Friday, October 16, 2009
Human genome in 3D
"The three-dimensional structure of the human genome has been mapped. Job Dekker of the University of Massachusetts Medical School in Worcester, Eric Lander of the Broad Institute in Cambridge, Massachusetts, and their co-workers identified segments of the genome that tend to sit close together. [...] The team found that each chromosome weaves between two compartments: one contains active genes; the other, more compact compartment houses inactive stretches of the genome. On a larger scale, the chromosomes are tightly packed into a 'fractal globule' (pictured) that remains unknotted to allow easy access to genes."
Labels: genomics, molecular structure
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."
The software is primarly distributed as Python source code and requires that Python 2.5 (or later) be installed on the target computer."
Labels: boolean networks, code, tools
Wednesday, July 08, 2009
Bacterial Photoshop
"To take control of biological systems, Tabor et al. argue, we need the ability to predict the behavior of complex genetic programs, which are analogous in some ways to electronic circuits that allow logical operations in computers. One strategy to obtain such an understanding is to build such circuits and to observe and to model mathematically their behavior. Tabor et al. used a combination of simple genetic circuits in combination to build a program that allowed a layer of bacteria on a Petri dish to function as an "edge detector" sensitive to areas of transition between high and low illumination (light-dark)." Editor's choice at Science Signaling.
Article:
J. J. Tabor, H. M. Salis, Z. B. Simpson, A. A. Chevalier, A. Levskaya, E. M. Marcotte, C. A. Voight, A. D. Ellington. A synthetic genetic edge detection program. Cell 137, 1272–1281 (2009).
Article:
J. J. Tabor, H. M. Salis, Z. B. Simpson, A. A. Chevalier, A. Levskaya, E. M. Marcotte, C. A. Voight, A. D. Ellington. A synthetic genetic edge detection program. Cell 137, 1272–1281 (2009).
Labels: bacteria, gene circuits
Tuesday, June 16, 2009
ten great inventions of evolution
A new book outlines the ten great inventions of evolution... See summary at the scientist.com.
Labels: evolution
adaptive immunity in lamprey
"The adaptive immune system, which can recognize, attack, and remember potentially harmful microbes, may have appeared on the evolutionary scene millions of years earlier than scientists thought. The immune system of the sea lamprey, a primitive, jawless fish, contains two cell types that recognize and respond to characteristic molecules associated with invading pathogens[...]" see article at the Scientist.com.
Labels: evolution, immune system
Friday, May 29, 2009
Synthetic Gene Networks That Count
"Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers." Full paper @ Science
Thursday, May 28, 2009
A Gene Changes How Mice Squeak
"People have a deep desire to communicate with animals, as is evident from the way they converse with their dogs, enjoy myths about talking animals or devote lifetimes to teaching chimpanzees how to speak. A delicate, if tiny, step has now been taken toward the real thing — the creation of a mouse with a human gene for language." Full article @ NYTimes.com
FOXP2 Gene
Wednesday, May 27, 2009
Ancient organism, modern immunity :The Scientist [27th May 2009]
"The adaptive immune system, which can recognize, attack, and remember potentially harmful microbes, may have appeared on the evolutionary scene millions of years earlier than scientists thought. The immune system of the sea lamprey, a primitive, jawless fish, contains two cell types that recognize and respond to characteristic molecules associated with invading pathogens". Full article @ The Scientist
Immunity can be lymph-less
"Researchers have overturned the long-standing notion that lymph nodes are always necessary for launching the mammalian immune response." (though B-cell mediated immune response seems to require lymph nodes). Full pice @ The Scientist
Tuesday, May 26, 2009
A virus DNA gate
"Tailed bacterial viruses (bacteriophages) are ubiquitously distributed in nature and are likely the most abundant organisms on the biosphere ( 1 1 ). Spending most of their time outside of the host, a bacterial cell, in often hostile external environments, they come to “life” upon encountering the receptor molecules on the host cell surface. The virus consists of a head (capsid) into which the DNA (genome) is packaged and a tail that delivers the genome into the bacterium. The capsid is pressurized because of packing of highly negatively-charged, relatively rigid dsDNA to near-crystalline density (≈500 μg/mL). The internal capsid pressure, ≈6 MPa or >10 times that of bottled champagne ( 1 2 ), provides a driving force for delivery of viral genome into host cell. One of the longstanding questions in phage biology has been how these viruses contain the DNA pressure and trigger release only upon recognition of a specific host cell. In this issue of PNAS, a study by Lhuillier et al. describes the pseudoatomic structure of a DNA gate from the Bacillus subtilis bacteriophage SPP1, which “zips” the capsid after the genome is packaged and unzips it when the virus is ready to infect the host. It is a compelling story, which began with the first in vitro virus assembly experiments described by Edgar and Wood >40 years ago ( 1 4 ) and is applicable not only to phages but also to large eukaryotic viruses such as herpes viruses." Full commentary @ PNAS
The paper: "Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating".
