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III. Ecosmos: A Revolutionary Organic Habitable UniVerse

E. A Thermodynamics of Life

Kaneko, Kunihiko and Chikara Furesawa. Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics. Annual Review of Biophysics. 47/273, 2018. University of Tokyo, Universal Biology Institute (see below) biophysicists contribute a unique notice of how microbial phenomena take upon a similar appearance, indeed as a common, manifest affinity, to these physical energies.

We present a macroscopic theory to characterize the plasticity, robustness, and evolvability of biological responses and their fluctuations. Overall, these results and support from the theoretical and experimental literature suggest a formulation of cellular systems akin to thermodynamics, in which a macroscopic potential is given by the growth rate (or fitness) represented as a function of environmental and evolutionary changes. (Abstract excerpt)

Elucidating the underlying mechanisms universal to all living organisms is one of the ultimate purposes of biological research. With advances in quantification and formulation in life science, expectations for research that provides guiding principles for the elucidation of these universal properties are constantly increasing. To this end, we founded the Universal Biology Institute by integrating research groups from theoretical biology and quantitative experimental biology at the University of Tokyo, with the goal of establishing a new world-class academic field. (UBI website)

Kempes, Christopher, et al. The Thermodynamic Efficiency of Computations Made in Cells across the Range of Life. arXiv:1706.05043. Kempes and David Wolpert, Santa Fe Institute, Zachery Cohen, University of Illinois, and Juan Perez-Mercader, Harvard University, theorize that evolution’s “subcellular to multicellular” course can be attributed to nested computational processes. This passage is tracked by their relative energetic usages from DNA replication efficiencies to the “collective computation of social groups.”

Biological organisms must perform computation as they grow, reproduce, and evolve. Moreover, ever since Landauer's bound was proposed it has been known that all computation has some thermodynamic cost. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. (Abstract excerpts)

Kleidon, Axel. How Does the Earth System Generate and Maintain Thermodynamic Disequilibrium and What does it Imply for the Future of the Planet?.. Philosophical Transactions of the Royal Society A. 370/1012, 2012. Reviewed more in A Living Planet, Kleidon’s web page as Director of Biospheric Theory and Modelling at the Max Planck Institute for Biogeochemistry lists him as mathematician, physicist, meteorologist, and his “research interests” as “atmosphere-biosphere interactions, geographic patterns of plant biodiversity, global vegetation modelling, non-equilibrium thermodynamics of Earth system processes, Gaia hypothesis, Earth system evolution, natural limits of renewable energies, geoengineering,” a leader in the theoretical explanation, fostering, and practice of A Thermodynamics of Life. With many colleagues, his well regarded papers such as this continue apace - search here and his website.

Kleidon, Axel. Thermodynamic Foundations of the Earth System. Cambridge: Cambridge University Press, 2016. The MPI for Biogeochemistry mathematical meteorologist (search) accomplishes a frontier synthesis of thermodynamic theories so as to apply to all manner of biospheric and anthropic realms. Typical chapters run from Energy and Entropy, and Dynamics, Structures, and Maximization to Hydrologic Cycling and Human Activity. Final sections consider how such findings can provide remedial guidance in Habitable Planets and Life, Planetary Evolution, Optimization, and Regulation, and A Sustainable Future.

The combination of dissipative structures and their interactions with the boundary conditions of the system can thus provide an extremely powerful theory to understand evolutionary dynamics in general terms. Evolutionary dynamics would reflect the overarching acceleration of the direction imposed by the second law, making dissipative structures more dissipative through the interaction with their boundary conditions and making processes evolve towards their thermodynamic limit. It would allow us to understand the evolutionary target of thermodynamic systems, from atmospheric convection to river networks, terrestrial vegetation, and the Earth system as a whole. (14)

Kleidon, Axel, et al, eds. Maximum Entropy Production in Ecological and Environmental Systems. Philosophical Transactions of the Royal Society. 365/1297, 2010. A special issue on this non-equilibrium thermodynamic theory with typical papers such as “It is not the entropy you produce, rather, how you produce it” by Tyler Volk and Olivier Pauluis, “The Constructal Law of Design and Evolution in Nature” by Adrian Bejan and Sylvie Lorente, and Roderick Dewar’s “Maximun Entropy Production and Plant Optimization Theories.”

