Monday, November 28, 2011


Winged Robots

Winged Robots Hint at the Origins of Flight - ScienceNOW

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Good introductory videos on network analysis :Annenberg Networks Network

Good introductory videos on network analysis by Mark Newman


Nature-inspired collective intelligence in theory and practice

A special issue worth looking into: ScienceDirect - Information Sciences : Nature-inspired collective intelligence in theory and practice


Friday, November 25, 2011


Exploring Complexity

Melanie Mitchell's blog withe perspectives on the sciences of complexity: Exploring Complexity

Tuesday, November 15, 2011


Computation Emerges from Adaptive Synchronization of Networking Neurons

"we show that computation can be seen as a feature emerging from the collective dynamics of an ensemble of networking neurons, which interact by means of adaptive dynamical connections. Namely, by associating logical states to synchronous neuron's dynamics, we show how the usual Boolean logics can be fully recovered, and a universal Turing machine can be constructed. Furthermore, we show that, besides the static binary gates, a wider class of logical operations can be efficiently constructed as the fundamental computational elements interact within an adaptive network, each operation being represented by a specific motif. Our approach qualitatively differs from the past attempts to encode information and compute with complex systems, where computation was instead the consequence of the application of control loops enforcing a desired state into the specific system's dynamics. Being the result of an emergent process, the computation mechanism here described is not limited to a binary Boolean logic, but it can involve a much larger number of states. As such, our results can enlighten new concepts for the understanding of the real computing processes taking place in the brain." Full paper @ PLoS ONE


Daniel Wolpert: The real reason for brains | Video on

Daniel Wolpert: The real reason for brains | Video on


Allan Jones: A map of the brain | Video on

Allan Jones: A map of the brain | Video on


Martin Hanczyc: The line between life and not-life | Video on

Martin Hanczyc: The line between life and not-life | Video on



Parasites drove human genetic variation : Nature News & Comment

Adapting to pathogens was more important than climate and diet in driving natural selection. News article @Nature News


Structure and dynamics of interactions in schooling fish

"The interactions revealed here may help account for the rapid changes in speed and direction that enable real animal groups to stay cohesive and amplify important social information". Full paper @ PNAS

Katz et al [2011]. PNAS November 15, 2011 vol. 108 no. 46 18720-18725

See also:

"Collective motion, where large numbers of individuals move synchronously together, is achieved when individuals adopt interaction rules that determine how they respond to their neighbors’ movements and positions. These rules determine how group-living animals move, make decisions, and transmit information between individuals. Nonetheless, few studies have explicitly determined these interaction rules in moving groups, and very little is known about the interaction rules of fish. Here, we identify three key rules for the social interactions of mosquitofish (Gambusia holbrooki)". Herbert-Read et al [2011].PNAS November 15, 2011 vol. 108 no. 46 18726-18731

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Monday, November 14, 2011


Evolution of Figures

Could you paint a replica of the Mona Lisa using only 50 semi transparent polygons? Yes, see: Genetic Programming: Evolution of Mona Lisa by Roger Alsing. See also the FAQ and source code.

Another implementation by Pierre Lindenbaun. See the Java source code.

Tuesday, November 08, 2011


Comparing shapes, understanding evolution

"The study of shape has intrigued some of the brightest minds of humanity, from Leonardo Da Vinci and Carl Friedrich Gauss to some of the top scientists of the modern era. [...]This is the topic addressed by the work of Boyer et al. (5) in PNAS, with a unique interdisciplinary team of anthropologists, archaeologists, computer scientists, and mathematicians." See commentary @ PNAS.

See also: Boyer DM, et al. (2011) Algorithms to automatically quantify the geometric similarity of anatomical surfaces. Proc Natl Acad Sci USA 108:18221–18226.

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Monday, November 07, 2011


Tinkering With Life

A decade's worth of engineering-infused biology. Full article @ The Scientist.

See also: Evolving Engineering: Exploiting the unique properties of living systems makes synthetic biologists better engineers, By George M. Church. and Synthesizing Life: Designing genomes from scratch will be the next revolution in biology, by J. Craig Venter.

Thursday, November 03, 2011


The Language of Dendrites

"Contrary to the assumption of McCulloch and Pitts, synapses are not made onto the soma (cell body) but onto dendrites, protrusions from the cell body separating the input and the action potential initiation zone. Dendrites filter, transform, and compute thresholds of synaptic input and can, in theory, implement basic arithmetic operations by themselves (2). I first became interested in dendrites during my Ph.D. work. Monitoring the properties of single synapses in hippocampal neurons, I found that dendrites can implement a negative feedback that regulates the amount of input each branch receives (3). Dendrites can thus independently process and regulate input information. Can these properties be used by single neurons to perform high-order computations?" Full article @ Science


Understanding the Human Brain

"Like most fields in biology, neuroscience is succumbing to an “epidomic” of data collecting. There are major projects under way to completely characterize the proteomic, metabolomic, genomic, and methylomic signatures for all of the different types of neurons and glial cells in the human brain. In addition, “connectomics” plans to provide the complete network structure of brains, and “synaptomics” aims to uncover all molecules and their interactions at synapses. This is a good time to pause and ask ourselves what we expect to find at the end of this immense omic brainbow." Full Editorial @ Science


pybool 1.1

pybool 1.1 for Linux - A package to infer Boolean networks - Softpedia

Tuesday, November 01, 2011


Transcription and Translation

A video shown in Class :


How a brain-manipulating virus turns caterpillars into zombies

"Behavior-modifying parasites are getting more press as of late, with reports of zombie ants and Toxoplamsa-infected rats that become sexually attracted to cats. But it's not just organisms that manipulate their hosts; there's at least one behavior-modifying virus. Just as the parasitic organisms do, baculoviruses change their host's behavior for their own benefit, ensuring their propagation. When infected with a baculovirus, European gypsy moth caterpillars behave in a way that healthy gypsy moth caterpillar never would." Full news article @ ARS Technica

Paper: Kelli Hoover, Michael Grove, Matthew Gardner, David P. Hughes, James McNeil, and James Slavicek [2011]. "A Gene for an Extended Phenotype". Science. 333 (6048), 1401.

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