Thursday, September 27, 2012


32 metronomes attaining spontaneous synchrony

I'm different, I'm different, I'm different... No i'm not, no I'm not, no I'm not.... 32 metronomes attaining spontaneous synchrony - Boing Boing

Thank you Mike Conover!

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Swapping DNA in the Womb

A new study finds male genes in women’s brains, the first evidence of microchimerism in the human brain. Full news article @ The Scientist

Article: Chan WFN, Gurnot C, Montine TJ, Sonnen JA, Guthrie KA, et al. (2012) Male Microchimerism in the Human Female Brain. PLoS ONE 7(9): e45592. doi:10.1371/journal.pone.0045592

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Wednesday, September 26, 2012


The early days of Pixar and L-Systems

Computer Recreations: Of fractal mountains, graftal plants and other computer graphics at Pixar (pdf) by A. K. Dewdney. Scientific American 255, 14-20 (December 1986) doi:10.1038/scientificamerican1286-14.

Thank you Max!



Proportion Control - Steven Strogatz

"No other number attracts such a fevered following as the golden ratio. Approximately equal to 1.618 and denoted by the Greek letter phi, it’s been canonized as the “Divine Proportion.” Its devotees will tell you it’s ubiquitous in nature, art and architecture. And there are plastic surgeons and financial mavens who will tell you it’s the secret to pretty faces and handsome returns. Not bad for the second-most famous irrational number. In your face, pi!" See full aricle @

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Friday, September 21, 2012


Evolving genomic transcriptional networks

"Combining transcriptomic and signaling data, we develop an evolutionary computational procedure that allows obtaining alternative genomic transcriptional regulatory network (GTRN) that still maintains its adaptability to dynamic environments. We apply our methodology to an E. coli GTRN and show that it could be rewired to simpler transcriptional regulatory structures." Full paper @

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Detecting Causality in Complex Systems

"Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. Here, 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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Genes behind feline spots and stripes

"Although long-studied, the underlying basis of mammalian coat patterns remains unclear. By studying a large number of cat species and varieties, Kaelin et al. identified two genes, Taqpep and Edn3, as critical factors in the development of feline pigment patterns."

See news piece @ NYTimes. Paper: Kaelin et al [2012]. "Specifying and Sustaining Pigmentation Patterns in Domestic and Wild Cats." Science. 337 (6101), 1536-1541.

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Saturday, September 08, 2012


The automatic chemist

"The Chematica network is a vast network that codifies and organises the known pathways through chemical space. The nodes of the network – molecules, elements and chemical reactions – are linked together by connecting reactants to products via the nexus of a known reaction. The full network contains around 7 million compound nodes and about the same number of reaction nodes". Full news article @ Chemistry World

Thursday, September 06, 2012


ENCODE Project

This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decadelong project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. “I don't think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle. Full analysis @ Science

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Wednesday, September 05, 2012


Far From ‘Junk,’ DNA Dark Matter Plays Crucial Role

"Among the many mys­ter­ies of hu­man bi­ol­ogy is why com­plex dis­eases like di­a­be­tes, high blood pres­sure and psy­chi­at­ric dis­or­ders are so dif­fi­cult to pre­dict and, of­ten, to treat. An equal­ly per­plex­ing puz­zle is why one in­di­vid­ual gets a dis­ease like can­cer or de­pres­sion, while an iden­ti­cal twin re­mains per­fect­ly healthy.
Now sci­en­tists have dis­cov­ered a vi­tal clue to un­rav­el­ing these rid­dles. The hu­man genome is packed with at least four mil­lion gene switch­es that re­side in bits of DNA that once were dis­missed as “junk” but that turn out to play crit­i­cal roles in con­trol­ling how cells, or­gans and oth­er tis­sues be­have. The dis­cov­ery, con­sid­ered a ma­jor med­ical and sci­en­tific break­through, has enor­mous im­pli­ca­tions for hu­man health be­cause many com­plex dis­eases ap­pear to be caused by tiny changes in hun­dreds of gene switch­es." Full article @ The New York Times

Tuesday, September 04, 2012


New DNA analysis shows ancient humans interbred with Denisovans

"A new high-coverage DNA sequencing method reconstructs the full genome of Denisovans — relatives to both Neandertals and humans — from genetic fragments in a single finger bone." Full news article @ Nature

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Cooperation and assortativity with dynamic partner updating

"[...] we report on a series of human subjects experiments in which groups of 24 participants played an iterated prisoner’s dilemma game where, critically, they were also allowed to propose and delete links to players of their own choosing at some variable rate. [...] we found that cooperators did punish defectors by severing ties, leading to higher levels of cooperation that persisted for longer." Full paper @ PNAS

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I585-I601 Presentation Langton and Pattee

Special Presentation - Jamie Murdock: Chris Langton's Artificial Life and discussion of Howard Pattee's Simulations, Realizations, and Theories of Life

From SciencePhotoLibrary

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