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

Santini, Francesco and Lodovico Galleni. Stability and Instability in Ecological Systems: Gaia Theory and Evolutionary Theory. Schneider, Stephen, et al, eds. Scientists Debate Gaia. Cambridge: MIT Press, 2004. The waning Genocentric emphasis is being replaced by an Organocentric synthesis that joins prior self-organization with subsequent selection. A further Biospherocentric realm is then proposed for the neglected interaction of organisms with their local and global environment.

….the inherent problems in the neo-Darwinian view of evolution, such as a lack of attention to biological hierarchies, to the importance of adaptive mutational systems and the epigenetic inheritance systems, to the developmental constraints caused by morphogenetic fields, and to phenomena of self-organization, and the emergent properties of complex systems. (354) Nowadays most workers have been forced to recognize that neo-Darwinian orthodoxy is a very partial explanation of the evolutionary processes, and that a more pluralistic and holistic theoretical framework is needed. (354)

Sapp, Jan. Genesis: The Evolution of Biology. Oxford: Oxford University Press, 2003. A historian of science achieves a detailed narrative of the 19th and 20th century growth of biological and evolutionary knowledge in its reductive phase. At the start of the 21st century, the discovery of symbiotic relations occurring in the life sciences such as molecular genetics, cytology and so on, along with new appreciations of the ubiquitous and constructive prevalence of cooperation, are helping these fields reconvene into a single coherent scenario.

Sarkar, Sahotra. Woese on the Received View of Evolution. RNA Biology. 11/3, 2014. We enter this paper for its content, and to record this special issue about Carl Woese (1928-2012), the physicist-biologist at the University of Illinois whose work laid out an integral approach to rightly view life’s innate natural emergence. Search for papers such as A New Biology for a New Century (2004) and Life is Physics (2011) with Nigel Goldenfeld. Here the UT Austin philosopher of biology reviews his deep concerns with the modern 1950s synthesis as inappropriate and inadequate. See also Constraint and Opportunity in Genome Innovation by James Shapiro, Carl Woese’s Vision of Cellular Evolution and the Domains of Life by Eugene Koonin, and Looking in the right Direction: Carl Woese and Evolutionary Biology by Nigel Goldenfeld. The 2018 paper Horizontal Transfer of Code Fragments between Protocells can Explain the Origins of the Genetic Code without Vertical Descent by Tom Froese, et al (search) in Nature Scientific Reports (8/3532) cites is an affirmation of Woese’s vision.

As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century: (1) according to Woese’s scenario of communal evolution during life’s earliest phase well-defined biological individuals did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. (Abstract excerpts)

Sato, Naoki. “Life-bearing Molecules” vs. “Life-embodying Systems:” Two Constrasting Views on What-is-Life from Molecular Biology to Post-genome Cell- and Organism-level Biology. Biosystems. 167/24, 2018. The University of Tokyo life scientist continues his efforts to express a full overview of organisms and evolution by here emphasizing these prime molecular and systems approaches. As the Abstract notes, biological studies have a long history of alternative fine focus or whole field perspectives. In the later 2010s as this vista opens to us, a complementary synthesis and resolve thus becomes evident. As a result, we are again invited to imagine and perceive a universal genesis via an innate creative force or impetus which instantiates and exemplifies in these bigender iconic modes. An earlier paper by Sato is Scientific Elan Vital: Entropy Deficit or Inhomogeneity as a Unified Concept of Driving Forces of Life in Hierarchical Biosphere Driven by Photosynthesis in Entropy (14/233, 2012)

“What is life?" is an ultimate biological quest for the principle that makes organisms alive. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. Another, prevalent idea emphasizes that life resides in the whole system of an organism, not in some particular molecules. The behavior of a complex system may be considered to embody the essence of life. The thermodynamic view of life system in the early 20th century was remodeled as physics of complex systems and systems biology. The two views contrast with each other, but they are no longer heritage of the historical dualism in biology, such as mechanism/materialism versus vitalism, or reductionism versus holism. In reality, molecules function in a context of systems, whereas systems presuppose functional molecules. Cell- or organism-level biology is destined to the dialectic of molecules and systems, but this antagonism can be resolved by dynamic thinking involving biological evolution. (Abstract edited excerpts)

Sayama, Hiroki, et al. Spontaneous Pattern Formation and Genetic Diversity in Habitats with Irregular Geographical Features. Conservation Biology. 17/3, 2003. How nonlinear dynamics complement selective effects.