The paper: "Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating".
Labels: molecular machinery, virus
Engineering Life
"Orthogonal, parallel and independent, systems are one key foundation for synthetic biology. The synthesis of orthogonal systems that are uncoupled from evolutionary constraints, and selectively abstracted from cellular regulation, is an emerging approach to making biology more amenable to engineering. Here, we combine orthogonal transcription by T7 RNA polymerase and translation by orthogonal ribosomes (O-ribosomes), creating an orthogonal gene expression pathway in Escherichia coli. We design and implement compact, orthogonal gene expression networks. In particular we focus on creating transcription–translation feed-forward loops (FFLs). The transcription–translation FFLs reported cannot be created by using the cells' gene expression machinery and introduce information-processing delays on the order of hours into gene expression. We refactor the rRNA operon, uncoupling the synthesis of the orthogonal 16S rRNA for the O-ribosome from the synthesis and processing of the rest of the rRNA operon, thereby defining a minimal module that can be added to the cell for O-ribosome production. The minimal O-ribosome permits the rational alteration of the delay in an orthogonal gene expression FFL. Overall this work demonstrates that system-level dynamic properties are amenable to rational manipulation and design in orthogonal systems. In the future this system may be further evolved and tuned to provide a spectrum of tailored dynamics in gene expression and investigate the effects of delays in cellular decision-making processes." Full paper: Synthesis of orthogonal transcription-translation networks — PNAS
Labels: engineering, gene circuits, systems biology
Molecular mechanisms responsible for the generation of Turing patterns
"The reaction–diffusion system is one of the most studied nonlinear mechanisms that generate spatially periodic structures autonomous. On the basis of many mathematical studies using computer simulations, it is assumed that animal skin patterns are the most typical examples of the Turing pattern (stationary periodic pattern produced by the reaction–diffusion system). However, the mechanism underlying pattern formation remains unknown because the molecular or cellular basis of the phenomenon has yet to be identified. In this study, we identified the interaction network between the pigment cells of zebrafish, and showed that this interaction network possesses the properties necessary to form the Turing pattern. When the pigment cells in a restricted region were killed with laser treatment, new pigment cells developed to regenerate the striped pattern. We also found that the development and survival of the cells were influenced by the positioning of the surrounding cells. When melanophores and xanthophores were located at adjacent positions, these cells excluded one another. However, melanophores required a mass of xanthophores distributed in a more distant region for both differentiation and survival. Interestingly, the local effect of these cells is opposite to that of their effects long range. This relationship satisfies the necessary conditions required for stable pattern formation in the reaction–diffusion model. Simulation calculations for the deduced network generated wild-type pigment patterns as well as other mutant patterns. Our findings here allow further investigation of Turing pattern formation within the context of cell biology.". Interactions between zebrafish pigment cells responsible for the generation of Turing patterns — PNAS
Labels: modeling, self-organization, turing
Evolution of cooperation by phenotypic similarity
"The advantage of mutual help is threatened by defectors, who exploit the benefits provided by others without providing benefits in return. Cooperation can only be sustained if it is preferentially channeled toward cooperators and away from defectors. But how? A deceptively simple idea is to distinguish cooperators from defectors by tagging them. It clearly is in the interest of cooperators to use some distinctive cue to assort with their like. Such an assortment, however, conflicts with the interests of the cheaters, who have every incentive to also acquire that tag. This makes for an inherently unstable situation. The history of evolutionary thinking on this issue is long. An article in this issue of PNAS by Antal et al. opens new ground by providing an in-depth analysis of a selection-mutation model." Full discussion by Karl Sigmund @ PNAS.
