Thursday, May 01, 2008

 

The Future of Computing

Silicon electronics are a staple of the computing industry, but researchers are now exploring other techniques to deliver powerful computers. Full article @ BBC NEWS | Technology



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Tuesday, April 29, 2008

 

Device 'spins silk like spiders'

A device that partially mimics the process by which spiders produce fine, yet super-strong, silks has been built. The team manufactured two genetically-engineered spider silk proteins using bacteria. These were fed into a device that consists of three channels etched into glass. More @ BBC NEWS | Science/Nature



A micrograph shows the artificial silk in more detail



Friday, April 25, 2008

 

Shedding Light on Life 

Advances in optical microscopy reveal biological processes as they unfold. Full article @ Harvard Magazine. Check out the videos too. Thanks to Erik Wennstrom for the link!



Microtubules (green) and clathrin-coated pits (red). The pits are indentations in a cell’s surface that mediate certain extracellular interactions.


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Saturday, April 19, 2008

 

Edward N. Lorenz

Edward N. Lorenz, the MIT meteorologist whose efforts to use computers to increase the precision of weather forecasts inadvertently led to the discovery of chaos theory and demonstrated that precise long-range forecasts are impossible, died of cancer Wednesday at his home in Cambridge, Mass. He was 90.
Edward N. Lorenz, 90; scientist developed influential chaos theory - Los Angeles Times




Friday, April 18, 2008

 

Your Cells Are My Cells

Many, perhaps all, people harbor a small number of cells from genetically different individuals--from their mothers and, for women who have been pregnant, from their children. What in the world do these foreigners do in the body?

Very interesting summary of maternal and fetal microchimerism. Full article at Scientific American.

A deeper article in Nature about a chimeric condition in children.




Thursday, April 17, 2008

 

US army develops robotic suits

On the big screen, films like Robocop, Universal Soldier and forthcoming release Iron Man show man-machines with superhuman powers. But in Utah they are turning science fiction into reality. Full story @BBC NEWS | Science/Nature

Friday, April 11, 2008

 

Darwinian Evolution on a Chip

Computer control of Darwinian evolution has been demonstrated by propagating a population of RNA enzymes in a microfluidic device. See article @ PLoS Biology



Friday, March 21, 2008

 

bat-inspired spy plane under development

A six-inch robotic spy plane modeled after a bat would gather data from sights, sounds and smells in urban combat zones and transmit information back to a soldier in real time. Full story @Physorg




Tuesday, March 18, 2008

 

Boston Dynamics: Big Dog

From Art:

BigDog is the alpha male of the Boston Dynamics family of robots. It is a quadruped robot that walks, runs, and climbs on rough terrain and carries heavy loads. BigDog is powered by a gasoline engine that drives a hydraulic actuation system. BigDog's legs are articulated like an animal’s, and have compliant elements that absorb shock and recycle energy from one step to the next. BigDog is the size of a large dog or small mule, measuring 1 meter long, 0.7 meters tall and 75 kg weight. Boston Dynamics: The Leader in Lifelike Human Simulation




 

Synthetic genomes brought closer to life : Article : Nature Biotechnology

An entire bacterial genome has been reconstructed by stitching together chemically synthesized DNA fragments, bringing the prospect of an artificial living organism one step closer. Full stoey @ Nature Biotechnology



Tuesday, March 11, 2008

 

Chemical brain controls nanobots

A tiny chemical "brain" which could one day act as a remote control for swarms of nano-machines has been invented. The molecular device - just two billionths of a metre across - was able to control eight of the microscopic machines simultaneously in a test. Full Story @
BBC NEWS|Science/Nature




Tuesday, March 04, 2008

 

kinetic sculptor

Thanks to Chris Schneider, I am posting the work of Theo Jansen, a Dutch "kinetic sculptor," uses genetic algorithms to model virtual life forms with only one purpose: To survive at all costs. ... [Theo] builds them at full scale out of whatever supplies are available, and sets them loose on the local beaches. They are powered solely by the wind and are designed to walk at random the hard sand of the local beaches forever.



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Mendel upended?

How the behavior of an Arabidopsis gene could overturn the classical laws of genetics. Full Story @ The Scientist




Friday, February 22, 2008

 

How Human Intelligence Evolved--Is It Science or 'Paleofantasy'? -- Balter 319 (5866): 1028a -- Science

AAAS ANNUAL MEETING: How Human Intelligence Evolved--Is It Science or 'Paleofantasy'? -- Balter 319 (5866): 1028a -- Science




 

Stealing Encrypted Data by Freezing

"A group led by a Princeton University computer security researcher has developed a simple method to steal encrypted information stored on computer hard disks." Full Story @ New York Times

I love how this method higlights the physical constarints on computing memory...



