This is the first book devoted to chimera states - peculiar partial synchronization patterns in networks. Providing an overview of the state of the art in research on this topic, it explores how these hybrid states, which are composed of spatially separated domains of synchronized and desynchronized behavior, arise surprisingly in networks of identical units and symmetric coupling topologies. The book not only describes various types of chimeras, but also discusses the role of time delay, stochasticity, and network topology for these synchronization-desynchronization patterns. Moreover, it addresses the question of robustness and control of chimera states, which have various applications in physics, biology, chemistry, and engineering.

Moghadam, S. Arbabi, et al. A Search for the Physical Basis of the Genetic Code. Biosystems. May, 2020. We cite because this entry by University of Alberta biophysicists including Jack Tuszynski discuss several ways that life’s genomic endowment can be rooted in and given a deeper substantial, innately fertile basis.

DNA contains the genetic code, which provides complete information about the synthesis of proteins in every living cell. Each gene encodes for a corresponding protein but most of the DNA sequence is non-coding. In addition to this non-coding part of the DNA, there is another redundancy, namely a multiplicity of DNA triplets (codons) corresponding to code for a given amino acid. In this paper we investigate possible physical reasons for the coding redundancy, by exploring free energy considerations and abundance probabilities as potential insights. (Abstract)

Racimo, Fernando, et al. Beyond Broad Strokes: Sociocultural Insights from the Study of Ancient Genomes. Nature Reviews Genetics. June, 2020. With prior hominids, migrations, primates, animal creatures and more now sequenced, and as techniques ever improve, University of Copenhagen and Universitat Pompeu Fabra, Barcelona researchers discuss a new phase which can reconstruct intangible behavioral, artifactual, and tribal features. So we wonder, what kind of temporal reality is this whereof a global species finally appears and becomes capable to recover, learn about and convert to knowledge all of whom and what went before. Why can we peoples do this, what is the great revelation and purpose?

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from large-scale supraregional studies to local perspectives of socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies, insights and methods to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines — such as anthropology, archaeology, linguistics and genetics — that have until recently evolved in separation. (Abstract)

Systems Evolution: A 21st Century Genesis Synthesis

Bapteste, Eric and Philippe Huneman. Towards a Dynamic Interaction Network of Life to Unify and Expand the Evolutionary Theory. BMC Biology. 16/56, 2018. In a unique contribution to a genesis synthesis, Sorbonne University philosophers of biology describe the pervasive, innate presence of network topologies as they serve to link altogether prior organismic parts across biomolecular, cellular, and organism phases. This late addition is seen to bolster the holobiont symbiosis model, and accord with scaffolded, process, and chimeric gene aspects. Once again, if by a philosophia mind to allow and view, life’s homologous developmental course takes on a webwork anatomy, physiology and neural appearance. With this in place, a shift toward network thinking, as everywhere else, would advance and unify evolutionary theory. See also Testing the “(Neo-) Darwinian” Principles against Reticulate Evolution by Nathalie Gontier in Information (11/7, 2020).

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology. (Abstract)

Fields, Chris and Michael Levin. Scale-Free Biology: Integrating Evolutionary and Developmental Thinking. BioEssays. June, 2020. As a 2020 integrative phase goes forward, a veteran philosopher of biology now based in France and a Tufts University, Allen Discovery Center developmental biologist propose and scope out an array of unifying perspectives which are guided by an insight that life’s oriented emergence repeats in similar ways and means across the nested phases it engenders.

When the history of life on Earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life can also be seen as the development of life. Here some fruitful research directions suggested by this perspective are highlighted. Variation and selection become bidirectional information flows between scales, while “cooperation” and “competition” become scale relative. The language of communication, inference, and information processing are more useful than the language of causation to describe homogeneous and heterogeneous living systems. Emerging scale‐free theories such as predictive coding and active inference can provide conceptual tools for the study of a unified, multiscale dynamical system. (Abstract)

Gontier, Nathalie. Testing the “(Neo-) Darwinian” Principles against Reticulate Evolution. Information. 11/7, 2020. The University of Lisbon evolutionary epistemologist has been at the conceptual forefront (search) of a 2010s revision of life’s developmental emergence. This paper continues her 2015 edited Reticulate Evolution volume by noting exemplary network topologies in symbiosis, lateral gene transfer, adaptive fitness, infective (viral) heredity, organismic mobility, species affordances, hybridization and more. A distinct approach of reticulate studies is proposed as an overdue phase of interconnective linkages between all the prior parts. In regard, an inclusion and endorsement of symbiotic mutual unions in their role as a prime evolutionary property is achieved. A history of symbiogenesis from the 1900s to the work of Lynn Margulis to current holobiont models braces the claim. See also Towards a Dynamic Interaction Network of Life to Unify and Expand the Evolutionary Theory by Eric Bapteste and Philip Huneman in BMC Biology (16/56, 2018) for another confirmation.

