life inspired

A lost essay by Wiener: "The year was 1949, and computers and robots were still largely the stuff of science fiction. Only a few farsighted thinkers imagined that they would one day become central to civilization, with consequences both liberating and potentially dire. [...] If we combine our machine-potentials of a factory with the valuation of human beings on which our present factory system is based, we are in for an industrial revolution of unmitigated cruelty. [...] We must be willing to deal in facts rather than in fashionable ideologies if we wish to get through this period unharmed. Not even the brightest picture of an age in which man is the master, and in which we all have an excess of mechanical services will make up for the pains of transition, if we are not both humane and intelligent." Full essay @ M.I.T. Scholar’s 1949 Essay on Machine Age Is Found - NYTimes.com

Labels: cybernetics, robots, Wiener

A Turing machine inside a Turing machine?

"The enormous scale of the invasion of vertebrate genomes by viral sequences has become apparent through analyses of complete genomes. Sequences derived from many kinds of RNA and DNA viruses have found a convenient resting place in host genomes during evolution, and the process is ongoing. Retroviral genomes, the major and best understood viral insertions, alone account for 6 to 14% of the genomes analyzed to date, including ∼8% of human DNA. These endogenous retroviruses (ERVs) comprise more genomic DNA than that encoding the host proteome. The functionality or otherwise of this "junk" DNA has become the focus of an intense debate. Here we consider a number of consequences of ERV acquisition (see the figure"). Full paper @ Scienve

Labels: dna, evolution, Turing machine, virus

"In 1953, Watson and Crick not only described the double-helix structure of DNA, but also embraced the idea that genes contained a code that expresses information and thereby changed our view of life. This article traces how these ideas entered biological thinking and highlights the connections between different branches of science at the time, exploring the power of metaphor in science." Full article @ Cell

Labels: cybernetics, dna, information, life

"Flies are among the most agile flying creatures on Earth. To mimic this aerial prowess in a similarly sized robot requires tiny, high-efficiency mechanical components that pose miniaturization challenges governed by force-scaling laws, suggesting unconventional solutions for propulsion, actuation, and manufacturing." Full article @ Science

Labels: bio-inspired computing, flying, insects, robots

"Logic gates evoke images of circuit boards, but cells are arguably equally good in relying on logic computations. [..] In recent years, there have been multiple reports on rationally designed, genetically encoded logic gates and circuits in living cells. [...] Two studies, [...] by Bonnet et al. and [...] Siuti et al., describe approaches that produce any of the 16 gates, including the notorious XNOR and XOR, in a compact manner by making relatively minor tweaks to the gates' genetic building blocks." Full discussion @ Science

Labels: DNA computing, logic, natural computing, synthetic biology

Very nice combination of computational biology and artificial life techniques to answer fundamental evolution questions: "Tooth development is used as a model to examine which aspects of phenotype can be optimized by natural selection; this reveals that the complexity of the relationship between genotypic and phenotypic variation can affect adaptation. " Full article @ Nature

Labels: evolution, genotype-phenotype map

"As the economy continues to chart its own tortuous, uncertain course, there seems to have been a fair amount of much-needed discussion on the kinds of skills new grads should possess." Blog post @ The Curious Wavefunction, Scientific American Blog Network,

Labels: complex systems, education

"Genome Biology speaks to a scientist involved in the discovery of the structure of DNA, and asks modern geneticists to highlight the key advances that have followed." News article @ The Scientist Magazine®. In-depth interview with Raymond Gosling @ Genome Biology.

Labels: dna, history, science

"[...]a brief history of the Evolving Cellular Automata (EvCA) project. In the EvCA project, a genetic algorithm was used to evolve cellular automata to perform certain (nontrivial) computational tasks, in an effort to gain more insight into the question: 'How does evolution produce sophisticated emergent computation in systems composed of simple components limited to local interactions?' Full article @ Complexity - Wiley Online Library

Labels: cellular automata, emergent computation, evolutionary algorithms

Another build-up on Golem on a build-up of Sim's paper: "This crazy looking thing is a simulated robot, made up of two different kinds of muscles along with bones and soft tissue for structure. This robot wasn't designed, it was evolved over a thousand virtual generations to move as fast, as far, and as functionally as possible." Full news article @ IEEE Spectrum. See the research from Jeff Clune.

