A thermodynamic theory of evolution

Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution

In this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and functions from an energetic perspective, by outlining relevant thermodynamic theory relating to molecular, metabolic, cellular, individual, population, species, ecosystem and biome organization. We next investigate the fundamental relationships between systems theory and thermodynamics in terms of the Earth system, examining the key characteristics of self-assembly, self-organization (including autonomy), emergence, non-linearity, feedback and sub-optimality. Finally, we examine the relevance of systems theory and thermodynamics with reference to two specific aspects: the tempo and directionality of evolution and the directional and predictable process of ecological succession. We discuss the importance of the entropic drive in understanding altruism, multicellularity, mutualistic and antagonistic relationships and how maximum entropy production theory may explain patterns thought to evidence the intermediate disturbance hypothesis.

Information and the Umwelt: A theoretical framework for the evolution of play

Play is phylogenetically widespread, and there are many proposed theories and fitness benefits of play. However, we still need a theoretical framework that unifies our understanding of the benefits that facilitated the evolution of play in so many diverse species. Starting with von Uexküll's theory of the Umwelt (i.e., the sensory-motor worlds of animals), together with the behavior systems approach, we propose that the Umwelt is an information processing system that serves basic biological functions. During development, the Umwelt undergoes a rapid expansion in the sensory and motor stimuli it processes. We argue that play is a process that converts surplus resources into information. By increasing the information content of the developing Umwelt, play confers fitness benefits. To demonstrate that play could evolve based on its information benefits, we present a model and simulation results of the evolution of a social play learning process that provides fitness-enhancing information in adult cooperative and competitive situations. Finally, we discuss this information-theoretic framework in relation to proposed hypotheses and fitness benefits of play.

The Entropy of Entropy: Are We Talking about the Same Thing?

In the last few decades, the number of published papers that include search terms such as thermodynamics, entropy, ecology, and ecosystems has grown rapidly. Recently, background research carried out during the development of a paper on "thermodynamics in ecology" revealed huge variation in the understanding of the meaning and the use of some of the central terms in this field-in particular, entropy. This variation seems to be based primarily on the differing educational and scientific backgrounds of the researchers responsible for contributions to this field. Secondly, some ecological subdisciplines also seem to be better suited and applicable to certain interpretations of the concept than others. The most well-known seems to be the use of the Boltzmann-Gibbs equation in the guise of the Shannon-Weaver/Wiener index when applied to the estimation of biodiversity in ecology. Thirdly, this tendency also revealed that the use of entropy-like functions could be diverted into an area of statistical and distributional analyses as opposed to real thermodynamic approaches, which explicitly aim to describe and account for the energy fluxes and dissipations in the systems. Fourthly, these different ways of usage contribute to an increased confusion in discussions about efficiency and possible telos in nature, whether at the developmental level of the organism, a population, or an entire ecosystem. All the papers, in general, suffer from a lack of clear definitions of the thermodynamic functions used, and we, therefore, recommend that future publications in this area endeavor to achieve a more precise use of language. Only by increasing such efforts it is possible to understand and resolve some of the significant and possibly misleading discussions in this area.

Entropy and institutional theory

Purpose

Once introduced and conceptualized as a factor that causes erosion and decay of social institutions and subsequent deinstitutionalization, the notion of entropy is at odds with predictions of institutional isomorphism and seems to directly contradict the tendency toward ever-increasing institutionalization. The purpose of this paper is to offer a resolution of this theoretical inconsistency by revisiting the meaning of entropy and reconceptualizing institutionalization from an information-theoretic point of view.

Design/methodology/approach

It is a theoretical paper that offers an information perspective on institutionalization.

Findings

A mistaken understanding of the nature and role of entropy in the institutional theory is caused by conceptualizing it as a force that counteracts institutional tendencies and acts in opposite direction. Once institutionalization and homogeneity are seen as a product of natural tendencies in the organizational field, the role of entropy becomes clear. Entropy manifests itself at the level of information processing and corresponds with increasing uncertainty and the decrease of the value of information. Institutionalization thus can be seen as a special case of an increase in entropy and a decrease of knowledge. Institutionalization is a state of maximum entropy.