We emphasize that the self-organization of dynamic patterns through multiscale interactions is a characteristic property of diverse complex systems, including spatially distributed living systems, and that recognition of this property can lead to deeper insights into community organization and evolution. (899)

Schaerli, Yolanda, et al. Synthetic Circuits Reveal how Mechanisms of Gene Regulatory Networks Constrain Evolution. Molecular Systems Biology. 14/9, 2018. As the 21st century complexity revolution advances, biologists with postings in Switzerland, Spain and the UK including Andreas Wagner achieve novel insights into the naturally innate occasion of life’s oriented development. As the quotes allude, and other late entries agree, something more than particulate nucleotides alone must be going on. Discrete genes are actually nodal entities in pervasive network linkages, which altogether carries procreative information. While random mutations occur, equally present multiplex topologies, which spring from an independent source, guide and channel toward preferred forms and pathways. This expansion in biological thinking to witness both genetic molecules and active connections as they compose whole genomes is the essence of a genesis synthesis. See also Inference of Developmental Gene Regulatory Networks beyond Classical Systems by Selene Fernandez-Valverde, et al (search) for another appreciation of GRN complements.

Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms are still poorly understood. Here we study evolutionary biases in two synthetic gene regulatory circuits expressed in Escherichia coli that produce a gene expression stripe—a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. (Abstract)

A mathematical model describing the regulatory mechanisms of the two networks allowed us to understand the differences between accessible novel phenotypes for the two networks. The model predictions are also supported by DNA sequencing data. We thus provide for the first time empirical evidence that GRNs with different regulatory mechanisms can cause different constrained variation, (10)

Since the 19th century, Darwinian evolutionary biology has focused on natural selection and its power to shape populations and species. Natural selection, however, requires phenotypic variation, and the molecular mechanisms by which DNA mutations produce novel phenotypes have only become understood in recent years. While orthodox evolutionary theory assumed, often tacitly, that DNA mutations may produce any kind of variation, the discovery of constrained phenotypic variation challenged this view. As we show here, constrained variation in simple yet important spatial gene expression patterns can be explained by the simple fact that genes are embedded in regulatory networks. What is more, the regulatory mechanisms of these GRNs can help explain why specific gene expression patterns originate preferentially. Given the pervasive nonlinearity of gene regulatory networks, we surmise that constraints like those we observe are inherent in biological pattern‐forming systems. (12)

Schlosser, Gerhard. The Role of Modules in Development and Evolution. Schlosser, Gerhard and Gunter Wagner, eds. Modularity in Development and Evolution. Chicago: University of Chicago Press, 2003. A lengthy overview and summary article that observes how common modular properties repeat everywhere in gene regulatory, cell signaling, position, and type, organ formation, and systemic networks. These “units of interacting elements” are then seen to support a new synthesis of embryology and phylogeny.

Modules of evolution are units of integrated and context-insensitive evolutionary change. (542) I have suggested here that developmental modularity promotes the evolution of complex systems in a self-organizing process, because it facilitates the redeployment and recombination of modules, thereby providing new opportunities for evolutionary change. (559)

Schlosser, Gerhard and Gunter Wagner, eds. Modularity in Development and Evolution. Chicago: University of Chicago Press, 2003. Over the past decade, within many areas of evolutionary investigation from genes to societies a universal tendency to form structural and functional modular components and processes has been recognized. This volume collects for the first time these new findings about modularity in four parts: its molecular and developmental basis, how to identify modules, their evolutionary origin and dynamics, and individuals as modules in higher-level units. The book tacitly assumes complexity theory and a nested scale of entities and networks where the same features recur at each stage. A balance of “autonomy or parcellation and integration” occurs as diverse, symbiotic modules join in “hierarchical clusters” such as gene regulatory systems, central nervous systems or as organs in organisms. The upshot is that “natural selection cannot do it alone,” something else and more is going on.

Modularity pervades every level of biological organization. From proteins to populations, larger biological units are built of smaller, quasi-autonomous parts. (Craig Nelson 17) The modular architecture of metazoan body plans is generated by a similarly modular genetic regulatory hierarchy. (CN 30)

Schoenemann, Thomas. Evolution of Brain and Language. Language Learning. 59/Supplement 1, 2009. Since our cerebral development and cognitive process is increasingly being appreciated as a complex network system, the Indiana University anthropologist finds a natural congruence with how speech and dialogue likewise evolved by the same nonlinear dynamics.

