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

Scott, Adam, et al. Phase Transitions in Evolutionary Dynamics. Chaos. December, 2022. We cite this paper by University of Missouri bio/neuro scientists AS, Dawn King, Stephen Ordway and Sonya Bahar to show how scientific frontiers are now advancing into an interdisciplinary expanse so to join living and physical systems by way of native complexity features.

Sharp changes in state, such as transitions from survival to extinction, are hallmarks of evolutionary dynamics in biological systems. In regard they can be studied by way of statistical physics and nonlinear complex systems. We discuss examples such directed percolation transitions in cellular automata and agent-based models of evolutionary activities. We also view phase transitions from chemistry to biochemistry at the origin of life and conclude with a review of multilevel selection and the major evolutionary transitions. (Excerpt)

Seilacher, Adolf and Alan Gishlick. Morphodynamics. Boca Raton: CRC Press, 2014. This unique work by Adolf Seilacher (1925-2014), a premier German paleontologist for six decades, and Alan Gishlick, a former graduate student and now an American science teacher, is a synthesis of his frontier insights into the evolutionary development of animal anatomies. Into the 21st century, a common array of independent structural principles can be identified, akin to D’Arcy Thompson and Jamie Davies, that are in manifest effect from life’s origins. As the chapters course through the range of extinct and living invertebrate kingdoms, the constant theme is a skeletal self-organization of fractal geometries.

Morphodynamics is defined as the unique interaction among environment, functional morphology, developmental constraints, phylogeny, and time—all of which shape the evolution of life. These fabricational patterns and similarities owe their regularity not to a detailed genetic program, but to extrinsic factors, which may be mechanical, chemical, or biological in nature. These self-organizing mechanisms are the focus of Morphodynamics.

Sendova-Franks, Ann and Nigel Franks. Self-assembly, Self-organization and Division of Labour. Philosophical Transactions of the Royal Society of London B. 354/1395, 1999. With the increasing employ and applicability of nonlinear theories in biology, this article strives to clarify and define core principles so that they can be used consistently in research studies from molecules to societies. An important insight is that self-organizing systems persistently divide tasks or functions as they complexify toward a higher whole.

Shapiro, James. A 21st Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering. Gene. 345/1, 2005. A paper from the 2005 Structural Approaches to Sequence Evolution: Molecules, Networks, Populations workshop at the Max Planck Institute, worthy of two excerpts because it glimpses the revolutionary shape of an evolutionary ascent that seems to know what it is doing and where it is going.

The last 50 years of molecular genetics have produced an abundance of new discoveries and data that make it useful to revisit some basic concepts and assumptions in our thinking about genomes and evolution. Chief among these observations are the complex modularity of genome organization, the biological ubiquity of mobile and repetitive DNA sequences, and the fundamental importance of DNA rearrangements in the evolution of sequenced genomes. (91)

Based on discoveries about genome system architecture and natural genetic engineering, it is now possible to formulate a series of basic concepts that lead to viewing evolution as something akin to a systems engineering process: * Genomes are formatted by repetitive elements and organized hierarchically for multiple information storage and transmission functions. * Major evolutionary steps occur by DNA rearrangements carried out by sophisticated cellular natural genetic engineering systems operating non-randomly. (97)

Shapiro, James. Evolution: A View from the 21st Century. Upper Saddle River, NJ: FT Press Science, 2011. For some two decades (search) the University of Chicago geneticist has been at the forefront of the on-going reconception of genomes from post-DNA particulate genes to their integration within complex, relational, modular, multiscale, informational systems. As other new volumes in this section such as Gissis and Jablonka, and elsewhere chime in, and Shapiro well articulates, this revolution is in addition revitalizing cellular, organismic matter with an internal, sentient, cognitive, personage. No longer subject to random mutations only, cells and creatures are now seen as proactively, intentionally responsive to changing conditions so as to better survive and prosper. An historic, expansive change of the nature and influence of genomic domains is thus underway from the 1970s “central dogma” of DNA to RNA to protein to this dynamic, multi-faceted source with many epigenetic reaches and constant environmental interactions.