The coupled biosphere–atmosphere system entails a vast range of processes at different scales, from ecosystem exchange fluxes of energy, water and carbon to the processes that drive global biogeochemical cycles, atmospheric composition and, ultimately, the planetary energy balance. These processes are generally complex with numerous interactions and feedbacks, and they are irreversible in their nature, thereby producing entropy. The proposed principle of maximum entropy production (MEP), based on statistical mechanics and information theory, states that thermodynamic processes far from thermodynamic equilibrium will adapt to steady states at which they dissipate energy and produce entropy at the maximum possible rate.

This issue focuses on the latest development of applications of MEP to the biosphere–atmosphere system including aspects of the atmospheric circulation, the role of clouds, hydrology, vegetation effects, ecosystem exchange of energy and mass, biogeochemical interactions and the Gaia hypothesis. The examples shown in this special issue demonstrate the potential of MEP to contribute to improved understanding and modelling of the biosphere and the wider Earth system, and also explore limitations and constraints to the application of the MEP principle. (1297)

Kupervasser, Oleg, et al. The Universal Arrow Time. Foundations of Physics. 42/9, 2012. In a paper available at arXiv:1011.4173, Physicists Kupervasser, Moscow State University, with Hrvoje Nikolic and Vinko Zlatic, Rudjer Boskovic Institute, Zagreb, make a sophisticated case for a vectorial cosmos seemingly on a developmental pathway toward dynamic unfoldings of increasingly complex and cognitive beings.

Statistical physics cannot explain why a thermodynamic arrow of time exists, unless one postulates very special and unnatural initial conditions. Yet, we argue that statistical physics can explain why the thermodynamic arrow of time is universal, i.e., why the arrow points in the same direction everywhere. Namely, if two subsystems have opposite arrow-directions initially, the interaction between them makes the configuration statistically unstable and causes a decay towards a system with a universal direction of the arrow of time. We present general qualitative arguments for that claim and support them by a detailed analysis of a toy model based on the baker’s map. (Abstract)

It should also be noted that our results are not in contradiction with the existence of dissipative systems (such as certain self-organizing biological systems) in which entropy of a subsystem can decrease with time, despite the fact that entropy of the environment increases. The full-system entropy (including the entropies of both the dissipative system and the environment) increases, which is consistent with the entropy-increase law. For such systems, it is typical that the interaction with the environment is strong, while results of our paper refer to weak interactions between the subsystems. For example, for existence of living organisms, a strong energy flow from the Sun is needed. (17)

Kurzynski, Michal. The Thermodynamic Machinery of Life. Berlin: Springer, 2006. Another Springer Frontiers Collection edition. We again quote from a web page, but as an example of an inappropriate mechanical paradigm of living systems. What will it take to realize a fundamental organic genesis creation?

The Thermodynamic Machinery of Life presents the relevant foundations of nonequilibrium thermodynamics as applied to biological processes taking place at the subcellular level. The biological cell is considered as a complex open thermodynamic system far from equilibrium that enzymatically controls various biochemical reactions and transport processes across internal and the cytoplasmatic membrane. The enzymatic free energy and signal transduction processes are described in detail. All the biological molecular machines, also pumps and motors are considered to be effective chemo-chemical free energy transducers. Special attention is paid to the role of the mesoscopic internal dynamics of biomolecules in the activity control of enzymes and the action of molecular machines.

Layzer, David. Cosmogenesis. New York: Oxford University Press, 1990. The Harvard astrophysicist provides theoretical insights into how an expanding universe can offset the second law by its generation of hierarchical order and information.

Lineweaver, Charles and Charles Egan. Life, Gravity and the Second Law of Thermodynamics. Physics of Life Reviews. 5/4, 2008. In this online journal, Australian astrophysicists contend that cosmic “gravitational collapse” is the driving source of free energy for evolving life. A “pyramid” thus accrues from baryon non-conservation to ‘heterotrophs’ (multicellular organisms) whose latest sapient human phase can trace such ancestry.

