Thermodynamics and the structure of living systems

Non-equilibrium physical systems, be they biological or otherwise, are powered by differences in intensive thermodynamic variables, which result in flows of matter and energy through the system. This thesis is concerned with the response of physical systems and ecosystems to complex types of boundary conditions, where the flows and intensive variables are constrained to be functions of one another. I concentrate on what I call negative feedback boundary conditions, where the potential difference is a decreasing function of the flow. Evidence from climate science suggests that, in at least some cases, systems under these conditions obey a principle of maximum entropy production. Similar extremum principles have been suggested for ecosystems. Building on recent work in theoretical physics, I present a statisticalmechanical argument in favour of this principle, which makes its range of application clearer. Negative feedback boundary conditions can arise naturally in ecological scenarios, where the difference in potential is the free-energy density of the environment and the negative feedback applies to the ecosystem as a whole. I present examples of this, and develop a simple but general model of a biological population evolving under such conditions. The evolution of faster and more efficient metabolisms results in a lower environmental energy density, supporting an argument that simpler metabolisms could have persisted more easily in early environments. Negative feedback conditions may also have played a role in the origins of life, and specifically in the origins of individuation, the splitting up of living matter into distinct organisms, a notion related to the theory of autopoiesis. I present simulation models to clarify the concept of individuation and to back up this hypothesis. Finally I propose and model a mechanism whereby systems can grow adaptively under positive reinforcement boundary conditions by the canalisation of fluctuations in their structure

Quantifying energy use efficiency via entropy production: a case study from longleaf pine ecosystems

Ecosystems are open systems that exchange matter and energy with their environment. They differ in their efficiency in doing so as a result of their location on Earth, structure and disturbance, including anthropogenic legacy. Entropy has been proposed to be an effective metric to describe these differences as it relates energy use efficiencies of ecosystems to their thermodynamic environment (i.e., temperature) but has rarely been studied to understand how ecosystems with different disturbance legacies respond when confronted with environmental variability. We studied three sites in a longleaf pine ecosystem with varying levels of anthropogenic legacy and plant functional diversity, all of which were exposed to extreme drought. We quantified radiative (effrad), metabolic and overall entropy changes – as well as changes in exported to imported entropy (effflux) in response to drought disturbance and environmental variability using 24 total years of eddy covariance data (8 years per site). We show that structural and functional characteristics contribute to differences in energy use efficiencies at the three study sites. Our results demonstrate that ecosystem function during drought is modulated by decreased absorbed solar energy and variation in the partitioning of energy and entropy exports owing to differences in site enhanced vegetation index and/or soil water content. Low effrad and metabolic entropy as well as slow adjustment of effflux at the anthropogenically altered site prolonged its recovery from drought by approximately 1 year. In contrast, stands with greater plant functional diversity (i.e., the ones that included both C3 and C4 species) adjusted their entropy exports when faced with drought, which accelerated their recovery. Our study provides a path forward for using entropy to determine ecosystem function across different global ecosystems.</p

Entropy Production in Ecosystems.

We present an extremely minimal ecosystem model which takes account of thermodynamic constraints on the organisms metabolism. This suggests a way to test the application of a hypothesised principle of Maximum Entropy Production to ecosystems. It also puts definite physical bounds on the rates at which matter can flow through the system and paves the way for more detailed models that have thermodynamic principles built in from the start. In providing the background for this model we point out some connections between thermodynamic principles and autopoiesis

Entropy Production in Ecosystems

Abstract. We present an extremely minimal ecosystem model which takes account of thermodynamic constraints on the organisms ’ metabolism. This suggests a way to test the application of a hypothesised principle of Maximum Entropy Production to ecosystems. It also puts definite physical bounds on the rates at which matter can flow through the system and paves the way for more detailed models that have thermodynamic principles built in from the start. In providing the background for this model we point out some connections between thermodynamic principles and autopoiesis.

Ecological indicators - Entropy

This article presents a scientific overview of ‘entropy’ as a thermodynamic basic function. A primary definition of entropy is stated in classical thermodynamics and statistical mechanics. The second law of thermodynamics states that, in any physical or chemical process, the quality of the energy in a system degrades, thus proving the existence of irreversibility in nature. From the second law descends the existence of the extensive state function, namely ‘entropy’, which measures the disorder degree of a system, and it is also an evidence of the unidirectional flow of time. Besides this classical interpretation, the role of entropy and energy with respect to evolution of life and complex systems has been a subject of widespread interest among the scientific community in the past century. Taking into account the theories of Ilya Prigogine, the far-from-equilibrium systems theory and the pivotal concept of negentropy by Schrödinger, it is nowadays possible to use the concept of entropy as a powerful instrument to deal with ecosystems, ecology, and definitely life. The assessment of entropy production in ecosystems has been diffusely applied as a thermodynamic indicator for understanding the development state of ecological systems