Labels: evolution, evolutionary robots, morphohology, robots

"Laurent Keller's passions go far beyond ants as he taps genomics, robots, and other approaches to answer evolutionary questions." Full profile @ Science. . See also the article:

 D.P. Mersch, A.Crespi, and L. Keller [2013]. "Tracking Individuals Shows Spatial Fidelity Is a Key Regulator of Ant Social Organization". Science 1234316.[DOI:10.1126/science.1234316]

Labels: ants, collective intelligence, robots

"Collective behavior comes through the ability of neighboring objects to communicate and interact with each other. Villar et al. [...] produced three-dimensionally patterned, interconnected networks of lipid-bounded structures functionalized with transmembrane proteins, which allowed electrical communication along specific pathways." Full article @ Science

Labels: biomimetics, collective behavior, development, self-assembly

"Scientists in the US have built and tested robotic ants that they say behave just like a real ant colony. The robots do not resemble their insect counterparts; they are tiny cubes equipped with two watch motors to power the wheels that enable them to move. But their collective behaviour is remarkably ant-like." News @ BBC News

Labels: ants, bio-inspired computing, collective intelligence, computation, robots

"For the first time, synthetic biologists have created a genetic device that mimics one of the widgets on which all of modern electronics is based, the three-terminal transistor. Like standard electronic transistors, the new biological transistor is expected to work in many different biological circuit designs. Together with other advances in crafting genetic circuitry, that should make it easier for scientists to program cells to do everything from monitor pollutants and the progression of disease to turning on the output of medicines and biofuels." Full news article @ ScienceNOW

Labels: circuits, computation, computational biology, systems biology

More evidence that DNA and RNA are directly involved in learning and memory in the brain... Connectionism seems not to be enough... "Scientists studying mice reported that normal neuronal activation stimulated by exposure to new environments can cause temporary DNA breaks—suggesting that transient damage may be involved in learning and memory." Full article @ Nature Neuroscience

Labels: dna, memory, neuroscience

"In a world overwhelmed by increasing amounts of data, finding new ways to store and process information has become a necessity. Conventional silicon-based electronics has experienced rapid and steady growth, thanks to the progressive miniaturization of its basic component, the transistor, but that trend cannot continue indefinitely." Special issue @ Science

Labels: computation, information, quantum computing

'I first read the paper by Fritz Lipmann titled "Metabolic generation and utilization of phosphate bond energy" (4). This historic paper introduced the notion of the "high-energy phosphate bond," symbolized by Lipmann's famous "squiggle," together with the accompanying key concepts of group potential and group transfer. This paper, even though published 3 years before Schrödinger's celebrated book, was most probably unknown to him. It clarified for the first time the second property singled out by Schrödinger in his definition of life: its ability to extract "negative entropy," better known to chemists as "free energy," from the environment and convert it into chemical and other forms of work.' Full letter @ Science

Labels: entropy; life; information

"Development, regeneration, and even day-to-day physiology require plant and animal cells to make decisions based on their locations. The principles by which cells may do this are deceptively straightforward. But when reliability needs to be high—as often occurs during development—successful strategies tend to be anything but simple. Increasingly, the challenge facing biologists is to relate the diverse diffusible molecules, control circuits, and gene regulatory networks that help cells know where they are to the varied, sometimes stringent, constraints imposed by the need for real-world precision and accuracy." Full review @ Science

Labels: cells, development

"Where once there was the genome, now there are thousands of ’omes. Nature goes in search of the ones that matter." News article @ Nature News

Labels: biology, omics

"Behold the latest curio in the cabinet of RNA oddities: naturally occurring circular RNA molecules that influence gene expression." News article @ Nature

