III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

D. Non-Equilibrium Thermodynamics of Living Systems

Jeffery, Kate, et al. On the Statistical Mechanics of Life: Schrodinger Revisited. Entropy. 21/12, 2019. At the verge of 2020, senior scientists Kate Jeffery, a University College London psychologist, Robert Pollack, a Columbia University biologist, and Carlo Rovelli, a University of Toulon polymath physicist proceed to revision cosmic, Earthly and human evolution as a single progression that arises from intrinsic energies and structures. Some 75 years after Erwin S. mused that the emergence of living beings must be rooted in and allowed by physical nature, his prescience can now be quantified and verified. To wit, novel insights about thermodynamic forces, (as herein reported), can indeed be seen to engender animate, evolving, recurrent, biospheric systems. One might even imagine we add, a “statistical organics” going forward also for quantum phenomena.

As an extended Abstract alludes, rather than entropic losses being a detriment, in this unique conception these currents are seen to foster orderly, oriented spatial and temporal growth. This vital process is well evinced by gregarious DNA nucleotides as they contain and convey prescriptive information. In this view, the major evolutionary transitions scale, here expanded to twelve steps from replicators to symbolic linguistics, can attributed to entropic and informative flows, as the second quote cites. A further significant consequence is a return of human beings to a consummate position, as per Section 12 and the third quote. Yet, within this grand scenario the word ”random” continues to appear. To reflect, if life’s informed ascent could be taken a big step further to its worldwise personsphere fulfillment, as V. Vernadsky and P. Teilhard did long ago and this site seeks to document, with a 2020 bicameral vision, a phenomenal discovery and destiny might accrue.

We study the statistical underpinnings of life and its increase in order and complexity over evolutionary time. We question some common assumptions about the thermodynamics of life. We recall that contrary to widespread belief, even in a closed system entropy growth can accompany an increase in macroscopic order. We view metabolism in living things as microscopic variables driven by the second law of thermodynamics, while viewing the macroscopic variables of structure, complexity and homeostasis as entropically favored because they open channels for entropy to grow via metabolism. This perspective reverses the conventional relation between structure and metabolism by emphasizing the role of structure for metabolism rather than the converse.

Structure extends in time, preserving information across generations, mainly in the genetic code, but also in human culture. We argue that increasing complexity is an inevitable tendency for systems with these dynamics and explain by way of metastable states, which are enclosed regions of the phase-space that we call “bubbles.” We consider that more complex systems inhabit larger bubbles, and also that larger bubbles are more easily entered than small bubbles. The result is that the system entropically wanders into ever-larger bubbles in the foamy phase space. This formulation makes intuitive why the increase in order/complexity over time is often stepwise and sometimes collapses as in biological extinction (Abstract)

The reason for this step structure can be explained by the statistical interpretation of life developed here: if life is the opening of stable channels for entropy to grow, then evolution, which is a slow random exploration of its phase space, reflects this effect by discovering new major channels into higher-entropy regions of the phase space. Each transition comes with an increase in biological diversity, understood as the acquisition of new stable pathways for entropy to grow, stabilised by the preservation of information in DNA. The earliest transitions were occasional – photosynthesis did not appear for around 2 billion years after life began, for example, while neurons arose only around 600 million years ago. Language appeared a mere 100,000 years ago, and has had a strong effect on the biosphere, via human culture and technological advance. (13)

To close, we turn to the human species; the product of a transitional step in evolution that has further increased the complexity of life’s activities. Humans have evolved a cognitive representational capability that allows us to create new correlations across time and space – that is, new forms of macroscopic order to funnel entropy into metabolism. This is manifest in many ways. For example, the experiential time of our species is much dilated, giving us a wide sense of time flow. We are aware of distant past and can plan far more ahead than any other species. Language allows humans to cooperate in learning and planning; the experience of one individual can be propagated to many others. Writing, and more recently electronic media, has amplified cultural transmissions, allowing us to develop technology that has extended our lifespans and our reach across the planet, and beyond. (14)

Jizba, Petr and Toshihico Arimitsu. The World According to Renyi: Thermodynamics of Multifractal Systems. Annals of Physics. 312/1, 2004. An example of the current shift in quantum and non-equilibrium statistical physics to include informational and dynamic system properties. Multifractals apply everywhere from cosmic strings to DNA sequences and financial markets.

Jorgensen, Sven, ed. Thermodynamics and Ecological Modelling. Boca Raton, FL: Lewis Publishers, 2000. A consideration of a proposed “fourth law of thermodynamics” that a growing number of investigators are trying to define in order to quantify the evident rise in animate complexity in cosmic and earthly nature.

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)

Kastner, Ruth. The Arrow of Time is Alive and Well but Forbidden Under the Received View of Physics. arXiv:2311.11456. In this eprint The University of Maryland physicist and author of The Transactional Interpretation of Quantum Mechanics (2022) defends the actual reality of a directional cosmic duration, along with noting its many prior twists and turns.

This essay offers a meta-level analysis in the sociology and history of physics in the context of the "Arrow of Time" or so-called "Two Times" problem. In effect, it argues that the two topics are intertwined, and it is only by coming to grips with the sociological aspects, involving adherence to certain metaphysical, epistemological and methodological beliefs and practices, that real progress can be made in the physics. (Abstract)

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)

Kondepudi, Dilip, et al. From Dissipative Structures to Biological Evolution: A Thermodynamic Perspective. Dambricourt Malasse, Anne, ed. Self-Organization as a New Paradigm in Evolutionary Biology. International: Springer, 2022. In this frontier collection, Wake Forest University and University of Connecticut theorists describe a further deep physical influence which serves to energize life’s organized emergence.

In the second half of the twentieth century, it was recognized that systems far from thermodynamic equilibrium can spontaneously self-organize into dissipative structures that exhibit oscillating chemical patterns. Many advances came from the Brussels School of Thermodynamics under the leadership of Ilya Prigogine. The 21st century, decade has given us a new perspective on the emergence of organism-like behavior in non-living systems. This chapter will review the relationship between this generative phenomena and biological evolution. (Abstract)

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.

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