V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

Jain, Kavita and Luca Peliti. Special Issue on a Statistical Theory of Biological Evolution. Journal of Statistical Physics. 172/1, 2018. An introduction by Jawaharfal Nehru Centre for Advanced Scientific Research, India and Santa Marinella Research Institute, Italy system physicists. Such a global collaboration and this edition are a good example of late 2010s syntheses as cosmic and living nature increasingly cross-fertilizes, informs, and becomes a unified vital procreation. Among the dozen papers are Stochastic Spatial Models in Ecology, Universality Classes of Interaction Structures for NK Fitness Landscapes, and Environmental Stochasticity and the Speed of Evolution. Of notice is how these expansive views of life’s development can easily meld together as they allow and imply guidance from a mathematical, genetic-like source. See also 2018 papers in Natural Algorithms (Bernini, et al) for another portal by our Earthropic sapience.

Jeong, Hawoong, et al. The Large-Scale Organization of Metabolic Networks. Nature. 407/651, 2001. A report from the Univerisity of Norte Dame physics group which has discovered a universality of invariant network principles.

Here we present a systematic comparative mathematical analysis of the metabolic networks of 43 organisms representing all three domains of life. We show that, despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems. This may indicate that metabolic organization is not only identical for all living organisms, but also complies with the design principles of robust and error-tolerant scale-free networks. (651)

Johnson, Brian and Sheung Kwan Lam. Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software. BioScience. 60/11, 2010. Circa late 2010, the pursuit of a more viable evolutionary theory, which begs a wholly revised synthesis, seems to be reaching a critical juncture and advance. As this site tries to document, it is increasingly evident that something else is going-on than random, gradual selection alone. In some real way, a prior, mathematical, informational, intrinsically generative force is being realized to impel and guide life’s nested ascent. While an old guard may give a nod, or not, and speak of “extended or expanded” versions, this large shift has not occurred. One reason has been that the multi-faceted complexity sciences, covered in A Cosmic Code, were in embryonic maturation until now.

In this paper, University of California, Berkeley, postdoctoral researchers give new admission and credence to these active, developmental influences, and show how they are indeed at work from proteins to organisms. Not to get ahead of themselves, this is done within a view of selective results, and phrased in mechanistic terms. As other ventures in this transition, it is then couched as a computerese “software,” which serves to proscribe creaturely “hardware.” Astutely, the authors situate this revolution not as an either-or divide between selection or organization, but a formative blend of both modes.

Self-organization is sometimes presented as an alternative to natural selection as the primary mechanism underlying the evolution of function in biological systems. Here we argue that although self-organization is one of selection's fundamental tools, selection itself is the creative force in evolution. The basic relationship between self-organization and natural selection is that the same self-organizing processes we observe in physical systems also do much of the work in biological systems. Consequently, selection does not always construct complex mechanisms from scratch. However, selection does capture, manipulate, and control self-organizing mechanisms, which is challenging because these processes are sensitive to environmental conditions. Nevertheless, the often-inflexible principles of self-organization do strongly constrain the scope of evolutionary change. Thus, incorporating the physics of pattern-formation processes into existing evolutionary theory is a problem significant enough to perhaps warrant a new synthesis, even if it will not overturn the traditional view of natural selection. (879)

The computer science concepts of hardware and software provide a useful metaphor for understanding the nature of biological systems. All the chemical compounds within a cell, and the stable organizational relationships among them, form the hardware of the biological system; this includes the cell membranes, organelles, and the DNA molecules. These structures and processes encompass information stored in genes, as well as information inherent in their organization. The software of the cell corresponds to programs implemented on the hardware for adaptive responses to the environment and for information storage and transmission. Such programs are contained not only in DNA but also in stable self-organization patterns, which are inherited across generations as ongoing processes. (883)

Jose, Marco. Rhythms Found in Human DNA. Physics World. November, 2004. The revolutionary ability of computer-based bioinformatics to sequence genomes can reveal an independent, prior nonlinear dynamics at work in their organization. This is seen as a challenge to the “belief that biological processes are governed by random mutations, genetic drift and natural selection.”

Joshi, Niknil, et al. The Minimal Complexity of Adapting Agents Increases with Fitness. PLoS Computational Biology. 9/7, 2013. As the Abstract cites, Joshi, Cal Tech, with Giulio Tononi, University of Wisconsin, and Christof Koch, Allen Institute for Brain Sciences, discern a parallel track between evolved organic intricacy and informed nervous systems. That is, the potential of any creature to survive and reproduce depends on its relative cognitive capacity. Pierre Teilhard would be pleased by this 21st century affirmation of his central vision of a tandem emergence of complexity and consciousness.