Full paper by Antal et al @ PNAS
Full paper by Antal et al @ PNAS
Labels: cooperation, evolution
Tuesday, May 12, 2009
Hints of a Helix, circa 1947
"An early DNA extraction experiment paved the way for James Watson and Francis Crick's discovery of the double helix". Full article @ The Scientist [2009-05-01]
Nondegraded DNA from calf thymus.
Monday, May 11, 2009
Decision-making ants
"Direct comparison of alternatives isn’t always the best way to make a decision – at least if you’re an ant. House-hunting rock ants collectively manage to choose the best nest-site without needing to study all their options, according to new research from the University of Bristol." Full press release @ Bristol University
Tuesday, May 05, 2009
The Science of Concentration
"You can drive yourself crazy trying to multitask and answer every e-mail message instantly. Or you can recognize your brain’s finite capacity for processing information, accentuate the positive and achieve the satisfactions of what Ms. Gallagher calls the focused life.". Fulla rticle @ NYTimes.com
RNA Activation
RNA is supposed to silence genes, not boost gene expression. So why are scientists seeing just that? Full article @ The Scientist
Monday, May 04, 2009
Where Is My Quantum Computer?
"The title question is echoed by electrical engineers and consumers alike. It has now been 15 years since quantum computing came to the forefront of popular science with its promise of superpowered computers for the future, so it is natural to be wondering when the first commercial products will appear on the market." Full article @ Science
Friday, May 01, 2009
Grafts guide gene exchange
"When two plants are grafted together, they share much more than water and minerals: They also swap genetic material, according to a study published in [...] Science. These findings muddy the distinction between naturally-occurring gene transfer in plants and the human-mediated mechanisms we generally refer to as genetic engineering." Article @ The Scientist
The full paper in Science.
The full paper in Science.
Thursday, April 30, 2009
On the Origin of The Immune System
"Did the immune system evolve to keep out harmful organisms, or is it like a bouncer at a nightclub, trained to allow the right microbes in and kick the less desirable ones out? In the fifth essay in Science's series in honor of the Year of Darwin, John Travis explores the evolution of the immune system." Ful article @ Science
Wednesday, April 29, 2009
Artificial bacterial flagella: Fabrication and magnetic control
"Inspired by the natural design of bacterial flagella, we report artificial bacterial flagella (ABF) that have a comparable shape and size to their organic counterparts and can swim in a controllable fashion using weak applied magnetic fields. The helical swimmer consists of a helical tail resembling the dimensions of a natural flagellum and a thin soft-magnetic “head” on one end. The swimming locomotion of ABF is precisely controlled by three orthogonal electromagnetic coil pairs. Microsphere manipulation is performed, and the thrust force generated by an ABF is analyzed. ABF swimmers represent the first demonstration of microscopic artificial swimmers that use helical propulsion. Self-propelled devices such as these are of interest in fundamental research and for biomedical applications." Full paper @ Applied Physics Letters
Tuesday, April 28, 2009
Henry Stewart Talk on Virus and Cancer
Monday, April 27, 2009
Slides for lecture 19 online
links to lecture 23
Immune System
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
T-Cell Selection Animation
Clonal Selection and Clonal Expansion
Collective Dynamics
Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks
Mexican Wave
Simulate Escape Panic
Lane Formation in a Street
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
T-Cell Selection Animation
Clonal Selection and Clonal Expansion
Collective Dynamics
Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks
Mexican Wave
Simulate Escape Panic
Lane Formation in a Street
Labels: collective behavior, immune system
Sunday, April 26, 2009
'Smart dust' to explore planets
"Tiny "smart" devices that can be borne on the wind like dust particles could be carried in space probes to explore other planets, UK engineers say." Full story @ BBC NEWS
