Thursday, October 20, 2016


Predictability and hierarchy in Drosophila behavior

Very cool hierarchical behavior control strategy; could be a general principle across species. "[...] we show that fly behavior exhibits multiple time scales and is organized into a hierarchical structure that is indicative of its underlying behavioral programs and its changing internal states." Full paper @ PNAS

Thursday, May 19, 2016


Learning from nature how to land aerial robots

"One of the main challenges for aerial robots is the high-energy consumption of powered flight, which limits flight times to typically only tens of minutes for systems below 2 kg in weight (1). This limitation greatly reduces their utility for sensing and inspection tasks, where longer hovering times would be beneficial. Perching onto structures can save energy and maintain a high, stable observation or resting position, but it requires a coordination of flight dynamics and some means of attaching to the structure. Birds and insects have mastered the ability to perch successfully and have inspired perching robots at various sizes. [Graule et al.] describe a perching robotic insect that represents the smallest flying robot platform that can autonomously attach to surfaces. At a mass of only 100 mg, it combines advanced flight control with adaptive mechanical dampers and electro-adhesion to perch on a variety of natural and artificial structures." Full perspective @ Science. See full article: M. A. Graule et al., Science 352, 978 (2016).

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Friday, April 01, 2016


Genetic circuit design automation

"As synthetic biology techniques become more powerful, researchers are anticipating a future in which the design of biological circuits will be similar to the design of integrated circuits in electronics. Nielsen et al. describe what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering." Full article @ Science

Friday, March 11, 2016


Bio-inspired rubber ball tires

"With magnetic levitation and a 3D-printed tread pattern inspired by brain coral, the sphere-shaped Eagle-360 could be the biggest advance to tyre tech since vulcanised rubber." Full news article @ BBC

Wednesday, February 24, 2016


Sex speeds adaptation

"We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations." Full article @ Nature

Tuesday, February 23, 2016


Cockroaches inspire a soft, legged robot

"Cockroaches intrude everywhere by exploiting their soft-bodied, shape-changing ability. We discovered that cockroaches traversed horizontal crevices smaller than a quarter of their height in less than a second by compressing their bodies’ compliant exoskeletons in half. Once inside vertically confined spaces, cockroaches still locomoted rapidly at 20 body lengths per second using an unexplored mode of locomotion—body-friction legged crawling. Using materials tests, we found that the compressive forces cockroaches experience when traversing the smallest crevices were 300 times body weight. Cockroaches withstood forces nearly 900 times body weight without injury, explaining their robustness to compression. Cockroach exoskeletons provided inspiration for a soft, legged search-and-rescue robot that may penetrate rubble generated by tornados, earthquakes, or explosions." Full article @ PNAS

Sunday, January 10, 2016


The physics of life

Physicists and their quest for laws of the macro-level behavior of life, while biologists seek micro-level genetic control---in my view, control has been more useful than understanding, but both are fascinating. "From flocking birds to swarming molecules, physicists are seeking to understand 'active matter' — and looking for a fundamental theory of the living world." Full news article @ Nature News & Comment


The Evolution of Cooperation

"When and why individual organisms work together at the game of life, and what keeps cheaters in check." Full review @ The Scientist Magazine®

Wednesday, December 23, 2015


CRISPR genome-editing, Breakthrough of the year

Yes, genes are material symbolic representations, we say: "accomplishments in genome editing across biological disciplines have been so remarkable that the method known as clustered regularly interspaced short palindromic repeats—or CRISPR—is Science's 2015 Breakthrough of the Year." News article @ Science

Tuesday, November 24, 2015


CRISPR-Powered Malaria Mosquito Gene Drive

"Using the precision gene-editing tool, researchers demonstrate an ability to create large populations of malaria parasite–resistant mosquitoes."CRISPR-Powered Malaria Mosquito Gene Drive | The Scientist Magazine®

Monday, November 23, 2015


Circuits within living plants

"Researchers have crafted flexible electronic circuits inside a rose. Eventually such circuitry may help farmers eavesdrop on their crops and even control when they ripen. The advance may even allow people to harness energy from trees and shrubs not by cutting them down and using them for fuel, but by plugging directly into their photosynthesis machinery." Full news article @ cience/AAAS | News

Wednesday, September 02, 2015


Eukaryotes really are special, and mitochondria are why

"Eukaryotes have four to five orders-of-magnitude more energy per gene than bacteria, meaning the number of proteins they can express increases by that much. Genome size is secondary." Letter @ PNAS. relevant original Full paper @ Nature.

