Saturday, October 30, 2010


Robot 'Hands' Write Without Fingers

"It turns out that opposable thumbs aren't critical for getting a good grip. Neither are fingers. Scientists have created a robotic arm that can do everything from serve drinks to draw pictures even though it has no digits.[...] Their robotic hand [...] is a thin rubber sack filled with coffee grains or small glass spheres." News piece @ ScienceNOW

Full Paper: Brown et al [2010] "Universal robotic gripper based on the jamming of granular material". PNAS, DOI: 10.1073/pnas.1003250107.

Thursday, October 28, 2010


What Is Epigenetics?

"The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)–genetics." Introduction to special issue of Science on Epigenetics.

RNA-directed deposition of epigenetic signals.


Autonomous Robotics Course

Autonomous Robotics -COGS Q360, CSCI B355 - Spring 2010

Class: Tuesdays and Thursdays, 9:30 - 10:45; Fridays, 9:05-9:55
Location: 833 Eigenmann
Instructor: Randall D. Beer
Autonomous Robotics


Human-robot interaction

Spring 2011

Selma Sabanovic
Assistant Professor
School of Informatics and Computing
Human-robot interaction: Debates and Challenges

Wednesday, October 27, 2010


Leopards change their spots

"William Allen and his colleagues at the University of Bristol, UK, analysed images of coat patterns in 35 cat species, including leopards, jaguars (pictured) and tigers. They used a mathematical model to link pattern development and function to habitat and behavioural traits." Full highlight @ Nature

Full paper: Allen et al [2010] "Why the leopard got its spots: relating pattern development to ecology in felids". Proc. R. Soc. B doi:10.1098/rspb.2010.1734.


Engineering of a synthetic electron conduit in living cells

"One idea for biosensors and bioenergy is to combine living cells with inorganic materials. Researchers have taken a step towards this goal by engineering the bacterium Escherichia coli to transmit electrons to inorganic materials." From

Full Paper: Engineering of a synthetic electron conduit in living cells — PNAS

An engineered Escherichia coli strain (yellow) attaching to solid iron oxide (black). (from ScienceDaily)


Shivering Shavenbaby

"Are redundant copies of noncoding DNA sequences due to poor genomic housekeeping, or do they function to improve the organism’s chances of survival?". Full news article @ The Scientist.

Full article: N. Frankel et al., “Phenotypic robustness conferred by apparently redundant transcriptional enhancers,” Nature, 466:490-93, 201.


Directing attention via machine

"A new brain-machine interface demonstrates how humans direct their thoughts". Full news article @
The Scientist

Full paper: Cerf et al [2010] "On-line, voluntary control of human temporal lobe neurons." Nature 467 , 1104–1108

Monday, October 25, 2010


A Turing Machine - Overview

Very nice physical implementation...


Boolean Network Modeling

"The goal of this software package is to provide intuitive and accessible tools for simulating biological regulatory networks in a boolean formalism. Using this simulator biologist and bioinformaticians can specify their system in a simple textual language then explore various dynamic behaviors via a web interface or an application programming interface (API) each designed to facilitate scientific discovery, data collection and reporting.

The software is primarly distributed as Python source code and requires that Python 2.5 (or later) be installed on the target computer."

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WolframTones: An Experiment in A New Kind of Music

Interesting use of cellular automata to make music. And you can download them as ringtones for your cell! Wolfram has extended cellular automata to every conceivable area...If you want to read his book (I had it autographed :) let me know! Its huge, over 1K pages.

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Thursday, October 14, 2010


Custom-Built Supercomputer Brings Protein Folding Into View

"Scientists have long been frustrated in their efforts to use computers to simulate the atomic detail of how proteins fold into their three-dimensional structures. The computing demands for simulating all the motions of a protein's atoms and the surrounding water are so high that scientists have had difficulty tracking the myriad atomic wiggles and gyrations for long enough to see the complete folding process. But now help is on the way. On page 341, computational biologists led by computer scientist and former hedge fund manager David Shaw report that they ran a specially built supercomputer for about 3 weeks to simulate a relatively small protein going through 15 rounds of folding and unfolding over 200 microseconds. They also tracked the folding gyrations of a similarly sized protein for more than a millisecond." Full news article @ Science

Wednesday, October 13, 2010


Why sex evolved

"Despite the obvious benefits of sex, it's an activity that's biologically disadvantageous under most conditions. Now, a new study published [...] in Nature helps explain why sex may have evolved, despite its downside". Full news story @ 5The Scientist


The green city that has a brain

"An eco-city in Portugal that its makers are aiming to build by 2015 takes its cues from the nervous system". Full article @ New Scientist

Tuesday, October 12, 2010


Lamarck's treatise at 200

"Fifty years before On the Origin of Species, a confusing, tiresome and prescient book laid the foundations of modern evolutionary theory, write Dan Graur, Manolo Gouy and David Wool.". Full book review @ Nature


Bacteria form electric circuits?

"Bacterial hair-like extensions appear to be capable of conducting electricity down their length, possibly playing a key role in respiration by allowing the cells to dump electrons at distances far outside the cell." Read more @ The Scientist. Full paper:

H.W. Harris, M.Y. El-Naggar, O. Bretschger, M. Ward, M. Romine, A. Obraztsova, and K.H. Nealson. Electrokinesis is a microbial behavior that requires extracellular electron transport, PNAS, 107(1), 326-331, 2010 doi:10.1073/pnas.0907468107

See NanoBio group at USC

Friday, October 08, 2010


Killer Bots Are Getting Human -- Bohannon 330 (6000): 30 -- Science

"Conscious Robots, a team of Spanish computer scientists, won the third annual 2K BotPrize, a competition to create artificially intelligent game-playing agents that can fool a judge into believing they are human. Its bot represents a leap forward for game AI because the team used machine consciousness rather than just mimicking human behaviors. It was incorrectly identified as human by the judges 32% of the time. By comparison, one human player was incorrectly identified as a machine 35% of the time." Fulla= article @ Killer Bots Are Getting Human -- Bohannon 330 (6000): 30 -- Science


The Gates of Immortality

"Could there be a mathematical description that might capture and explain biology’s fallibility? The theory of evolution, as formulated by Darwin, stands in its remarkable simplicity as an example of a single set of rules applicable to all biological systems. This theory, in its original expression, was remarkably devoid of mathematics (although it has since been described with great success in mathematical models). But biology in general appears to be so subject to deviations, exceptions, and diversification, rather than convergences, that it is difficult to derive simple and general principles. Nonetheless, it was this possibility of convergence that drove me to biology in the first place.

Read more:The Gates of Immortality - The Scientist - Magazine of the Life Sciences

Thursday, October 07, 2010

Featuring the latest in theoretical and applied research, evo* topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimization, evolutionary algorithms, machine learning and data mining techniques in the biosciences, in numerical optimization, in music and art domains, in image analysis and signal processing, in hardware optimization and in a wide range of applications to scientific, industrial, financial and other real-world problems.

Monday, October 04, 2010


ECAL 2011, 20th anniversary edition. Back to the origins of ALife

"ECAL, the European Conference on Artificial Life, is a biennial event that alternates with the US-based Alife conference series." ECAL 2011, 20th anniversary edition. Back to the origins of ALife


How to visually interpret biological data using networks

"Networks in biology can appear complex and difficult to decipher. Merico et al. illustrate how to interpret biological networks with the help of frequently used visualization and analysis patterns." Full article @ Nature Biotechnology

Mathematical representation of networks and three alternate visualizations of the same data. (Nature Biotechnology 27, 921 - 924 (2009))

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