What is the relationship between the complexity and the fitness of evolved organisms, whether natural or artificial? It has been asserted, primarily based on empirical data, that the complexity of plants and animals increases as their fitness within a particular environment increases via evolution by natural selection. We simulate the evolution of the brains of simple organisms living in a planar maze that they have to traverse as rapidly as possible. Their connectome evolves over 10,000s of generations. We evaluate their circuit complexity, using four information-theoretical measures, including one that emphasizes the extent to which any network is an irreducible entity. We find that their minimal complexity increases with their fitness. (Abstract)

It has often been asserted that as organisms adapt to natural environments with many independent forces and actors acting over a variety of different time scales, they become more complex. We investigate this question from the point of view of information theory as applied to the nervous systems of simple creatures evolving in a stereotyped environment. We performed a controlled in silico evolution experiment to study the relationship between complexity, as measured using different information-theoretic measures, and fitness, by evolving animats with brains of twelve binary variables over 60,000 generations. We compute the complexity of these evolved networks using three measures based on mutual information and one measure based on the extent to which their brain contain states that are both differentiated and integrated. All measures show the same trend - the minimal complexity at any one fitness level increases as the organisms become more adapted to their environment, that is, as they become fitter. Above this minimum, there exists a large degree of degeneracy in evidence. (Author Summary)

Judson, Olivia. The Energy Expansions of Evolution. Nature Ecology & Evolution. Online April 28, 2017. In this new journal, the biological science author (Amazon) with an Oxford University doctorate in philosophy proposes an innovative, succinct view of life’s ascendance by way of five stages of geothermal, sunlight, oxygen, flesh, and fire energy source and usage. In contrast to other studies (e.g. Lenton 2016) she takes a biospheric view to take in the sequential formations of a life-planet system. As a result, …the lens reveals a fundamental, recursive interplay between events in the evolution of life and the development of the planetary environment. (7)

The history of the life–Earth system can be divided into five ‘energetic’ epochs, each featuring the evolution of life forms that can exploit a new source of energy. These sources are: geochemical energy, sunlight, oxygen, flesh and fire. The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the transformation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change. Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life–planet systems elsewhere. (Abstract)
In short, this Perspective of energy expansions suggests that the likely development of a life–planet system will depend on the interplay between the planet's cosmic situation, its intrinsic properties, and the paths that evolving life can potentially take. The example of this life–planet system suggests that the development of a flourishing, complex biosphere depends on a virtuous circle between evolving life forms and transformations of their planetary home. (8)

Karsenti, Eric. Self-Organization in Cell Biology. Nature Reviews: Molecular Cell Biology. 9/3, 2008. A European Molecular Biology Laboratory (Heidelberg) senior researcher and group leader surveys the historical acceptance of such dynamical theories in the life sciences, and then goes on to advise their further utilization. And the growing admission per the second quote that “living matter” indeed possesses such deep attributes augurs for a cosmic revolution proper to their presence.

Over the past two decades, molecular and cell biologists have made important progress in characterizing the components and compartments of the cell. New visualization methods have also revealed cellular dynamics. This has raised complex issues about the organization principles that underlie the emergence of coherent dynamical cell shapes and functions. Self-organization concepts that were first developed in chemistry and physics and then applied to various morphogenetic problems in biology over the past century are now beginning to be applied to the organization of the living cell. (255)

The principles that are associated with self-organization processes tend to indicate that the driving force behind the diversity of life and its evolution is not mainly selection. Instead, it may derive largely from the intrinsic properties of living matter and the combination of various self-organized functional modules. (261)

Keller, Evelyn Fox. Ecosystems, Organisms, and Machines. BioScience. 55/12, 2005. For a special section on “new thinking in biology,” the MIT philosopher of science reviews the historical perception from Immanuel Kant to mid 20th century cybernetics to current nonlinear dynamical theory of an animate, developing nature that organizes itself. See also Keller’s article DDS: Dynamics of Developmental Systems in Biology and Philosophy (20, 2-3, 2005) for more on a necessary clarification of terms.

