life inspired

Lecture 15 - Genetic Algorithms

Labels: evolution, evolutionary algorithms

Robot Self-replication
Cornell CCSL: Self replication

Modeling Evolution
From Artificial Evolution to Artificial Life (1999), Tim Taylor's PhD Dissertation. Check his overview of open-ended evolution.
Introduction to Genetic Algorithms
Genetic Algorithm Viewer
Biomorph Viewer
Omnipotence
Biomorph game
Biomorphs with Crossover
Dawkins' Biomorphs
J-Biomorph
Icosystem - The Hunch Engine™
The Golem Project
Illustrating Evolutionary Computation with Mathematica

LifeSpacies. More. Christa Sommerer

Labels: evolutionary algorithms

7. Modeling Evolution: Evolutionary Computation

Labels: evolution, evolutionary algorithms, self-organization

In the past few decades group selection has made a quiet comeback among evolutionary theorists. E. O. Wilson of Harvard University and David Sloan Wilson (no relation) of Binghamton University are trying to give group selection full-fledged respectability. They are rebranding it as multilevel selection theory: selection constantly takes place on multiple levels simultaneously. And how do you figure the sum of those selections in any real-world circumstance? “We simply have to examine situations on a case-by-case basis,” Sloan Wilson says. Full article @ Scientific American

Labels: evolution, group selection, multilevel selection, natural selection

Single genes, chromosomal regions and even entire genomes can undergo duplication. What good can come of these extra copies? Evolution seems to use several tricks to take advantage of the situation. Full paper @ Nature

Also see Gene duplication and the adaptive evolution of a classic genetic switch

Labels: evolution, genetics, non-coding DNA

"Members of the public across Europe are being asked to look in their gardens or local green spaces for banded snails as part of a UK-led evolutionary study. ". Full article @ BBC NEWS

BNS is a software tool for computing attractors in Boolean Networks with Synchronous update. Synchronous Boolean networks [1] are used for the modeling of genetic regulatory networks.

Paper: "A SAT-Based Algorithm for Computing Attractors in Synchronous Boolean Networks", E. Dubrova, M. Teslenko, available at http://arxiv.org/abs/0901.4448, submitted to the International Conference on Computer-Aided Verification (CAV'2009), June 26 - July 2, 2009 Grenoble, France.

Labels: computation, Cyborgs

"How can something be dependent and autonomous at the same time? And why do so many systems in nature show this hierarchical organization? No one has answered these questions, but in Complexity, computer scientist Melanie Mitchell of the Santa Fe Institute, New Mexico, offers a valuable snapshot of the growing field of complex-systems science from which the answers may eventually arise." Full review @ Nature

"Talk about a royal scandal. When a termite king and queen have been in power for some time, the king begins mating with his royal daughters to populate the colony. Now, researchers report that one termite species has found a way around this incest: The queen produces offspring that have only her genes. That way, when the king mates with a daughter, he's effectively still having sex with the queen.". Full Story @ ScienceNOW

Biomimicry - The practice of developing sustainable human technologies inspired by nature. Sometimes called Biomimetics or Bionics, it's basically biologically inspired engineering. See The 15 Coolest Cases of Biomimicry

Lecture 14 - Open-ended Evolution

Labels: open-ended evolution

"Proving that a new approach can secure victory in a classic strategy game, a team from England's Southampton University has won the 20th-anniversary Iterated Prisoner's Dilemma competition, toppling the long-term winner from its throne. The Southampton group, whose primary research area is software agents, said its strategy involved a series of moves allowing players to recognize each other and act cooperatively". Full Story @ Wired News.

Labels: Agent-based modeling, Prisoner's Dilemma, social agents

"Biofilms are spatially structured communities of microbes whose function is dependent on a complex web of symbiotic interactions. Localized interactions within these assemblages are predicted to affect the coexistence of the component species, community structure and function, but there have been few explicit empirical analyses of the evolution of interactions11. Here we show, with the use of a two-species community, that selection in a spatially structured environment leads to the evolution of an exploitative interaction. Simple mutations in the genome of one species caused it to adapt to the presence of the other, forming an intimate and specialized association. The derived community was more stable and more productive than the ancestral community. Our results show that evolution in a spatially structured environment can stabilize interactions between species, provoke marked changes in their symbiotic nature and affect community function." Full article @ Evolution of species interactions in a biofilm community : Article : Nature

Labels: evolution

Courtesy of Art Kolchinsky:

Nylon-eating bacteria @ Wikipedia

and

Mutating micro-organisms on MIR space station

Labels: biology, evolution

A study provided clear evidence of multigenerational effects of environmental exposure. A spotlight on a hot paper in epigenetics @The Scientist

