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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Evolutionary Development Organizes Itself: A 2020s Genesis Synthesis

A. A Major Emergent Evolutionary Transitions Scale

Rosslenbroich, Bernd. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Heidelberg: Springer, 2014. In this book, I develop the proposal that a recurring central aspect of macroevolutionary innovations is an increase individual organismal autonomy in the sense of emancipation from the environment with changes in the capacity for flexibility, self-regulation, and self-control of behavior. (3) The University of Witten/Herdecke physiologist provides a book-length treatment of his hypothesis that a progressive manifestation of personal liberties, within reciprocal symbiotic groupings, is a main axial trend and vector of life’s episodic emergence. The text opens with an historic and current survey, noting the companion 2015 work of Alvaro Moreno and Matteo Mossio (search). Chapters proceed from major transitions in the early Cambrian to complex dynamic functions across bodies to brains, and onto increasing freedoms in supportive communities.

In recent years ideas about major transitions in evolution are undergoing a revolutionary change. The author states that a recurring central aspect of macroevolutionary innovations is an increase in individual organismal autonomy whereby it is emancipated from the environment with changes in its capacity for flexibility, self-regulation and self-control of behavior. The first chapters define the concept of autonomy and examine its history and its epistemological context. Later chapters demonstrate how changes in autonomy took place during the major evolutionary transitions and investigate the generation of organs and physiological systems. They synthesize material from various disciplines including zoology, comparative physiology, morphology, molecular biology, neurobiology and ethology. It is argued that the concept is also relevant for understanding the relation of the biological evolution of man to his cultural abilities. Finally the relation of autonomy to adaptation, niche construction, phenotypic plasticity and other factors and patterns in evolution is discussed.

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)

Schuster, Peter. Major Transitions in Evolution and in Technology. Complexity. Online March, 2016. The University of Wien biochemist is president of the Austrian Academy of Sciences and editor-in-chief of this journal. Since being conceived by John Maynard Smith and Eors Szathmary in the 1990s, this perception of a recurrent, nested emergent scale from biomolecules to human cultures has become increasingly accepted, verified, and expanded. This contribution goes on to find these common principles to be repeated in some manner in the creation of technological artifacts.

Sela, Itamar, et al. Selection and Genome Plasticity as the Key Factors in the Evolution of Bacteria. Physical Review X. 9/031018, 2018. In this physics journal, aided by current affirmations of a common repetition in kind everywhere, National Center for Biotechnology Information theorists I. Sela, Yuri Wolf and Eugene Koonin report that genomic phenomena takes on the form of a nested scale across many domains or classes. As their Summary below notes, the present re-unification and re-rooting of life in an increasingly fertile cosmos is well served by such evidential findings. See also a reference Family Specific Scaling Laws in Bacterial Genomes by Eleonora De Lazzari, et al in Nucleic Acids Research (45/13, 2017, second quote).

In microbes, different functional classes of genes, such as those involved in information processing, metabolism, and regulation, show scaling exponents with the genome size. However, there is no general theory to explain these “universal laws” of microbial genome evolution. Here, we describe a mathematical model that recovers the differential scaling of functional gene classes in bacterial genomes, includes only two parameters to characterize genomes, selection coefficient and plasticity. After testing the model against genomic data, we conclude that genome plasticity is a key evolutionary factor. Our findings suggest that at least some key aspects of genome evolution can be captured by general theoretical models akin to those widely used in physics. (Sela Summary)

Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, which share a specific functional annotation across genomes of given size. The size of these functional categories change, on average, as power-laws in the total number of protein-coding genes. Here, we show that such regularities are not restricted to the behavior of high-level functional categories, but exist at the level of single evolutionary families of protein domains. Under the common assumption that selection is driven solely or mainly by biological function, these findings point to fine-tuned and interdependent roles of specific protein domains. (De Lazzari Abstract)

Suki, Bela. The Major Transitions of Life from a Network Perspective. Frontiers in Fractal Physiology. 3/Article 94, 2012. The major transitions theory of an episodic, recurrent evolution from biomolecules to genomes, cells, mammals, brains, primates, and language, first proposed in 1995, has gained much acceptance. In the years since, a new nature has been realized as vitally suffused with complex, dynamical systems. A Boston University professor of Biomedical Engineering can now deftly elucidate the role of ubiquitous network topologies in this nested emergence, as the quotes attest. In regard, the addition of these propensities leads to several implications. A generic sequence becomes apparent for stage changes akin to phase transitions in statistical physics. The dynamic recast of evolution then infers an iterative self-organization at work at each scale. Finally, from 2012, Bela Suki muses whether we might be in the midst of a further ascent to a worldwide humankind noopshere.

