Artificial life & collective behavior

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1 Artificial Life - History
2 Chemical Systems
- 2.1 Catalyst
- 2.2 Auto-catalysis
3 Reaction Diffusion Systems
4 The Amazing Belousov-Zhabotinskii Reaction
5 A-Life Large Scale Integration

Artificial Life - History

VonNewman CA
- Complex study of mechanical reproduction

Conway's Game of Life - CA
- Simplification, global rules, cellular patterns

Core Wars
- Inspired by computer viruses
- Virtual machine protects environment uses simple instructions
- Linear address space
- Economy…time slice & battle for memory

Tierra - Rom Ray
- Robust instruction set allowed
- Genetic operations, i.e. mutation
- Parasites develop - steal time and reproduce other organisms
- Immunity and self repair develop
- Introduce size/complexity trade off
- No locality in model

2D Code Worlds
- CA + code in the cell e.g. AVIDA - Chris Adam et.al
- Exhibits locality
- Cellular patterning
- Cellular competition

In these four screen rmages of Tom Ray's Tierra computer world, we see a survwal of the-fittest drama played out In the first frame we see a population dominated by red creatures represented by red line segments along with a few blue creatures into which some yellow parasites represented by the yellow line segments have started to invade In the second frame the population of red creatures has been severely diminished by the parasites. In the third frame we begin to see the blue creatures which are immune to the parasites, increasing in number and forcing the parasites toward the top of the screen. In the last frame the blue creatures have largely forced the parasites out and are now the dominant creatures.

Chemical Systems

Catalyst

Helps a reaction to take place quickly without being "used up" itself

Here the catalyst Z assists with creating C from A & B

Catalyst work by providing molecular template that help "line up" bonding sites.

Auto-catalysis

A matrix of reactions which produces the catalysts it requires.

Here A & B combine to make C and C also serves as a catalyst for its own production.

Here A & B combine to make C, D & E make F and C & F act as catalysts for the reaction for each other.

Complex networks of auto catalytic reactions may have been the pre-DNA precursors for life.

Reaction Diffusion Systems

Autocatalytic systems which form patterns because of differences in the rate of diffusion between the 2 agents.

Activation
- Self-catalyzing & Inhibitor Catalyzing.
- Diffuses slowly
Inhibitor
- Diffuses quickly

Pattern formation by autocatalysis and long-range inhibition. (a) Reaction scheme. An activator catalyses its own production and that of its highly diffusing antagonist, the inhibitor. (b-e) Stages in pattern formation after a local perturbation. Computer simulation in a linear array of cells. A homogeneous distribution of both substances is unstable. A minute local increase of the activator (—) grows further until a steady state is reached in which self-activation and the surrounding cloud of inhibitor ( ---- ) are balanced.

Additional seashell examples

The Amazing Belousov-Zhabotinskii Reaction

Here is a tried and tested recipe for this oscillatory reaction:

500 millililres of sulphuric acid (1 molar)
I4-30 grams malonic acid
5-22 grams potassium bromate
0.548 grams ammonium uric nitrate
I-2 millilitres of ferroin (0.025 molar)

(Make the ferroin by dissolving 1.485 grams of 1,10-phenanthroline and 0.685 grams of hydrated ferrous sulphate in 100 of water.)

Stir the mixture continuously. The resulting oscillations between blue and red with a period of about 1 minute will last for several hours.

If you pour some ofthe mixture as a thin layer into a Petridish, beautiful patterns, with blue concentric circles, called targets, on a red background will develop.

We can split the reaction into three overall processes. In process A, bromate ions oxidize bromide ions to produce bromine.

1. Br0₃^- +Br^- +2H⁺ → HBrO₂ + HOBr
2. HBrO₂ + Br^- + H⁺ → 2HOBr
3. HOBr + Br^- + H⁺ → Br₂ + H₂O

As the concentration of bromide ions decreases, so does the rate of step 2. The bromate ions then compete for reaction with the hypobromous acid (HBrO₂) and switch the system to process B. In this part of the reaction, cerium oxidizes from oxidation state (III) to oxidation state (IV). This gives the color change from red to blue.

4. BrO₃^- + HBrO₂ + H⁺ → 2BrO₂ + H₂O
5. BrO₂ + Ce(III) + H⁺ → HBrO</sub>2</sub> + Ce(IV)
6. ZHBrO₂ → BrO</sub>3</sub> + HOBr + H⁺

Because two BrO₂ radicals are produced in step 4, and each reacts rapidly to form an HBrO</sub>2</sub>, molecule, this part ofthe reaction constitutes an autocatalytic cycle. The autocatalysis causes the rate of this process to increase very quickly once it has switched on, so red changes rapidly to blue. The growth in the concentration of HBrO₂, is limited by step 6. The switch between processes A and B will occur when the rates of steps 2 and 4 are approximately equal.

The final stage, process C, must regenerate the bromide ion and reduce the catalyst back to its lower oxidation state. We do not understand this part of the reaction but we can use the following representation. Malonic acid (MA) reacts with bromine to give bromomalonic acid (BrMA). If this is then oxidized by the cerium (IV), we will regain bromide and cerium (III). The oxidized form of the catalyst can also react directly with malonic acid, so we may get fewer than one bromide ion per cerium (III) ion produced.

So we describe process C as:

7. MA + Br₂ → BrMA + Br^- + H⁺
8. 2Ce(IV) + MA + BrMA → fBR^- + 2Ce(III) and other products

where f is known as thc 'stoichiometric factor'. In the simplest computer analyses, f is assumed to be a constant, say f ≈ 1.

In modelling used to match complex oscillations, wc attempt to allow f (the number of bromide ions produced as two cerium ions are reduced) to be a function of the instantaneous concentrations of other species, such as HOBr. Process C sees the blue change to red and resets the chemical clock for the next oscillation.

BZ Reaction demo video - Steven Strogatz

A-Life Large Scale Integration

A-life systems combine multiple ingredients

L-systems

Not just a grammar based system also a simulation of real context sensitive process

Reaction Diffusion Systems
Swarm behavior - Boids, examples:
- Avoid collision
- Avoid being alone (center)
- Copy direction/speed of near boids

See CB of N Boids program See Star Logo slime, firefly, wolf-sheep examples

Sim-city style ecological simulation
Genetics
- Database of information
- Instructions for construction
- Instructions for behavior
- Mechanism for variation