Originality/value

It is explained why institutionalization and institutional persistence are what to be expected in the long run and why information entropy contributes to this tendency. Contrary to the tenets of the institutional work perspective, no intentional efforts of individuals and collective actors are needed to maintain institutions. In this respect, the paper contributes to the view of institutional theory as a theory of self-organization.

Transitions in nutation trajectory geometry in peppermint (Mentha x piperita L.) with respect to lunisolar acceleration

Nutations of plant organs are significantly affected by the circatidal modulation in the gravitational force exerted by the Moon and Sun (lunisolar tidal acceleration, Etide). In a previous study on nutational rotations of stem apices, we observed abrupt alterations in their direction and irregularities of the recorded trajectories. Such transitions have not yet been analysed in detail. Peppermint plants were continuously recorded with time-lapse photography and aligned with contemporaneous time courses of the Etide estimates. Each nutational stem tip movement path was assigned to one of two groups, depending on its geometry, as: (i) regular elliptical movements and (ii) irregular movements (with a random type of trajectory). Analyses of the correlation between the plant nutation trajectory parameters and Etide, as well as of the trajectory geometry of the individual plants were performed. The trajectory geometry of young mint stem apices was related to the velocity of the apex rotation and significantly affected by the gravitational force estimated from the Etide. A low velocity of nutational movement, associated with the random character of the trajectory, usually occurred simultaneously with local minima or maxima of Etide. As the mint plant ages, the transitions in the stem tip trajectory were limited; no correspondence with Etide dynamics was observed. The results indicate that the plant tip geometry path transitions with respect to the changing gradient of lunisolar tidal acceleration could be interpreted as manifestation of a continuous accommodation of the shoot apical part to the state of minimum energy dissipation.

Microbial bioenergetics of coral-algal interactions

Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time) and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify microbial impacts on reef health.

Life's Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives

In memoriam Jeffrey S. Wicken (1942-2002)-the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken's legacy. (i) Connecting life's origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic 'charging' of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called 'microspheres' is more realistic as a kinetic transition model of primal biogenesis than 'hypercycle replication' theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic 'microspheres'. On the 'continuist vs. miraculist' schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic 'continuist' views and agenda.

Ribosomal history reveals origins of modern protein synthesis

The origin and evolution of the ribosome is central to our understanding of the cellular world. Most hypotheses posit that the ribosome originated in the peptidyl transferase center of the large ribosomal subunit. However, these proposals do not link protein synthesis to RNA recognition and do not use a phylogenetic comparative framework to study ribosomal evolution. Here we infer evolution of the structural components of the ribosome. Phylogenetic methods widely used in morphometrics are applied directly to RNA structures of thousands of molecules and to a census of protein structures in hundreds of genomes. We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17) and the oldest substructure (the ribosomal ratchet) in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.

EXTREMAL PRINCIPLES WITH SPECIAL EMPHASIS ON EXERGY AND ASCENDENCY — THE MODERN APPROACH IN THEORETICAL ECOLOGY

Extremal principles or ecological orientors or goal functions are the most modern approach in theoretical ecology. There are many such principles proposed by different theoretical ecologists. In this paper, the most important extremal principles are discussed based on their theoretical backgrounds. Two widely accepted goal functions, i.e. exergy and ascendency are optimized and treated in a quantitative manner in an aquatic ecosystem model of planktonic and fish systems for their appropriateness. In the model varied body sizes of phytoplankton and zooplankton are considered. Parameter values varied according to the allometric principle with the body sizes. For self-organization of the model system two goal functions predict different results, however both are realistic.

Speculation on quantum mechanics and the operation of life giving catalysts

The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life's emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.

Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae

Background

Protein subcellular localization and differences in oxidation state between subcellular compartments are two well-studied features of the the cellular organization of S. cerevisiae (yeast). Theories about the origin of subcellular organization are assisted by computational models that can integrate data from observations of compositional and chemical properties of the system.

Presentation and implications of the hypothesis

I adopt the hypothesis that the state of yeast subcellular organization is in a local energy minimum. This hypothesis implies that equilibrium thermodynamic models can yield predictions about the interdependence between populations of proteins and their subcellular chemical environments.