Indeed, it is claimed that the emergence of life itself can be seen as a self-organized critical phenomenon. Life is incorporated not into the category of structurally complex “self-organizing” machines, as it had been in the 1950’s and 1960’s, but into the nonlinear dynamics of structurally simple, physical-chemical systems. What has happened here? In this assimilation of life and familiar physical processes, is biology being reduced to physics, or is physics being revived by the infusion of life? (1072) Such arguments may lead us to think of everything as a self-organizing system, but doing so need not be bad – as long as it comes with the understanding that the most interesting kinds of self-organizing systems are those that require the participation and interaction of many different kinds of selves. (1073)

Keller, Laurent, ed. Levels of Selection in Evolution. Princeton: Princeton University Press, 1999. Papers on the conceptual expansion from a gene centered model to multilevel stages from replicators to societies.

Kirschner, Mark and John Gerhart. The Plausibility of Life. New Haven: Yale University Press, 2005. These senior biologists – Kirschner is chair of Systems Biology at Harvard, Gerhart a professor at the University of California, Berkeley – argue that the standard Darwinian theory is correct but “incomplete.” Blind mutation and selection is not enough to explain how organisms originate and become more complex. Life is “plausible” because of a build-up of “evolvability” via “conserved core processes” that favor viable genotype (genetic) variations increasingly biased by the active behavior of phenotypes (creatures). An inherent propensity for modular body plans and “compartmentalization,” along with topological constraints, adds a further impetus.

Now when this work is taken together with a growing literature making a similar case, such as Endless Forms Most Beautiful (Sean Carroll), Evolution in Four Dimensions (Eva Jablonka and Marion Lamb), Developmental Plasticity and Evolution (Mary Jane West Eberhard), Evolution and Learning (Bruce Weber and David Depew, eds.) and others, not only is a major revision and advance in evolutionary theory in the air, but to a radically new version which begins to look like an oriented development, an embryogenesis.

By subdividing the animal into smaller, largely independent domains, the evolution of structures in that domain can be uncoupled from the evolution of structures in other domains. (203) The main accomplishment of the theory of facilitated variation is to see the organism as playing a central part in determining the nature and degree of variation, thus giving selection more abundant viable variation on which to act. (243) Facilitated variation definitely implies a biased output of phenotypic variation by an organism, even though the initial input of mutation over the entire genome is random. This bias in inevitable, because variation is based on reuse of the existing phenotype in new ways and hence starts with a given structure, a given bias. (246)

Klarreich, Erica. Life on the Scales. Science News. February 12, 2005. A report on and synthesis of recent advances in uncovering constant mathematical relations throughout nature. Geoffrey West, James Brown, Brian Enquist, James Gillooly, and others over the last 10 years have found a universal scale of body size and metabolism, trees in a forest, ecological communities, and so on. The consequence is that we are finally able to understand the natural realm as much more than a chaotic, tangled jumble, rather it expresses a deep, intelligible order.

Knoll, Andrew and Richard Bambach. Directionality in the History of Life. Paleobiology. 26/4 Supplement, 2000. Work iA Harvard University biologist, and Virginia Polytechnic Institute geologist offer glimpses in this year toward an evolutionary trend from the origin of life through various microbial, eukaryotic, multicellular, and technological stages. n process toward elucidating an evolutionary trend from the origin of life through its microbial, eukaryotic, multicellular, and technological stages.

Issues of directionality in the history of life can be framed in terms of six major evolutionary steps, or megatrajectories (Maynard Smith and Szathmáry 1995): (1) evolution from the origin of life to the last common ancestor of extant organisms, (2) the metabolic diversification of bacteria and archaea, (3) evolution of eukaryotic cells, (4) multicellularity, (5) the invasion of the land and (6) technological intelligence. Within each megatrajectory, overall diversification conforms to a pattern of increasing variance bounded by a right wall as well as one on the left. However, the expanding envelope of forms and physiologies also reflects—at least in part—directional evolution within clades. Each megatrajectory has introduced fundamentally new evolutionary entities that garner resources in new ways, resulting in an unambiguously directional pattern of increasing ecological complexity marked by expanding ecospace utilization. The sequential addition of megatrajectories adheres to logical rules of ecosystem function, providing a blueprint for evolution that may have been followed to varying degrees wherever life has arisen. (Abstract)

Each metatrajectory has introduced fundamentally new evolutionary entities that garner resources in new ways, resulting in an unambiguously directional pattern of increasing ecological complexity marked by expanding ecospace utilization. (1)

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