Monday, May 09, 2022

 

Links for "Self-Reproduction and Open-Ended Evolution" Lecture

Robot Self-replication
Cornell Creative Machines Lab: Self replication
Soft Robotics Evolution


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 and demos.

Self-reproducing loops

Langton's Loop Applet .






Self-reproducing Xenobots.







autocatalytic networks
Lack of evolvability in self-sustaining autocatalytic networks
Darwinian properties and their trade-offs in autocatalytic RNA reaction networks

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Full Lecture Notes: Evolutionary Systems

Chapter 7 Modeling Evolutionary Systems now available. The entire lecture notes for 2022 also available, including in a pdf booklet.

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Monday, May 02, 2022

 

New Lecture Notes: Chapter 6 - Von Neumann and Natural Selection

6. Von Neumann and Natural Selection

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links for "Immune System" lecture



Immune System
Overview of the Immune System
Immunology movies at Cells Alive!
An Interpretative Introduction to the Immune System. by S. A. Hofmeyr.
Immunology as information processing. by S. Forrest and S. A. Hofmeyr.





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Tuesday, April 19, 2022

 

links for Collective Behavior and Swarms lectures



Chemotaxis, Stigmergy, Termites and Ant Clustering and Sorting
Artificial Termites.
Mitchel Resnick
Ant-like task allocation and recruitment in cooperative robots
Cells Solving mazes and optimal paths
Self-generated gradients of chemicals and physical tension, cells in the body steer themselves to vital destinations.
Swarm Robotics @ Bristol Robotics Laboratory.
NetLogo





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




Collective Behavior
Boids
Boids Demo. Experiment with different interaction ruleson another demo.
Javascript for Boids. Implementing boids in Python.
EPFL Laboratory for Intelligent Systems
A Swarm of One Thousand Robots

Boid -flocking Simulation with python


Flocking with fixed-wing robots at EPFL


Particle Swarm Optimization
Particle Swarm Optimization Paper by Kennedy and Eberhart..
Particle Swarm Optimization Demos.
Particle Swarm Optimization Visualization by Axel Thevenot.
Software Resources for PSO. PySwarm (Python code). Tutorial for coding PSO in Python.
PSO for prediction of protein-ligand interaction

Ant Colony Optimization
Ant Colony Optimization Resources
Ant Colony Optimization Demo


Swarm-bots
Collective Robotic Intelligence Project (CRIP)
Braitenberg (reactive) Vehicles. A simulation of Braitenberg Vehicles.



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 and Simulation of Multi-lane traffic. A video with stop-and.go dynamics
Mexican Wave
Simulate Escape Panic. Crowd Turbulence







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Monday, April 11, 2022

 

Lecture Notes Chapter 5: Life is Stranger than Fiction

Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology?


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Lecture Notes (Chapter 4): Self-organization and emergent complex behavior

4. Self-Organization and Emergent Complex Behavior

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Links for "Evolutionary Algorithms" Lectures

Modeling Evolution

Introduction to Genetic Algorithms
Illustrating Evolutionary Computation with Mathematica
Genetic Algorithm Tutorial with Java Code
Simple Genetic Algorithm in NetLogo
Genetic Algorithm Walkers
PyGAD - Python Genetic Algorithm and paper with details




The Golem Project Genetic Programming Resources
Annual "Humies" Awards For Human-Competitive Results Produced By Genetic And Evolutionary Computation
Eureqa: a software tool for detecting equations and hidden mathematical relationships in data. Older version.
gplearn: Genetic Programming in Python



Biomorph demo and Python code
Biomorph Demo
Icosystem - The Hunch Engine™




From Artificial Evolution to Artificial Life (1999), Tim Taylor's PhD Dissertation. Check his overview of open-ended evolution.


BEACON: Center for the Study of Evolution in Action. biologists, computer scientists, and engineers study evolution as it happens and apply this knowledge to solve real-world problems.

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Thursday, April 07, 2022

 

How Cells Conquer Mazes

"Researchers are beginning to understand more about how migrating cells navigate through the body." Full article @ Quanta Magazine.

