Thursday, February 28, 2013


Big biology: The ’omes puzzle

"Where once there was the genome, now there are thousands of ’omes. Nature goes in search of the ones that matter." News article @ Nature News

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Circular RNAs throw genetics for a loop

"Behold the latest curio in the cabinet of RNA oddities: naturally occurring circular RNA molecules that influence gene expression." News article @ Nature

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Thursday, February 21, 2013


Quorum sensing

"bacteria, seemingly the most basic and solitary of life forms, are, in fact, communicating with each other. They are counting themselves, their cousin species, and the unrelated 'others' in their vicinity and changing their behavior as a group in response to the results of this census. Researchers who study this behavior, known as quorum sensing, believe this ability is the origin of multicellularity and communal behavior. It may also yield important practical benefits, such as new approaches for combating drug-resistant bacterial infections in humans." Full article @ PNAS

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Friday, February 15, 2013


Structural Biological Materials

"Spider silk is extraordinarily strong, mollusk shells and bone are tough, and porcupine quills and feathers resist buckling. How are these notable properties achieved? The building blocks of the materials listed above are primarily minerals and biopolymers, mostly in combination; the first weak in tension and the second weak in compression. The intricate and ingenious hierarchical structures are responsible for the outstanding performance of each material. Toughness is conferred by the presence of controlled interfacial features (friction, hydrogen bonds, chain straightening and stretching); buckling resistance can be achieved by filling a slender column with a lightweight foam. Here, we present and interpret selected examples of these and other biological materials. Structural bio-inspired materials design makes use of the biological structures by inserting synthetic materials and processes that augment the structures' capability while retaining their essential features. In this Review, we explain this idea through some unusual concepts." Full article @ Science


Tuesday, February 12, 2013


Evolution of fairness in the one-shot anonymous Ultimatum Game

"Here we show that using stochastic evolutionary game theory, where agents make mistakes when judging the payoffs and strategies of others, natural selection favors fairness." Full article @ PNAS

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Observability of complex systems

"A quantitative description of a complex system is inherently limited by our ability to estimate the system’s internal state from experimentally accessible outputs. Although the simultaneous measurement of all internal variables, like all metabolite concentrations in a cell, offers a complete description of a system’s state, in practice experimental access is limited to only a subset of variables, or sensors. A system is called observable if we can reconstruct the system’s complete internal state from its outputs. Here, we adopt a graphical approach derived from the dynamical laws that govern a system to determine the sensors that are necessary to reconstruct the full internal state of a complex system. We apply this approach to biochemical reaction systems, finding that the identified sensors are not only necessary but also sufficient for observability. The developed approach can also identify the optimal sensors for target or partial observability, helping us reconstruct selected state variables from appropriately chosen outputs, a prerequisite for optimal biomarker design. Given the fundamental role observability plays in complex systems, these results offer avenues to systematically explore the dynamics of a wide range of natural, technological and socioeconomic systems." Full article @ PNAS

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Biomimetic buildings

"The more technology advances, the more there seems to be a basic human yearning to return to nature. This is reflected in a growing number of designers, architects, and artists who are turning to nature’s example to model uses of new technology." Full article Biomimetic buildings

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Monday, February 11, 2013


Physical Laws Shape Biology

"Because there are still naysayers who question whether simple physical laws operate in living systems, we want to emphasize the existence of numerous examples in which the laws of physics have been used to provide mechanistic insights on complex behaviors of living organisms." Full letter @ Science



Connecting a Connectome to Behavior

"We develop a neuroanatomically-grounded model of salt klinotaxis, a form of chemotaxis in which changes in orientation are directed towards the source through gradual continual adjustments. We identify a minimal klinotaxis circuit by systematically searching the C. elegans connectome for pathways linking chemosensory neurons to neck motor neurons, and prune the resulting network based on both experimental considerations and several simplifying assumptions. We then use an evolutionary algorithm to find possible values for the unknown electrophsyiological parameters in the network such that the behavioral performance of the entire model is optimized to match that of the animal. Multiple runs of the evolutionary algorithm produce an ensemble of such models. We analyze in some detail the mechanisms by which one of the best evolved circuits operates and characterize the similarities and differences between this mechanism and other solutions in the ensemble." Full article @ PLOS Computational Biology

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Wednesday, February 06, 2013


In retrospect: On Growth and Form

"First published in 1917, with the modern synthesis of neo-Darwinian biology two or three decades away and genes still a nascent concept, On Growth and Form looked in some ways archaic by the time the second edition appeared — yet it continues to inspire. Thompson's agenda is captured in the book's epigraph from statistician Karl Pearson [...]: 'I believe the day must come when the biologist will — without being a mathematician — not hesitate to use mathematical analysis when he requires it.' Thompson presents mathematical principles as a shaping agency that may supersede natural selection, showing how the structures of the living world often echo those in inorganic nature." Full review @ Nature


Tuesday, February 05, 2013


Complexity Explorer

"Santa Fe Institute's Introduction to Complexity course is now enrolling!
This free online course is open to anyone, and has no prerequisites. Watch the Intro Video to learn what this course is about and how to take it"

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Sunday, February 03, 2013


Emergent Sensing

"The capacity for groups to exhibit collective intelligence is an often-cited advantage of group living. Previous studies have shown that social organisms frequently benefit from pooling imperfect individual estimates. However, in principle, collective intelligence may also emerge from interactions between individuals, rather than from the enhancement of personal estimates. Here, we reveal that this emergent problem solving is the predominant mechanism by which a mobile animal group responds to complex environmental gradients. Robust collective sensing arises at the group level from individuals modulating their speed in response to local, scalar, measurements of light and through social interaction with others. This distributed sensing requires only rudimentary cognition and thus could be widespread across biological taxa, in addition to being appropriate and cost-effective for robotic agents." Fullarticle @ SCience

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