Labels: genomics, RNA, transcription

"bacteria, seemingly the most basic and solitary of life forms, are, in fact, communicating with each other. They are counting themselves, their cousin species, and the unrelated 'others' in their vicinity and changing their behavior as a group in response to the results of this census. Researchers who study this behavior, known as quorum sensing, believe this ability is the origin of multicellularity and communal behavior. It may also yield important practical benefits, such as new approaches for combating drug-resistant bacterial infections in humans." Full article @ PNAS

Labels: bacteria, collective behavior, quorum sensing

"Spider silk is extraordinarily strong, mollusk shells and bone are tough, and porcupine quills and feathers resist buckling. How are these notable properties achieved? The building blocks of the materials listed above are primarily minerals and biopolymers, mostly in combination; the first weak in tension and the second weak in compression. The intricate and ingenious hierarchical structures are responsible for the outstanding performance of each material. Toughness is conferred by the presence of controlled interfacial features (friction, hydrogen bonds, chain straightening and stretching); buckling resistance can be achieved by filling a slender column with a lightweight foam. Here, we present and interpret selected examples of these and other biological materials. Structural bio-inspired materials design makes use of the biological structures by inserting synthetic materials and processes that augment the structures' capability while retaining their essential features. In this Review, we explain this idea through some unusual concepts." Full article @ Science

Labels: materials; biomimetics

"Here we show that using stochastic evolutionary game theory, where agents make mistakes when judging the payoffs and strategies of others, natural selection favors fairness." Full article @ PNAS

Labels: Agent-based modeling, cooperation, evolutionary algorithms, social agents

"A quantitative description of a complex system is inherently limited by our ability to estimate the system’s internal state from experimentally accessible outputs. Although the simultaneous measurement of all internal variables, like all metabolite concentrations in a cell, offers a complete description of a system’s state, in practice experimental access is limited to only a subset of variables, or sensors. A system is called observable if we can reconstruct the system’s complete internal state from its outputs. Here, we adopt a graphical approach derived from the dynamical laws that govern a system to determine the sensors that are necessary to reconstruct the full internal state of a complex system. We apply this approach to biochemical reaction systems, finding that the identified sensors are not only necessary but also sufficient for observability. The developed approach can also identify the optimal sensors for target or partial observability, helping us reconstruct selected state variables from appropriately chosen outputs, a prerequisite for optimal biomarker design. Given the fundamental role observability plays in complex systems, these results offer avenues to systematically explore the dynamics of a wide range of natural, technological and socioeconomic systems." Full article @ PNAS

Labels: biocomplexity, complex systems, control

"The more technology advances, the more there seems to be a basic human yearning to return to nature. This is reflected in a growing number of designers, architects, and artists who are turning to nature’s example to model uses of new technology." Full article Biomimetic buildings

Labels: architecture, biomimetics

"Because there are still naysayers who question whether simple physical laws operate in living systems, we want to emphasize the existence of numerous examples in which the laws of physics have been used to provide mechanistic insights on complex behaviors of living organisms." Full letter @ Science

Labels: biocomplexity

"We develop a neuroanatomically-grounded model of salt klinotaxis, a form of chemotaxis in which changes in orientation are directed towards the source through gradual continual adjustments. We identify a minimal klinotaxis circuit by systematically searching the C. elegans connectome for pathways linking chemosensory neurons to neck motor neurons, and prune the resulting network based on both experimental considerations and several simplifying assumptions. We then use an evolutionary algorithm to find possible values for the unknown electrophsyiological parameters in the network such that the behavioral performance of the entire model is optimized to match that of the animal. Multiple runs of the evolutionary algorithm produce an ensemble of such models. We analyze in some detail the mechanisms by which one of the best evolved circuits operates and characterize the similarities and differences between this mechanism and other solutions in the ensemble." Full article @ PLOS Computational Biology

Labels: animal behavior, connectome, robots

"First published in 1917, with the modern synthesis of neo-Darwinian biology two or three decades away and genes still a nascent concept, On Growth and Form looked in some ways archaic by the time the second edition appeared — yet it continues to inspire. Thompson's agenda is captured in the book's epigraph from statistician Karl Pearson [...]: 'I believe the day must come when the biologist will — without being a mathematician — not hesitate to use mathematical analysis when he requires it.' Thompson presents mathematical principles as a shaping agency that may supersede natural selection, showing how the structures of the living world often echo those in inorganic nature." Full review @ Nature

