Monday, May 09, 2022
Links for "Self-Reproduction and Open-Ended Evolution" Lecture
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.
Langton's Loop Applet .
Lack of evolvability in self-sustaining autocatalytic networks
Darwinian properties and their trade-offs in autocatalytic RNA reaction networks
Full Lecture Notes: Evolutionary Systems
Monday, May 02, 2022
New Lecture Notes: Chapter 6 - Von Neumann and Natural Selection
links for "Immune System" lecture
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.
Tuesday, April 19, 2022
links for Collective Behavior and Swarms lectures
Chemotaxis, Stigmergy, Termites and Ant Clustering and Sorting
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.
Michael Conrad's Work
Sim Life and Spore (More on Spore).
Boids Demo. Experiment with different interaction ruleson another demo.
EPFL Laboratory for Intelligent Systems
A Swarm of One Thousand Robots
Flocking with fixed-wing robots at EPFL
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 Resources
Ant Colony Optimization Demo
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).
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
Simulate Escape Panic. Crowd Turbulence
Monday, April 11, 2022
Lecture Notes Chapter 5: Life is Stranger than Fiction
Lecture Notes (Chapter 4): Self-organization and emergent complex behavior
Links for "Evolutionary Algorithms" Lectures
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
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.
Thursday, April 07, 2022
How Cells Conquer Mazes
When researchers built a miniature replica of the hedge maze at Hampton Court Palace in England, social slime-mold amoebas (Dictyostelium discoideum) solved it efficiently, as seen in this time-lapse video. Chemical gradients created by the cells leading the way discouraged the cells behind them from going down dead ends.
Monday, April 04, 2022
Links for "Genes as Turing Tape" Lecture
Brenner, Sydney. . "History of Science. The Revolution in the Life Sciences". Science 338 (6113): 1427-8.
Brenner, Sydney. . "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
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
Monday, March 28, 2022
Links for "Design Principles of Computation" Lecture
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)
The Antikythera Mechanism Research Project
NOVA: Ancient Computer
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
Cool implementation of Babbage's Difference Engine using LEGO! Photos, description of adder and carry propagation logic, mechanical issues, etc. at: By Andy Carol
Monday, March 21, 2022
Links for "Computation in Cellular Automata" lecture
Game of Life Demo
Game of Life Applet
3-D Game of Life
Rule 110 and Universal Computation
Computation Theory of Cellular Automata
A Computational Mechanics Reading List by Cosma Shalizi
links for "Cellular Automata and Edge of Chaos" lecture
Devin Acker's Elementary CA Demo
Cellular Automata rules lexicon
Cellular Automata Rules
New Kind of Science Applets
Wolfram CA Demos
Langton's Lambda Parameter
Edge Of Chaos CA
Lambda Parameter Applet
Monday, March 14, 2022
Engineered Biological Switches
Monday, March 07, 2022
Links for "Boolean Networks and Self-Organization" lecture
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.
Spontaneous Order and Self Organization @ Scholarpedia
Companion Links for chaos and logistic map lecture
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.
Thursday, March 03, 2022
How We Can Make Sense of Chaos
Monday, February 28, 2022
Companion links for "Dynamical Systems and Attractor Behavior" lecture
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.
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.
Monday, February 21, 2022
Lecture notes (Chapter 3): Formalizing and Modeling the World
Companion links for Self-Similarity and L-Systems Lecture
- A good description and demos by Chris Jennings
- Source Code from Gary Flake's Computational Beauty of Nature Book
- Generate an L-System. An alternative generator, and Another HTML Generator.
- Code for a L-System Explorer
- The Algorithmic Beauty of Plants
- Self-similar syncopations: Fibonacci, L-systems, limericks and ragtime.
- Musical L-Systems by Stelios Manousakis and the Symbolic Composer
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.
Wednesday, February 16, 2022
Lecture Notes (Chapter 2): The Logical Mechanisms of Life
Monday, February 07, 2022
Companion links for "Modeling Principles of Organization" lecture
- Fibonacci numbers in Nature. The Romanesco Vegetable.
- Fibonacci Spiral Demo. Another Demo.
- Fibonacci Music
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.
- In retrospect: On Growth and Form by Phillip Ball.
- D'Arcy Thompson's Affine Fish Transformations @ Wolfram
- S.J. Gould.  "D'Arcy Thompson and the Science of Form". New Literary History, 2 (2): 229-258
- W. Arthur . "D'Arcy Thompson and the theory of transformations".Nature Reviews Genetics 7, 401-406.
- Geometry of Growth and Form: Commentary on D'Arcy Thompson
- Java applet for shell sketching
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!"
Monday, January 31, 2022
Links for Information Lecture 2
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
Sunday, January 30, 2022
Monday, January 18, 2021
3D underwater collective behaviors in a fish-inspired robot swarm
Tuesday, January 14, 2020
Friday, October 18, 2019
Self-healing, path solving mould
Saturday, March 23, 2019
Robotic collectives inspired by biological cells
Tuesday, December 18, 2018
A neural data structure for novelty detection
Thursday, July 05, 2018
Programming self-organizing multicellular structures
Thursday, May 03, 2018
Fractal-like hierarchical organization of bone