life inspired

"Traces of genetic material from non-retroviruses have unexpectedly turned up in the genomes of several mammal species, including humans." See commentary @ The Scientist. The actual report:

Horie1, M. et al [2010]. "Endogenous non-retroviral RNA virus elements in mammalian genomes". Nature 463, 84-87.

Labels: evolution, RNA, virus

"More findings confirm that small RNAs work in mysterious ways. Nearly 20 years after its discovery, RNA interference (RNAi) is part of biology’s orthodoxy. Small RNA molecules can disrupt gene expression by degrading messenger RNAs (mRNAs) on their way to becoming proteins, or otherwise interfering with translation. But the discovery that these same small RNA molecules might be able to do just the opposite—enhance gene expression—was somewhat heretical". Full article @ The Scientist.com.

Labels: RNA, transcription

I really prefer the institutional video awards...

Labels: Darwin, genetics, life

"Sitting over the microscope, whilst listening to music the idea popped up to combine
microscopic imagery with electronic music. The Scientist will certainly see more than
a carpenter, but both might enjoy the beauty. Concerning the used music, it is
Venetian Snares (oh another biological toppic) "Szamar madar", a masterpiece (in my ear) in blending classical music with electronic break core music. " Dirk Pacholsky

Labels: cell

"Darwin referred to the origin of species as "that mystery of mysteries", and despite decades of study, evolutionary biologists still cannot agree on the underlying processes that have produced the great diversity of life around us. Most contentious of all has been the question of whether speciation can occur within a population (sympatrically). On page [...] van Doorn et al. suggest that mating preferences can halt the movement of genes within a population. Their work gives credibility to the concept of sympatric speciation, which has long been the ugly duckling of evolutionary biology, and suggests that both local adaptation and sexual selection may play a far more important role in speciation than previously thought". Full commentary @ Science Magazine.

Labels: evolution, natural selection, sexual selection, speciation

Science Magazine's Breakthrough of the Year:

"Fifteen years after its discovery, Ardipithecus ramidus, the oldest known skeleton of a putative human ancestor, was finally unveiled in 11 papers in print and online in October. The discoverers of the 4.4-million-year-old fossil proposed that she was a new kind of hominin, the family that includes humans and our ancestors but not the ancestors of other living apes. They say that Ardi's unusual anatomy was unlike that of living apes or later hominins, such as Lucy. Instead, Ardi reveals the ancient anatomical changes that laid the foundation for upright walking. Not all paleoanthropologists are convinced that Ar. ramidus was our ancestor or even a hominin. But no one disputes the importance of the new evidence." Full Text @ Science Magazine.

Labels: evolution, hominim, paleontology

"Brain-Like Chip May Solve Computers' Big Problem: Energy. The future of computing may depend on embracing the chaos that defines human thinking". Full article @ discover.com.

Labels: biomimetics, computation, natural computing

"Søren Brunak at the Technical University of Denmark and Kasper Lage, now at the Broad Institute in Boston, developed a computational method to predict which proteins most likely cause a particular disease. [...] This study was one of the first to use computational methods to predict a gene–phenotype relationship." article @ TheScientist.com.

Labels: computational biology, disease, genetics, genomics, proteomics

"Swarm Chemistry" is the pilot research project run by Hiroki Sayama in the Department of Bioengineering at Binghamton University, as well as the interactive simulation software developed and used for the project.

We study the collective dynamics of heterogeneous self-propelled particle swarms and develop novel methods of decentralized control and interactive design of self-organizing decentralized systems. Swarm agents steer their motion according to a set of simple kinetic rules, similar to those in Craig Reynolds' "Boids". Each agent in our model has its own kinetic parameters that may be different from others, so that we can mix several different types of swarm agents into a single population and see how they kinetically react and form a dynamic pattern.

Labels: Artificial Life, simulation, Swarms

"The FOXP2 gene is implicated in the development of human speech and language. A comparison of the human and chimpanzee FOXP2 proteins highlights the differences in function in the two species." Full article @ Nature.com.

Labels: dna, evolution, genetics, natural language

DNA polymerase enzymes that are responsible for DNA replication can work faster than previously thought. Full paper @ PNAS.

Labels: dna, replication

"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

"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."

Labels: boolean networks, code, tools

"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).

Labels: bacteria, gene circuits

A new book outlines the ten great inventions of evolution... See summary at the scientist.com.

Labels: evolution

"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

"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

"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

"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

"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

"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".

Labels: molecular machinery, virus

"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

"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

"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

Labels: cooperation, evolution

"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]

"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

"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 is supposed to silence genes, not boost gene expression. So why are scientists seeing just that? Full article @ The Scientist

"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

"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.

"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

"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

Recommended by Ahmed:

Henry Stewart Talk on Virus and Cancer

Lecture 19 - The Immune System

Labels: immune system

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

Labels: collective behavior, immune system

"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

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

"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

Labels: emotion, robots

Complex Systems: From Chemistry to Systems Biology Special Issue — PNAS

"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

"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

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

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

"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...

Labels: computation

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

Labels: nanobots, robots, Swarms

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

Labels: robots

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

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

Labels: Cyborgs, robots

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!

Labels: life, technology

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

Labels: bio-materials, synthetic biology

Labels: collective behavior, collective intelligence

Lecture 18 - Swarms, Stigmergy and Collective Intelligence

Labels: ant colony optimization, collective behavior, stigmergy, Swarms

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

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

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 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

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

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).

Labels: ants, stigmergy

"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

"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

"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

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

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

Labels: evolution, robots

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

Labels: robots

"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

"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

"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

Labels: emergent computation, 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