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
Labels: biomimetics, robots, toys
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'
Wednesday, April 22, 2009
Complex Systems Special Issue on PNAS
Complex systems: Cooperative network dynamics : Article : Nature
"Nested, or hierarchically arranged, mutualisms allow ecosystems to support more species than they otherwise would. But in this and other contexts, the growth of such networks could carry a heavy price." Full article @ Nature
Major evolutionary jumps might be caused by changes in gene regulation rather than the emergence of new genes
"One of the great challenges in molecular and evolutionary biology is to explain the link between giant evolutionary leaps, such as the colonization of land by plants or the emergence of vertebrates, and the underlying genetic and genomic changes. For a long time, biologists thought that such profound changes in phenotype would be accompanied—if not driven by—equally dramatic upheavals at the genetic level. Similarly, the emergence of the flowering plants within the plant kingdom, or mammalian vertebrates, must surely have been marked by recognizable changes in the genome. Yet in fact, it turns out that the genomic changes that enabled these evolutionary developments were far more subtle—it is the regulation, rather than the modification or creation, of genes that has driven macroscopic events throughout evolution. Full article @ "EMBO Reports
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
Labels: artificial intelligence, cognitive science, natural language
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
Labels: bio-materials, biomimetics
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...
I love how this method higlights the physical constarints on computing memory...
Labels: computation
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
BBC NEWS|Science/Nature
Labels: nanobots, robots, Swarms
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
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
Labels: robots
Tuesday, April 21, 2009
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
Labels: biomimetics, robots
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
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.
Labels: life, technology
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
Labels: bio-materials, synthetic biology
Naomi Leonard on Collective Motion and Sensing Networks
Slides for lecture 18 online
Lecture 18 - Swarms, Stigmergy and Collective Intelligence
Labels: ant colony optimization, collective behavior, stigmergy, Swarms
Monday, April 20, 2009
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
Labels: genetics, social agents, Swarms
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.
Labels: animal behavior, flocking, robots
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
Labels: social agents, Swarms
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
Labels: biomimetics, robots, social agents
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.
Labels: art, genetic algorithms, robots
links for lecture 18
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).
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).
Friday, April 17, 2009
Hip hop Darwin
"This year, biologists, philosophers, and historians have been celebrating Charles Darwin's birth and his profound contributions to biology. As the year of Darwin nears its halfway point, a rapper is adding his unique Darwin tribute to the mix and making Charles Darwin a little bit more like Chuck D." Full story @ The Scientist
Thursday, April 16, 2009
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
Labels: animal behavior, ants
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
Labels: collective behavior, collective intelligence, Swarms
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.
Labels: biomimetics
Robo-salamander's evolution clues
A robot is being used by a Franco-Swiss team to investigate how the first land animals on Earth might have walked. Full story @ BBC NEWS | Science/Nature
The ethical dilemmas of robotics
If the idea of robot ethics sounds like something out of science fiction, think again, writes Dylan Evans. Scientists are already beginning to think seriously about the new ethical problems posed by current developments in robotics.