The coevolution of language and brain can be understood as the result of a complex adaptive system. Complex adaptive systems are characterized by interacting sets of agents (which can be individuals, neurons, etc.), where each agent behaves in an individually adaptive way to local conditions, often following very simple rules. The sum total of these interactions nevertheless leads to various kinds of emergent, systemwide orders. Biological evolution is a prime example of a complex adaptive system: Individuals within a species (a “system”) act as best they can in their environment to survive, leading through differential reproduction ultimately to genetic changes that increase the overall fitness of the species. In fact, “evolution” can be understood as the name we give to the emergent results of complex adaptive systems over time. (163)

Schultz, Emily. Resolving the Anti-Antievolutionism Dilemma: A Brief for Relational Evolutionary Thinking in Anthropology. American Anthropologist. 111/2, 2009. The academic humanities often bend themselves out of shape over which school, method, or worldview is approved, and to be held to. A St. Cloud State University, Minnesota, anthropologist tries to sort through her field’s course toward an evolutionary basis, but which at the same time is troubled by its ultra-Darwinist strictures. Agustin Fuentes (search) and colleagues are on a similar mission. A resolve is here offered via the 21st century synthesis shift to leaven random selection with nature’s self-organizing integrations, as broached in the quote. Another good exercise beyond the box to try to include novel “structural, functional, and process” propensities quite going on across life’s nested hierarchy.

Evolutionary theory, however, comes in many forms. Relational evolutionary approaches such as Developmental Systems Theory, niche construction, and autopoiesis–natural drift augment mainstream evolutionary thinking in ways that should prove attractive to many anthropologists who wish to affirm evolution but are dissatisfied with current “neo-Darwinian” hegemony. Relational evolutionary thinking moves evolutionary discussion away from reductionism and sterile nature–nurture debates and promises to enable fresh approaches to a range of problems across the subfields of anthropology. (Abstract, 224)

Schuster, Peter. Increase in Complexity and Information through Molecular Evolution. Entropy. Online November, 2016. The emeritus University of Wien, Austria theorist (search) is also co-editor of the journal Complexity. His latest 37 page, mathematical essay is still another indication and expression of an imminent 21st century synthesis. As the quotes say, the presence of cooperative behaviors, symbiotic assemblies, and a major transitions scale are now well accepted. A competition-cooperation-mutation model is broached which effects transformative rise by way of informative genomic complexities, which suggests this generic reciprocity at work. But as due to one man, akin to Kevin Laland’s project (search) and others, it remains a partial advance. An admission of a greater genesis with its own source, gestation, and human destiny yet eludes. A good sign is that the “progress” word is allowed in the text.

Biological evolution progresses by essentially three different mechanisms: (I) optimization of properties through natural selection in a population of competitors; (II) development of new capabilities through cooperation of competitors caused by catalyzed reproduction; and (III) variation of genetic information through mutation or recombination. Simplified evolutionary processes combine two out of the three mechanisms: Darwinian evolution combines competition (I) and variation (III) and is represented by the quasispecies model, major transitions involve cooperation (II) of competitors (I), and the third combination, cooperation (II) and variation (III) provides new insights in the role of mutations in evolution.

A minimal kinetic model based on simple molecular mechanisms for reproduction, catalyzed reproduction and mutation is introduced, cast into ordinary differential equations (ODEs), and analyzed mathematically in form of its implementation in a flow reactor. Stochastic aspects are investigated through computer simulation of trajectories of the corresponding chemical master equations. The competition-cooperation model, mechanisms (I) and (II), gives rise to selection at low levels of resources and leads to symbiontic cooperation in case the material required is abundant. Accordingly, it provides a kind of minimal system that can undergo a (major) transition. (Abstract excerpts)

Symbiosis is indeed one straightforward way among others to increase substantially the amount of genetic information: The genomes of two or more organisms become available for the superorganism and the same is true for semantic information. Eukaryotic cells formed by endosymbiosis are presumably the best understood examples: The nucleus and the organelles share their genetic information but processing of information reveals hierarchical control. (30)

Schwartzman, David. Biological Evolution is Coarsely Deterministic. Journal of Big History. 4/2, 2020. This paper was presented by the veteran Howard University biologist at the Life in the Universe: Big History, SETI and the Future conference in Milan in July 2019. In essence, it continues his insightful views that “playing the tape over again” would necessarily lead to life’s development into human-like beings and cognitive capabilities because biochemical and thermal properties of the geobiosphere would again impel and channel it that way.

Starting with the origin of life, I argue that the general pattern of the tightly coupled evolution of biota and climate on Earth has been the very probable outcome from a relatively small number of possible histories at the macroscale, given the same initial conditions. Thus, the evolution of the biosphere self-selects a pattern of biotic evolution that is coarsely deterministic, with critical constraints likely including surface temperature as well as oxygen and carbon dioxide levels in the atmosphere. Environmental physics and chemistry drive the major events in biotic evolution, including photosynthesis and oxygenic photosynthesis, the emergence of new cell types (eucaryotes) from the merging of complementary metabolisms, multicellularity and even encephalization. (Abstract)

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