Thursday, August 20, 2015


Avery Discovers Genes Are Made of DNA

Anyone who has taken one of my classes knows about this landmark experiment, but Dr. Flexner's Suitcase encapsulates it in a nutshell rather well. Besides, never too much to insist on ansering the DNA question right! The answer to "Who discovered DNA?" summarized @ Dr. Flexner's Suitcase

Wednesday, August 19, 2015


web-like eukaryotic genome evolution

"A comparative genomic study shows that, during evolution, nucleus-containing cells acquired DNA from bacteria primarily by endosymbiosis — the uptake and integration of one cell by another." Full news article @ Nature

Thursday, July 02, 2015


Machine ethics: The robot’s dilemma

"Working out how to build ethical robots is one of the thorniest challenges in artificial intelligence." Full news article @ Nature News & Comment

Wednesday, July 01, 2015


Cells that flock together

"A burgeoning field of research on collective cell motion is drawing on mathematics originally developed to model animal flocks." Full news article 2 PNAS

Monday, June 15, 2015


The X-rule: universal computation in a non-isotropic Life-like Cellular Automaton

"We present a new Life-like cellular automaton (CA) capable of logic universality -- the X-rule." Full paper @ ArXiv.

Tuesday, June 02, 2015


DNA Memory: What's old is new again

"Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA have opened an unprecedented window into the history of life on Earth. In just a few decades, the study of ancient DNA has gone from a scientific curiosity to an extremely powerful method for reconstructing past biological phenomena." News article @ The Scientist Magazine®

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Wednesday, May 27, 2015


Robotics: Ethics of artificial intelligence

"Four leading researchers share their concerns and solutions for reducing societal risks from intelligent machines." News article @ Robotics: Ethics of artificial intelligence

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From evolutionary computation to the evolution of things

"We discuss how evolutionary computation compares with natural evolution and what its benefits are relative to other computing approaches, and we introduce the emerging area of artificial evolution in physical systems." Full article @ Nature

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Robots that can adapt like animals

"we introduce an intelligent trial-and-error algorithm that allows robots to adapt to damage in less than two minutes in large search spaces without requiring self-diagnosis or pre-specified contingency plans. Before the robot is deployed, it uses a novel technique to create a detailed map of the space of high-performing behaviours. This map represents the robot’s prior knowledge about what behaviours it can perform and their value. When the robot is damaged, it uses this prior knowledge to guide a trial-and-error learning algorithm that conducts intelligent experiments to rapidly discover a behaviour that compensates for the damage. Experiments reveal successful adaptations for a legged robot injured in five different ways, including damaged, broken, and missing legs, and for a robotic arm with joints broken in 14 different ways. This new algorithm will enable more robust, effective, autonomous robots, and may shed light on the principles that animals use to adapt to injury." Ful paper @ Nature


Tuesday, May 19, 2015


CRISPR gene editing

"Just a few years ago, molecular biologists hoping to alter the genome of their favorite organisms faced an arduous task and likely weeks of genetic tinkering. Today, those scientists can quickly destroy or edit a gene with a new technology called CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9. [...]It really opens up the genome of virtually every organism that’s been sequenced to be edited and engineereg." Overview @ PNAS

Monday, May 18, 2015


Turing patterns in zebrafish skin

"The zebrafish is a model organism for pattern formation in vertebrates. Understanding what drives the formation of its coloured skin motifs could reveal pivotal to comprehend the mechanisms behind morphogenesis. The motifs look and behave like reaction–diffusion Turing patterns, but the nature of the underlying physico-chemical processes is very different, and the origin of the patterns is still unclear. Here we propose a minimal model for such pattern formation based on a regulatory mechanism deduced from experimental observations. This model is able to produce patterns with intrinsic wavelength, closely resembling the experimental ones. We mathematically prove that their origin is a Turing bifurcation occurring despite the absence of cell motion, through an effect that we call differential growth. This mechanism is qualitatively different from the reaction–diffusion originally proposed by Turing, although they both generate the short-range activation and the long-range inhibition required to form Turing patterns." Full paper @ Nature Communications

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Friday, May 15, 2015


Genetic control in the Evolution of Social Bees

Genetic control of social behavior: "“The study suggests that there has been an increase in the complexity of gene regulation with increased social complexity.” News article @ The Scientist Magazine. Full original paper:

Kapheim et al [2015]. "Genomic signatures of evolutionary transitions from solitary to group living." Science DOI:10.1126/science.aaa4788.