Full story @ BBC NEWS | Technology
Full story @ BBC NEWS | Technology
Labels: robots
Genes Show Limited Value in Predicting Diseases
"The era of personal genomic medicine may have to wait. The genetic analysis of common disease is turning out to be a lot more complex than expected." Full article @ NYTimes.com
Distilling Free-Form Natural Laws from Experimental Data
"For centuries, scientists have attempted to identify and document analytical laws that underlie physical phenomena in nature. Despite the prevalence of computing power, the process of finding natural laws and their corresponding equations has resisted automation. A key challenge to finding analytic relations automatically is defining algorithmically what makes a correlation in observed data important and insightful. We propose a principle for the identification of nontriviality. We demonstrated this approach by automatically searching motion-tracking data captured from various physical systems, ranging from simple harmonic oscillators to chaotic double-pendula. Without any prior knowledge about physics, kinematics, or geometry, the algorithm discovered Hamiltonians, Lagrangians, and other laws of geometric and momentum conservation. The discovery rate accelerated as laws found for simpler systems were used to bootstrap explanations for more complex systems, gradually uncovering the "alphabet" used to describe those systems." Full paper @ Science
Labels: evolutionary programming, symbolic regression
How Do Cells Count?
"Researchers provide insight into an old mystery in cell biology, and offer up new clues to understanding cancer. Scientitists have unraveled the mystery of how cells count the number of centrosomes, the structure that regulates the cell’s skeleton, controls the multiplication of cells, and is often transformed in cancer" > read full article on
ScienceDaily
ScienceDaily
Labels: emergent computation, evolution
'Reverse Evolution' In Real Time Provides Key Insights Into Basic Mechanisms Of Evolution
"Evolutionary biology tells us that replaying life's tape will not not look at all like the original. The outcome of evolution is contingent on everything that came before. Now, scientists have turned back the clock on the evolution in the fruit fly to provide key insights into the basic mechanisms of evolution. ... > read full article on ScienceDaily
Labels: evolution
Wednesday, April 15, 2009
Can evolution explain how minds work?
"Biologists have tended to assume that closely related species will have similar cognitive abilities. Johan J. Bolhuis and Clive D. L. Wynne put this evolutionarily inspired idea through its paces.". Full article @ Nature
Labels: cognitive science, evolution
Butterfly Wings Could Lead to Better Solar Panels
From Mike Conover:
"Biomimicry is the act of applying biological principles to to human designs. Velcro is the most obvious example (see more of them in our Nature-Inspired Innovations slideshow). The latest discovery has to do with butterfly wings and solar cells". Full story @ TreeHugger
"Biomimicry is the act of applying biological principles to to human designs. Velcro is the most obvious example (see more of them in our Nature-Inspired Innovations slideshow). The latest discovery has to do with butterfly wings and solar cells". Full story @ TreeHugger
Labels: bio-materials, biomimetics
Tuesday, April 14, 2009
Eusociality
"Darwin identified eusocial evolution, especially of complex insect societies, as a particular challenge to his theory of natural selection. A century later, Hamilton provided a framework for selection on inclusive fitness. Hamilton's rule is robust and fertile, having generated multiple subdisciplines over the past 45 years. His suggestion that eusociality can be explained via kin selection, however, remains contentious. I review the continuing debate on the role of kin selection in eusocial evolution and suggest some lines of research that should resolve that debate". Full article: Darwin's ‘one special difficulty’: celebrating Darwin 200 by Joan M Herbers.
Labels: evolution, multilevel selection
Monday, April 13, 2009
slides for lectures 17 online
Lecture 17 - Collective Behavior
Labels: ant clustering algorithm, boids, collective behavior, Particle Swarm Optimization
The secret, social lives of bacteria
From Mike Conover:
"Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves." See follow-up interview. TED Blog: The secret, social lives of bacteria: Exclusive interview with Bonnie Bassler
"Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves." See follow-up interview. TED Blog: The secret, social lives of bacteria: Exclusive interview with Bonnie Bassler
Labels: bacteria, collective intelligence, communication, semiotics
links for lecture 17
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
The Boids!
