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

D. Non-Equilibrium Thermodynamics of Living Systems

Chaisson, Eric. Non-equilibrium Thermodynamics in an Energy-Rich Universe. Kleidon, Alex and Ralph Lorenz, eds. Non-Equilibrium Thermodynamics and the Production of Entropy. Berlin: Springer, 2005. A recent summary of Chaisson’s thought in this regard.

And it is non-equilibrium thermodynamics of open, complex systems that best characterizes resources flowing in and wastes flowing out, all the while system entropy actually decreases locally while obeying thermodynamics’ cherished law that demands environmental entropy increase globally. (28)

Conte, Tom, et al. Thermodynamic Computing. arXiv:1911.01968. This is a report from an NSF supported CCC (Computing Community Consortium) workshop held January 3-5, 2019 at the Prince Wakiki Hotel, Honolulu. Some 40 expert invitees such as Jim Crutchfield, Lidia del Rio, Massimiliano Esposito, Ilya Nemenman, Gavin Crooks, Seth Lloyd, and David Wolpert came together to scope out the necessary transit from earlier macro stages (see Abstract) into deeper energetic, complex, intrinsically self-organizing domains. Its opening phase revisited contacts between physics, information, and thermodynamics over 200 years in a table which runs from Carnot and Babbage through Gibbs, Boltzmann, Turing, Shannon, Prigogine, onto to Hopfield, Landauer, and Hinton. Current interfaces are then noted between past and future via a passage from classical to thermal to quantum methods. In sum, the endeavor continues to trace a path to better mimic natural cosmic, biological, and neural processes.

The hardware and software basics laid in the 20th Century have transformed the world, but the current paradigm faces limits from several perspectives. In terms of hardware, devices have become so small that the effects of thermodynamic fluctuations take over, which are unavoidable at the nanometer scale. In terms of software, our ability to imagine and program implementations are challenged in several domains. These difficulties - device scaling, software complexity, adaptability, energy consumption, and fabrication economics – have run their course. We propose that progress in computing can continue under a united, physically grounded, computational paradigm centered on thermodynamics. We propose a research agenda that accordingly involves complex, non-equilibrium, self-organizing systems in a holistic way that will harness nature's innate computational capacity. (Abstract excerpts)

Coveney, Peter and Roger Highfield. The Arrow of Time. New York: Fawcett Columbine, 1991. An accessible explanation of how a far-from-equilibrium thermodynamics drives a universal evolution which develops in a fractal-like manner toward intelligent life.

Cross, Michael and Henry Greenside. Pattern Formation and Dynamics in Nonequilibrium Systems. Cambridge: Cambridge University Press, 2009. In a graduate text in nonlinear science, CalTech and Duke University physicists open with a good statement of why it is important to study and learn these pervasive principles. It is necessary to realize today that cosmic nature in fact resides in a nonequilibrium state throughout, with a stratified self-similar, emergent universality that invites our recognition and comprehension. The abiding cosmos is not dust to dust,nothing to nothing, after all, as a mechanical Ptolemaic physics is wont to conclude, but in some real way winding itself up by these iterative, complex, genetic-like traces that our human phenomenon seems meant to discover.

We can suggest three reasons why nonequilibrium systems are worthy of study. First, observation tells us that most of the Universe consists of nonequilibrium systems and that these systems possess an extraordinarily rich and visually fascinating variety of spatiotemporal structure. So one answer is sheer basic curiosity: where does this rich structure come from and can we understand it? Experiments and simulations further tell us that many of these systems – whether they be fluids, granular media, reacting chemicals, lasers, plasmas, or biological tissues – often have similar dynamical properties. This then is the central scientific puzzle and challenge: to identify and to explain the similarities of different nonequilibrium systems, to discover unifying themes, and if possible, to develop a quantitative understanding of experiments and simulations. (xiii)

We can say why the Universe is interesting rather than boring: the Universe was born in a cosmological Big Bang and is still young when measured in units of the lifetime of a star. Thus the Universe has not yet lasted long enough to come to thermodynamic equilibrium: the Universe as a whole is a nonequilibrium system. (3, bold in the original)

Damiani, Giuseppe. The Fractal Borderland Between the Deterministic Order and the Unpredictable Chaos. Benci, Vieri, et al, eds. Determinism, Holism, and Complexity. New York: Kluwer Academic, 2003. The chapter title catches the theme of still another volume which tries to express our nascent encounter with a radically different cosmos where the entire Universe is a complex dissipative system, in a non-equilibrium state. Damiani also floats a “Binary Theory of Everything” by way of an innate self-similar universality.

