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Roger D. Jones

Publications and source records attributed to Roger D. Jones.

7 recordsLinked to original sources
arXiv2026

What is Life?

Since Schrodinger's \emph{What Is Life?}, the physical basis of biological organization has been understood in terms of the interplay between matter, energy, and information. Subsequent developments in molecular biology, information theory, nonequilibrium thermodynamics, and evolutionary theory have clarified how hereditary information is stored, maintained, and modified through natural selection. Here, we extend this program by asking what minimal physical principles are required for adaptable life. We propose six postulates governing adaptive living systems: the existence of an entropy source, longevity of information, fast response to environmental change, repeatable operation, energetic efficiency, and networks of multiple interacting switches. These principles are introduced as a minimal foundation for biological information processing and adaptation. We examine their implications and compare them with observations across multiple levels of biological organization, including genetic inheritance, epigenetic regulation, cellular signaling, neural computation, metabolic networks, and ecological systems. The resulting framework suggests that adaptability emerges from the interplay of energy flow, information storage, information processing, and natural selection in systems maintained far from thermodynamic equilibrium. Although the proposed principles are qualitative and not yet predictive, they provide a unified perspective on the physical constraints governing adaptive behavior and offer a starting point for the development of a quantitative theory of adaptable life.

q-bio.MN↗
arXiv2026

Information Transmission and Processing in G-Protein-Coupled-Receptor Complexes

G-protein-coupled receptors (GPCRs) are central to cellular information processing, yet the physical principles governing their switching behavior remain incompletely understood. We present a first principles theoretical framework, grounded in nonequilibrium thermodynamics, to describe GPCR switching as observed in light-controlled impedance assays. The model identifies two fundamental control parameters: (1) ATP/GTP-driven chemical flux through the receptor complex, and (2) the free-energy difference between phosphorylated and dephosphorylated switch states. Together, these parameters defin the switch configuration. The model predicts that GPCRs can occupy one of three quasi-stable configurations, each corresponding to a local maximum in information transmission. Active states support chemical flux and exist in an on or off switch configuration, whereas inactive states lack flux, introducing a distinction absent in conventional phosphorylation models. The model takes two ligand-derived inputs: fixed structural features and inducible conformations (e.g. cis or trans). It shows that phosphatase activity, modeled as an energy barrier, chiefly governs on/off occupancy, whereas the kinase sustains flux without directly determining the switch configuration. Comparison with experimental data confirms the predicted existence of multiple quasi-stable states modulated by ligand conformation. Importantly, this framework generalizes beyond GPCRs to encompass a wider class of biological switching systems driven by nonequilibrium chemical flux.

q-bio.MN↗
arXiv2025

Plumbing Analog of Molecular Computation

Biological information processing often arises from mesoscopic molecular systems operating far from equilibrium, yet their complexity can make the underlying principles difficult to visualize. In this study, we introduce a macroscopic hydraulic model that serves as an intuitive analog for the molecular switching behavior exhibited by G protein-coupled receptors (GPCRs) on the cell membrane. The hydraulic system reproduces the essential structural and functional features of the molecular switch, including the presence of up to three distinct steady state solutions, the characteristic shapes of these solutions, and the physical interpretation of the control parameters governing the behavior of the system. By mapping water flow, energy barrier height, and siphoning dynamics onto biochemical flux, activation energy, and state transitions, the model provides a transparent representation of the mechanisms that regulate GPCR activation. The correspondence between the hydraulic analog and the molecular system suggests several experimentally testable hypotheses about GPCR function. In particular, the model highlights the central role of energy flux, driven by imbalances in ATP/ADP or GTP/GDP concentrations, in activating the molecular switch and maintaining nonequilibrium signaling states. It also identifies two key parameters that primarily determine switch behavior: the energy difference between the active and inactive states and the effective height of the energy barrier that separates them. These results imply that GPCR signaling dynamics may be governed by generalizable physical principles rather than by biochemical details alone. The hydraulic framework thus offers a tractable platform for interpreting complex molecular behavior and may aid in the development of predictive models of GPCR function in diverse physiological contexts.

q-bio.SC↗
arXiv2025

Thermodynamics of Biological Switches

We derive a formulation of the First Law of nonequilibrium thermodynamics for biological information-processing systems by partitioning entropy in the Second Law into microscopic and mesoscopic components and by assuming that natural selection promotes optimal information processing and transmission. The resulting framework demonstrates how mesoscopic information-based subsystems can attain nonequilibrium steady states (NESS) sustained by external energy and entropy fluxes, such as those generated by ATP/ADP imbalances in vivo. Moreover, mesoscopic systems may reach NESS before microscopic subsystems, leading to ordered structures in entropy flow analogous to eddies in a moving stream.

cond-mat.stat-mech↗
arXiv2004

Information Flow and Computation in the Maxwell Demon Problem

In this paper we examine the Maxwell Demon problem from an information theoretic and computational point-of-view. In particular we calculate the required capacity of a communication channel that transports information to and from the Demon. Equivalently, this is the number of bits required to store the information on a computer tape. We show that, in a simple model for the Maxwell Demon, the entropy of the universe increases by at least an amount eta=0.83999552 bits per particle in going from unsorted to sorted particles and by an amount eta*=2.37314 in going from one sorted state to another sorted state.

physics.class-ph↗
arXiv2003

The Maxwell Demon and Market Efficiency

This paper addresses two seemingly unrelated problems, (a) What is the entropy and energy accounting in the Maxwell Demon problem? and (b) How can the efficiency of markets be measured? Here we show, in a simple model for the Maxwell Demon, the entropy of the universe increases by an amount eta=0.839995520 in going from a random state to an ordered state and by an amount eta*=2.731382 in going from one sorted state to another sorted state. We calculate the efficiency of an engine driven by the Maxwell sorting process. The efficiency depends only on the temperatures of the particles and of the computer the Demon uses to sort the particles. We also show the approach is general and create a simple model of a stock market in which the Limit Trader plays the role of the Maxwell Demon. We use this model to define and measure market efficiency.

physics.class-ph↗