Monday, February 18, 2008

 

Engineers create new adhesive that mimics gecko toe hairs

A new anti-sliding adhesive developed by engineers at the University of California, Berkeley, may be the closest man-made material yet to mimic the remarkable gecko toe hairs that allow the tiny lizard to scamper along vertical surfaces and ceilings. Full story @ Physorg



Wednesday, December 05, 2007

 

Slides for lectures 23 and 24

Lecture 23 - Collective Intelligence and the Immune System

Lecture 24 - The Adaptive Immune System

Special Presentation - Al Abi-Haidar: Artificial Immune Systems

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Immune System Animations

Shown by Al:









T-Cell Selection Animation
Clonal Selection and Clonal Expansion

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Monday, December 03, 2007

 

links to lecture 23

Overview of the Immune System
Immunology movies at Cells Alive!
Immunobiology animations
An Interpretative Introduction to the Immune System. by S. A. Hofmeyr.
Immunology as information processing. by S. Forrest and S. A. Hofmeyr.
Immune System by Paul Bugl
Gary Carlson Biomedical images


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Wednesday, November 28, 2007

 

A cool 3D L-system rendering tool

Ken sent this 3-D L-System Rendering Tool out, and it is very cool:

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A couple of interesting programs

Ralf sent these and I must say they are great!


The first one deals with the prisoner's dilemma at it's core.




The second take an interesting view on how this inspired our view of genes and ultimately trans- and deformed our society. Btw the first 3 mins of each program are identical.


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Monday, November 19, 2007

 

Slides for Lecture 22 plus special presentation online

Lecture 22 - Swarm Algorithms

Special Presentation - Joseph Renneisen: Helbing et al "Simulating dynamical features of escape panic" Paper


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Links for Lecture 22

Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks
Mexican Wave
Simulate Escape Panic
Lane Formation in a Street


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Thursday, November 15, 2007

 

A Robotic Future

Special Issue on Robotics @ Science/AAAS | Table of Contents: 16 November 2007; 318 (5853)

See:

Making Machines That Make Others of Their Kind. (Though this piece continues the tradition of looking at self-replication as the main concept behind Von neumann's scheme, when its greatest insight is open-ended evolution).

Self-Organization, Embodiment, and Biologically Inspired Robotics: "Robotics researchers increasingly agree that ideas from biology and self-organization can strongly benefit the design of autonomous robots. Biological organisms have evolved to perform and survive in a world characterized by rapid changes, high uncertainty, indefinite richness, and limited availability of information. Industrial robots, in contrast, operate in highly controlled environments with no or very little uncertainty. Although many challenges remain, concepts from biologically inspired (bio-inspired) robotics will eventually enable researchers to engineer machines for the real world that possess at least some of the desirable properties of biological organisms, such as adaptivity, robustness, versatility, and agility".



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Robot Cockroach Tests Insect Decision-Making Behavior

"Robot cockroaches coated with pheromones are so well accepted by the household pests that the robots become part of the insects' collective decision-making process". Full article @ Science


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Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. Full article @ Science

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Is There Progress on Talking Sensibly to Machines?

Several research projects are closing in on ways to allow humans to effectively communicate with machines in natural language. Full article @ Science


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Who's the Queen?

Biologists are finding that in some social insects nature, not nurture, determines whether offspring become workers or royalty. Full article @ Science


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Wednesday, November 14, 2007

 

Slides for lecture 21 online

Lecture 21 - Swarms, Stigmergy and Collective Intelligence


Ant-based clustering


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links for lecture 21

Stigmergy
Dynamic Concepts Stigmergy Robots. Paper with rules used.
AntZ Trailer
Ant Colony Optimization Resources



Swarm-bots
Collective Robotic Intelligence Project (CRIP)
Braitenberg (reactive) Vehicles. A simulation of Braitenberg Vehicles from Rolf Pfeifer's group.

IdMind. Leonel Moura's robot art including RAP (Robot Action Painter).

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Mathematica Demos

Wolfram has prepared a very nice showcase with visualizations and implementations of several models (many with discrete dynamical systems, of course) in Mathematica.