Shapiro goes on to press his descriptive phrase “natural genetic engineering” as: “The collective set of biochemical capabilities that cells have to restructure their genomes by cleaving, splicing, and synthesizing DNA chains.” In addition, a “symbiogenesis” is seen to play a prime role in the evolution of nucleated eukaryotic cells and multicellular organisms. Taken altogether, and it is not the author’s charge to do so, one can broadly observe not only a revised theory and model, but an epochal shift and revolution from the aimless, contingent passivity of the old mechanical materialism to a once and future 21st century resuscitation of a developmental genesis cosmos.

While that determination (exclude any external help) fits with the naturalistic boundaries of science, the continued insistence on the random nature of genetic change by evolutionists should be surprising for one simple reason: empirical studies of the mutational process have inevitably discovered patterns, environmental influences, and specific biological activities at the roots of novel genetic structures and altered DNA sequences. (2) Over time, conditions inevitably change, and the organisms that can best acquire novel inherited functions have the greatest potential to survive. The capacity of living organisms to alter their own heredity is undeniable. Our current ideas about evolution have to incorporate this basic fact of life. (2)

The contemporary concept of life forms as self-modifying beings coincides with the shift in biology from a mechanistic to informatic view of living organisms. (4) Paralleling the contemporaneous transformation from a largely mechanical-industrial society to a densely interconnected information-driven society, the life sciences have converged with other disciplines to focus on questions of acquiring, processing, and transmitting information to ensure the correct operation of complex vital systems. (4) Genomes are sophisticated data storage organelles integrated into the cellular and multicellular life cycles of each distinct organism. Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-based random walk through the limitless space of possible DNA configurations. (6)

The selected cases just described are examples where molecular biology has identified specific components of cell sensing, information transfer, and decision-making processes. In other words, we have numerous precise molecular descriptions of cell cognition, which range all the way from bacterial nutrition to mammalian cell biology and development. The cognitive, informatic view of how living cells operate and utilize their genomes is radically different from the genetic determinism perspective articulated most succinctly, in the last century, by Francis Crick’s famous “Central Dogma of Molecular Biology.” (24)

Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth, and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities. (143) Cells are built to evolve; they have the ability to alter their hereditary characteristics rapidly through well-described natural genetic engineering and epigenetic processes as well as by cell mergers. (143) The science of the 21st century deals with the interactions between the multiple components of complex systems, ranging from aggregates of elementary particles (each of which has its own multivalent set of properties) to the behavior of the largest structures in the cosmos. (145) Today, a major focus in scientific inquiry is to understand how systems change over time, whether they are atoms, molecules, organism, ecosystems, climates, galaxies, black holes, or universes. (145)

Shapiro, James. Living Organisms Author Their Read-Write Genomes in Evolution. Biology. Online December, 2017. In this 75 page, 720 reference posting, the senior University of Chicago biologist and author continues his luminous theories about the holistic literacy of genetic phenomena. A natural writing and reading, aka engineering, is seen to proceed throughout evolutionary life’s emergent development. To horizontal, mobile, and “domain module” DNA transfers which he conceives, this latest posting adds a “symbiogenetic” factor in play. By page 21 one reaches a “syntactical organization of genomes,” while a closing section is Genome Rewriting as a Core Biological Capability. To extrapolate, our human phase via CRISPR systems and more can radically continue life’s narrative script. The article is a lead entry in a Biology in the Early 21st Century: Evolution Beyond Selection issue, see a third quote summary.

Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations. (Abstract excerpt)

Our view of what genomes are has changed fundamentally since genetics and evolution first combined in the early 20th Century to form the Modern Synthesis [412]. At that time, geneticists could only examine genome function by the mutational analysis of phenotypes, recombinational mapping, and cytological examination of chromosome structure and behavior. The nature of genome analysis changed in the middle of the 20th Century, beginning with a series of key discoveries: DNA as the carrier of genetic information [413], the DNA double helix [414], regulation of DNA-encoded protein synthesis [415], and the existence of mobile DNA elements that were capable of altering genome structure and patterns of genome expression [416]. This section will review some consequences of these discoveries from a conceptual perspective leading to a detailed empirical discussion of the key roles that mobile repetitive DNA elements play in evolutionary variation. (21)

