM1), has been unclear. In a Perspective in the 18 Dec 2007 issue, M. Dalod discussed recent findings -- made possible by the generation and study of SARM1 reporter and SARM1-deficient mice -- showing that SARM1 downmodulates TLR3 and TLR4 responses in human leukocytes and also contributes to neuronal apoptosis in response to metabolic stress. Together with insights into the functions of the worm ortholog of SARM1 and other reports on the role of TLRs in neuronal development and responses to injury in mammals, these new results suggest that further studies of SARM1-deficient animals may uncover unexpected similarities between the ways in which immune and neuronal cells respond to danger.

Also in STKE this month:
-- P.W. Majerus highlighted two recent Science papers that defined a signaling function for the inositol pyrophosphate IP7 (11 Dec 2007)
-- E.N. Benveniste and H. Qin discussed the molecular basis for the anti-inflammatory properties of type I interferons and their therapeutic potential in autoimmune and inflammatory diseases (11 Dec 2007)
-- Schwertassek et al. described the use of mechanism-based kinetic trapping to assess the oxidoreductase reactivity of cell-surface proteins within their native environment (18 Dec 2007)
-- The STKE editors offered highlights from the 2007 ASCB Annual Meeting, which took place Dec 1-5 in Washington, DC.