The Mathematics of Familiar Strangers We live in an image-dominated age, and popular science abounds with visuals: eye-popping photographs, gorgeous graphics and slick information design. Amidst all this eye candy, not much attention is paid to figures accompanying articles in scientific journals and white papers. Even if they're utilitarian and low-resolution, though — or perhaps because of that — these figures are a sort of scientific folk art. They convey complex findings or principles with simplicity and grace, and sometimes even beauty. On the following pages are Wired Science's favorite research graphics of 2013. They're in no particular order, except that the first are particular favorites. Based on a population-wide analysis of bus ridership in Singapore, they depict a little-appreciated type of social network: that of "familiar strangers," or the people we encounter while going about our everyday routines. Above is the encounter network of a single bus and its 214 regular passengers. Below and at left is a single individual's "encounter network" over the course of a week; to the right are the formal chances of bumping into a familiar stranger a given time. Even at a glimpse, the figures quantify a truth intuited by commuters: beneath urban life's chaotic, seemingly random surface lies pattern and order. Citation: "Understanding metropolitan patterns of daily encounters." By Lijun Sun, Kay W. Axhausen, Der-Horng Lee, Xianfeng Huang. Proceedings of the National Academy of Sciences, Vol. 110 No. 34, August 20, 2013.

An Unexpected Engine of Evolution It's often thought that evolution is fueled by competition, with red-in-tooth-and-claw dynamics generating new, better-adapted forms and species. But sometimes — perhaps frequently — new species just happen. Above and at right is a map of greenish warbler distribution, color-coded according to local genetic signatures, around the Tibetan plateau. The warblers are what's known as a ring species, occupying a horseshoe-shaped range; as neighboring populations intermingle, genes flow around the horseshoe, but populations at its tips no longer interbreed and eventually become different species. At left is a computational model of this process. According to the model, no adaptations or differences in reproductive fitness are necessary to produce new species. Rather, they seem to arise as a function of time and space; evolution itself is a generative, diversifying force. Citation: “Evolution and stability of ring species.” By Ayana B. Martins, Marcus A. M. de Aguiar and Yaneer Bar-Yam. Proceedings of the National Academy of Sciences, March 11, 2013.

A Fossil Insect's Forest Tale At first glance, this computer re-creation of a 110 million-year-old fossil lacewing larvae might seem like eye candy. But what makes it special is the information it provides — not just about the insect's anatomy and the evolutionary history of its family, but the Early Cretaceous forests in which it lived. In modern lacewings, those frond-like shell structures catch small, fine hairs that grow on the surface of ferns, creating a fern-like camouflage coat. The fossil lacewing, surmise researchers, lived in forests burned regularly by wildfires, opening habitat in which ferns could grow. Citation: "Early evolution and ecology of camouflage in insects." By Ricardo Pérez-de la Fuente, Xavier Delclòs, Enrique Peñalver, Mariela Speranza, Jacek Wierzchos, Carmen Ascaso, and Michael S. Engel. Proceedings of the National Academy of Sciences, Vol. 109 No. 52, December 26, 2012.

Alan Turing's Fingers Nearly six decades after Alan Turing's death, the British mathematician is still celebrated as a Nazi code-breaking World War II hero and father of modern computer science. His most enduring legacy, though, may be in biology: Late in his life, Turing theorized that a particular type of chemical interaction could account for many patterns observed in nature. In subsequent decades, scientists would find these Turing patterns in everything from cheetah spots to organ formation. In the image above, Turing patterns can be seen in the development of mouse fingers, just as they're seen in fish fin development — suggesting, say researchers, that some Turing-type mechanism is an ancestral feature of vertebrate evolution. Citation: "Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism." By Rushikesh Sheth, Luciano Marcon, M. Félix Bastida, Marisa Junco, Laura Quintana, Randall Dahn, Marie Kmita, James Sharpe, Maria A. Ros. Science, Vol. 338 No. 6113, 14 December 2012.

The Sleep-Deprived Genome If you miss a night's sleep, you feel like a zombie — a phenomenon described at the genomic level in this comparison of gene expression in well-rested and sleep-deprived people. The two groups differ, not only in genes linked to sleep and circadian rhythms, but also to immune function cell, repair and stress response.

