Thursday, October 25, 2012


Detecting Causality in Complex Ecosystems

"Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm)." Full article @ Science

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Tuesday, October 23, 2012


How social and genetic factors predict friendship networks

"Our results suggest that individuals with similar genotypes may not actively select into friendships; rather, they may be placed into these contexts by institutional mechanisms outside of their control. Our work highlights the fundamental role played by broad social structures in the extent to which genetic factors explain complex behaviors, such as friendships." Full articke @ PNAS

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Active, motor-driven mechanics in a DNA gel

"Cells are capable of a variety of dramatic stimuli-responsive mechanical behaviors. These capabilities are enabled by the pervading cytoskeletal network, an active gel composed of structural filaments (e.g., actin) that are acted upon by motor proteins (e.g., myosin). Here, we describe the synthesis and characterization of an active gel using noncytoskeletal components. " Full article @ PNAS

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Think Like Turing

"Biomedical researchers would benefit from emulating the logically rigorous reasoning of the late Alan Turing, British mathematician, computer scientist, and master cryptographer." Opinion: Think Like Turing | The Scientist Magazine®

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Thursday, October 11, 2012


Bacterial Quorum Sensing and Metabolic Incentives to Cooperate

"The opportunistic pathogen Pseudomonas aeruginosa uses a cell-cell communication system termed “quorum sensing” to control production of public goods, extracellular products that can be used by any community member. Not all individuals respond to quorum-sensing signals and synthesize public goods. Such social cheaters enjoy the benefits of the products secreted by cooperators. There are some P. aeruginosa cellular enzymes controlled by quorum sensing, and we show that quorum sensing–controlled expression of such private goods can put a metabolic constraint on social cheating and prevent a tragedy of the commons." Full report @ Science

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A Dynamical-Systems View of Stem Cell Biology

"During development, cells undergo a unidirectional course of differentiation that progressively decreases the number of cell types they can potentially become. Stem cells, however, keep their potential to both proliferate and differentiate. A very important issue then is to understand the characteristics that distinguish stem cells from other cell types and allow them to conduct stable proliferation and differentiation. Here, we review relevant dynamical-systems approaches to describe the state transition between stem and differentiated cells, with an emphasis on fluctuating and oscillatory gene expression levels, as these represent the specific properties of stem cells. Relevance between recent experimental results and dynamical-systems descriptions of stem cell differentiation is also discussed." Full perspective @ Science

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Developmental Pattern Formation: Insights from Physics and Biology

"The spatial organization of cell fates during development involves the interpretation of morphogen gradients by cellular signaling cascades and transcriptional networks. Recent studies use biophysical models, genetics, and quantitative imaging to unravel how tissue-level morphogen behavior arises from subcellular events. Moreover, data from several systems show that morphogen gradients, downstream signaling, and the activity of cell-intrinsic transcriptional networks change dynamically during pattern formation. Studies from Drosophila and now also vertebrates suggest that transcriptional network dynamics are central to the generation of gene expression patterns. Together, this leads to the view that pattern formation is an emergent behavior that results from the coordination of events occurring across molecular, cellular, and tissue scales. The development of novel approaches to study this complex process remains a challenge." Full review @ Science

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Tuesday, October 09, 2012


Slime Mold Memory

"The yellow slime mold Physarum polycephalum exploring an agar plate. Courtesy of Audrey Dussutour
The slime mold Physarum polycephalum remembers where it’s been, allowing the single-cell amoeboid to more efficiently navigate its environment. The key [is] a kind of externalized spatial memory system, based on the trail of translucent slime it leaves in its wake, that allows the organism to recognize and avoid already-explored areas." Full news article @ The Scientist Magazine. Original article:

Reid et al [2012] "Slime mold uses an externalized spatial 'memory' to navigate in complex environments." PNAS. 10.1073/pnas.1215037109

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Friday, October 05, 2012


Mysteries of the Brain

"For this special section, our news team identify and explore some of the brain's enduring mysteries. The scientific puzzles we chose for a closer examination here encompass medical science, evolutionary biology, cognitive science, and more—and leave many provocative questions to another time. " Special issue @ Science

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Monday, October 01, 2012


Complexity and information: Measuring emergence, self-organization, and homeostasis at multiple scales - Gershenson - 2012 - Complexity - Wiley Online Library

"we use information theory to provide abstract and concise measures of complexity, emergence, self-organization, and homeostasis. The purpose is to clarify the meaning of these concepts with the aid of the proposed formal measures. In a simplified version of the measures (focusing on the information produced by a system), emergence becomes the opposite of self-organization, while complexity represents their balance." Full article @ Complexity

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Understanding the Flight of the Bumblebee

"Bumblebees are remarkable navigators. While their flight paths may look scattered to the casual eye, all that buzzing about is anything but random. Like the travelling salesman in the famous mathematical problem of how to take the shortest path along multiple stops, bumblebees quickly find efficient routes among flowers. And once they find a good route, they stick to it. The same goes for other animals from hummingbirds to bats to primates that depend on patchy resources such as nectar and fruit. Perhaps this is not such a surprising feat for animals with relatively high brain power. But how do bumblebees, with their tiny brains, manage it? " Full synopsis @ PLOS Biology

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