Small and Simple Systems That Favor the Arrow of Time.

The 2nd law of thermodynamics yields an irreversible increase in entropy until thermal equilibrium is achieved. This irreversible increase is often assumed to require large and complex systems to emerge from the reversible microscopic laws of physics. We test this assumption using simulations and theory of a 1D ring of N Ising spins coupled to an explicit heat bath of N Einstein oscillators. The simplicity of this system allows the exact entropy to be calculated for the spins and the heat bath for any N, with dynamics that is readily altered from reversible to irreversible. We find thermal-equilibrium behavior in the thermodynamic limit, and in systems as small as N=2, but both results require microscopic dynamics that is intrinsically irreversible.

Entropy and the Second Law of Thermodynamics-The Nonequilibrium Perspective.

An alternative to the Carnot-Clausius approach for introducing entropy and the second law of thermodynamics is outlined that establishes entropy as a nonequilibrium property from the onset. Five simple observations lead to entropy for nonequilibrium and equilibrium states, and its balance. Thermodynamic temperature is identified, its positivity follows from the stability of the rest state. It is shown that the equations of engineering thermodynamics are valid for the case of local thermodynamic equilibrium, with inhomogeneous states. The main findings are accompanied by examples and additional discussion to firmly imbed classical and engineering thermodynamics into nonequilibrium thermodynamics.

Responses to commentaries on "The gene: An appraisal".

The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.

The Winding Road from Origin to Emergence (of Life).

Humanity's strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin's Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the "organic-molecules-paradigm" became increasingly difficult to ignore, culminating in Erwin Schrödinger's 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far.