Mutation

Mutation is the re-roll a genome takes each time it is copied. Every mitosis, every bud and every plasmodium pinch builds the daughter from a re-rolled copy of the parent’s genome, and that roll runs at two speeds. Only two processes change a living cell’s genome without a division.

The two speeds

The drift floor. At the shipped division settings every parameter of every gene steps every division, by 0.08% to 0.4% of the value it starts from. Most parameters step proportionally; the pH optimum steps by a fraction of its range instead, so an unbiased walk rests at neutral rather than sliding acid.

The event. On the shipped 0.57% roll per gene copy, every parameter that gene owns is drawn from the large band at once: a step of 30% to 80%, a jump of 1.35x to 2.2x either way on a proportional axis. The roll is per gene, not per parameter, so a genome of many genes throws more events than one of few whatever their parameter counts, and an event lands as one organelle changing rather than one knob moving. The large step is not softened as it nears a parameter’s limit, though the result is clamped into range.

The mutation pass

One pass walks the genome in a fixed order.

The rate rises by running the pass more than once, not by raising any of the numbers above. A contaminant lineage runs one extra pass per division, and every pass a banked mutagen dose buys runs another. A cell the player owns runs slower than either: one authored scale below 1 damps its mutation rate, its drift magnitude, its copy-change rates and its odds of gaining a gene, together. Ownership is the whole gate.

A few counts are fixed:

• Temperature tolerance is single-copy with a deletion chance of zero, so nothing takes it off a cell.
• Cilia neither duplicates nor deletes.
• The vacuole gains copies but never falls below one.
• Enzyme modifiers are dropped outright if no digestive enzyme survives the pass.

Drift direction

Most parameters walk without direction. The pH and temperature optima do not: they are pulled toward the substrate sampled where the daughter lands, not where the parent sat. Mitosis samples each daughter at its own pole, so a division across a steep border splits them harder; a bud samples its parent’s centre.

The pull scales with how committed the ground is: nothing inside a small deadzone, 3:1 against a counter-gradient step just outside it, 8:1 on fully committed ground, with the with-gradient step scaled up 1.6x on top. It never becomes a gate, and a step against the grain is always possible. Extremity raises mutation itself as well: at crystal-level ground the magnitude band rises to 1.75x and the event rate to 3x, so events cluster where the dish is harsh.

Deliberate mutation

Dosing is how a player mutates a cell on purpose, and it reaches player-owned cells only. F charges the player for one dose of every armed non-trophin compound and delivers it to each selected owned cell. Mutagen particles dose a cell on contact and are consumed. Banked hits convert to whole extra passes at a fixed threshold, and a division spends and clears the bank, so they accumulate only inside one division interval. Those bought passes are exempt from the owned-lineage brake, which is what makes a dose faster than the lineage’s ambient rate.

A banded compound overrides the ground rather than averaging with it: a cell given an acid-band mutagen while it stands on alkaline substrate aims its optimum acid.

A paid trophin dose is the other way to aim mutation, and it reads the ground the cell stands on. On off-neutral ground it aims that axis’s tolerance optimum at the local field, closing a fifth to two fifths of the remaining gap at the next division. On mottled ground, whose spread is wider than the cell’s own band, it widens the band instead. Each axis is judged on its own.

Two paths skip division. A digestive enzyme carrying the Mutagenic modifier runs a whole mutation pass over the living cell it lands on, one gene guaranteed to mutate, and it samples no position, so that rewrite is not steered by the ground. Clicking a ready nucleus in an amoeba duplicates the nucleus, and the copy’s genome is built through the same pass.

Strain divergence

A strain forks when a member is far enough from its founder snapshot, frozen when the strain was created and never measured against its parent. Three things clear the gate:

1. A change in comparable gene count, gene type or a gene’s parameter count, any of which is divergence outright whatever the magnitudes say.
2. One weighted axis past the per-axis threshold.
3. The weighted mean across all compared axes past the average threshold.

Axes are not equal. Contract-visible traits (enzyme fire rate, cilia thrust and speed, ER emission rate) carry heavier weights, so the same drift forks a line sooner there than on a housekeeping trait. Both thresholds are scene-tunable, and hosted-symbiont genes are exempt, so an infection does not fork a bud into a new strain.

The first condition is why gaining a second mitochondrion renames a line and a long quiet walk may not. Identifying a drifted cell with M starts a new strain from that cell and freezes a new founder, which is the only thing that moves a baseline. The fork is announced at most once per strain, and only on a division that actually named something.

Divergence marks

Each division stamps up to three ranked divergence marks on the daughter: which gene moved, and which way. Direction carries no worth anywhere in the system, deliberately: a lineage shedding motility in a still dish is adapting. Ranking is by score alone and never asks what kind of change a mark is, so a large enough scalar jump outranks an acquisition:

No surface prints a mark as words. A daughter that carried any mark reads DRIFTING on its lineage node for a while after that division, and a strain’s first divergence pays one perk pick flavoured by its marks: a pH move offers the pH perks, a temperature or metabolism move the metabolic ones, an enzyme move the enzyme ones. A card presents that pick and holds the dish paused for it, and a declined pick is banked rather than lost.