In an influential work, Maynard Smith and Szathmáry argued that the majority of the increase in complexity is not gradual, but it is associated with a few so-called major transitions along the way of the evolution of life. For each major transition, they identified specific mechanisms that could account for the change in complexity related to information transmission across generations. In this work, I propose that the sudden and unexpected improvement in the functionality of an organism that followed a major transition was enabled by a phase transition in the network structure associated with that function. The increase in complexity following a major transition is therefore directly linked to the emergence of a novel structure–function relation which altered the course of evolution. As a consequence, emergent phenomena arising from these network phase transitions can serve as a common organizing principle for understanding the major transitions. As specific examples, I analyze the emergence of life, the emergence of the genetic apparatus, the rise of the eukaryotic cells, the evolution of movement and mechanosensitivity, and the emergence of consciousness. (Abstract)

Here I will argue that the basis of the new kind of behavior post-transition is a fundamental change in the structure pre-transition. If each major transition can be linked to the emergence of a novel structure, then there man by a common mechanism behind these transitions related to the complexity of the underlying structural organization. (1) The theory of complexity has much to offer to understand life and its major transitions. Specifically, complexity deals with systems that show emergent behavior resulting from the interactions of many components or subunits of the system. A convenient way to discuss such systems is to consider the interactions among the units as a network. (1-2) If we accept the notion that the structural basis of life is a network, then the “emergence” of living matter maybe associated with the emergence of a suitable network structure that allows processes associated with life. (4) Thus, network phenomena under non-equilibrium conditions mist have played a key role in the very first major transition, the origin of life, independent of the precise details of chemistry. (5)

As mentioned earlier, fractal structures and long-range correlated fluctuations naturally appear at the critical point during phase transitions providing thus an intriguing link between non-equilibrium conditions, ordered structures and the corresponding novel functions related to the major transitions of life. (9) If the major transition are indeed a network associated phase transition, then, to some extent, they should be independent of the details of the system. With regard to the first transition, the origin of life, does this suggest that a transition is likely to occur in any sufficiently rich soup of raw materials largely independent of the specifics of chemistry? Given the steady discovery of Earth-like planets, an important implication of this would be that some sort of a self-sustaining primitive life should abound in the universe. (10)

What is the expected impact of a new transition, biological or other, on human society? It is evident that even over the short time period of human evolution, various new networks have emerged and transitions occurred. A recent and perhaps most revolutionizing network in terms of human experience is the internet. As the complexity of the internet increases, is it possible to live through a phase transition such that the internet acquires some form of intelligence or consciousness? Also, consciousness is certainly an emergent phenomenon arising from the neural network connectivity of the brain. Could the human species undergo yet another phase transition? (11)

Szathmary, Eors. Cultural Processes: The Latest Major Transition in Evolution. Nadel, Lynn, editor-in-chief. Encyclopedia of Cognitive Science. London: Nature Publishing Group, 2003. A concise summary of the late John Maynard Smith and Szathmary’s theory of evolution as a sequential emergence from molecular gene to human social levels. This increase in complexity proceeds through a recurrent process of divergence, symbiosis, and epigenesis which goes on to form a “higher” whole entity. Each stage is also characterized by a new genetic template from DNA to language. And this scenario is just what would be found if life’s evolution is in fact a self-organizing complex adaptive system.

Szathmary, Eors. Evolution of Language as One of the Major Evolutionary Transitions. Nolfi, Stefano and Marco Mirolli, eds. Evolution of Communication and Language in Embodied Agents. Berlin: Springer, 2010. The cofounder with John Maynard Smith of this large conceptual advance expands on its current linguistic phase. Since social discourse is appreciated as a main formative agency for hominid group culture, language is to be rightly seen as a “novel inheritance system.”

Major transitions happened a number of times in evolution, and always resulted in a significant increase in complexity. For example, the eukaryotic cell is a result of the coming together and coevolution of some initially independent microbial lineages, or multicellular living being arose either through the sticking together or aggregation of related cells. There are some recurrent themes in the major transitions: (1) Independently replicating units come together to form a higher-level unit. (2) Appearance of novel inheritance systems. (3) Division of labor or combination of functions. (4) Contingent irreversibility. (5) Central Control. (49-50)

Szathmary, Eors. Toward Major Evolutionary Transition Theory 2.0. Proceedings of the National Academy of Sciences. 112/10104, 2015. A presentation at the October 2014 NAS Sackler Colloquium: Symbioses Becoming Permanent: The Origins and Evolutionary Trajectories of Organelles by the Eotvos University, Hungary, biologist and founder with John Maynard Smith in 1995 of this natural iterative scale. This 20 year review and update of nuances and verifications serves to aver its current mainstream acceptance. From protocells at life’s origin to nucleotides, eukaryotic cells, plastid organelles, organisms, eusocial cooperation onto symbolic human sapience, a nested sequence was facilitated in each case by a novel informational “inheritance system.” Gradual Darwinian selection is not mentioned, presently replaced by this axial oriented emergence, which quite bodes for a genesis synthesis.