Davies, Paul. Emergent Complexity, Teleology, and the Arrow of Time. Dembski, William and Michael Ruse, eds. Debating Design. Cambridge: Cambridge University Press, 2004. A notable article because it definitively sets aside the old heat death model in light of a new expansive universe which innately develops into viable complexity. Physicist Davies own words exemplify the imminent cosmic Copernican Revolution.

The history of the universe, then, is one of entropy rising but chasing a moving target, because the expanding universe is raising the maximum entropy at the same time. (200) As I have explained, the rapid expansion of the universe just after the Big Bang created a huge entropy gap, which has been funding the accumulating complexification ever since, and which will continue to do so for a long while yet. Thus the history of the universe is not so much one of entropic degeneration and decay as a story of the progressive enrichment of systems on all scales, from atoms to galaxies. (203)

However, this picture of a dying universe, which for 150 years has provoked nihilistic and atheistic commentary, may be overly simplistic. Modern cosmology reveals that the universe is expanding, and that it is subject to subtle gravitational effects that complicate the traditional “order into chaos” theme. Moreover, the discovery of self-organizing and self-complexifying processes in nature suggests that alongside the degenerative arrow of time there exists a creative arrow, pointing in the direction of increasing richness, diversity, and potential. (208)

Deffner, Sebastian and Christopher Jarzynski. Information Processing and the Second Law of Thermodynamics. Physical Review X. 3/041003, 2013. In a paper highlighted by the journal, a University of Maryland biochemist and a biophysicist offer novel insights into the communicative essence of nature’s fundamental generative energies. And to reflect, it ought to be noted interest, and concern, that a century and half after Ludwig Boltzman, projects like this abound on arXiv and the professional journals, for we still do not have a sufficient theoretical handle on what is really going on. Some inhibiting reasons might be that scientists can’t figure out what the universe may actually be doing, if anything, or a main mindset that cannot even imagine or accepts its default denial.

We obtain generalizations of the Kelvin-Planck, Clausius, and Carnot statements of the second law of thermodynamics for situations involving information processing. To this end, we consider an information reservoir (representing, e.g., a memory device) alongside the heat and work reservoirs that appear in traditional thermodynamic analyses. We derive our results within an inclusive framework in which all participating elements—the system or device of interest, together with the heat, work, and information reservoirs—are modeled explicitly by a time-independent, classical Hamiltonian. We place particular emphasis on the limits and assumptions under which cyclic motion of the device of interest emerges from its interactions with work, heat, and information reservoirs. (Abstract)

In this paper, we take a different approach. To the traditional thermodynamic analyses that employ heat and work reservoirs, we add an information reservoir in place of an external observer. The information reservoir captures the physical consequences of Maxwell’s demon, or more precisely, its memory. We then use a single time-independent Hamiltonian to describe a collection of thermodynamic elements, including a device, one or more heat baths, a work reservoir, and an information reservoir (like, for instance, a stream of bits). As a main result, we generalize several classic formulations of the second law of thermodynamics, such as the Kelvin-Planck, Clausius, and Carnot statements, to situations involving information processing. Our paper provides a general conceptual framework for further development and explorations in the cross-disciplinary field of thermodynamic theories of information processing. (041003-2)

Demetrius, Lloyd. Boltzmann, Darwin and Directionality Theory. Physics Reports. 530/1, 2013. The author has a doctorate in mathematical biology from the University of Chicago with currents appointments at the Department of Organismic and Evolutionary Biology, Harvard University, and the Max Planck Institute for Molecular Genetics. This extensive, theoretical, wise contribution proceeds in the 21st century to conceive an integral unity of thermodynamic forces with life’s sequential emergence. A capsule for Ludwig Boltzman (1844-1906) is given as “Thermodynamic entropy increases as the composition of the aggregate changes under molecular collision.” For Charles Darwin it is “Fitness increases as the composition of the population changes under variation and natural selection.” As the Abstract notes, a “directionality principle” is then advanced to join these areas of statistical energetic interactions with populations of reproducing, evolving organisms.

We include several quotes from many analytical pages on which serve to integrate “inanimate matter and living cells.” By a natural philosophy reflection, what may be lately realized is a true “universe” wherein creaturely beings can once again be known to seamlessly flow from nature’s generative spontaneity. A fertile cosmos seems to exist on its own, and by such propensities is made and meant to develop into embryonic life and inquisitive persons. The presence of constant, iterative principles can be gleaned whence thermal energies fuel both individual struggles and group incentives of mutual self-assembly. By this advance, a scientific verification of nature’s ubiquitous me entity and communal we reciprocity is achieved. In closing, a role for these joint forces or agencies in the popular “major evolutionary transitions” approach is also specified. For recent embelishments see Evolutionary Entropy and the Second Law of Thermodynamics by LD and Christian Wolf at arXiv:2005.10332 and Directionality Theory and the Origin of Life by LD at 2304.14873.