Mental CLARITY A new technique for dissolving fatty molecules in biological tissue can be used to render organs transparent (below). Known, appropriately, as CLARITY, the technique's power becomes evident when combined with fluorescent tags that affix to particular cell types. The result: translucent, color-coded brains, such as the mouse brain above, that could give researchers a literal window into neurological function and anatomy. Citation: "Structural and molecular interrogation of intact biological systems." By Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron S. Andalman, Thomas J. Davidson, Julie J. Mirzabekov, Kelly A. Zalocusky, Joanna Mattis, Aleksandra K. Denisin, Sally Pak, Hannah Bernstein, Charu Ramakrishnan, Logan Grosenick, Viviana Gradinaru & Karl Deisseroth. Nature, online publication 10 April 2013.

How Much Is a Forest Worth? Jungle cleared late in the 19th century to build the Panama Canal grew back quickly; by 2000, when the United States gave control of the canal to Panama, the forests had largely recovered. Soon, however, they were threatened by commercial and residential development. This is problematic for many reasons: not only is the juncture of North and South America a biodiversity hotspot, but canal operations rely on dry-season water flows impacted by changes in forest cover. Of course, when weighed against short-term profit, such well-meaning but fuzzy-sounding environmental arguments often lose. Enter ecosystem services, which quantifies nature's bottom-line financial worth to humans. For the map above, researchers calculated the annual value of sustainably managed Panamanian forests. They're worth far more as water-gathering, carbon-sequestering timber than as parking lots. Citation: Bundling ecosystem services in the Panama Canal watershed." By Silvio Simonit and Charles Perrings. Proceedings of the National Academy of Sciences, Vol. 110 No. 23, 4 June 2013.

Parasitic Complexity For decades, parasites were viewed primarily as pests: something to ignore, perhaps with a sniff of disgust, unless they harmed humans, in which case they were enemies. In recent years, though, scientists have come to appreciate the nuanced, often important roles played by parasites in animal life. Much of that appreciation involves the relationship between parasites and immune system function, but there's an ecological angle, too. Witness this computer-modeled food web: When parasites are included in its parameters, it's revealed as a far more complex system than it appeared without them. Citation: "Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity." By Jennifer A. Dunne, Kevin D. Lafferty, Andrew P. Dobson, Ryan F. Hechinger, Armand M. Kuris, Neo D. Martinez, John P. McLaughlin, Kim N. Mouritsen, Robert Poulin, Karsten Reise, Daniel B. Stouffer, David W. Thieltges, Richard J. Williams, Claus Dieter Zander. PLoS Biology, Vol. 11 No. 6, 11 June 2013

A Genome Is Not a Book Until very recently, genomes were treated as linear strings of genetic information — something that could be read sequentially, DNA molecule by DNA molecule, like lines in a book. Inside our cells, though, our chromosomes are tangled in fabulously complex ways, and the shape of these tangles may be inseparable from their function. New methods are being now developed to study real-time, real-shape genomes. Above is one such analysis: in a series of cell-nucleus snapshots, it captures gene activity across time and space. Activity proved to be coordinated in far-flung regions of the genome, but in ways that fluctuated over time. Structure itself is a form of information. Citation: "Micron-scale coherence in interphase chromatin dynamics." By Alexandra Zidovska, David A. Weitz, and Timothy J. Mitchison. Proceedings of the National Academy of Sciences, online publication 9 September 2013.

A Lost Underground Kingdom Soil isn't just dirt. It's rich microbial ecosystems integral to the life that grows above. In the Great Plains, these ecosystems have been almost entirely wiped out: as tallgrass prairies were converted to farmland, soil composition changed, too. The microbial relationships that sustained one of Earth's great biomes were lost to time. Yet a few prairie fragments remain; by taking DNA samples from their soils, researchers reconstructed this vanished underground world. Citation: "Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States." By Noah Fierer, Joshua Ladau, Jose C. Clemente, Jonathan W. Leff, Sarah M. Owens, Katherine S. Pollard, Rob Knight, Jack A. Gilbert, Rebecca L. McCulley. Science, Vol. 342 No. 6158, 1 November 2013.