The Cosmic Web
Introduction to Special Issue

Stars and galaxies are not randomly strewn about our universe, but rather are entwined in a filamentous network of dark and visible matter that pervades the cosmos. A special section of the 4 Jan 2008 Science considered the latest research into the origins and evolution of this so-called cosmic web. A News story described the many techniques astronomers are using to trace the web, including using telescopes to catalog the number of galactic clusters; a method called weak gravitational lensing, which allows researchers to detect (dark) matter by how it affects passing light; and viewing the universe through microwave and other radiation outside the usual optical and infrared wavelengths. Three Perspective articles discussed the search for the lumps of dark matter that lace the halos of galaxies, supercomputer simulations that have enhanced our understanding of where the cosmic web came from, and the mystery of the missing baryons -- the protons and atomic nuclei that constitute the ordinary matter of which stars and planets are made. The continuing efforts of astronomers and physicists promise to reveal even more intriguing details about how the universe came to be and how it is evolving.


Missing Stardust

Comets -- celestial bodies made of ice, rock, and dust -- are thought to contain large amounts of the most primitive material in the solar system, including dust from other stars and interplanetary dust particles from the rubble disk out of which the planets grew. That was the expectation of researchers analyzing particles from comet 81P/Wild 2, which were collected by the Stardust spacecraft and returned to Earth in January 2006. But according to a Report by Ishii et al. in the 25 Jan 2008 Science, ancient specks from the outer nebula are nowhere to be found in the Stardust samples. Instead, silicate grains in the captured comet dust look more like the silicates in meteorites from the inner solar system’s asteroid belt (see the related News story by R. A. Kerr). Grains similar to interplanetary dust components known as GEMS (glass embedded with metal and sulfides) were found in the Stardust samples, but the team showed that these particles were actually created during the high-speed impact of the comet with the spacecraft’s sample collector. The researchers made some themselves by shooting mineral particles into collector material at Stardust velocities. Overall, the findings imply that there is a continuum between asteroids and comets and that interplanetary dust particles gathered from our stratosphere are a precious source of the most cosmically primitive astromaterials.


Explosion of Early Life

Most of the major living groups of animals emerged during the so-called Cambrian explosion between 542 million and 520 million years ago. Now, a Report in the 4 Jan 2008 Science suggests that the oldest known complex multicellular organisms -- a fossil assemblage known as the Ediacara biota dating to about 575 million years ago -- emerged in a similar explosion of life. Shen et al. performed a comprehensive analysis of the morphological characters and patterns observed in Ediacara fossils. Their characterization of Ediacara morphospace -- a graphic representation of the possible shapes and forms assumed by these organisms -- indicates a rapid evolution of body plans followed by taxonomic diversification, and then rapid decline, similar to the pattern of the Cambrian explosion. Since many of the organisms, which resemble leaf-like fronds and fractal forms, emerged abruptly over about 25 million years during the Avalon period, the team has named the event the Avalon explosion. A related ScienceNOW story published on 3 Jan 2008 by P. Berardelli noted that "[i]f confirmed, the find reinforces the idea that major evolutionary innovations occurred in bursts."


Nonvolcanic-Tremor Triggers

Seismic activity termed nonvolcanic tremor and accompanying slow slip have recently been observed at tectonic plate boundaries (subduction zones) in Japan and Cascadia -- which stretches from Vancouver Island, Canada to Northern California. These geophysical phenomena occur over long time scales (days to months) and have physical characteristics different from those of "normal" earthquakes. Two studies reported in the 11 Jan 2008 Science offered insights into the forces that trigger these events. Rubinstein et al. (published online 22 Nov 2007) recorded three nonvolcanic tremor episodes in the Puget Sound/southern Vancouver Island portion of the Cascadia subduction zone and noted clear pulsing of tremor activity with periods of about 12.4 and 24 to 25 hours, which match the periods of the lunar and lunar-solar tides. Because tremor is more sensitive to tidal forces than normal earthquakes, the researchers surmise that tremor occurs on very weak faults. Gomberg et al. (also published online 22 Nov), meanwhile, identified seven locations along the North American-Pacific plate boundary in California, from the desert southeast of Los Angeles to Napa Valley in the north, where nonvolcanic tremor was triggered by the 2002 Denali earthquake in Alaska. Their findings imply that the conditions essential for nonvolcanic tremor exist in a range of tectonic environments. An accompanying Perspective by E. Richardson and C. Marone highlighted the studies.