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Wednesday, May 13, 2015


Splicing does the two-step

"An intricate recursive RNA splicing mechanism that removes especially long introns (non-coding sequences) from genes has been found to be evolutionarily conserved and more prevalent than previously thought." Full News article @ Nature

Tuesday, May 12, 2015


Deep-ocean microbe is closest living relative of complex cells

"Genomic study of 'Loki' supports a revisionist view of the origin of eukaryotes". NEws article @ Science


How a well-adapted immune system is organized

"The adaptive immune system uses the experience of past infections to prepare its limited repertoire of specialized receptors to protect organisms from future threats. What is the best way of doing this? Building a theoretical framework from first principles, we predict the composition of receptor repertoires that are optimally adapted to minimize the cost of infections from a given pathogenic environment. A naive repertoire can reach these optima through a biologically plausible competitive mechanism. Our findings explain how limited populations of immune receptors can self-organize to provide effective immunity against highly diverse pathogens. Our results also inform the design and interpretation of experiments surveying immune repertoires." Full article @ PNAS

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Monday, May 11, 2015


The Search for a New Machine

"With the end of Moore's law in sight, chip manufacturers are spending billions to develop novel computing technologies." Full article @ Scientific American


Cellular Small Talk

"Neighboring cells exchange molecular information through channels that directly connect them. Disruption of this signaling system can lead to disorders ranging from hearing loss to heart disease." Full article @ Scientific American

Saturday, May 09, 2015


Grades are in!

The grades are in. Many awesome projects. Thank you and I hope you enjoyed learning more about bio-inspired computing during this semester. Go and have a fantastic Summer!

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Tuesday, May 05, 2015


3D Printing Soft Materials: What Is Possible?

"roundtable discussion [...] talking about 3D printing soft materials. [...] cutting edge of the technology, and is also likely to have quite important disruptive effects. [Discussion] about the prospects, what is exciting about it, and some of the limitations. Full roundtable discussion @ "Soft Robotics

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Thursday, April 30, 2015


Slides for "The Adaptive Immune System and Artificial Immune Systems" lecture, April 29 2015 online

I485/H400 - Lecture 24 - The Adaptive Immune System and Artificial Immune Systems

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Wednesday, April 29, 2015


links for "Immune System" lecture

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, by Gary Kaiser

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Bio-inspired computing complete set of lecture notes

All lecture notes, updated for 2015, are now on the course site. All chapters are also available as a single file.

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New lecture notes: Modeling Evolution

7. Modeling Evolution: Evolutionary Computation

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Monday, April 27, 2015


Slides for "Turing’s Tape, Von Neumann and the design principle of open-ended, multi-level complexity", April 27, 2015 lecture online

I485/H400 - Lecture 23 - Turing’s Tape, Von Neumann and the design principle of open-ended, multi-level complexity

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Slides for EXTRA lecture "Swarms, Stigmergy and Collective Intelligence" online

I485/H400 - Lecture 22 - Swarms, Stigmergy, and Collective Intelligence

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Ants Swarm Like Brains Think

"The behavior of each individual in the group is set by the rate at which it meets other ants and a set of basic rules. Its behavior alters that of its neighbors, which in turn affects the original ant, in a classic example of feedback. The result is astonishing, complex behavior." Full article @ Nautilus

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Links for "Self-Reproduction" Lecture

Robot Self-replication
Cornell Creative Machines Lab: Self replication
Stochastic Modular Assembly (Programmable Matter)

An implementation of Von Neumann's Self_reproducing Automata. See Modifications by Tim Hutton.

Self-Reproducing Loops: from Langton's to Evoloop. Hiroki Sayama's Website.

Self-reproducing loops

Langton's Loop Applet .

Bibliography on Self-replicating automata

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Links for "Swarms, Stigmergy and Collective Intelligence" lecture

Ant Colony Optimization Resources
Dynamic Concepts Stigmergy Robots. Report with rules used.

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

Swarm Paintings and a conceptual update (using pheromone fields by Vitorino Ramos).

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

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

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

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Sunday, April 26, 2015


New Lecture Notes: Von Neumann and Natural Selection

6. Von Neumann and Natural Selection (pdf)

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Slides for "Ant Clustering Algorithm" April 22, 2015 lecture online

H400/I485 - Lecture 21 - Ant Clustering Algorithm

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