# Thermodynamics of life

September 23, 2014 — May 30, 2017

buzzword

compsci

life

statmech

time series

Statistical mechanics of living things.

What is happening in this area, since everyone got tired of handwaving about “dissipative systems”? Prigogene’s work in that area seems to have sunk into… disregard? disrepute? But there is a revival of some of the formalisms.

Shinier and newer, Jeremy England is hip… others?

Popsci. Jeremy England: A new physics theory of life

John Baez and friends’ Entropy and information in biological systems shows when Shannon and Boltzmann entropy relate and how that is important in an interesting class of systems:

A workshop! Non-Equilibrium Thermodynamics in Biology

## 1 References

Altaner. 2017. “Nonequilibrium Thermodynamics and Information Theory: Basic Concepts and Relaxing Dynamics.”

*Journal of Physics A: Mathematical and Theoretical*.
Apell, Neidrauer, Papazoglou, et al. 2012. “Physics of Wound Healing I: Energy Considerations.”

*arXiv:1212.3778*.
Baez, and Pollard. 2015. “Relative Entropy in Biological Systems.”

Bagnoli, and Bergstrom. 1989. “Log-Concave Probability and Its Applications.”

Beretta. 2020. “The Fourth Law of Thermodynamics: Steepest Entropy Ascent.”

*Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences*.
Boyd, Crutchfield, and Gu. 2020. “Thermodynamic Machine Learning Through Maximum Work Production.”

Clarke. 2004. “Is There a Universal Temperature Dependence of Metabolism?”

*Functional Ecology*.
Crooks. 1999. “The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences.”

*Physical Review E*.
Crutchfield. 1992. “Semantics and Thermodynamics.” In

*Nonlinear Modeling and Forecasting*. Santa Fe Institute Studies in the Sciences of Complexity, XII.
de Vladar, and Barton. 2011. “The Contribution of Statistical Physics to Evolutionary Biology.”

*Trends in Ecology & Evolution*.
England. 2013. “Statistical Physics of Self-Replication.”

*The Journal of Chemical Physics*.
Fodor, Nardini, Cates, et al. 2016. “How Far from Equilibrium Is Active Matter?”

*Physical Review Letters*.
Gallucci. 1973. “On the Principles of Thermodynamics in Ecology.”

*Annual Review of Ecology and Systematics*.
Ghavasieh, Nicolini, and De Domenico. 2020. “Statistical Physics of Complex Information Dynamics.”

*Physical Review E*.
Goldt, and Seifert. 2017. “Stochastic Thermodynamics of Learning.”

*Physical Review Letters*.
Harvey, Lahiri, and Ganguli. 2020. “A Universal Energy Accuracy Tradeoff in Nonequilibrium Cellular Sensing.”

Judson. 2017. “The Energy Expansions of Evolution.”

*Nature Ecology & Evolution*.
Kolchinsky, and Wolpert. 2018. “Semantic Information, Autonomous Agency, and Nonequilibrium Statistical Physics.”

Krakauer, and Flack. 2010. “Better Living Through Physics.”

*Nature*.
Lane, and Martin. 2010. “The Energetics of Genome Complexity.”

*Nature*.
Lang, Fisher, Mora, et al. 2014. “Thermodynamics of Statistical Inference by Cells.”

*Physical Review Letters*.
Lotka. 1922. “Natural Selection as a Physical Principle.”

*PNAS*.
Marsland, and England. 2018. “Limits of Predictions in Thermodynamic Systems: A Review.”

*Reports on Progress in Physics*.
Martyushev, and Seleznev. 2006. “Maximum Entropy Production Principle in Physics, Chemistry and Biology.”

*Physics Reports*.
McLeod. 1998. “Hyperbolic Decay Time Series.”

*Journal of Time Series Analysis*.
Morowitz, and Smith. 2007. “Energy Flow and the Organization of Life.”

*Complexity*.
Nguyen, Qiu, and Vaikuntanathan. 2021. “Organization and Self-Assembly Away from Equilibrium: Toward Thermodynamic Design Principles.”

