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

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)

Krotov, Dmitry, et al. Morphogenesis at Criticality. Proceedings of the National Academy of Sciences. 111/3683, 2014. Princeton University, Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, theorists, including William Bialek, contend that genome phenomena, as it informs developing morphologies, is effectively poised or “tuned” to a critical state. One may add, just as brains are now found to be.

Spatial patterns in the early fruit fly embryo emerge from a network of interactions among transcription factors, the gap genes, driven by maternal inputs. Such networks can exhibit many qualitatively different behaviors, separated by critical surfaces. At criticality, we should observe strong correlations in the fluctuations of different genes around their mean expression levels, a slowing of the dynamics along some but not all directions in the space of possible expression levels, correlations of expression fluctuations over long distances in the embryo, and departures from a Gaussian distribution of these fluctuations. Analysis of recent experiments on the gap gene network shows that all these signatures are observed, and that the different signatures are related in ways predicted by theory. Although there might be other explanations for these individual phenomena, the confluence of evidence suggests that this genetic network is tuned to criticality. (Abstract)

Biological networks are described by many parameters, and the behavior of a network is qualitatively different (monostable, bistable, oscillating, etc.) in different parts of parameter space. Critical points and surfaces are the borders between such qualitatively different regimes, as with phase transitions in equilibrium thermodynamics. We argue that, as expected from the thermodynamic case, genetic regulatory networks should exhibit behaviors near criticality that are independent of most molecular details. Analyzing recent experiments on the gap gene network in the early Drosophila embryo, we find that these signatures of criticality can be seen, quantitatively. This raises the question of why evolution has tuned this network to such a special point in its parameter space. (Significance)

Kul, Kaveli. Adaptive Evolution without Natural Selection. Biological Journal of the Linnean Society. Online July, 2013. The University of Tartu, Estonia, semiotics scholar advises one more way that something innately prescriptive is going on prior to selective eliminations. By this view, life’s temporal, scalar development from microbes to people is seen as most facilitated constant communicative behaviors. This proactive agency is said to deserves much merit as informing and guiding an evolutionary emergence.

A mechanism of evolution that ensures adaptive changes without the obligatory role of natural selection is described. According to this mechanism, the first event is a plastic adaptive change (change of phenotype), followed by stochastic genetic change which makes the transformation irreversible. This mechanism is similar to the organic selection mechanism as proposed by Baldwin, Lloyd Morgan and Osborn in the 1890s and later developed by Waddington, but considerably updated according to contemporary knowledge to demonstrate its independence from natural selection. Conversely, in the neo-Darwinian mechanism, the first event is random genetic change, followed by a new phenotype and natural selection or differential reproduction of genotypes. Due to the role of semiosis in the decisive first step of the mechanism described here (the ontogenic adaptation, or rearrangement of gene expression patterns and profile), it could be called a semiotic mechanism of evolution. (Abstract)

Laland, Kevin, et al. The Extended Evolutionary Synthesis: Its Structure, Assumptions and Predictions. Proceedings of the Royal Society B. Vol. 282/Iss. 1813, 2015. Within growing realizations that the 1950s Modern Evolutionary Synthesis, which remains in place, has become quite inadequate, leading theorists including Eva Jablonka, Gerd Muller, and Kim Sterelny continue their efforts to scope out an appropriate 21st century version. Older random mutation and post selection alone can be amended and surpassed by a “reciprocal causation” between organism and environment such as niche construction, epigenetic inheritance, directional phenotypic variation, evolutionary developmental biology, and so on. Something else and far more is going on which is not accidental, but still in need, we add, of a physical rooting in a cosmic, self-organizing, vivifying genesis. See also Schism and Synthesis at the Royal Society, a review by KL of the November, 2016 meeting New Trends in Evolutionary Biology (Trends in Ecology and Evolution February 2017).

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. (Abstract)

Landis, Michael and Joshua Schraiber. Pulsed Evolution Shaped Modern Vertebrate Body Sizes. Proceedings of the National Academy of Sciences. 114/13224, 2017. We cite this paper by Yale and Temple University biologists to show how evolutionary theorists are finding an independent mathematical process as it generates and guides corporeal creatures across widely diverse clades. See also in Systematic Biology Phylogenetic Analysis Using Levy Processes by Landis, et al (62/2, 2013) and Inference of Evolutionary Jumps in Large Phylogenies Using Levy Processes by Pablo Duchin, et al (66/6, 2017).

The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner. (Significance)

Lane, Nick, et al. Energy, Genes and Evolution: Introduction to an Evolutionary Synthesis. Philosophical Transactions of the Royal Society B. 368/20120253, 2013. An overview for this special issue on Energy Transduction and Genome Function: An Evolutionary Synthesis. As the Abstract excerpts sample, life’s ancient evolutionary heritage keeps expanding beyond just mutation and selection and deeper into its dynamic substrate of a physical cosmos. The thesis and claim is that a proper, complete understanding need have a bioenergetic, thermodynamic dimension and source. Salient papers could be “The Inevitable Journey to Being” by Michael Russell, et al, “Early Biochemical Evolution” by Filipa Sousa, et al, and “Why did Eukaryotes Evolve only Once? Genetic and Energetic Aspects of Conflict and Conflict Mediation” by Neil Blackstone. See also a companion issue “The Evolutionary Aspects of Bioenergetic Systems” in Biochimica et Biophysica Acta - Bioenergetics (1827/2, 2013) with some of the same authors.

Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. No energy, no evolution. The ‘modern synthesis’ of the past century explained evolution in terms of genes, but this is only part of the story. While the mechanisms of natural selection are correct, and increasingly well understood, they do little to explain the actual trajectories taken by life on Earth. From a cosmic perspective—what is the probability of life elsewhere in the Universe, and what are its probable traits?—a gene-based view of evolution says almost nothing. Irresistible geological and environmental changes affected eukaryotes and prokaryotes in very different ways, ones that do not relate to specific genes or niches. Questions such as the early emergence of life, the morphological and genomic constraints on prokaryotes, the singular origin of eukaryotes, and the unique and perplexing traits shared by all eukaryotes but not found in any prokaryote, are instead illuminated by bioenergetics. If nothing in biology makes sense except in the light of evolution, nothing in evolution makes sense except in the light of energetics. This Special Issue of Philosophical Transactions examines the interplay between energy transduction and genome function in the major transitions of evolution, with implications ranging from planetary habitability to human health. (Abstract, Lane, et al)

Life is evolutionarily the most complex of the emergent symmetry-breaking, macroscopically organized dynamic structures in the Universe. Members of this cascading series of disequilibria-converting systems, or engines in Cottrell's terminology, become ever more complicated—more chemical and less physical—as each engine extracts, exploits and generates ever lower grades of energy and resources in the service of entropy generation. Each one of these engines emerges spontaneously from order created by a particular mother engine or engines, as the disequilibrated potential daughter is driven beyond a critical point. Exothermic serpentinization of ocean crust is life's mother engine. It drives alkaline hydrothermal convection and thereby the spontaneous production of precipitated submarine hydrothermal mounds. (Abstract, Russell et al)

Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. (Abstract, Sousa, et al)

According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly. (Abstract, Blackstone)

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