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Insect communication/`No entry/' signal in ant foraging : Nature

"Forager ants lay attractive trail pheromones to guide nestmates to food, but the effectiveness of foraging networks might be improved if pheromones could also be used to repel foragers from unrewarding routes". Full article @ Nature


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fish-bots

The world's first autonomous robotic fish are the latest attraction at the London Aquarium. Biologically inspired by the common carp, the new designs can avoid objects and swim around a specially designed tank entirely of their own accord. Full article at BBC News.


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Bee social activity tied to gene

A gene involved in egg production also helps honeybees exhibit some crucial social behaviors that distinguish them from solitary insects, researchers report in PLoS Biology this week. Full Story @ The Scientist


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Tuesday, November 13, 2007

 

From Ants to People, an Instinct to Swarm

"By studying army ants — as well as birds, fish, locusts and other swarming animals — Dr. Couzin and his colleagues are starting to discover simple rules that allow swarms to work so well. Those rules allow thousands of relatively simple animals to form a collective brain able to make decisions and move like a single organism." Full Story @ New York Times



Monday, November 12, 2007

 

slides for lectures 20 online

Lecture 20 - Collective Behavior


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links for lecture 20

Artificial Ecosystems
Special Issue on Michael Conrad's Work
PolyWorld
Sim Life and Spore (More on Spore).

Collective Behavior
Boids
e-floys
Boids Applet
Art Boids
EPFL Laboratory for Intelligent Systems
Flocking Robots: The Seven Dwarves
Cybots Kit from the University of Reading





Particle Swarm Optimization
Particle Swarm Optimization Paper by Kennedy and Eberhart..
Particle Swarm Optimization Applet. Another one.
Particle Swarm Optimization Visualization Applet.





Termites and Ant Colony Clustering and Sorting
Artificial Termites. Another artificial termine applet.
Mitchel Resnick
termites @ Flake's site
Ant-like task allocation and recruitment in cooperative robots
Bristol Robotics Laboratory, and its previous Intelligent Autonomous Systems Laboratory


Resources
NetLogo
Swarm Simulation Environment
Vectors

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Slides for Lectures 19 online

Lecture 19 - Genetic Programming


Emergent architecture


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The Thinking Machine

Jeff Hawkins created the Palm Pilot and the Treo. Now he says he’s got the ultimate invention: software that mimics the human brain. Full article @
Wired 15.03


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Emotion robots learn from people

"Making robots that interact with people emotionally is the goal of a European project led by British scientists. Feelix Growing is a research project involving six countries, and 25 roboticists, developmental psychologists and neuroscientists:. Full Article @ BBC NEWS | Technology

The robots exhibit imprinted behaviour - following the 'mother around'

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Chips push through nano-barrier

"The next milestone in the relentless pursuit of smaller, higher performance microchips has been unveiled. Chip-maker Intel has announced that it will start manufacturing processors using transistors just 45 nanometres (billionths of a metre) wide". Full Story: BBC NEWS | Technology | Chips push through nano-barrier


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Wednesday, October 31, 2007

 

Circuits and Innate Behaviour

"In recent years, neuroscientists have made great strides in understanding the mechanisms and processes of innate behaviour as well as the circuits (both anatomical and molecular) that mediate them. For instance, a new Nature paper describes a powerful method to uniquely label individual cells within a population, and thereby distinguish adjacent neurons and cellular processes. This genetic labelling of neurons with multiple distinct colours allows for the large-scale analysis of neuronal circuits". Full web feature @ Circuits and Innate Behaviour : Web focus : Nature



 

links for lecture 18

Simple Symbolic Regression Using Genetic Programming à la John Koza
Truck Demo
Genetic Programming Resources
36 Human-Competitive Results Produced by Genetic Programming


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Tuesday, October 30, 2007

 

Student snags maths prize

The simple 2,3 Turing Machine (a head with only two states and a tape that can use 3 symbols) is shown to be capable of universal computation. Full article @ Nature News


The state of the head (up or down droplet) and the pattern of colour (orange, yellow and white) in a given row depends upon the row above. A simple start can lead to an incredibly complex picture. (Wolfram Institute)



 

Small-scale technique hits the big time :

Nanostructure-initiator mass spectrometry (NIMS), can now be used to identify individual molecules in biological samples, down to the single-cell level. Full article @
Nature News



 

Personalized genomes go mainstream

Commercial personal genome services could help people to understand more about their family medical history. Full article @ Nature News

Monday, October 29, 2007

 

Links for Lectures 17 and 18

Modeling Evolution
From Artificial Evolution to Artificial Life (1999), Tim Taylor's PhD Dissertation. Check his overview of open-ended evolution.
Introduction to Genetic Algorithms
Genetic Algorithm Viewer
Biomorph Viewer
Omnipotence
Biomorph game
Biomorphs with Crossover
Dawkins' Biomorphs
J-Biomorph
Icosystem - The Hunch Engine™
Evolvica
The Golem Project
Illustrating Evolutionary Computation with Mathematica


LifeSpacies. More. Christa Sommerer


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Artificial Chemistry

Tim Hutton's computational chemistry applet and papers.


