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Special Issue "Equilibrium and Non-Equilibrium Entropy in the Origin of Life"


A special issue of Entropy (ISSN 1099-4300).

Deadline for manuscript submissions: closed (30 December 2012)

Special Issue Editor

Guest Editor
Dr. Eric Smith (Website)

Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
Phone: 505-946-2764
Interests: origin of life; non-equilibrium systems; population processes; early evolution of metabolism; statistical mechanics on structured domains

Special Issue Information

Dear Colleagues,

Boltzmann (Populäre Schriften, 1905) characterized the Darwin/Malthus struggle for existence as a struggle for free energy, and Schrödinger (What is Life?, 1944) centered the physics of life around rejection of entropy from biomass to the nonliving environment.  The rise of the paradigms of self-organization and dissipative structures have since led to proposals that the emergence of life might be understood as a spontaneous rejection of entropy, perhaps carried out by processes related to those that maintain life today.

The half-century since Schrödinger has seen major advances of two kinds in our understanding of entropy as it might pertain to the origin of life.  The first is within equilibrium thermodynamics: more is known about sources of free energy that sustain life on earth, and more diverse and complete quantitative models exist for biochemistry, physiology, and ecology.  In parallel, advances in non-equilibrium statistical mechanics and its large-deviation theory have shown how the concept of entropy maximization continues to explain the emergence and robustness of non-equilibrium ordered states, in cases where the rate functions defining the appropriate entropies (now, effective actions) differ from the equilibrium free energies.  The latter advances show how kinetics may preempt equilibrium thermodynamics as the source of relevant constraints on the formation and persistence of ordered non-equilibrium states.

In this volume we seek to bring together mathematical insights from both equilibrium and non-equilibrium thermodynamics with expertise from empirical domains relevant to the emergence and early evolution of life, including planetary and space chemistry, biochemistry, evolutionary dynamics ranging from physical self-organization to population processes, the dynamics of both chemically homogeneous (e.g. RNA) and heterogeneous populations of molecules, and separations of time and spatial scales that lead to the emergence of memory, compartmentalization, control systems, individuality, or levels of development and selection.  Collaborations that unify such domains are especially solicited.

Dr. Eric Smith
Guest Editor


  • chemoautotrophy
  • proto-metabolism
  • Hadean atmosphere, ocean, and mineralogy
  • hydrothermal vents
  • mineral-mediated organosynthesis
  • network combinatorics and autocatalysis
  • hypergraphs and stoichiometry
  • syntrophy and ecological stoichiometry
  • systems biology
  • synthetic biology
  • control systems
  • requisite variety
  • tiny RNA
  • genome integration and regulation
  • compartmentalization
  • compositional inheritance models
  • emergence and evolution of individuality
  • population processes
  • horizontal gene transfer
  • innovation sharing
  • stochastic chemistry and Gillespie algorithms
  • metal-ligand interactions
  • catalysis
  • kinetic theory
  • reaction-diffusion theory
  • Kolmogorov-Sinai entropy
  • effective action and stochastic effective action
  • Martin-Siggia-Rose, Doi-Peliti, and Freidlin-Wentzell methods
  • fluctuation-dissipation theorems
  • additivity principles
  • intensive thermodynamic parameters
  • dynamic large deviations
  • (chemical and other) non-equilibrium work relations
  • maximum entropy
  • maximum entropy production (MEP)
  • information
  • information physics
  • optimal information processing
  • Bayesian probability theory

Published Papers (1 paper)

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Open AccessArticle Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data
Entropy 2013, 15(10), 4066-4083; doi:10.3390/e15104066
Received: 22 February 2013 / Revised: 10 September 2013 / Accepted: 11 September 2013 / Published: 25 September 2013
Cited by 8 | PDF Full-text (869 KB) | HTML Full-text | XML Full-text | Supplementary Files
Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth. HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex [...] Read more.
Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth. HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex mixture. Here we use a computational model based on graph grammars as a means of exploring the chemical spaces of HCN polymerization and hydrolysis. A fundamental issue is to understand the combinatorial explosion inherent in large, complex chemical systems. We demonstrate that experimental data, here obtained by mass spectrometry, and computationally predicted free energies together can be used to guide the exploration of the chemical space and makes it feasible to investigate likely pathways and chemical motifs even in potentially open-ended chemical systems. Full article
(This article belongs to the Special Issue Equilibrium and Non-Equilibrium Entropy in the Origin of Life)

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