Not-So-Natural Streams

Pioneering studies of natural streams in the eastern United States have been fundamental to our understanding of how rivers and floodplains develop and have contributed to the widely accepted model of a natural stream as a single-channel meandering form. Now, in a Research Article in the 18 Jan 2008 Science, Walter and Merritts present results suggesting that many of the streams and rivers considered to be natural actually bear the stamp of extensive human influence. Mapping and dating of sediment deposits along mid-Atlantic streams, as well as historical maps and records, show that before European settlement, the streams consisted of small branching channels that flowed across broad vegetated wetlands. However, tens of thousands of milldams constructed for water-powered milling operations between the 17th and 19th centuries, along with widespread deforestation for agriculture, drastically changed these riverscapes. Extensive sedimentation behind the dams buried presettlement wetlands, creating a series of milldam ponds and confining streams to meandering channels. As noted in an accompanying Perspective by D. R. Montgomery, "[t]he results parallel findings in Europe and the Pacific Northwest of how historical clearing of large wood and logjams altered river morphology. Walter and Merritts discussed the study and its implications for river restoration efforts in the U.S. and Europe in a related podcast interview.


Improved Face Recognition

Face-recognition technology has the potential to be a valuable resource for national security and crime prevention -- but current systems make too many mistakes to be practical. That’s because none can cope with common types of image variability such as blurriness or poor lighting. But in a Brevium in the 25 Jan 2008 Science, Jenkins and Burton reported that a simple process of image averaging, whereby different photos of a face are merged to form a single image, can dramatically boost the performance of a commercial face recognition system (see the related ScienceNOW article by Y. Bhattacharjee). The team modeled their image averaging process after the way human beings learn to recognize faces: through repeat encounters. The team tested the procedure at a Web site that contains a database of celebrity pictures and uses a face-recognition algorithm that allows visitors with a personal photo and find out which celebrity they most resemble. Remarkably, the researchers found that using an "average" image of a celebrity, in which 20 pictures taken over several decades and under various light conditions were merged, increased the accuracy of the system from 54% (when individual images were used) to 100%. Similar to the way the humans learn a particular face, averaging the pictures has the effect of blocking out extraneous factors such as lighting, pose, or facial expression and distilling the essence of a face into a reliable image. Dr. Jenkins discussed the work in a related podcast segment.


New Viral Cancer Culprit?

Merkel cell carcinoma (MCC) is a rare but aggressive human skin cancer that typically affects elderly and immunosuppressed individuals such as transplant recipients and AIDS patients. In a Report published online on Science Express on 17 Jan 2008, Feng et al. provided tantalizing evidence that this cancer could be caused by a previously uncharacterized human polyomavirus -- a type of small double-stranded DNA virus. The researchers made their discovery using a technique called digital transcriptome subtraction, which involved sequencing all of the RNA from several MCC tumor samples and comparing those sequences to known human genome sequences. The team then took tumor sequences that did not align with human sequences, compared those to known viral sequences, and found that one of them was similar to, but distinct from all known polyomaviruses -- suggesting that it represented a new type of polyomavirus (which the team named Merkel cell polyomavirus, or MCV). MCV sequences appeared in 80% of MCC tumors sampled, but only 8% of control tissues from various parts of the body. Moreover, the viral sequences were found to be integrated within the tumor genome in a pattern suggesting that MCV infection occurred before the tumors started growing. In an interview in the 18 Jan Science Podcast, senior author of the study Dr. Patrick Moore noted that further research is needed to address whether MCV plays a causal role in MCC development.


HIV Helpers

HIV is a remarkably simple virus, equipped with only 9 genes that code for a mere 15 proteins. As a result, the virus must exploit multiple host cell functions in order to ensure its own survival and replication. In a Research Article published online in Science Express on 10 Jan 2008, Brass et al. described their systematic approach to identifying which host human proteins in particular are required for HIV infection. Using RNA interference (RNAi) technology, which enables researchers to inhibit the expression of specific genes one at a time, the team screened more than 20,000 human genes and identified 273 HIV-dependency factors -- proteins that help the virus wreak its havoc on the immune system (see the related News story by J. Cohen). These factors -- of which only 36 had previously been identified -- participate in a broad array of cellular functions including nuclear transport, sugar modification of proteins, and vesicular trafficking, and implicate new pathways in the viral life cycle. The new work demonstrates the power of RNAi to probe the dependencies of human pathogens such as HIV, and to identify potential new targets for therapy. The senior author on the study, Dr. Stephen Elledge, discussed the study in a related podcast interview.


