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

• Main Authors: Charles W. Carter, Peter R. Wills
• Format: Article
• Language: English
• Published: MDPI AG 2021-02-01
• Series: Biomolecules
• Subjects: genetic coding; free energy transduction; non-equilibrium thermodynamics; transition-state stabilization; conformational change; aminoacyl-tRNA synthetases
• Online Access: https://www.mdpi.com/2218-273X/11/2/265

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. In each example, a paradox is resolved by coupling “if, and only if” conditions for reciprocal transitions between levels, such that the consequent of the first test is the antecedent for the second. Each condition thus restricts fluxes through, or “gates” the other. Reciprocally-coupled gating, in which two gated processes constrain one another, is self-referential, hence maps onto the formal structure of “strange loops”. That mapping uncovers two different kinds of forces that may help unite the axioms underlying three phenomena that distinguish biology from chemistry. As a physical analog for Gödel’s logic, biomolecular strange-loops provide a natural metaphor around which to organize a large body of experimental data, linking biology to information, free energy, and the second law of thermodynamics.