Directionality theory is a quantitative model of the Darwinian argument of evolution by variation and selection. This mathematical theory is based on the concept evolutionary entropy, a statistical measure which describes the rate at which an organism appropriates energy from the environment and reinvests this energy into survivorship and reproduction. According to directionality theory, microevolutionary dynamics, that is evolution by mutation and natural selection, can be quantitatively explained in terms of a directionality principle: Evolutionary entropy increases when the resources are diverse and of constant abundance; but decreases when the resource is singular and of variable abundance. We exploit this analytic relation between the thermodynamic and evolutionary tenets to propose a physico-chemical model of the transition from inanimate matter which is under thermodynamic selection, to living systems which are subject to evolutionary selection. (Abstract excerpts)

Organic evolution is thus a dynamical process driven by the combined forces of mutation and selection. The outcome of this process is determined by differences in the rate at which the competing types appropriate resources from the external environment. The mean turnover time, that is the cycle time or generation time of the population, now becomes a critical factor in predicting evolutionary change. Hence, evolutionary dynamics can be considered as an analogue of thermodynamic systems in which the concept of temperature, an organizing variable in thermodynamic theory, is replaced by cycle time, the coordinating parameter in evolutionary systems. (2)

Our analysis of energy transformation in inanimate matter and living organisms will be based on a distinction between what we will call lineal and hierarchical modes of selection. Lineal modes of selection refer to stabilization of a selective unit within a given lineage. Selection will discriminate between the individual units on the basis of the stability, thermodynamic or kinetic, of the different energy distributions. Hierarchical modes of selection pertain to cooperation of elements within a lower level hierarchy to produce a higher level unit. The lower level unit is defined in terms of a set of related individuals. The relatedness between the units confers on the higher level unit certain properties which are not defined at the lower level. The higher level unit can be considered a collective with properties which are functions of the degree of relatedness of the units that make up the group. (106-107)

Lineal modes of organization are driven or regulated by thermodynamic and kinetic selection. Hierarchical modes of organization are driven by self-assembly or self-organization. New structure will form depending on the affinity or relatedness of the different elements that make up the collective. The persistence of the collective will depend on its kinetic stability – a property determined by evolutionary entropy. The non-equilibrium steady states are characterized by states which maximize evolutionary entropy. An example of a hierarchical mode of selection is the transition from a group of activated nucleotides to their encapsulation in a vesicle. The evolutionary entropy of the collective unit will depend on the degree of cooperation that exists between the individual elements in the vesicle. (107-108)

We will appeal to the notions of lineal and hierarchical transitions to provide an analytic framework for the evolutionary process. Lineal transitions are characterized by the consolidation of one type of organization within the given lineage. We will call this process competitive. Hierarchical transitions involve the organization of elements at a lower level hierarchy to generate a higher level system with emergent attributes. We call these process cooperative. (109) The transformation from inanimate matter to a primitive protocell thus involves the integration of two classes of selection events: (a) a cooperative transition which is defined by the integration of related units to form a higher level unit, (b) a competitive transition which is defined by the replacement of one unit by another as a result of variation and selection. (111)

Dewar, Roderick, et al, eds. Beyond the Second Law: Entropy Production and Non-equilibrium Systems. Berlin: Springer, 2013. With co-editors Charles Lineweaver, Robert Niven, and Klaus Regenauer-Lieb, a volume from a series of workshops, especially 2011 at Australian National University, Canberra, about the Maximum Entropy Production principle. To wit “(MEP) states that systems are driven to steady states in which they produce entropy at the maximum possible rate given the prevailing constraints” (search Kleidon). Sample chapters could be “Use of Receding Horizon Optimal Control to Solve MaxEP-Based Biogeochemistry Problems” by Joseph Vallino, et al, and “Earth Systems Dynamics Beyond the Second Law,” Axel Kleidon, et al. In regard I heard Joe Vallino, Woods Hole Marine Biological Laboratory, speak at the University of Massachusetts, Amherst, in December 2013, about these efforts which are broadly intended to get a better theoretical handle, with consistent terminology, on the evident presence of an energetically driven cosmos, fertile earth, and lifekind.

