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

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 Godel'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.

Automated summary

Bioenergetics, genetic coding, and catalysis are crucial processes of biology that are hard to emerge without pre-existing historical context. Resolving paradoxes through coupling is essential in understanding the underlying contradictions in these processes.