Particle Swarm Optimization
Particle Swarm Optimization Paper by Kennedy and Eberhart..
Particle Swarm Optimization Applet. Another one.
Particle Swarm Optimization Visualization Applet.
PSO for prediction of protein-ligand interaction
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
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
The Boids!
Particle Swarm Optimization
Particle Swarm Optimization Paper by Kennedy and Eberhart..
Particle Swarm Optimization Applet. Another one.
Particle Swarm Optimization Visualization Applet.
PSO for prediction of protein-ligand interaction
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
Labels: Artificial ecology, boids, collective behavior, flocking, Particle Swarm Optimization, Swarms
Sunday, April 12, 2009
How Human Intelligence Evolved
AAAS ANNUAL MEETING: How Human Intelligence Evolved--Is It Science or 'Paleofantasy'? -- Balter 319 (5866): 1028a -- Science
Labels: evolution, intelligence
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".
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".
Labels: embodiment, Emergence, open-ended evolution, robots, self-organization, self-reproduction, synthetic biology
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
Labels: evolution, natural computing
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.
Very interesting summary of maternal and fetal microchimerism. Full article at Scientific American.
A deeper article in Nature about a chimeric condition in children.
Bio-Plastic Factories
"Scientists at San Diego–based Genomatica, Inc., have announced success in manipulating the bacteria to directly produce butanediol (BDO), a chemical compound used to make everything from spandex to car bumpers, thereby providing a more energy-efficient way of making it without oil or natural gas." Full article @
Scientific American
Scientific American
Labels: bacteria, bio-materials
Friday, April 10, 2009
Molly mating mystery
Researchers have proposed an explanation for how three species of tiny fish manage to coexist despite having seemingly incompatible modes of reproduction. Full story @ The Scientist
Flight Plan
"To fly with precision, flying animals need to be able to maneuver and stabilize their course and orientation immediately following a change of direction. However, the dynamics of turning are poorly understood. Hedrick et al develop a framework for predicting maneuverability and stability in flying animals, then use it to predict turning dynamics of seven very different flying animals (including insects, bats, and birds). Geometrically similar animals have turning dynamics in "wingbeat time" regardless of size; fruit flies and hummingbirds both require the same number of wingbeats to finish a turn. An increase in wingbeat frequency allows animals to enhance both maneuverability and stability, two properties previously thought to be in opposition." Full article @ Science
Ribosome Profiling
"Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non–adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible." Full article @ Science
Leishmania Exploit Sex
"Protozoan parasites of the genus Leishmania (Kinetoplastida:Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis is responsible for overwhelming fatal epidemics, and cutaneous leishmaniasis can lead to destructive and life-threatening mucocutaneous lesions. Since the discovery of these disease agents more than a century ago, there has been debate as to whether they reproduce entirely clonally or undergo genetic exchange [...] That debate is now over. Akopyants et al. provide evidence for genetic exchange in Leishmania. This represents the latest in a series of discoveries of sexual cycles operating in eukaryotic pathogens previously thought to be asexual ". Full article @ Science:
Tuesday, April 07, 2009
Human genes are multitaskers
Gene Expression--Where to Start?
"To convert the encoded genetic information from eukaryotic DNA into proteins, base sequences of genes are first transcribed into RNA by RNA polymerase II. To produce functional RNA molecules, dozens of accessory factors are needed to define the proper locations for RNA polymerase II to begin and end transcription. Although we have some basic knowledge about how these factors work, it is still not possible to take a eukaryotic genome sequence and accurately predict what RNA species it will produce. Recent efforts to map and sequence "transcriptomes" have only increased the challenge by revealing a much more complex set of RNAs than expected, including many that do not produce proteins". Full article @ Science
Labels: gene regulation, genomics, RNA
A virus's virus
Researchers have discovered the first virus to infect another virus, according to a study appearing tomorrow in Nature. The new virus was found living inside a new strain of the viral giant, mimivirus. Full story @ The Scientist : NewsBlog : A virus's virus [6th August 2008]
Labels: virus
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
Wired 15.03
Labels: biomimetics, computation
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)
Labels: computation
Brain 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
Labels: neuroscience
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
Nature News
Labels: molecular structure
Personalized genomes go mainstream
Commercial personal genome services could help people to understand more about their family medical history. Full article @ Nature News
Labels: genomics
Artificial Chemistry
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.
