URT in Biology: Efficiency, Folding Funnels, Replication Fidelity, and Molecular Motor Dynamics

This paper presents an empirical translation of Unified Recursion Theory (URT) into biological systems. Rather than introducing new biological models or mechanisms, it maps existing experimental measurements in molecular and cellular biology onto the universal URT variables of informational stiffness (σ) and recursion efficiency (λ).

Biological processes such as protein folding, enzyme catalysis, RNA folding, DNA replication, molecular motor stepping, and cellular metabolism are treated as discrete physical state transitions. Each transition carries a measurable energetic cost and entropy change, allowing direct comparison with the URT proportionality relation between energy expenditure and informational change.

Free-energy landscapes widely used in biophysics are interpreted geometrically, with stiffness corresponding to landscape curvature. Measured biological efficiencies—folding yields, catalytic turnover, motor work efficiency, and replication fidelity costs—are identified directly with the recursion efficiency λ. Across all systems examined, efficiencies cluster within bounded intermediate ranges, consistent with finite stiffness rather than near-reversible or frozen dynamics.

A central result is the distinction between passive and active recursion regimes. Passive systems terminate recursion through constraint excess as stiffness diverges. Biological systems, by contrast, require continuous energy throughput to maintain finite stiffness. Recursion terminates in biology through energy limitation, when available metabolic input is insufficient to sustain structured landscapes against entropic decay.

The paper introduces no new physical laws and does not imply biological optimization. URT predicts bounded efficiency bands imposed by landscape geometry and energetic constraint, not optimal design. Biological measurements are shown to be consistent with the empirically convergent efficiency scale λ₀ identified in prior URT work; biology constrains this convergence but does not define it.

Falsifiable predictions are presented, including efficiency–temperature scaling, landscape-modification responses, load-dependent motor behavior, fidelity–energy tradeoffs, and maintenance-energy thresholds. Agreement across these tests supports URT universality in living systems; systematic deviation would falsify the framework in this domain.

This paper establishes biology as a primary empirical validation domain for Unified Recursion Theory and completes the cross-domain extension of URT from quantum and gravitational systems into real, actively maintained physical systems.

URT PAPER FAMILY

This work forms part of the Unified Recursion Theory (URT) research program, which develops a cross-domain framework for physical evolution based on constrained informational recursion and an energy–entropy proportionality law. Each paper in the series is self-contained, while collectively establishing the theoretical structure across quantum, geometric, biological, cosmological, and particle-level domains.

Related URT works available on Zenodo:

FOUNDATIONAL PAPERS

1. Unified Recursion Theory — Core Framework (URT Core)

DOI: 10.5281/zenodo.17642761
Record: https://zenodo.org/records/17642761

2. Discrete Admissible Regimes in Unified Recursion Theory: Operator Closure, Constraint Topology, and the Necessity of Five Operators

DOI: 10.5281/zenodo.18148192
Record: https://zenodo.org/records/18148193

3. Informational Field Theory in Strong Curvature (IFT-SC)

DOI: 10.5281/zenodo.17850379
Record: https://zenodo.org/records/17850379

4. Dynamical Evolution of the Informational Stiffness Field (ISW Theory)

DOI: 10.5281/zenodo.17860533
Record: https://zenodo.org/records/17860533

RESOLUTION PAPERS (PHYSICAL PARADOXES)

5. Informational Recursion and the Dissolution of the Black Hole Information Paradox

DOI: 10.5281/zenodo.17868662
Record: https://zenodo.org/records/17868662

6. ORM and the Quantum Measurement Problem (ORM)

DOI: 10.5281/zenodo.17881944
Record: https://zenodo.org/records/17881944

BRIDGING / CONSTRAINT PAPER

7. Distinguishability Geometry in Informational State Space

DOI: 10.5281/zenodo.17957062
Record: https://zenodo.org/records/17957062

Provides the geometric foundation for informational state space.
Underpins the emergence of spacetime, efficiency universality, and landscape geometry.

THEORETICAL EXPANSION PAPERS

8. Emergent Spacetime from Informational Recursion

DOI: 10.5281/zenodo.17885555
Record: https://zenodo.org/records/17885555

9. λ-Universality Across Scales (λ-UAS)

DOI: 10.5281/zenodo.17934065
Record: https://zenodo.org/records/17934065

10. Free-Energy Landscape Geometry in Unified Recursion Theory

DOI: 10.5281/zenodo.17940995
Record: https://zenodo.org/records/17940995

BIOLOGY / COMPLEXITY PAPER

11. URT in Biology: Efficiency, Folding Funnels, Replication Fidelity, and Molecular Motor Dynamics

DOI: 10.5281/zenodo.17945209
Record: https://zenodo.org/records/17945209

COSMOLOGICAL EXTENSIONS

12. Cyclic Cosmology from Informational Recursion

DOI: 10.5281/zenodo.17955043
Record: https://zenodo.org/records/17955043

13. Antimatter as Inverse Recursion: Temporal Operator Asymmetry and Matter–Antimatter Imbalance in Unified Recursion Theory

DOI: 10.5281/zenodo.17955043
Record: https://zenodo.org/records/17955625