PEBBLE BioFusion | Part 2

Damage feedback and repair decline

After the minimal model, what changes when damage can accelerate its own accumulation and weaken repair?

Terminal cells-
Mean terminal damage-
Damage range-
Correlation with O-history-
Cells that died-
Lineage tree: each dot is one cell; colour is damage
O edge: larger inherited shareN edge: smaller inherited sharelow damagehigh damage✕ cell died before dividing
Terminal damage distribution
Present state versus ancestry
Single-cell damage trajectory: current feedback/repair decline versus no feedback
no feedback or repair decline: f = q = 0current f and q valuesdeterministic update: no noise, partitioning, or death

Pair challenges

  1. Start with 1. Symmetric. Before running, predict whether the O-history plot should have a slope.
  2. Choose 2. Asymmetric. Increase asymmetry from 0.18 to 0.30. Which plot changes most, and why?
  3. Choose 3. More repair. Does repair erase the branch pattern, or merely shrink damage values?
  4. Choose 4. Death threshold. Which branches disappear first, and why does this create selection among lineages?
  5. For the trajectory chart, set feedback = 0 and repair decline = 0, then increase one parameter at a time. Which parameter makes the curve bend upward, and why?
  6. Make one evidence-based claim: “Changing ___ caused ___ in the ___ plot; therefore ___.”
The extended toy model: before division, a cell repairs a fraction of its old damage, accumulates new damage and noise, then dies if its damage exceeds the threshold.
reff = r / (1 + q Dt)
aeff = a (1 + f Dt)
Pt = max(0, (1 - reff) Dt + aeff + εt)
if Pt ≥ T: cell dies before division
DOt+1 = (0.5 + s) Pt,   DNt+1 = (0.5 - s) Pt
Here f is damage feedback, q is repair decline, and aeff is the damage newly generated in the current cycle; the remaining symbols have the same meaning as in Part 1. Damage feedback lets already-damaged cells accumulate damage faster; repair decline lets high damage weaken repair. Partitioning moves damage between daughters; only repair removes it.