Regulatory State Space as a Dynamical System: How Autocatalytic Network Structure, Methylation-Coupled Landscape Reshaping, Sampling Bias in Boolean Models, Control-Theoretic Aging Frameworks, and Ecological Interaction Signatures Jointly Constrain the Architecture of Biological Self-Organization

Version 2 — revised in response to an external structural review and an automated critique pass. See "Response to Review" appendix in the PDF for the change log.

Biological systems at every scale — from gene regulatory networks to ecological communities — share a structural problem: they must maintain functional identity against perturbation while remaining capable of state transitions when conditions demand. This paper synthesizes five to seven findings from recent q-bio preprints (categories q-bio.MN, q-bio.PE, q-bio.GN, q-bio.BM) to argue for a **candidate heuristic reading** — explicitly not a derivation — of biological self-organization as a multi-timescale, state-space architecture in which slow dynamical coordinates constrain fast expression or behavioral dynamics, network topology determines reachable state sets, and sampling assumptions invisibly shape what we believe those state sets look like. Specifically, we draw on: (1) a control-theoretic reframing of aging as progressive loss of safe controllability, in which intervention order is predicted to matter because vector fields on biological state space do not commute [corpus:arxiv:2605.16781] — a preprint (v2) whose central claims remain experimentally unvalidated as of the submission date; (2) a dynamical reframing of DNA methylation as a slow internal coordinate that autonomously reshapes expression landscapes rather than merely stabilizing them, validated in silico in minimal model systems [corpus:arxiv:2605.14562]; (3) a formal unification of two autocatalysis frameworks showing that collective self-sustaining reaction networks are, under mild conditions, also stoichiometrically self-amplifying — a result that applies to chemical reaction networks and whose extension to gene regulatory networks is heuristic [corpus:arxiv:2605.25523]; (4) a demonstration that uniform sampling of Boolean network functions — a standard null model — introduces systematic bias in sensitivity estimates and thus in conclusions about regulatory robustness, with the direction and magnitude of propagated error requiring the full analysis to assess [corpus:arxiv:2606.05196]; (5) a characterization of ecological interaction strength distributions as Pareto-tailed and taxon-conserved, documented in two empirical plant-animal network datasets [corpus:arxiv:2605.17220]; and, as a weakly-connected addendum presented separately from the primary argument, (6) elemental stoichiometry as a biosignature framework that extends the notion of constrained chemical space to ecological scales [corpus:arxiv:2605.19252]. The bridge across scales is a shared structural motif — constrained state spaces navigated by slow coordinates — identified by heuristic reading, not formal derivation. The central falsification path is: if methylation dynamics can be experimentally decoupled from transcription-factor binding kinetics without altering fate commitment statistics, the slow-coordinate model is falsified at the molecular level; if aging intervention outcomes prove order-independent in controlled combinatorial trials, the non-commutativity prediction is falsified at the systems level. ---

Authorship: Saluca Agentic AI Research Team (Saluca LLC). AI-drafted from arXiv preprint corpus on the date in the filename.

Cited arXiv preprints: 2605.14562, 2605.16781, 2605.17220, 2605.19252, 2605.21945, 2605.25523, 2605.29958, 2606.03071, 2606.05196, 2606.07372, 2606.08493

AI disclosure. This work was produced with an agentic AI research apparatus operated by Saluca Labs. The apparatus drafted, searched and analysed under direction. Cristian Ruvalcaba is the human author and is accountable for the content. No AI system is listed as an author or contributor, because authorship entails accountability that a model cannot hold; this disclosure is the credit, and it is deliberately the whole of it.