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program. Several of these aspects have been called “Darwinian principles.” However, we will here describe the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. Because “Darwinian principles” are brought about by both vertical and reticulate processes, they should contribute to a more pluralistic theory of evolution, one that surpasses the Modern and Neo-Darwinian Synthesis. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (Abstract excerpt)

Reticulate: the formation of a net or web- work topology, or the presence of net structures such as veins of a leaf, or a nervous system.

Nathalie Gontier: I’m a philosopher of evolutionary sciences, with special interest in the nature and scope of evolutionary explanations, how they evolved within the overall genealogy of thought; how they are applied within the biological, sociocultural and linguistic sciences; and how they are depicted in hierarchical diagrams such as cycles, timelines, trees and networks.

Evolving a Major Transition in the Internet Age. evolution-institute.org/evolving-a-major-transition-in-the-internet-age. This 2020 posting by the veteran environmentalist and filmmaker in collaboration with the SUNY Binghamton evolutionary practitioner and author David Sloan Wilson is located on Wilson’s The Evolution Institute site. By way of text and a DSW interview, a project is scoped out is based upon a likely but rare perception that a further emergent stage of global proportions can be seen as much underway. By this extension, our anthropocene phase is composed of wholly interconnected information but beset by disjointed nations and societies. A vital need is to implement the “new ways to cooperate at higher levels of complexity” that usually distinguish and facilitate these transitions. To date, this is only concerted effort to carry forth life’s ascendant, quickening scale to its sustainable planetary fulfillment.

PROSOCIAL is a framework for improving the efficacy of groups that is being developed by the Evolution Institute. It is based on eight core design principles – originally derived by Elinor Ostrom for groups who manage natural resources – that are needed by most groups whose members must work together to achieve common goals: Strong group identity and understanding of purpose; Fair distribution of costs and benefits; Inclusive decision-making; Monitoring agreed-upon behaviors; Fast and fair conflict resolution; Appropriate relations with other groups. (Alan Honick website)

Sandora, McCullen and Joseph Silk. Biosignature Surveys to Exoplanet Yields and Beyond. arXiv:2005.04005. University of Pennsylvania and Johns Hopkins University cosmologists propose a more comprehensive guide for future search phases as they proceed to quantify the presence and stage of evolutionary life. As per the second quote, the major transitions scale finds service since each level from microbes to a metropolis will have a characteristic atmospheric signature, along with other indicators. In regard we want to record the wide acceptance and application of this episodic emergence, which is a major structural feature of a genesis synthesis.University of Pennsylvania and Johns Hopkins University cosmologists propose a more comprehensive guide for future search phases as they proceed to quantify the presence and stage of evolutionary life. As per the second quote, the major transitions scale finds service since each level from microbes to a metropolis will have a characteristic atmospheric signature, along with other indicators. In regard we want to record the wide acceptance and application of this episodic emergence, which is a major structural feature of a genesis synthesis.

Upcoming biosignature searches focus on indirect indicators to infer the presence of life on other worlds. Aside from just signaling the presence of life, however, some biosignatures can contain information about the state that a planet's biosphere has achieved. This additional information can be used to measure what fractions of planets achieve certain key stages of the advent of life, photosynthesis, multicellularity and technological civilization. Our approach is probabilistic and relies on large numbers of candidates rather than detailed examination of individual exoplanet spectra. The dependence on survey size, likeliness of the transition, and degrees of confidence are discussed. (Abstract excerpt)

The life history of our own planet can be seen as a sequence of transitions wrought by evolutionary innovations, from biogenesis to the evolution of photosynthesis, multicellularity, and technological civilization. As far as these transitions can be expected to be generic, they can each be sought for independently through their characteristic atmospheric imprints. The question we address here is, what fraction of planets undergoes each transition, and more importantly, which can be measured with upcoming surveys? By quantifying the uncertainty in measurements of each of these quantities, we provide a framework for understanding how they depend on proposed mission designs as well as on atmospheric modeling. (1)

DiFrisco, James and Johannes Jaeger. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. BioEssays. 42/6, 2020. A biological studies advance, KU Leuven philosopher and a Complexity Science Hub, Vienna systems biologist seek to add a relational network vista which can inform the historic turn from discrete nucleotides to whole entities, be it genomes or organisms.