Labels: mathematical biology

"Santa Fe Institute's Introduction to Complexity course is now enrolling!
This free online course is open to anyone, and has no prerequisites. Watch the Intro Video to learn what this course is about and how to take it"

Labels: complex systems, complexity, course

"The capacity for groups to exhibit collective intelligence is an often-cited advantage of group living. Previous studies have shown that social organisms frequently benefit from pooling imperfect individual estimates. However, in principle, collective intelligence may also emerge from interactions between individuals, rather than from the enhancement of personal estimates. Here, we reveal that this emergent problem solving is the predominant mechanism by which a mobile animal group responds to complex environmental gradients. Robust collective sensing arises at the group level from individuals modulating their speed in response to local, scalar, measurements of light and through social interaction with others. This distributed sensing requires only rudimentary cognition and thus could be widespread across biological taxa, in addition to being appropriate and cost-effective for robotic agents." Fullarticle @ SCience

Labels: collective behavior, collective intelligence

"Unusual strains of the pathogen Candida albicans have been found that contain a single set of chromosomes. Formation of such haploid strains weeds out damaged copies of genes to promote evolution in the human body. Fungi exhibit the most complex and diverse strategies for mating and sexual reproduction in nature. [...] Hickman et al. report the isolation of C. albicans strains that have shed one copy of each chromosome, leading to a haploid state. These haploid strains can mate to regenerate diploid strains, and can undergo all of the developmental life-cycle stages normally seen in the organism." Full news article @ Nature. Original article: Nature (2013) doi:10.1038/nature11865.

Labels: mating; genome organization;

"In the fire ant Solenopsis invicta, the existence of two divergent forms of social organization is under the control of a single Mendelian genomic element marked by two variants of an odorant-binding protein gene4, 5, 6, 7, 8. Here we characterize the genomic region responsible for this important social polymorphism, and show that it is part of a pair of heteromorphic chromosomes that have many of the key properties of sex chromosomes. [...] most of the genes with demonstrated expression differences between individuals of the two social forms reside in the non-recombining region. These findings highlight how genomic rearrangements can maintain divergent adaptive social phenotypes involving many genes acting together by locally limiting recombination." Full paper @ Nature 493, 664–668

Labels: ants; evolution; social behavior; collective behavior

"We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic of automata. This results in straightforward measures to quantify canalization in an automaton (micro-level), which is in turn integrated into a highly scalable framework to characterize the collective dynamics of large-scale automata networks (macro-level). This way, our approach provides a method to link micro- to macro-level dynamics -- a crux of complexity. Several new results ensue from this methodology: uncovering of dynamical modularity (modules in the dynamics rather than in the structure of networks), identification of minimal conditions and critical nodes to control the convergence to attractors, simulation of dynamical behaviour from incomplete information about initial conditions, and measures of macro-level canalization and robustness to perturbations. We exemplify our methodology with a well-known model of the intra- and inter cellular genetic regulation of body segmentation in Drosophila melanogaster. We use this model to show that our analysis does not contradict any previous findings. But we also obtain new knowledge about its behaviour: a better understanding of the size of its wild-type attractor basin (larger than previously thought), the identification of novel minimal conditions and critical nodes that control wild-type behaviour, and the resilience of these to stochastic interventions. Our methodology is applicable to any complex network that can be modelled using automata, but we focus on biochemical regulation and signalling, towards a better understanding of the (decentralized) control that orchestrates cellular activity -- with the ultimate goal of explaining how do cells and tissues 'compute'." Full pre-print:

M. Marques-Pita and L.M. Rocha [2013]. "Canalization and control in automata networks: body segmentation in Drosophila Melanogaster". PLOS ONE, In Press.