Ants, Acacias, and Herbivores

The close interaction between acacia trees and their resident ants is one of the best-known examples of mutualism -- an ecological relationship in which both parties gain. Colonies of stinging ants help defend the tree against ravaging insects and hungry herbivores, and in return, the trees exude nectar for nourishment and grow hollow thorns where ants can seek shelter. In a Report in the 11 Jan 2008 Science, Palmer et al. showed that large mammalian herbivores such as giraffes and elephants play an important role in the maintenance of this mutually beneficial alliance. Ten years of exclusion of large herbivores from plots in an African savanna reduced the nectar and housing provided by plants to ants and led to decreases in the colony size of the dominant ant species on acacia trees. Subsequent colonization of the trees by a related, less vigilant ant species resulted in increased attack by stem-boring beetles, slower tree growth, and increased tree mortality. The results suggest that the decline of large herbivores throughout Africa due to human activities could have strong and unanticipated consequences for the broader ecosystems in which these animals live. An accompanying News story by M. Leslie highlighted the study.


Small Fish Think Big

The sophisticated cognitive abilities of humans and other primates are usually associated with highly specialized brain areas containing very high densities of interconnected neurons. Now, a Report in the 4 Jan 2008 shows that intelligent behavior can arise from a surprisingly small neural circuitry. Schlegel and Schuster studied the rapid decision-making abilities of archerfish, freshwater fish renowned for their ability to spit precisely aimed jets of water to knock potential prey off twigs suspended above the water, and then retrieve them. To assess what drives these quick movements, the researchers designed a set of experiments in which they placed insects on platforms, out of view of the fish, and then blew the insects into the water using bursts of air. The fish responded just as quickly--in as little as 40 milliseconds--to unseen prey blown off the platforms as to prey they shot down themselves, indicating that the fish don’t have to know how or when the insects are shot to pinpoint their landing spot. As explained in a related ScienceNOW story by E. Pennisi, the archerfish instead use a small neural network to first take visual stock of the speed, direction, and height of airborne prey. This information is combined with signals coding the fish’s spatial position relative to the insect’s path and then conveyed to motor neurons that enable the fish to turn and move so as to end up at the right spot when the prey drops. Dr. Schuster discussed the study in a related podcast interview.


Early Brain Organization

In early development, the cortex of the mammalian brain is built layer by layer from the inside out -- starting from a one-cell-thick sheet of stem cells. In a Research Article in the 18 Jan 2008 Science, Mangale et al. revealed new insights into how cells destined for the cortex are specified at the earliest stages of brain development. Using mouse genetic mosaics -- animals engineered with different populations of genetically distinct cells -- and a series of carefully timed gene inactivation experiments, the team showed that the Lhx2 gene instructs stem cells to become cerebral cortex cells and suppresses alternative cell fates during a narrow but critical period in early development. Moreover, the team found that cortical stem cells that don’t express the Lhx2 gene turn into cortical hem cells, which induce neighboring cells to develop and organize into the hippocampus -- an intricate cortical structure important for memory formation and spatial orientation. An accompanying Perspective by E.A. Grove highlighted the study.

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In Science Signaling

(Note: Science’s STKE changed its name to Science Signaling starting with the first issue in January 2008. For more information see the Science Magazine website.)


Synapse Formation in the Balance The neuromuscular junction (NMJ), where a motor neuron communicates with a skeletal muscle fiber through the neurotransmitter acetylcholine, is a well-studied chemical synapse and has served as a tractable model system to clarify how synapse formation occurs. Proteins on both the presynaptic (neuron) and postsynaptic (muscle) side of the NMJ contribute to one of the junction’s most salient features: the high-density accumulation of acetylcholine receptors (AChRs) on the postsynaptic side. Binding of acetylcholine to AChR is the signal that triggers muscle excitation. In a Perspective in the 15 Jan 2008 issue, F. Ono highlighted a series of advances that have shed new light on the molecules and signaling pathways involved in AChR accumulation and formation of the NMJ. It turns out that two opposing pathways are involved: A pathway required to cluster AChRs, and an opposing pathway that disperses AChRs in the extrasynaptic regions of the muscle. Ono notes that progress in the field of NMJ formation has greatly benefited from the creation of knockout animals lacking specific synaptic molecules, but that more work is necessary before the whole picture becomes clear.

Also in Science Signaling this month:
-- The Science Signaling editors highlighted the top cell signaling breakthroughs of 2007, ranging from research into the signals that regulate the state of chromatin in the cell nucleus to those signals that modulate the social behavior of organisms (8 Jan 2008).
-- Natoli and Chiocca explained how ubiquitination and degradation of NF-kappaB complexes in the nucleus provide a mechanism by which pro-inflammatory responses are terminated (8 Jan 2008)
-- Fearon and Cohen-Fix discussed recent work demonstrating the involvement of the endoplasmic reticulum in cyclin regulation during the cell cycle (22 Jan 2008)