Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Reciprocally-coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis

Version 1 : Received: 31 December 2020 / Approved: 4 January 2021 / Online: 4 January 2021 (16:21:16 CET)

A peer-reviewed article of this Preprint also exists.

Carter, C.W., Jr.; Wills, P.R., Jr. Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis. Biomolecules 2021, 11, 265. Carter, C.W., Jr.; Wills, P.R., Jr. Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis. Biomolecules 2021, 11, 265.

Journal reference: Biomolecules 2021, 11, 265
DOI: 10.3390/biom11020265

Abstract

Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a “Chicken and Egg” problem; its resolution is concisely described by de Grasse Tyson: “the egg was laid by a bird that was not a chicken”. The concision and generality of that answer furnish no details—only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. The paradox in each example is resolved by coupling if, and only if, conditions for two related transitions between levels. One drives, and each restricts fluxes through, or “gates” the other. That reciprocally-coupled gating, in which two gated processes constrain one another, maps onto the formal structure of “strange loops”. That mapping may help unite the axiomatic foundations of genetics, bioenergetics, and catalysis. As a physical analog for Gödel’s logic, biomolecular strange-loops provide a natural metaphor around which to organize these data, linking biology to the physics of information, free energy, and the second law of thermodynamics.

Subject Areas

Genetic coding; free energy transduction; non-equilibrium thermodynamics; transition-state stabilization; conformational change; aminoacyl-tRNA synthetases; emergent phenomena

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