Testing the hypothesis

Three types of tests are proposed. First, there should be correlations between modeled and observed oxidation states for different compartments. Second, there should be a correspondence between the energy requirements of protein formation and the order the appearance of organelles during cellular development. Third, there should be correlations between the predicted and observed relative abundances of interacting proteins within compartments.

Results

The relative metastability fields of subcellular homologs of glutaredoxin and thioredoxin indicate a trend from less to more oxidizing as mitochondrion – cytoplasm – nucleus. Representing the overall amino acid compositions of proteins in 23 different compartments each with a single reference model protein suggests that the formation reactions for proteins in the vacuole (in relatively oxidizing conditions), ER and early Golgi (in relatively reducing conditions) are relatively highly favored, while that for the microtubule is the most costly. The relative abundances of model proteins for each compartment inferred from experimental data were found in some cases to correlate with the predicted abundances, and both positive and negative correlations were found for some assemblages of proteins in known complexes.

Conclusion

The results of these calculations and tests suggest that a tendency toward a metastable energy minimum could underlie some organizational links between the the chemical thermodynamic properties of proteins and subcellular chemical environments. Future models of this kind will benefit from consideration of additional thermodynamic variables together with more detailed subcellular observations.

Complementarity of ecological goal functions

This paper summarizes, in the framework of network environ analysis, a set of analyses of energy-matter flow and storage in steady-state systems. The network perspective is used to codify and unify ten ecological orientors or extremal principles: maximum power (Lotka), maximum storage (Jørgensen-Mejer), maximum empower and emergy (Odum), maximum ascendency (Ulanowicz), maximum dissipation (Schneider-Kay), maximum cycling (Morowitz), maximum residence time (Cheslak-Lamarra), minimum specific dissipation (Onsager, Prigogine), and minimum empower to exergy ratio (Bastianoni-Marchettini). We show that, seen in this framework, these seemingly disparate extrema are all mutually consistent, suggesting a common pattern for ecosystem development. This pattern unfolds in the network organization of systems.

The physical base of marine bacterial ecology

Specific affinity theory is compared with traditional ways of understanding the nutrient concentration dependency of microbial growth. It is demonstrated that the Michaelis constant increases with the ratio of metabolic enzyme to membrane permease content of bacteria so that small values can reflect specialization for nutrient collection. When compared to the specific affinity, Kt gives a measure of oligotrophic capacity. Specific affinity, on the other hand, reflects nutrient collection ability directly, and increases with the number of permeases. It can be estimated, along with the other kinetic constant, Vmax, by use of isotopes in natural samples. Because of systematic errors in estimating Vmax, specific affinity is the preferred measure of substrate accumulation ability. The advantage of simultaneous collection of multiple substrates in dilute solution is demonstrated. The structural basis of this advantage is computed from collision frequency and recollision probability, computations that further show that multisubstrate usage is essential for bacterial growth under low-nutrient conditions. Computed growth rates from specific affinities require that several substrates be used simultaneously for growth at measured concentrations. Formulations anticipate that the surface of oligobacteria should be occupied by a diversity of transporter types, that each type of transporter should occupy only a small portion of the cell surface, and the number of cytoplasmic enzymes can be small, allowing small cell size to give a large surface-to-volume ratio for high specific affinity. The large number of substrate types that may be accumulated by a single oligobacterial species is consistent with extensive species diversity.

Natural self-organization of polynucleotides and polypeptides in protobiogenesis: appearance of a protohypercycle

Basic thermal polyamino acids or proteinoids have been reported to be catalytic for both self-instructing polymerization of amino acids and internucleotide synthesis. We show theoretically that a complex suspension of thermal proteinoids, free amino acids, nucleotides and ATP as an energy source can exhibit an evolutionary character. The suspension can produce a prototype of Eigen's hypercycle, or protohypercycle, for which translation proceeds from amino acid to nucleotide. The protohypercycle is suggested to be an evolutionary precursor of the hypercycle, in which translation is from nucleotide to amino acid. The possibility that the Fox-Nakashima microsphere containing both lysine-rich and acidic proteinoids may work as a model of a protohypercycle is considered.