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Monday, April 04, 2022

 

Links for "Genes as Turing Tape" Lecture



Brenner, Sydney. [2012]. "History of Science. The Revolution in the Life Sciences". Science 338 (6113): 1427-8.
Brenner, Sydney. [2012]. "Turing centenary: Life's code script. Nature 482 (7386) (February 22): 461-461.
The virtual Cell
Inside the Cell
Cell Biology at the Biology Project
More on Cells from Wikipedia
The Cell Image Library and highMag
Colonial Algae


Genetics and Genomics

Watson and Crick's Molecular structure of Nucleic Acids 1953 article
Journey into DNA
Cracking the Code of Life (PBS Show)
Explore a stretch of code

Translation and Protein Synthesis
Interactions between the Translation Machinery and Microtubules

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Monday, March 28, 2022

 

Links for "Design Principles of Computation" Lecture

The Lebombo Bone and Other Ancient Mathematical Objects


  The Ishango Bone

Turing Machine Simulator
Turing Machine Simulator 2
Turing Machine Simulator 3 (Java)

A Turing Machine Overview
BTW, my thoughts on the recent Turing Biopic and a related news article.


The Manchester Baby (1948)




MESM 1950 (Kyev)


Some resources about the Abacus
The Abacus in Various Number Systems
Demo (The Chinese Abacus)
Mechanical Calculators
The Pascaline




The Antikythera Mechanism

The Antikythera Mechanism Research Project
NOVA: Ancient Computer


Another video of the Antikythera Mechanism
Babbage, Lovelace and the Analytical Engine
The Difference Engine
The Analytical Engine
9 Neat Facts About the World's First Computer Programmer, Ada Lovelace 
Ada Lovelace and the Analytical Engine
Helping Ada Lovelace with her Homework: Classroom Exercises from a Victorian Calculus Course








It Started Digital Wheels Turning


Cool implementation of Babbage's Difference Engine using LEGO! Photos, description of adder and carry propagation logic, mechanical issues, etc. at: By Andy Carol


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Monday, March 21, 2022

 

Links for "Computation in Cellular Automata" lecture

Conway's Game of Life

Game of Life Demo
Game of Life Applet
3-D Game of Life

Turing Machine Implemented in Game of Life

Rule 110
Rule 110 and Universal Computation
Computation Theory of Cellular Automata
A Computational Mechanics Reading List by Cosma Shalizi

Neural Cellular Automata For Art Recreation

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links for "Cellular Automata and Edge of Chaos" lecture

Boolean networks beyond Systems Biology: Musical Morphogenesis


Devin Acker's Elementary CA Demo
Cellular Automata rules lexicon
Cellular Automata Rules
Cellab
New Kind of Science Applets
MCell
Wolfram CA Demos



Langton's Lambda Parameter
Edge Of Chaos CA
Lambda Parameter Applet

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Monday, March 14, 2022

 

Engineered Biological Switches

Scientists created DNA nanotube rails that branch in multiple directions, with each unique track made up of unique DNA patterns. Protein motors designed to recognize these patterns then carry their cargo down the desired tracks. Nanoswitchyards should help scientists better test and understand the real thing inside cells. They may also eventually help researchers steer different drug cargoes to different tissues or engineer novel DNA computers that respond to their environment. In the video, proteins called dyneins have been engineered to glide along DNA tracks. At a branch point, different DNA patterns of the tracks steer dyneins carrying orange fluorescent cargo to the left and dyneins carrying cyan fluorescent compounds to the right.

Video @ Science

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Monday, March 07, 2022

 

Links for "Boolean Networks and Self-Organization" lecture

Random Boolean Networks Tutorial by Carlos Gershenson
Random Boolean Network Simple Examples
Random Boolean Networks Demo by Wolfram
BooleSim by Mathias Bock
Discrete Dynamics Lab
Booleannet tool for simulating biological regulatory networks in a boolean formalism by Istvan Albert.
CANA Control and Redundancy in Boolean Networks by Rion Correia and CASCI.

Muramator Robot

Spontaneous Order and Self Organization @ Scholarpedia

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Companion Links for chaos and logistic map lecture

Logist Map Plots and Analysis by Dirk Brockman for Complexity Explorer
Wolfram demo for the Logistic map and detailed study.
Java Code for Time Series of Logistic Map
GDScript Code for Logistic Map


Andrew Clem ~ Chaos theory contains a very nice explanation of the logistic map and the white bands of periodic behavior inside the chaotic range. Try r=3.84 in the demo used in class, to see a cycle of 3 arise.

See also The birth of period 3, revisited.



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Thursday, March 03, 2022

 

How We Can Make Sense of Chaos

"Dynamical systems can be chaotic and impossible to predict, but mathematicians have discovered tools to help understand them". Full article by David S. Richeson at Quanta Magazine.

