zebbeni/protozoa

A simulation of protozoan behavior and evolution

Protozoa

A simulation of organisms navigating their environment according to inherited traits and decision trees. Rendered with ebitengine

Simulation Rules

Protozoa randomly generates a number of organisms and food items on a 2D grid. Per render cycle, each organism chooses a simple action (eat, move, turn, attack etc.) based on a randomly-generated decision tree with which it was initialized. Organisms that survive long enough can spawn offspring with very slight mutations, thus propagating successful traits and behaviors.

Environment

The environment consists of a 2D wraparound grid. Each location contains a ph value (0-10). These ph values play a large role in organism health, and are likewise affected by certain organism actions (ie. growth).

Each cycle, ph values diffuse between neighboring grid locations at a regular rate, such that the whole environment will gradually approach a single ph value in the absence of organism activity.

Low ph (acidic) locations appear green, high ph (alkaline) locations are pink, and neutral locations (~5.0 ph) are black.

Additionally, the environment can be separated by walls into 'pools' with small openings allowing diffusion and movement in between. This is meant to allow different families of organisms to develop in isolation longer than would otherwise be possible. (The existence and size of these pools can be set in the configuration json files in settings/)

Food

'Food' items are generated when organisms die. Each food item is represented by a dark gray square and contains a value between 0 and 100, representing how much the food item contains. When an organism sees a food item directly ahead, it can choose to 'eat' it, subtracting some value from the food and adding it to its own health. If a food item's value is reduced to 0, it disappears from the grid. Conversely, when an organism's health is reduced to 0 it 'dies' and is immediately replaced with a food item, whose value is set equal to the organism's size at death.

Apart from feeding organisms, food items also prevent movement. Organisms and food items cannot occupy the same location, and an organism facing a food item directly ahead cannot move through it.

Organisms

Organisms are represented by colored squares of different sizes, and they perform actions in their environment according to a set of genetic traits and a single decision tree. 'Health' and 'energy' are the same thing for organisms, and an organism's actions (moving, eating, etc.) may reduce its own health by some small amount to represent the energy exertion needed to do them. Further, an organism unable to tolerate the ph of its location will also have its health reduced until conditions improve.

An organism's health is limited by its current size, so an organism of size 50 will have a max health of 50. When an organism gains more health than its size allows, it 'grows' in size by some fraction of the excess health gain.

Traits

Initial organisms are generated with random values for several 'genetic' traits that define its size limitations, its ph tolerance, the time it waits betweeen spawning, etc. When spawning a new organism, the traits of the parent are adjusted by small random amounts and passed down to the new child.

• Color - generated from random hue, saturation, and brightness
• MaxSize - the maximum size an organism can grow
• SpawnHealth - the initial health given to a spawned child, which is also subtracted from the parent's health
• MinHealthToSpawn - the minimum health required by the parent to spawn a new child (never less than SpawnHealth)
• MinCyclesBetweenSpawns - the minimum number of cycles that must pass before the organism can produce another child
• ChanceToMutateDecisionTree - The chance of the organism passing a mutated version of its decision tree onto each spawned child
• IdealPh - The middle of the organism's ph tolerance range
• PhTolerance - The absolute ph distance the organism can go from its ideal ph without adverse effects. (eg. An ideal ph of 3 and ph tolerance of 1 provide a tolerance zone of 2-4 ph)
• PhEffect - the positive or negative factor the organism's growth has on the ph level of its location)

Decision Trees

Each organism's behavior is governed by a decision tree composed of various conditions and actions. Organisms generated at simulation start are given randomly-selected trees built from these decision nodes, while spawned children inherit an identical or similar variation of their parents' decision tree. and chosen from the following:

Conditions

• CanMoveAhead - checks if the organism can move forward (false if a food item or another organism directly ahead)
• IsRandomFiftyPercent - returns true if a randomly generated float is less than .5
• IsFoodAhead - true if a food item directly ahead
• IsFoodLeft - true if a food item lies 90 degrees to the left
• IsFoodRight - true if a food item lies 90 degrees to the right
• IsOrganismAhead - true if an organism directly ahead
• IsOrganismLeft - true if an organism lies 90 degrees to the left
• IsOrganismRight - true if an organism lies 90 degrees to the right
• IsBiggerOrganismAhead - true if an organism of greater size directly ahead
• IsRelatedOrganismAhead - true if an organism with a shared ancestor directly ahead
• IsRelatedOrganismLeft - true if an organism with a shared ancestor lies 90 degrees to the left
• IsRelatedOrganismRight - true if an organism with a shared ancestor lies 90 degrees to the right
• IfHealthAboveFiftyPercent - true if organism's health values more than half its current size
• IsHealthyPhHere - true if the ph level at current location is within the organism's tolerance - having no harmful health effects and allowing for chemosynthesis
• IsHealthierPhAhead - true if the ph level directly ahead is closer to the organism's ideal ph than the ph at its current location tolerance

Actions

• Chemosynthesis - generates a small amount of health, if performed at a location with healthy ph
• Eat - consumes a small amount of health to consume any food that lies directly ahead
• Move - consumes a small amount of health to move forward, if no food or organism directly ahead
• TurnLeft -- consumes a small amount of health to turn 90 degrees left
• TurnRight - consumes a small amount of health to turn 90 degrees right
• Attack - consumes a large amount of health to reduce the health of any organism directly ahead
• Feed - transfers a small amount of health to any organism directly ahead

Decision Tree Health Effects

Because decision trees are randomly generated and mutated, many trees will have areas of redundancy and illogic, containing branches that have no possibility of ever being reached. As a way to reward logical algorithms, Organisms lose a very small amount of health each cycle for every node in their decision tree, as a way to simulate the energy needed to process complicated decision-making. Thus, over time, subsequent mutations to decision trees should allow more efficient organisms to outpace those with similar behaviors but less efficient algorithms.

Display

Clicking on an organism in the simulation grid will display its traits and decision tree in the left-hand panel, as shown:

As printed, each conditional statement (eg. "If Can Move Ahead") is followed by a line that splits into two branches. The first, top-most branch is the logic the organism will follow if the checked condition returns true. The second, bottom branch will evaluate if the condition returns false. All decision tree nodes evaluated in the previous cycle are followed by "◀◀". Thus, the example decision tree shows - in the previous cycle - the selected organism checked 'If Can Move Ahead' (true), checked 'If Food Right' (false), and so it chose the 'Move Ahead' action.

Setup

go get
go run main.go

Run Options

-config Use overriden simulation constants. Ex:

go run main.go -config=settings/small.json
go run main.go -config=settings/big.json

-seed Set the random seed used by the simulation. Ex:

go run main.go -seed=2

-debug Display memory usage and FPS

go run main.go -debug=true

Config

You can create your own .json config files to override simulation constants at runtime. To print the default settings as json (you can paste and edit this in a new configuration .json file)

go run main.go -dump-config

Run Headless

• Single trial:

go run main.go -headless

• Multiple trials:

go run main.go -headless -trials=10

Test

go test test/utils_test.go