Complexity Digest 2006.32: Digital World Reveals Architecture of Evolution.
Labels: complex networks, evolution
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
Labels: Agent-based modeling, cooperation
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
Labels: complex networks, computation
Flying dinos had bi-plane design
The first flying dinosaurs took to the air in a similar way to a World War I bi-plane, a study shows. Full Story @ BBC NEWS
The similarities may reflect a common solution to the same problem (Image: Jeff Martz)
Labels: natural design
Flea protein may repair arteries
Computing, 2016: What Won't Be Possible?
"Computer science is not only a comparatively young field, but also one that has had to prove it is really science. Skeptics in academia would often say that after Alan Turing described the concept of the ''universal machine'' in the late 1930's -- the idea that a computer in theory could be made to do the work of any kind of calculating machine, including the human brain -- all that remained to be done was mere engineering." Full Story @ NY Times
Labels: computation
Sabretooth's surprising weak bite
"The sabretooth tiger may have looked a fearsome sight with its massive canines but its reputation takes something of a knock with a new piece of research. Scientists who have studied the extinct creature's skull in detail say it had a relatively weak bite - compared with, say, a modern lion". Full Story @ BBC NEWS | Science/Nature
Finite Element Analysis of Skull: "Hot" colours indicate where the skull is stressed
Labels: biology, engineering
'Spider-man' suit secret revealed
"Natural technology used by spiders and geckos could help a human climb the side of a building or hang upside down from a roof, the analysis suggests". Full Story @ BBC NEWS | Science/Nature
Labels: biomimetics, technology
Slides for Lectures 16 online
Monday, April 06, 2009
links for lecture 16
Simple Symbolic Regression Using Genetic Programming à la John Koza
Truck Demo
Genetic Programming Resources
36 Human-Competitive Results Produced by Genetic Programming
Truck Demo
Genetic Programming Resources
36 Human-Competitive Results Produced by Genetic Programming
Labels: evolutionary algorithms, evolutionary programming
Re-engineering Humans
We challenged experts across fields to imagine a new way to solve the problems of human aging. Full story @ The Scientist
Labels: biology, synthetic biology
What Can Systems Biology Do for You?
Four computational modeling strategies and the data that build them. Full story @ The Scientist
Labels: systems biology
3-D vision of life’s dawn
"A new technique allowing virtual dissections of half-billion-year-old fossil embryos is producing the first three-dimensional images of the dawn of life. It reveals a universe of detail impossible using previous methods, and researchers said it was pushing back the frontiers of science much as the scanning electron microscope did half a century ago." Full Story @ MSNBC: Breakthrough gives 3-D vision of life’s dawn - Science - MSNBC.com
Labels: Artificial Life, origin, visualization
'Human-animal' embryo green light
"Regulators have agreed in principle to allow human-animal embryos to be created and used for research." Full story @ BBC NEWS | Health
Building the Cortex in Silicon
"An ambitious project to model the cerebral cortex in silicon is under way at Stanford. The man-made brain could help scientists understand how the most recently evolved part of our brain performs its complex computational feats, allowing us to understand language, recognize faces, and schedule the day. It could also lead to new neural prosthetics." Full article @ MIT Technology Review.
Labels: biomimetics
Sunday, April 05, 2009
Labs
I have been wanting to comment about the I485 labs for a while. We have been very impressed with some of your results! For instance, Corey Davis produced the L-System forest below, which is all procedurally generated.Good work!
Labels: L-systems