Ecological indicators - Entropy

This article presents a scientific overview of ‘entropy’ as a thermodynamic basic function. A primary definition of entropy is stated in classical thermodynamics and statistical mechanics. The second law of thermodynamics states that, in any physical or chemical process, the quality of the energy in a system degrades, thus proving the existence of irreversibility in nature. From the second law descends the existence of the extensive state function, namely ‘entropy’, which measures the disorder degree of a system, and it is also an evidence of the unidirectional flow of time. Besides this classical interpretation, the role of entropy and energy with respect to evolution of life and complex systems has been a subject of widespread interest among the scientific community in the past century. Taking into account the theories of Ilya Prigogine, the far-from-equilibrium systems theory and the pivotal concept of negentropy by Schrödinger, it is nowadays possible to use the concept of entropy as a powerful instrument to deal with ecosystems, ecology, and definitely life. The assessment of entropy production in ecosystems has been diffusely applied as a thermodynamic indicator for understanding the development state of ecological systems

Energy and ecology : on entropy production and the analogy between fluid, climate and ecosystems

We derive an expression for the thermodynamic entropy production (EP) of both phototrophic and chemotrophic ecosystems, and we apply this to simple models of generalized Lotka-Volterra ecosystems in a chemostat set-up in order to describe explicitly the coupling between the ecosystem and its environment. This allows us to determine the irreversibility of biological processes, whether the EP is an ecological goal function, whether the EP increases if a system is driven further out of equilibrium, and whether there are connections between EP and stability, competition, predation, biodiversity, efficiency or other hypothetical goal functions such as exergy. The EP as a candidate goal function also relates with the maximum entropy production (MaxEP) hypotheses applied in multiple physical systems, especially fluid and climate systems. We give a schematic classification of 11 different EP principles and hypotheses. We present an omnivore ecosystem as a counterexample for all MaxEP hypotheses in the non-linear response regime. We also formulate a practical definition of dissipative structures, and we apply this to ecosystems. Finally, we discuss an intriguing correspondence between ecosystems and fluid and climate systems. We demonstrate that the dynamical equations of a simple chemotrophic ecosystem correspond with the Lorenz equations for Rayleigh-Bénard convective fluid systems. Then we derive the size of convection cells by using an ecological competition principle. More generally, we postulate that the interactions of streams and whirls form a food web for the fluid or climate system.1 General introduction 1.1 Overview thesis 1.2 The most important results 2 Entropy production in ecosystems 2.1 Introduction 2.2 Fundamental problems in thermodynamic ecology 2.3 Chemotrophic ecosystems 2.4 Phototrophic ecosystems 3 A thermodynamic perspective on food webs: quantifying the entropy production associated with resource processing 3.1 Introduction 3.2 Model formulation 3.3 (Quasi) steady state analysis 3.4 Thermodynamic analysis of ecosystems 3.5 Discussion and conclusion 3.6 The correspondence between ecological and climate systems 4 Entropy production within classical ecological models: Lotka-Volterra revisited 4.1 Introduction 4.2 The generalized Lotka-Volterra chemostat dynamics 4.3 Entropy production rates 4.4 Discussion: a comparison of entropy production expressions 4.5 Summary 5 Classification of entropy production principles and hypotheses 5.1 MaxEP or MinEP? 5.2 Why a classification? 5.3 The classification 5.4 Non-Variational MaxEP 5.5 Partial Steady State MaxEP 5.6 Total Steady State MaxEP 5.7 Non-linear Lyapunov EP 5.8 Non-linear Non-Lyapunov MaxEP 5.9 Gradient Response 6 Testing entropy production hypotheses in ecosystems 6.1 Introduction 6.2 The resource-consumer-omnivore ecosystem 6.3 The test 6.4 Discussion: Entropy production, ecosystem stability and biodiversity 7 Testing ecological goal functions and efficiency measures 7.1 Introduction 7.2 Definitions for goal functions 7.3 General set-up and thermodynamic problems 7.4 The resource-consumer-predator model 7.5 Goal function proposals 7.6 Testing the goal function proposals 7.7 Efficiency measures 7.8 Searching for relationships between the measures 7.9 Conclusion 7.10 Appendix: Parameter constraints and model simplifications 7.11 Appendix: Derivation of the exergy function 8 Ecosystems and dissipative structures: Does life increase the entropy production? 8.1 Introduction 8.2 A definition of dissipative structures 8.3 Biological structures as dissipative structures? 8.4 The phototrophic ecosystem 8.5 The chemotrophic ecosystem 8.6 Conclusions and further discussion 9 A useful correspondence between fluid convection and ecosystem operation 9.1 Introduction 9.2 The Rayleigh-Bénard convection system 9.3 The resource-consumer ecosystem 9.4 The correspondence 9.5 Energy flows along energetic pathways 9.6 Competitive exclusion and fitness 9.7 Conclusions and further discussions 9.8 Appendix: The RCW ecosystem 9.9 Appendix: The XYZ Lorenz system 10 Further discussion 10.1 From the Lorenz model to a biological model 10.2 Predating fluid motion 10.3 Convection pattern deformations and ecological evolution 10.4 Turbulent fluids and complex food webs 10.5 The megascopic scale: A new hope for MaxEP? 10.6 The microscopic scale and underlying mechanisms 10.7 Solving the basic problem in thermodynamic ecology? 10.8 The state of the field: Where do we stand? 11 Summary of most important results 12 Endnote and personal confession A Glossary B Notational conventions C Samenvattingen C.1 Samenvatting voor het brede publiek C.2 Wetenschappelijke resultatenstatus: publishe