*Annual Review of Condensed Matter Physics*.
Nicholson. 2019. “Is the Cell Really a Machine?”

*Journal of Theoretical Biology*.
Odum. 1973. “Energy, Ecology, and Economics.”

*Ambio*.
Perunov, Marsland, and England. 2016. “Statistical Physics of Adaptation.”

*Physical Review X*.
Pollard. 2016. “Open Markov Processes: A Compositional Perspective on Non-Equilibrium Steady States in Biology.”

*arXiv:1601.00711 [Cond-Mat, Physics:physics]*.
Reiss, Hammerich, and Montroll. 1986. “Thermodynamic Treatment of Nonphysical Systems: Formalism and an Example (Single-Lane Traffic).”

*Journal of Statistical Physics*.
Ricotta, and Szeidl. 2006. “Towards a Unifying Approach to Diversity Measures: Bridging the Gap Between the Shannon Entropy and Rao’s Quadratic Index.”

*Theoretical Population Biology*.
Salthe. 1997. “The Overall Pattern of the Evolution of Information in Dissipative, Material Systems.”

*World Futures*.
———. 2005. “Energy and semiotics: the Second Law and the origin of life.”

*Cosmos and History: The Journal of Natural and Social Philosophy*.
———. 2010. “Development (and Evolution) of the Universe.”

*Foundations of Science*.
Sarkar, and England. 2019. “Design of Conditions for Emergence of Self-Replicators.”

*Physical Review E*.
Schneider, and Kay. 1994. “Life as a Manifestation of the Second Law of Thermodynamics.”

*Mathematical and Computer Modelling*.
Schwab. 2012. “The Energetic Costs of Cellular Computation.”

*Proceedings of the National Academy of Sciences*.
Seifert. 2012. “Stochastic Thermodynamics, Fluctuation Theorems and Molecular Machines.”

*Reports on Progress in Physics*.
Smith. 2008a. “Thermodynamics of Natural Selection I: Energy Flow and the Limits on Organization.”

*Journal of Theoretical Biology*.
———. 2008b. “Thermodynamics of Natural Selection II: Chemical Carnot Cycles.”

*Journal of Theoretical Biology*.
Stanley, Amaral, Goldberger, et al. 1999. “Statistical Physics and Physiology: Monofractal and Multifractal Approaches.”

*Physica A: Statistical and Theoretical Physics*.
Still, Sivak, Bell, et al. 2012. “Thermodynamics of Prediction.”

*Physical Review Letters*.
Stumpf. 2022. “More Is Different with a Vengeance.”

*Cell Systems*.
Ulanowicz, and Abarca-Arenas. 1997. “An Informational Synthesis of Ecosystem Structure and Function.”

*Ecological Modelling*.
van den Broeck. 2010. “The Many Faces of the Second Law.”

*Journal of Statistical Mechanics: Theory and Experiment*.
Ventola, Braun, Yu, et al. 2023. “Probabilistic Circuits That Know What They Don’t Know.” arXiv.org.

Vinković, and Kirman. 2006. “A Physical Analogue of the Schelling Model.”

*Proceedings of the National Academy of Sciences*.
West, Savage, Gillooly, et al. 2003. “Why Does Metabolic Rate Scale with Body Size?”

*Nature*.
West, Woodruff, and Brown. 2002. “Allometric Scaling of Metabolic Rate from Molecules and Mitochondria to Cells and Mammals.”

*Proceedings of the National Academy of Sciences*.
Whitfield. 2004. “Ecology’s Big, Hot Idea.”

*PloS Biology*.
———. 2018. “Overview of Information Theory, Computer Science Theory, and Stochastic Thermodynamics for Thermodynamics of Computation.”

———. 2021. “Fluctuation Theorems for Multiple Co-Evolving Systems.”

*arXiv:2003.11144 [Cond-Mat]*.
Yang, Heinemann, Howard, et al. 2021. “Physical Bioenergetics: Energy Fluxes, Budgets, and Constraints in Cells.”

*Proceedings of the National Academy of Sciences*.