life inspired

"we use digital evolution to show that changing environments facilitate the simultaneous evolution of high mutation rates and a distribution of mutational effects skewed toward beneficial phenotypes. The evolved mutational neighborhoods allow rapid adaptation to previously encountered environments, whereas higher mutation rates aid adaptation to completely new environmental conditions. By precisely tracking evolving lineages and the phenotypes of their mutants, we show that evolving populations localize on phenotypic boundaries between distinct regions of genotype space. Our results demonstrate how evolution shapes multiple determinants of evolvability concurrently, fine-tuning a population’s adaptive responses to unpredictable or recurrent environmental shifts".Full paper @ PNAS.

Labels: #evolution, #evolvability

"The study of flocking in biological systems has identified conditions for self-organized collective behavior, inspiring the development of decentralized strategies to coordinate the dynamics of swarms of drones and other autonomous vehicles. Previous research has focused primarily on the role of the time-varying interaction network among agents while assuming that the agents themselves are identical or nearly identical. Here, we depart from this conventional assumption to investigate how inter-individual differences between agents affect the stability and convergence in flocking dynamics." Full article at the ArXiv.

Labels: #collectivebehavior, #flocking

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.

Labels: #adaptiveImmunity, #ArtificialImmuneSystems, #immunesystem, Class Links

Chemotaxis, Stigmergy, Termites and Ant Clustering and Sorting
Artificial Termites.
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
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
Braitenberg (reactive) 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
Pedestrian dynamics: Spontaneous lane formation, congestion and patterns in a simple model for interacting pedestrians

Labels: #AntClusteringAlgorithm, #ants, #Artificialecology, #boids, #ClassLinks, #collectivebehavior, #flocking, #ParticleSwarmOptimization, #Swarms

Chapter 7 Modeling Evolutionary Systems now available. The entire lecture notes for 2024 also available, including in a pdf booklet.

Labels: #evolution, #evolutionaryalgorithms, #selfOrganization, #Semioticclosure, #Semiotics

6. Von Neumann and Natural Selection

Labels: #cellularAutomata, #Darwin, #evolution, #infomation, #Mendel, #self-reproduction, #Turing, #VonNeumann

Modeling Evolution

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


Stanley, K.O. et al. [2019]. "Designing neural networks through neuroevolution". Nat Mach Intell 1, 24–35.
Genobots: Generative Representations for Design Automation
The Golem Project
Genetic Programming Resources
Annual "Humies" Awards For Human-Competitive Results Produced By Genetic And Evolutionary Computation
Eureqa models, part of DataRobot: a software tool for detecting equations and hidden mathematical relationships in data. Older version, also at softsea.com.
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.
Evolved Open-Endedness, Not Open-Ended Evolution, By Howard Pattee and Hiroki Sayama

Labels: #Biomorphs, #evolution, #evolutionaryalgorithms, #evolutionaryComputation, #geneticAlgorithms, Class Links

Richerson et al. [2021]. "Modern theories of human evolution foreshadowed by Darwin’s Descent of Man". Science372.
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.
Al-Hashimi, H. [2023]. "Turing, von Neumann, and the computational architecture of biological machines",PNAS 120 (25) e2220022120.
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

Labels: #Cell, #CellBiology, #dna, #evolution, #information, #SidneyBrenner, #Turing, #VonNeumann, Class Links