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Monday, February 28, 2022

 

Companion links for "Dynamical Systems and Attractor Behavior" lecture

 Gravitational Pendulum

The Icosystem Game
Turing Reaction-Diffusion Model of Morphogenesis by Kele W. Cable: a demo by Chris Jennings .
Graphics Research on Reaction-Diffusion
synthetic texture using reaction-diffusion
Reaction-Diffusion in gene expression of digit determination (in mouse)
Validation of predicted patternsin Turing diffusion (in abiological droplets)
Revising the Turing model with biological evidence (in zebrafish)
Turing-type polyamide membranes for water purification
Expanding theoretical models (ABM and others)
Reaction-Diffusion in various areas.



Reaction-Diffusion in Nature

3-Body Gravitational Problem 3-Body Problem in JavaScript


Lorenz Attractor Demo
Wolfram Projects Demo
Plotting Edward Lorenz's 1963 "Deterministic Nonperiodic Flow" in a 3-dimensional space using mplot3d.
Sensitive dependence on initial conditions in the Lorenz Attractor (Python code). Wolfram Sensitivity To Initial Conditions Demo.


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Monday, February 21, 2022

 

Lecture notes (Chapter 3): Formalizing and Modeling the World

Formalizing and Modeling the World. CHapter 3 of lecture notes now online.

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Companion links for Self-Similarity and L-Systems Lecture

Fractals



L-Systems




Evolutionary Robots
3D Genbots using L-systems
The GOLEM Project.

See also the research pages pages of Karl Sims, Jordan Pollack, Hod Lipson, Josh Bongard, and Dario Floreano.

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Wednesday, February 16, 2022

 

Lecture Notes (Chapter 2): The Logical Mechanisms of Life

The Logical Mechanisms of Life

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Monday, February 07, 2022

 

Companion links for "Modeling Principles of Organization" lecture

Pi the Movie

Fibonacci Sequence

The magic of Fibonacci numbers by Arthur Benjamin


Peter Hilton (1923-2010) discusses intriguing number tricks that can be explained by analysing the properties of Fibonacci numbers and the related Lucas numbers. The explanations themselves benefit from further explanations which, in their turn, lead to further discoveries. Recorded at Imperial College London during the 1996 London Mathematical Society Popular Lecture series.


D'Arcy Thompson

Patterns of Life – D’Arcy Thompson, Structuralism and the Shape of Life


Treasures of the Library 5. D'Arcy Thompson, On growth and form


BLOOMS: Strobe Animated Sculptures Invented by John Edmark from Charlie Nordstrom on Vimeo. "This series of 3D printed sculptures was designed in such a way that the appendages match Fibonacci's Sequence, a mathematical sequence that manifests naturally in objects like sunflowers and pinecones. When the sculptures are spun at just the right frequency under a strobe light, a rather magical effect occurs: the sculptures seem to be animated or alive!"

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Monday, January 31, 2022

 

Links for Information Lecture 2

Lectures Slides: What is Life? and Uncertainty-based Information

Information Basics
Entropy Applet
Letter frequency in English
Word and Letter Frequency in English
Entropy of English
Text Mechanic - Text Manipulation Tools
1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com

Claude Shannon Demonstrating Theseus

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Sunday, January 30, 2022

 

Lecture notes (chapter 1): What is Life?

Welcome to Life-Inspired, SSIE 483X/583X Spring 2022 Class. On this blog you will see many types of posts related to the class, from links to multimedia materials used in class, to breaking research on related topics. The first chapter of the course's lecture notes is now available: SSIE483X/583X: What is Life?

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Monday, January 18, 2021

 

3D underwater collective behaviors in a fish-inspired robot swarm

"most underwater robot collectives rely on centralized, above-water, explicit communication and, as a result, exhibit limited coordination complexity. Here, we demonstrate 3D collective behaviors with a swarm of fish-inspired miniature underwater robots that use only implicit communication mediated through the production and sensing of blue light. We show that complex and dynamic 3D collective behaviors—synchrony, dispersion/aggregation, dynamic circle formation, and search-capture—can be achieved by sensing minimal, noisy impressions of neighbors, without any centralized intervention." Full paper @ Science Robotics.

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Tuesday, January 14, 2020

 

Programmable organisms

Exciting work bridging biology and computing from josh Bongard and Michael Levin, who "present a method that designs completely biological machines from the ground up: computers automatically design new machines in simulation, and the best designs are then built by combining together different biological tissues." Full article @ PNAS.