The logic of genetic discovery remains in place, but the focus of biology is shifting from genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the reductionist view of genes as privileged causes is re‐examined. The scope of genetic effects in complex regulatory systems, in which dynamics are driven by feedback and hierarchical interactions across levels, are considered. This review argues that genes can be treated as specific difference‐makers for the molecular regulation of their expression. However, they are not stable, proportional or specific as causes of the behavior of regulatory networks. Proper dynamical models can illuminate cause‐and‐effect in complex biological systems so to gain an integrative understanding of underlying complex phenotypes. (Abstract edit)

Brun-Usan, Miguel, et al.. How to Fit In: The Learning Principles of Cell Differentiation. PLoS Computational Biology.. April, 2020. University of Southampton, UK, computer scientists including Richard Watson continue their revisionary studies of biological metabolisms by viewing them through a learning lens. A cerebral perspective, as this section reports, can provide better insights into cellular processes because both evolution and learning are explorations in search of solutions. A further step is to integrate this view with gene regulatory networks so these common models can reinforce each other. Altogether this approach implies that life’s oriented emergence is trying to achieve some manner of its own self-description and comprehension.

Cell differentiation in multicellular organisms requires cells to respond to complex combinations of extracellular cues, such as morphogen concentrations. But a general theory describing how cells integrate multi-dimensional signals is still lacking. In this work, we propose a framework from learning theory to understand the relationships between environmental cues (inputs) and phenotypic responses (outputs) underlying cell plasticity.. Altogether, these results illustrate the functional parallelisms between learning in neural networks and the action of natural selection on environmentally sensitive gene regulatory networks. This offers a theoretical framework for responses that integrate information from multiple cues, a phenomenon that underpins the evolution of multicellularity and developmental robustness. (Abstract excerpt)

Earth Life Emergence: Development of Body, Brain, Selves and Societies

Cornacchia, Loreta, et al. Self-Organization of River Vegetation Leads to Emergent Buffering of River Flows and Water Levels. Proceedings of the Royal Society B. July, 2020. As complexity studies of “tangled banks” continue to reveal inherent patterns and processes, Dutch and British geoecologists based at the Royal Netherlands Institute for Sea Research quantify how they riverine environs dynamically organize themselves so as to keep up with ever changing conditions.

Global climate change will impact hydrodynamic conditions in stream ecosystems but there is limited understanding of how they interact and change. By mathematical modelling of field data, we demonstrate that bio-physical feedback between plant growth and flow redistribution causes spatial self-organization of in-channel vegetation that buffers for changed hydrological conditions. The interplay of vegetation growth and hydrodynamics results in a separation of the stream into densely vegetated, low-flow zones divided by unvegetated channels of higher flow velocities. Our results provide important evidence of how plant-driven self-organization allows stream ecosystems to adapt to changing hydrological conditions, maintaining suitable hydrodynamic conditions to support high biodiversity. (Abstract excerpt)

Baross, John, et al. The Environmental Roots of the Origin of Life. Meadows, Victoria, et al, eds. Planetary Astrobiology. Tempe: University of Arizona Press, 2020. University of Washington, Carleton College and University of St. Andrews Earth system scientists first review of origin studies from J. B. Haldane and A. Oparin to current bottom up prebiotic chemistry and top down paleogenetics along with RNA and metabolism first views. The paper then digs deep into Hadean geologic, thermal and elemental conditions and on to early organic activities such as polymerization, compartments and cellularity. Again within the book paradigm of a whole biospherical active process, a global chemical and catalytic reactor is described. With this retrospect survey in place, the relative likelihood and biosignature detection of astrocosmic life occurrences is previewed.

The ongoing quest to understand how Earth life emerged and evolved converges on four aspects: the earliest evidence of life, geochemical properties of the environmental setting, and the life forms based on molecular and biochemical data. The fourth is how life got started which involves complex chemical and biochemical reactions that led to metabolism, genetics, and evolving organisms. One of the goals of this review is to identify the interrelationship of the Hadean environmental and geochemical conditions with critical biochemical determinants involved in the origin of life that could be helpful in our search for Earth-like life elsewhere. (Abstract excerpt)

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