The Second Law of Thermodynamics governs the average direction of all non-equilibrium dissipative processes. However it tells us nothing about their actual rates, or the probability of fluctuations about the average behaviour. The last few decades have seen significant advances, both theoretical and applied, in understanding and predicting the behaviour of non-equilibrium systems beyond what the Second Law tells us. Novel theoretical perspectives include various extremal principles concerning entropy production or dissipation, the Fluctuation Theorem, and the Maximum Entropy formulation of non-equilibrium statistical mechanics. However, these new perspectives have largely been developed and applied independently, in isolation from each other. The key purpose of the present book is to bring together these different approaches and identify potential connections between them: specifically, to explore links between hitherto separate theoretical concepts, with entropy production playing a unifying role; and to close the gap between theory and applications. The aim of this overview chapter is to orient and guide the reader towards this end. We begin with a rapid flight over the fragmented landscape that lies beyond the Second Law. We then highlight the connections that emerge from the recent work presented in this volume. Finally we summarise these connections in a tentative road map that also highlights some directions for future research. (Overview Chapter Abstract)

Planet Earth is a thermodynamic system far from equilibrium and its functioning—obviously—obeys the second law of thermodynamics, at the detailed level of processes, but also at the planetary scale of the whole system. Here, we describe the dynamics of the Earth system as the consequence of sequences of energy conversions that are constrained by thermodynamics. We first describe the well-established Carnot limit and show how it results in a maximum power limit when interactions with the boundary conditions are being allowed for. To understand how the dynamics within a system can achieve this limit, we then explore with a simple model how different configurations of flow structures are associated with different intensities of dissipation. When the generation of power and these different configuration of flow structures are combined, one can associate the dynamics towards the maximum power limit with a fast, positive and a slow, negative feedback that compensate each other at the maximum power state. We close with a discussion of the importance of a planetary, thermodynamic view of the whole Earth system, in which thermodynamics limits the intensity of the dynamics, interactions strongly shape these limits, and the spatial organization of flow represents the means to reach these limits. (Kleidon Abstract)

Dyson, Freeman. How We Know. New York Review of Books. March 10, 2011. Within a review of James Gleick’s new book The Information, the octogenarian philosopher physicist goes on to deftly set aside an entropy doom touted in the current science press. If to think about it, life’s ascendant evolution is characterized by increasing degrees of complex structure, and most of all embodied information. Such an emergent vector counters disorder which thus repeals the old “heat death” fate, the paradox is removed. Since gravitation is the dominant form of energy, temperature differences in space will not equilibrate out but rather their wide range enables a universe hospitable to life wherein vital communication and content can ever grow.

Gravitation reverses the usual relation between energy and temperature. As a result, temperature differences in the astronomical universe tend to increase rather that decrease as time goes on. There is no final state of uniform temperature, and there is no heat death. Gravitation gives us a universe hospitable to life. Information and order can continue to grow for billions of years in the future, as they have evidently grown in the past. The vision of the future as an infinite playground, with an unending sequence of mysteries to be understood by an unending sequence of players exploring an unending supply of information, is a glorious vision for scientists.

Endres, Robert. Entropy Production Selects Nonequilibrium States in Multistable Systems. Nature Scientific Reports. 7/14437, 2017. The Imperial College London biophysicist (search) continues his multidiscipline project to describe these nonlinear qualities of microbial and cellular entities and systems. This paper serves to emphasize active thermodynamic properties.

Far-from-equilibrium thermodynamics underpins the emergence of life, but how has been a long-outstanding puzzle. Best candidate theories based on the maximum entropy production principle could not be unequivocally proven, in part due to complicated physics, unintuitive stochastic thermodynamics, and the existence of alternative theories such as the minimum entropy production principle. Here, we use a simple, analytically solvable, one-dimensional bistable chemical system to demonstrate the validity of the maximum entropy production principle. To generalize to multistable stochastic system, we use the stochastic least-action principle to derive the entropy production and its role in the stability of nonequilibrium steady states. This shows that in a multistable system, all else being equal, the steady state with the highest entropy production is favored, with a number of implications for the evolution of biological, physical, and geological systems. (Abstract)

England, Jeremy. Dissipative Adaptation in Driven Self-Assembly. Nature Nanotechnology. 10/11, 2015. The MIT thermodynamicist continues his studies (search) which show how this field, after two centuries from Carnot and Boltzman to Prigogine and Tsallis, is still open to conjecture and advance. An overview would be that the second law and equilibrium closure is being superseded by open, far-from-equilibrium systems that increasingly imply an innate animate development.

In a collection of assembling particles that is allowed to reach thermal equilibrium, the energy of a given microscopic arrangement and the probability of observing the system in that arrangement obey a simple exponential relationship known as the Boltzmann distribution. Once the same thermally fluctuating particles are driven away from equilibrium by forces that do work on the system over time, however, it becomes significantly more challenging to relate the likelihood of a given outcome to familiar thermodynamic quantities. Nonetheless, it has long been appreciated that developing a sound and general understanding of the thermodynamics of such non-equilibrium scenarios could ultimately enable us to control and imitate the marvellous successes that living things achieve in driven self-assembly. Here, I suggest that such a theoretical understanding may at last be emerging, and trace its development from historic first steps to more recent discoveries. Focusing on these newer results, I propose that they imply a general thermodynamic mechanism for self-organization via dissipation of absorbed work that may be applicable in a broad class of driven many-body systems.

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