The conventional NeoDarwinian appraisal of evolution is based on corresponding pillars of random genetic variation and selection via differential fitness. This Special Issue will offer several differing perspectives on evolutionary development and phylogeny that extend beyond Darwinian selection. The role of cellular cooperativity, cellular cognition, self-reference, niche construction, stigmergy, self-organization, epigenetic modifications, genetic transfer and mobility, endosymbiosis, hologenomics, and non-stochastic genetic mechanisms will be addressed. Over many years, movement towards a substantial revision of the NeoDarwinian synthesis has gained slow momentum through many diverging approaches. (Biology in the Early 21st Century)

Shapiro, James. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process. Biology. 5/2, 2016. In a Beyond the Modern Evolutionary Synthesis issue, the University of Chicago geneticist and author (search) continues his insights about life’s natural self-engineered, edited, oriented emergence. In the decades since the 1950s modern synthesis and especially into the 21st century, many advances such as pervasive symbiogenesis, information processing systems, whole scale genome restructuring, horizontal transfers, and more have yet to be factored in. By these revisions, much more than accidental copying-errors or mutations is going on amongst active genomic phenomena.

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. (Abstract)

Smith, Jillian, et al. Looked at Life from Both Sides. Life. 4/4, 2014. With advice from Joni Mitchell, Emory University biochemists and biologists neatly reflect how chemistry and life, ground and genesis, are coming together, cross-fertilizing, as one natural animation. With some 150 references, an increasingly organic, fecund, complementary nature is well being articulated and affirmed. We may have reached the point where the creation of a mutualistic chemical ecology can be used to inform the progressive growth of molecular information on Earth.

As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers. (Abstract)

Sole, Ricard and Sergi Valverde. Spontaneous Emergence of Modularity in Cellular Networks. Santa Fe Institute Working Papers. 07-06-013, 2007. The persistent formation of modular nodes and links in evolving metabolisms occurs due to advantageous intrinsic propensities of scale-free network topologies, prior to external selection. Another indication of a radical revision in evolutionary thinking to admit such a self-existing, endemic, creative force. (Available on the SFI website.)

Modularity is known to be one of the most relevant characteristics of biological systems and appears to be present at multiple scales. Given its adaptive potential, it is often assumed to be the target of selective pressures. Under such interpretation, selection would be actively favouring the formation of modular structures, which would specialize in different functions. Here we show that, within the context of cellular networks, no such a selection pressure is needed to obtain modularity. Instead, the intrinsic dynamics of network growth by duplication and diversification is able to generate it for free and explain the statistical features exhibited by small subgraphs. The implications for the evolution and evolvability of both biological and technological systems are discussed.

Sole, Ricard, et al. Selection, Tinkering, and Emergence in Complex Networks. Complexity. 8/1, 2003. An exploration of similar, ubiquitous principles in effect from genomes to ecosystems, lexicons and economies. As a result, ‘a different view of evolution’ is possible. In place of a random selection of objects, a predictable emergence occurs due to common network interconnections.

We conjecture that there is a largely universal principle that pervades the evolution of scale-free nets (optimal communication) and that the observed topological features of bionets reflect this feature together with constraints arising form other causes, such as the need of modular organization. (31)

Stadler, Barbel, et al. The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change. Journal of Theoretical Biology. 213/2, 2001. A sophisticated mathematical theory which proposes that a limited range of geometries which preceed selection effects constrain genetic programs and organismic form.

If phenotypes are organized according to genetic accessibility, the resulting space…is formalized by an unfamiliar structure, known as a pre-topology. Patterns of phenotypic evolution - such as punctuation, irreversibility, modularity - result naturally from the properties of space. The classical framework, however, addresses these patterns by exclusively invoking natural selection on suitably imposed fitness landscapes. We propose to extend the explanatory level for phenotypic evolution from fitness considerations alone to include the topological structure of phenotype space. (241)

Staune, Jean. Darwinism Design and Purpose. www.metanexus.net/conference2005/papers.asp#S. The General Secretary of the Universite Interdisciplinare de Paris contends that a materialist neoDarwinism does not rule in Europe as it does in America (also England per Richard Dawkins). On the continent, evolutionary theory has moved beyond vicarious genes and selection to envision a constantly self-organized, fractally nested, emergence. By these properties, evolution reflects an internal, teleological logic and impetus. Rather than a contingency, this directional process will inevitably converge toward human-like beings. Prepared for the Metanexus Institute June 2005 conference on "Science and Religion: Global Perspectives," the paper is a good example of an imminent shift or revolution between the two options.

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