Genome Actions Reference

Note

This file was generated using Claude

Detailed breakdown of all genome-driven actions in the CLANS3 simulation, extracted from the Processing source code (Cells.pde, constant.pde).

Overview

Only APEX (Sprout) cells execute genome commands. The genome system has three execution paths depending on cell state:

1. Growth — when no conditions are defined in the active gene
2. Body commands — when the APEX has a parent (is part of a multicellular organism)
3. Lone commands — when the APEX has no parent (is a free-roaming single cell)

Execution Flow (per tick)

APEX evaluates active gene:
  ├─ Check condition 1 (bytes 3-4)
  ├─ Check condition 2 (bytes 5-6)
  │
  ├─ Both conditions unused (gene value > 67)?
  │   └─ GROW using bytes 0-2 → APEX becomes WOOD
  │
  ├─ At least one condition met (none return -1)?
  │   ├─ Has parent? → execute body command (byte 9)
  │   │   └─ success → gene byte 10, failure → gene byte 11
  │   ├─ No parent? → execute lone command (byte 15)
  │   │   └─ success → gene byte 16, failure → gene byte 17
  │   └─ No valid command? → jump to gene byte 7
  │
  └─ At least one condition NOT met?
      ├─ Has parent? → execute body command (byte 12)
      │   └─ success → gene byte 13, failure → gene byte 14
      ├─ No parent? → execute lone command (byte 18)
      │   └─ success → gene byte 19, failure → gene byte 20
      └─ No valid command? → jump to gene byte 8

Growth (No Conditions Active)

Who: APEX cells (both body and lone) When: Both condition slots in the active gene have values > 67 (maxIF) Effect: The APEX creates up to 3 new cells (left/forward/right) based on bytes 0-2, then transforms into WOOD.

Growth Byte Encoding (each of bytes 0, 1, 2)

Growth Requirements

• Energy cost: (WORK + ORGANIC_CELL) = 20 energy per new cell
• Total energy must be >= cell_count * 20 or growth is skipped entirely
• Target position must be empty (cellsIndx == 0), otherwise that branch is silently skipped
• The growing APEX becomes WOOD after growth
• If no branches can be created and cell is alone, active gene resets to 0

Growth Side Effects

• New APEX children: parent WOOD sets energyTo[] flag toward them (will send energy)
• New LEAF/ROOT/ANTN children: child sets energyTo[] flag toward parent (will send energy back)
• Mutation: ~1% chance per new APEX child — copies genome, changes 1 random byte

Body Commands (APEX with parent, gene value 0-14)

These commands are available when the APEX is part of a multicellular organism (has a parent).

Fire/Seed Collision Behavior (setNewSEED)

When the target position (one step ahead) is occupied:

• If occupied by same genome → adds (ORGANIC_CELL+WORK+30) energy to that cell
• If occupied by different genome → marks that cell for death
• Either way, costs the creating cell (ORGANIC_CELL+WORK+30) energy
• If target is a wall (cellsIndx < 0) → fails, returns false

Lone Commands (APEX without parent, gene value 0-17)

These commands are available when the APEX is a free-roaming single cell (no parent).

Conditions (68 total, IDs 0-67)

Conditions are checked before commands execute. Each gene has two condition slots (bytes 3-4 and 5-6). A condition slot is “unused” if the gene value > 67 (maxIF).

Return Values

• 1 — condition met
• -1 — condition not met
• 0 — condition slot unused (gene value > maxIF)

Condition Table

Non-Genome Cell Behaviors (Automatic, Every Tick)

These are not genome-driven — they happen automatically based on cell type.

SEED

• Costs 0.5 energy/tick
• Dies if energy < 0
• If energy > 512 while attached → detaches (destroyAllLinks())
• If detached and restTime > 0: counts down, moves 1 cell/tick if move=true
  • Collision: kills the hit cell, seed stops moving (move=false, returns false → seed dies)
  • Movement costs 1 energy/step
• When restTime reaches 0: transforms into APEX at gene 0, level=0, age=AGE

WOOD (Transport)

• Costs 0.04 energy/tick
• If energy > 0: transmits energy to all cells marked in energyTo[], split evenly
• If energy <= 0: loses 1 age tick (starts at AGE=3)
• Dies when age reaches 0
• If detached (no parent) and has no children → dies immediately

LEAF (Green)

• Photosynthesis: OrganicMap[x][y] * free_neighbor_count * 0.0008
  • free_neighbor_count starts at LIGHTENERGY=10
  • Each occupied neighbor (8 checked): -1 from count
  • If ANY adjacent cell is LEAF: returns 0 (mutual shading — complete shutdown)
• Costs 0.04 energy/tick
• Transmits surplus energy toward parent
• Dies when age reaches 0 OR if parent == -1 (detached)

ROOT (Red)

• Extracts up to ROOT_CAN=1 organic/tick from OrganicMap at position
• Immune to organic poisoning (can survive OrganicMap >= 512)
• Costs 0.04 energy/tick
• Transmits surplus energy toward parent
• Dies when age reaches 0 OR if detached

ANTN (Blue)

• Extracts up to ANTN_CAN=1 energy/tick from EnergyMap at position
• Immune to energy poisoning (can survive EnergyMap >= 512)
• Costs 0.04 energy/tick
• Transmits surplus energy toward parent
• Dies when age reaches 0 OR if detached

APEX (Sprout)

• Costs 1 energy/tick
• Dies if energy + engP + engM < 0
• If energy > 1024 while attached → detaches and resets to gene 0
• If detached → level resets to 0

Energy Transfer System

• Uses double-buffer (engP/engM) with alternating phase (EnergyTransportPeriod flips between +1/-1 each tick)
• Cells receive buffered energy at start of tick
• transmitEnergy(): splits cell’s energy evenly among all flagged energyTo[] directions
• If nowhere to send and has parent: redirects to parent, also tells parent to stop sending energy back
• If nowhere to send and no parent: dumps energy into EnergyMap, loses 1 age tick

Key Constants

Source Code Notes

• Bug in condition 1: The code for conditions 0 and 1 is identical (< param*2). SIMULATION.md describes condition 1 as >=, so this appears to be a copy-paste bug in the original Processing source.
• “Light” conditions (26-31): “Light” actually measures organic matter at 3 cells distance in the given direction, excluding poisoned cells (organic >= 512 counts as 0). This is because photosynthesis depends on soil organic.
• Directional (9) scans (32-58): These sample a 3x3 grid offset 2 cells in the given direction, not the 3x3 around the cell itself.
• Eat (lone cmd 16): Checks all 8 neighbors (4 cardinal + 4 diagonal via 0.5-step increments). Only eats types < WOOD (APEX=0, LEAF=1, ANTN=2, ROOT=3). WOOD and SEED are spared.
• Command 3 vs Command 1: Both set move=true and restTime=8, but only command 1 calls destroyAllLinks(). Command 3 stays attached, meaning it won’t actually fly until either energy exceeds MAX_SEED_ENERGY (512) causing auto-detach, or it dies.