Labels: automata, biocomplexity, boolean networks, canalization, complex systems, modularity, self-organization

"Our knowledge of the principles by which organ architecture develops through complex collective cell behaviours is still limited. Recent work has shown that the shape of such complex tissues as the optic cup forms by self-organization in vitro from a homogeneous population of stem cells. Multicellular self-organization involves three basic processes that are crucial for the emergence of latent intrinsic order. Based on lessons from recent studies, cytosystems dynamics is proposed as a strategy for understanding collective multicellular behaviours, incorporating four-dimensional measurement, theoretical modelling and experimental reconstitution." Full paper @ Nature

Labels: develo, self-organization, stem cells

"Researchers have done it again—encoding 5.2 million bits of digital data in strings of DNA and demonstrating the feasibility of using DNA as a long-term, data-dense storage medium for massive amounts of information." News article @ The Scientist Magazine®. Original article:


N. Goldman et al., “Towards practical, high-capacity, low-maintenance information storage in synthesized DNA,” Nature, doi: 10.1038/nature.11875, 2013.

Labels: DNA; memory;

"Dissecting the genetic basis of a species' physical features is regular research fodder. So why not do the same for the inanimate objects that some animals produce, such as beehives or beaver dams? On page 402 of this issue, Weber and colleagues show that the sophisticated burrows of oldfield mice can be understood using straightforward genetics, shedding light on how this classic 'extended phenotype' evolved ()." News article @ Nature. Full article: J. N. Weber et al. Nature 493, 402–405; 2013

Labels: genetics; evolution;

On December 11th, 2012, the Calouste Gulbenkian Foundation hosted The Alan Turing Centenary Symposium, organized by the Instituto Gulbenkian de Ciência, to celebrate Alan Turing's centenary and discuss his legacy. Among the invited speakers were Sidney Brenner, Nobel Laureate in Physiology or Medicine 2002, the writer David Leavitt, and the scientists Luís Rocha (Instituto Gulbenkian de Ciência and Indiana University), António Machiavelo (Universidade do Porto) and Christof Teuscher (Portland State University). A video library with all the talks at this conference is available. The videocasts are also shown below in three blocks:

Labels: artificial intelligence, Artificial Life, biocomplexity, computation, informatics, turing

"How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates." Full Article @ Science

Labels: evolution, Phenotypic complexity, RNA, vertebrates

"The human brain is exceedingly complex and studying it encompasses gathering information across a range of levels, from molecular processes to behavior. The sheer breadth of this undertaking has perhaps led to an increased specialization of brain research and a concomitant fragmentation of our knowledge. A potential solution is to integrate all of this knowledge into a coherent simulation of the brain". Full article @ Science

Labels: brain, cognitive science, complex systems, simulation

"Before he became America's first de facto science adviser and before he helped lay the foundation for the National Science Foundation, Vannevar Bush was a professor of Electrical Engineering and, eventually, dean of Engineering and vice president at the Massachusetts Institute of Technology (MIT). In those capacities, he came in contact with some of the nation's best and brightest minds in their formative years. But after two decades in such a rarified academic environment, Bush had become disenchanted by the increasing specialization of undergraduate curricula in science and engineering in America (1). He felt that education in these fields placed too much emphasis on information transferral from teacher to student and too little on deep understanding and intellectual synthesis by the student. Bush was among the first to anticipate that massive amounts of information would someday be universally and readily available to all, such that our ability to communicate knowledge through classes would become far less important than our ability to inspire students to do something creative, and valuable, with it." Full article @ Science

Labels: complex systems, cybernetics, education, simulation

I485/H400 - Lecture 23 - The Adaptive Immune System and Artificial Immune Systems
I585/I601 - Lecture 22 - The Immune System

Labels: artificial immune systems, immune system

I485/H400 - Lecture 21 - Collective Intelligence

I485/H400 - Lecture 22 - The Immune System

I585/I601 - Lecture 21 - Swarms, Stigmergy, and Collective Intelligence

Labels: Ant Colony optimization, art, collective intelligence, 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

Labels: immune system

Collective Dynamics

Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks and Simulation of Multi-lane traffic. A video with stop-and.go dynamics
Mexican Wave
Simulate Escape Panic. Crowd Turbulence
Lane Formation in a Street

Labels: art, collective intelligence, social dynamics