Source
Zhao, Wytock, Reynolds and Motter (2024), LIT-854, read in full in NOTE-655, with the Supplementary Text. The thesis is the paper’s own reading of its model result, stated in its abstract and discussion; its concrete prediction is that a transient crp knockdown leaves zraR, melR or rhaRS in a changed state (NOTE-655, C8).
What is asserted
That regulation by transcription factors, with no epigenetic marking and no change of environment, is enough for a bacterium’s expression state to remember a past disturbance: a temporary change to one regulator flips a self-maintaining part of the network, which then holds the new state after the cause is gone. Genotype would then fix a set of possible expression states, and history would choose among them.
What the Active account establishes toward it
THEORY-178 holds what was shown: in an ensemble of sign-consistent Boolean rules on the 87-gene core, many single genes admit a transient knockout or overexpression after which the network settles in a different attractor, and every such gene reaches a strongly connected component with a positive circuit. That is a model ensemble. The weak support from adaptive evolution under a permanent crp knockout (NOTE-655, C7) is not a transient perturbation.
What would confirm or reject it
The promote_when above. The authors’ own caveat, that noise in cells can turn a permanent state into a long-lived one, is the slow-return confound it asks to exclude (THEORY-136). The positive-circuit condition is not part of this thesis: as a general law of synchronous Boolean networks it fails (THEORY-178, note of 2026-10-19).
Provenance
Filed on 2026-10-20 by the narrowing-loss sweep (ADR-047 v4, batch 068), from the wider title THEORY-178 carried before it was narrowed on 2026-10-19.