All dissipative structures in the universe including all forms of life, owe their existence to the fact that the universe started in a low entropy state and has not yet reached equilibrium. The low initial entropy was due to the low gravitational entropy of the nearly homogeneously distributed matter and has, through gravitational collapse, evolved gradients in density, temperature, pressure and chemistry. These gradients, when steep enough, give rise to far from equilibrium dissipative structures (e.g., galaxies, stars, black holes, hurricanes and life) which emerge spontaneously to hasten the destruction of the gradients which spawned them. (Abstract)

Lineweaver, Charles, et al, eds. Complexity and the Arrow of Time. Cambridge: Cambridge University Press, 2013. Leading thinkers such as Paul Davies, Eric Chaisson, Seth Lloyd, Simon Conway Morris, David Krakauer, and Philip Clayton, explore nature’s evident propensity from universe to humankind to become more intricately arranged, organic, and cognizant. Its main sections cover Cosmological, Physical, Biological, Evolutionary, Informational, and Philosophical perspectives. Search each name above, especially Chaisson, for more commentary.

Ma, Tian and Shouhong Wang. Phase Transition Dynamics. Berlin: Springer, 2014. Sichuan University and Indiana University mathematicians draw upon statistical physics to formulate an innovative thermodynamic theory for equilibrium and nonequilibrium phenomena. With a view that natural systems are situated and poised in an active fluidity, these theories are effectively applied to Geophysical and Climate Dynamics such as El Nino oceanic and atmospheric circulation, and Dynamic Transition in Chemistry and Biology with regard to bacterial chemotaxis and speciations.

Mahulikar, Shripad and Priti Kumari. Scale-Invariant Entropy-Based Theory for Dynamic Ordering. Chaos. 24/033120, 2014. As the quotes explain, Indian Institute of Technology senior researchers propose this conceptual basis to explain how life naturally arises and self-emerges into consistent forms and viabilities. By way of sophisticated mathematics another window is opened upon the innate developmental essence of a holistic, habitable universe.

Dynamically Ordered self-organized dissipative structure exists in various forms and at different scales. This investigation first introduces the concept of an isolated embedding system, which embeds an open system, e.g., dissipative structure and its mass and/or energy exchange with its surroundings. Thereafter, scale-invariant theoretical analysis is presented using thermodynamic principles for Order creation, existence, and destruction. The sustainability criterion for Order existence based on its structured mass and/or energy interactions with the surroundings is mathematically defined. This criterion forms the basis for the interrelationship of physical parameters during sustained existence of dynamic Order. It is shown that the sufficient condition for dynamic Order existence is approached if its sustainability criterion is met, i.e., its destruction path is blocked. This scale-invariant approach has the potential to unify the physical understanding of universal dynamic ordering based on entropy considerations. (Abstract)

Dynamically ordered self-organized dissipative structures, e.g., convection cells, hurricanes, living systems, ecosystems, and accretion disks around black holes, are not just systems with low disorder. In spite of the validity of the Entropy Principle, they possess a low specific entropy relative to their immediate surroundings. In contrast, static order, e.g., crystals are created in the vicinity of global equilibrium based on the minimization of free energy, which follows from Prigogine’s theorem of minimum entropy production. Self-organization is a fundamental process of living organisms at all hierarchical levels, from molecule to organ. An expanded view of non-equilibrium thermodynamics led to the understanding that the spontaneous production and existence of dynamic Order are the expected consequences of basic physical laws. Life is a subset of the general class of dissipative structures. (1)

Ecosystems self-organize by degrading the incoming solar radiation in to lower quality exergy, by lowering the reradiated temperatures. The more developed the ecosystem, the colder its surface temperature, i.e., the more degraded its reradiated energy. Ecosystems develop hierarchical far-from equilibrium patterns and functions, whose maintenance requires a continuous flow of resources. Living cells are dissipative, open, and far-from-equilibrium systems that lower their entropy by an influx of energy and molecular material in a multi-compartment structure, with specific functional characteristics. Heat is dissipated, and waste products are excreted by the cell so that excess entropy in the environment is balanced by structure and information generation, thereby lowering the cell’s entropy. (4)

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