From Lower to Higher Level Evolutionary Units The first common feature is the transition from independent replicators to form higher level units: for example, genes ganged up in protocells, prokaryotes joined to constitute the eukaryotic cell, protist cells stacked together to form multicellular organisms, and so on. In order for such a transition to be successful, evolution at the lower level must be somehow constrained by the higher level. I adopt the view of (Andrew) Bourke (search), who suggested that major transitions should typically be cut into three phases: the formation, maintenance, and transformation of social groups. (10104)

Turney, Peter. Modeling Major Transitions in Evolution with the Game of Life. arXiv:1908.07034. We cite this entry (bio below) as a rate exercise to consider and model a further phase of this iterative, nested emergent sequence as it may reach a worldwise personsphere individuality. See also Conditions for Major Transitions in Biological and Cultural Evolution at by the author at arXiv:1806.07941 and Symbiosis Promotes Fitness Improvements in the Game of Life in Artificial Life (26/3, 2020).

Maynard Smith and Szathmáry's book The Major Transitions in Evolution describes eight events in the evolution of life on Earth and a common theme that unites them. In each case, smaller entities came together to form larger, inclusive stages by way of symbiosis and/or cooperation. Here we present a computational simulation of evolving entities that includes symbiosis with shifting levels of selection. The experiments show that a small amount of symbiosis, added to the other layers, significantly increases the fitness of the population. We suggest that, in addition to providing new insights into biological and cultural evolution, this model of symbiosis may have practical applications in evolutionary computation, such as in the task of learning deep neural network models. (Abstract)

Dr. Peter Turney is a scientist based in Gatineau, Quebec, Canada. He is currently a Research Scholar with the Ronin Institute since 2018. He was a Senior Research Scientist at the Allen Institute for Artificial Intelligence from 2015 to 2017, a Principal Research Officer at the National Research Council of Canada (NRC) from 1989 to 2014, and an Adjunct Professor at the University of Ottawa.

Waring, Timothy and Zachary Wood. Long-term Gene-culture Coevolution and the Human Evolutionary Transition. Proceedings of the Royal Society B. May, 2021. University of Maine sustainability scholars provide a latest, thorough study of how our homocene to anthropocene, local to global, emergence can well be appreciated as a further spherical scale. A bibliography from Alfred Kroeber and Herbert Spencer to current work conveys how such a “superorganic” phase has long been suggested. Herein, a historic passage from genetic to cultural “inheritance,” from genome to memory, is found to be a prime causal rationale. Thus we reach Section 4. Rethinking the Human Evolutionary Transition in Individuality. But as we often say, it would be of much benefit to realize that this planetary progeny appears to be learning and gaining knowledge on her/his own.

It has been suggested that the human species may be undergoing an evolutionary transition in individuality (ETI). But an issue is how to apply the ETI framework to our species, and whether culture is a cause or consequence. Some have argued that culture steers human evolution, while others propose that genes hold culture on a leash. We review the literature and evidence on long-term GCC in humans and find a set of common themes. First, culture appears to hold more adaptive potential than inheritance. The evolutionary impact of culture occurs mainly through organized human groupings of many kinds. Second, the role of culture appears to be overtaking genetic evolution. Altogether, these findings suggest that human GC coevolution constitutes an evolutionary transition in inheritance (from genes to culture) and in individuality (from genetic individual to cultural group). (Abstract excerpt)

Warrell, Jonathan and Mark Gerstein. Cyclical and Multilevel Causation in Evolutionary Processes. Biology & Philosophy. 35/Art.50, 2020. Yale University computational biophysicists and geneticists (search MG) post a 36 page careful consideration of how novel machine learning techniques and models seem able to gain deeper insights about into life’s structured developmental advance, better ways to understand and mitigate diseases and a sense of identities.

We develop here a general theoretical framework for analyzing evolutionary processes drawing on recent approaches to causal modeling developed in the machine-learning literature, which have extended Pearls do-calculus to incorporate cyclic causal interactions and multilevel causation. We show how our causal framework helps to clarify conceptual issues in the contexts of complex trait analysis and cancer genetics, including assigning variation in an observed trait to genetic, epigenetic and environmental sources in the presence of epigenetic and environmental feedback processes, and variation in fitness to mutation processes in cancer using a multilevel causal model respectively. Finally, we consider the potential relevance of our framework to biology and evolution, including supervenience, multilevel selection and individuality. (Abstract excerpt)

West, Stuart, et al. Major Evolutionary Transitions in Individuality. Proceedings of the National Academy of Sciences. 112/10112, 2015. A paper for the 2014 NAS Sackler Colloquium entitled Symbioses Becoming Permanent: The Origins and Evolutionary Trajectories of Organelles about confirmations of life’s communal emergence as due to pervasive symbiotic unions. In accord with Eors Szathmary’s presentation at this meeting (search), this nested, manifest scale could be seen as regnant, liberated persons in relative communities.

The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven’t taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved. (Abstract)

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