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Friday, October 18, 2019

 

Self-healing, path solving mould

"A yellow organism which looks like fungus but acts like an animal has gone on display at the Paris Zoological Park. The slime mould - Physarum polycephalum - has almost 720 sexes and has been described as one of "nature's mysteries" by scientists. It can heal itself in two minutes if cut in half, and detect and digest food despite not having eyes, a mouth or a stomach." From BBC News.

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Saturday, March 23, 2019

 

Robotic collectives inspired by biological cells

"A robotic system has been demonstrated in which the random motion of individual components leads to deterministic behaviour, much as occurs in living systems. Environmental and medical applications could follow." News article and full paper @ Nature.

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Tuesday, December 18, 2018

 

A neural data structure for novelty detection

"Novelty detection is a fundamental biological problem that organisms must solve to determine whether a given stimulus departs from those previously experienced. [The authors show] the algorithmic basis of an important neurobiological problem and offers strategies for novelty detection in computational systems." Full paper @ PNAS.

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Thursday, July 05, 2018

 

Programming self-organizing multicellular structures

"A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multi-domain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. The ability of these networks to drive complex structure formation illustrates the power of interlinking cell signaling with cell sorting: signal-induced spatial reorganization alters the local signals received by each cell, resulting in iterative cycles of cell fate branching. These results provide insights into the evolution of multi-cellularity and demonstrate the potential to engineer customized self-organizing tissues or materials."

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Thursday, May 03, 2018

 

Fractal-like hierarchical organization of bone

" By combining three-dimensional electron tomography with two-dimensional electron microscopy, Reznikov et al. observed structural ordering from the nanoscale upward. At the smallest scale, needle-shaped mineral units form platelets that organize into stacks bridging multiple collagen units." Full article @ Science.

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Saturday, October 14, 2017

 

Robot that can change its texture on the fly

"Most robots stick out in nature like a sore thumbdrive. Now, scientists have found a new way to help them blend in—by changing not only the color, but also the texture of their skin. Inspired by cephalopods—squid, octopus, and cuttlefish—which use ring-shaped muscles to squeeze small bumps on their skin into large bulges that mimic rocks and algae, researchers created similar reversible protrusions with sheets of stretchy silicone. " Full news @ Science.




Thursday, August 31, 2017

 

Octopus embodiment and intelligence

"Even asking how much the body contributes to intelligent action presupposes a division between brain and body that seems not to apply to the octopus. The octopus’s body is pervaded by nervousness: it is not a thing controlled by the animal’s thinking part, but itself a thinking thing". Full book review at London Review of Books. Thank you to Thiago Carvalho for sharing.



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Wednesday, June 28, 2017

 

mathematical sculptors create compelling forms

"[...] many math sculptors also aim to connect their pieces to the observable, natural world. A gypsum sculpture by David Bachman, for example, looks just like a seashell in both shape and color. But it’s wholly artificial: Bachman first drew—on a computer screen—a curve representing the profile of the shell. Then, he used a computer program to generate equations to describe the spiral shape seen on the outside, as well as the twisting internal structure. Bachman sent his design to a 3D printer, and a convincingly real shell emerged layer by layer. It’s so convincing that the first thing people do when they see it, he says, is put it to their ear. “I wanted to prove the point that you can create a very natural looking thing with mathematics,” he says." Full article at PNAS.




Friday, March 03, 2017

 

DNA Fountain enables a robust and efficient storage architecture

DNA Fountain approaches the theoretical maximum for information stored per nucleotide. Efficient encoding of information is demonstrated by storing a full computer operating system, movie, and other files with a total of 2.14 × 106 bytes in DNA oligonucleotides and perfectly retrieved the information after multiple rounds of polymerase chain reaction. Full paper @ Science



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Wednesday, February 22, 2017

 

Studying swarms of ants could help speed up your commute

Studying collective behavior could be used to manage traffic in urban areas. Full news article @ Wired.uk.

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Monday, January 09, 2017

 

Efficient Switches in Biology and Computer Science

"Biological systems are adapted to respond quickly to changes in their environment. Signal processing often leads to all-or-none switch-like activation of downstream pathways. Such biological switches are based on molecular interactions that form positive feedback loops. [...] We discuss here how the structure and dynamical features of a computational algorithm resemble the behaviour of a large class of biological switches and what makes them work efficiently." Full article @ PLOS Computational Biology






Biological networks with switching dynamics.

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