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Digital World Reveals Architecture of Evolution

"The architecture that pervades biological networks gives them an evolutionary edge by allowing them to evolve to perform new functions more rapidly than an alternative network design, according to computer simulations conducted at the University of Chicago".
Complexity Digest 2006.32: Digital World Reveals Architecture of Evolution.


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Re-engineering Humans

We challenged experts across fields to imagine a new way to solve the problems of human aging. Full story @ The Scientist


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Selfish genes may drive out diseases

"Genetic elements that select for their own survival could establish disease-resistance genes in insect populations." Full article @ The Scientist

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Slow Down, Multitaskers; Don’t Read in Traffic

Confident multitaskers of the world, could I have your attention? Think you can juggle phone calls, e-mail, instant messages and computer work to get more done in a time-starved world? Read on, preferably shutting out the cacophony of digital devices for a while. Full article @ New York Times



 

slides for lecture 17 online

Lecture 17 - Evolutionary Algorithms

Special Presentation - Didem Kadihasanoglu: Varela, Maturana and Uribe's Autopoiesis


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Wednesday, October 24, 2007

 

What Can Systems Biology Do for You?

Four computational modeling strategies and the data that build them. Full story @ The Scientist



 

New lecture notes on evolutionary computation

7. Modeling Evolution: Evolutionary Computation


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Slides for Lecture 14 online

Self-Reproduction and Open-ended Evolution


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Monday, October 22, 2007

 

Links for Lecture 16

An implementation of Von Neumann's Self_reproducing Automata



Self-Reproducing Loops: from Langton's to Evoloop. Hiroki Sayama's Website.
Self-reproducing loops
Langton Loop Applet. Applet 2.
Bibliography on Self-replicating automata



Robot Self-replication
Cornell CCSL: Self replication


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On the right scent

Searching for the source of a smell is hampered by the absence of pervasive local cues that point the searcher in the right direction. A strategy based on maximal information could show the way. Summary at Nature. Also see the Infotaxis Full Paper.


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If Leonardo Had Made Toys



LEONARDO DA VINCI’S 15th-century vision of mechanical flight apparently never included fixed wings assisted by propellers or jet engines. His chief inspiration was birds, reflected in drawings of a flying machine fashioned to stay aloft by flapping its wings. More than 500 years later, WowWee, a robotics and entertainment products company, shares that vision. Next month, it plans to release a mass-produced, functional ornithopter, a device that flies in birdlike fashion — in this case, a radio-controlled toy that mechanically flaps its Mylar wings. Full Story @ New York Times

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New Lecture Notes

6. Von Neumann and Natural Selection (pdf)


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Wednesday, October 17, 2007

 

Slides for Leacture 15 online

Lecture 15 - Cellular Automata and Computation

Special Presentation - Mike Conover: Dorigo et al "Ant Colony Optimization-- Artificial Ants as a Computational Intelligence Technique" Paper

BTW: here is some sample C code to generate 1D CAs---such as rule 110 (there's a project in here!). This page also has code for 2D CA such as the game of life.


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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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COOPERATION, COLLECTIVES FORMATION AND SPECIALIZATION

Cooperation in spatial evolutionary game theory has revealed various interesting insights into the problem of the evolution and maintenance of cooperative behavior. In social dilemmas, cooperators create and maintain a common resource at some cost to themselves while defectors attempt to exploit the resource without contributing. (...) Here we review recent advances in the dynamics of cooperation... Adv. Complex Sys. Full Article

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A twenty-first century science

"If handled appropriately, data about Internet-based communication and interactivity could revolutionize our understanding of collective human behaviour". Full essay @A twenty-first century science : Article : Nature


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Biology's next revolution

"The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself.[...] Here we explain why we foresee such a dramatic transformation, and why we believe the molecular reductionism that dominated twentieth-century biology will be superseded by an interdisciplinary approach that embraces collective phenomena." Full article @ Biology's next revolution : Article : Nature


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The Boids!

From Mike Conover:
The Boids! » Blog Archive » The Boids #1 - If I Had A Hammer…



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