Labels: epigenetics

It's not easy making a human. Getting from a fertilized egg to a full-grown adult involves a near-miracle of orchestration, with replicating cells acquiring specialized functions in just the right places at the right times. So you'd think that, having done the job once, our bodies would replace cells when required by the simplest means possible. Oddly, they don't. Our tissues don't renew themselves by mere copying, with old skin cells dividing into new skin cells and so forth. Instead, they keep repeating the laborious process of starting each cell from scratch. Now scientists think they know why: it could be nature's way of making sure that we don't evolve as we grow older. Full Story @nature.com

Labels: development, evolution, multicellular

The scientists compared twins, who are 100% genetically alike, with each other and with their brothers, who share on average 50% of their genes. Twins used the same strategy more often than brothers did in the roughly 50 trials, suggesting that "there are qualitative differences in how individuals think, and these differences have a substantial genetic component,". Article @ Science

Paper: Koten et al [2009]. "Genetic Contribution to Variation in Cognitive Function: An fMRI Study in Twins". Science. 323 (5922): 1737 - 1740

How the behavior of an Arabidopsis gene could overturn the classical laws of genetics. Full Story @ The Scientist

Labels: epigenetics, inheritance, Mendel

Self-Reproduction and Open-ended Evolution

Labels: open-ended evolution, Von Neumann

LNCS Author Instructions| Springer

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 Loop Applet. Applet 2.
Bibliography on Self-replicating automata

Labels: open-ended evolution, self-reproduction

These maps are always interesting even if no two-dimensional map can do justice to such an interdisciplinary field---at leas it makes a coolScience t-shirt...

Labels: complex systems, complexity

Lecture 12 - Cellular Automata: From the Edge of Chaos to Computation

BTW: here is some sample C code to generate 1D CAs---such as rule 110 (there's a project in here!). This page also has code for 2D CA such as the game of life.

Labels: cellular automata, computation

6. Von Neumann and Natural Selection (pdf)

Labels: cellular automata, evolution, self-reproduction, Von Neumann

Interesting use of cellular automata to make music. And you can download them as ringtones for your cell! Wolfram has extended cellular automata to every conceivable area...If you want to read his book (I had it autographed :) let me know! Its huge, over 1K pages.

Labels: cellular automata, music

A bacterium found in sewage sludge uses its tail-like flagellum to lasso a symbiotic archaeon and keep it close at bay so that the two microbial partners can synchronize their metabolism, a Japanese research team reports in the Mar. 20 issue of Science. News report @ The Scientist

Cellular Automata Applet for Many Rules

Langton's Lambda Parameter

Edge Of Chaos CA
Lambda Parameter Applet


Conway's Game of Life

Game of Life Applet
Game of Life Applet II

3-D Game of Life
Turing Machine Implemented in Game of Life

Rule 110
One-Dimensional CA Applet
Rule 110 and Universal Computation
Computation Theory of Cellular Automata
A Computational Mechanics Reading List by Cosma Shalizi

Labels: cellular automata, complexity, computation, edge of chaos, game of life, self-organization, self-reproduction

Canadian poet Christian Bök plans to encode his verse into DNA that will sit within the genome of a live bacterium. He tells Nature why he wants to create an organism that will translate its own poetic response. Full article @ Nature

A humanoid robot is teaching itself to walk and eventually run around a California research lab. Full Story @ BBC NEWS | Technology

Labels: robots

Lecture 11 - Celular Automata and the Edge of Chaos

Labels: boolean networks, cellular automata, dynamical systems, edge of chaos

"Some peculiar microorganisms are showing systems biology can color in what's missing from models of biochemical and cellular networks." Full article @ The Scientist

Labels: complex systems, systems biology

Wolfram has prepared a very nice showcase with visualizations and implementations of several models (many with discrete dynamical systems, of course) in Mathematica.

Labels: computation, dynamical systems, tools

Spontaneous Order and Self Organization @ Scholarpedia

Cellular Automata rules lexicon
Cellular Automata Rules
Cellab
New Kind of Science Applets
More CA rules

Labels: boolean networks, cellular automata, edge of chaos, self-organization

Charles Darwin’s ideas have spread widely, but his revolution is not yet complete. Full article @ The Economist

Lecture 10 - The Logistic Map and Boolean Networks

Labels: boolean networks, chaos, discrete dynamical systems

A team engineers microbes to perform AND, OR, NAND and NOR logic operations. Full story @Science News

Labels: bacteria, natural computing

"Almost every important gene and pathway will be regulated at multiple levels by a variety of microRNAs," predicts Deepak Srivastava of the University of California, San Francisco. "It's really an entirely new layer of biology."
See Full article @ The Scientist

Labels: RNA

"Dimmer switches that control the level of protein created from a given gene may regulate the development, function and, ultimately, the life span of cells that begin to vanish from the brain at the onset of Parkinson's disease". Full Story at Scientific American

Labels: RNA