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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

2. Microbial Colonies

Leander, Brian. A Hierarchical View of Convergent Evolution in Microbial Eukaryotes. Journal of Eukaryotic Microbiology. 55/2, 2008. The University of British Columbia botanist via his “Leander Lab of Marine Serendipity and Spectaculars” (Google) makes the important contribution that even in bacterial realms, a robust convergences are evident. See also Jules Lukes, Leander and Patrick Keeling’s “Cascades of Convergent Evolution: The Corresponding Evolutionary Histories of Euglenozoans and dinoflagellates” in Proceedings of the National Academy of Sciences (106/Suppl. 1, 2009)

Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence—"parallel,” "proximate," and "ultimate" — that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. (59)

The pervasiveness and adaptive significance of convergent evolution at the microbial scale is only just beginning to be explored and characterized. (67) Accordingly, a more complete understanding of the hierarchical structure of convergent evolution and the overall history of life will require further advancement in the following research areas: (1) describing the overall diversity of microbial life, (2) reconstructing the Tree of Eukaryotes by establishing robust internal phylogenies for major eukaryotic groups, (3) experimentally demonstrating the selective forces operating at microbial scales within functional and ecological contexts, and (4) characterizing the patterns and processes associated with the development of complex subcellular systems in eukaryotic cells. (67)

Li, Si and Michael Purugganan. The Cooperative Amoeba. Trends in Genetics. 27/2, 2011. NYU Center for Genomics and Systems Biology researchers contend that while propensities for socially interactive groupings are pervasive among Metazoan species, a genetic basis for such constant palliative altruism has eluded. Since bacteria are in fact found to epitomize this behavior, they make a good candidate for its study. And indeed Dictyostelium colonies are happy to contribute the molecular bases and mechanisms underlying their salutary sharing.

Lowery, Colin, et al. Interspecies and Interkingdom Communication Mediated by Bacterial Quorum Sensing. Chemical Society Reviews. 37/1337, 2008. Scripps Research Institute biochemists write a tutorial article on the pervasiveness and survival value of uni- and multi- cellular groups which strive for an agreed consensus, e.g., on nutrient availability and location, or predator avoidance.

In total, because of the many relationships that can be mediated, QS may represent a more global language of communication that spans across every kingdom of life and human interpretation of this language will impart a deeper knowledge of prokaryotic lifestyles and provide the opportunity for an appropriate response. (1345)

Macktoobian, Matin. Self-Organizing Nest Migration Dynamics Synthesis for Ant Colony Systems. arXiv:2210.03975. A University of Alberta, Canada computer scientist describes how even social insect movements like this can be found to express and exemplify nature’s universal mathematic generative source program by way of common, multiplex, entity/edge network topologies.

In this study, we synthesize a novel dynamical approach for ant colonies enabling them to migrate to new nest sites in a self-organizing fashion. In other words, we realize ant colony migration as a self-organizing phenotype-level collective behavior. The proposed theoretic and empirical mechanism effectively shows that an ant colony can migrate to the vicinity of a new nest site in a self-organizing manner without any external supervision.

Macktoobian, Matin. Self-Organizing Nest Migration Dynamics Synthesis for Ant Colony Systems. arXiv:2210.03975. A University of Alberta, Canada computer scientist describes how even social insect movements like this can be found to express and exemplify nature’s universal mathematic generative source program by way of common, multiplex, entity/edge network topologies. Once again, as everywhere, here is an archetypal instance.

In this study, we synthesize a novel dynamical approach for ant colonies enabling them to migrate to new nest sites in a self-organizing fashion. In other words, we realize ant colony migration as a self-organizing phenotype-level collective behavior. The proposed theoretic and empirical mechanism effectively shows that an ant colony can migrate to the vicinity of a new nest site in a self-organizing manner without any external supervision.

Maree, Athanasius and Paulien Hogeweg. How Amoeboids Self-organize into a Fruiting Body. Proceedings of the National Academy of Sciences. 98/3879, 2001. A paper which has become seen as one of the first achievements of a full mathematical, computational analysis of the emergence of a complex organic assembly.

Marijuan, Pedro, et al. On Prokaryotic Intelligence. BioSystems. 99/2, 2010. A team from the Grupo de Bioinformación y Biología de Sistemas, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain advocates a deep confluence between “the cellular way of life” and an innate creative self-organization. Drawing upon various theories from earlier autopoiesis and symbiogenesis to complex adaptive systems and biosemiotics, such constant, vital environment-sensing activity from genomes to ecosystems ought to be appreciated most of all as engaged in information-gaining, neural network cognition. See also Judith Armitage, et al.

Marlow, Jeffrey and Rogier Braakman. Team Players. Scientific American. November, 2018. Harvard and MIT biologists present a popular, graphic article about how prevalent and important reciprocal cooperation is beyond a prior emphasis on competition among isolate microbes.

McFall-Nagl, Margaret, et al. Animals in a Bacterial World, a New Imperative for the Life Sciences. Proceedings of the National Academy of Sciences. 110/3229, 2013. Some 26 biological and medical scientists at major institutions in the USA and Europe from Hawaii to Croatia, including Andrew Knoll, Scott Gilbert, and Angela Douglas, propose a novel vista of life’s temporal and spatial evolution as if a singular phylogenesis, suffused and informed by a proactive microbial milieu. In regard, features such as Interdomain Communication via quorum sensing, Nested Ecosystems, and pervasive Symbiosis would gain more inclusion and import.

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world. (Abstract)

For much of her professional career, Lynn Margulis (1938-2011), a controversial visionary in biology, predicted that we would come to recognize the impact of the microbial world on the form and function of the entire biosphere, from its molecular structure to its ecosystems. The weight of evidence supporting this view has finally reached a tipping point. The examples come from animal-bacterial interactions, as described here, and also from relationships between and among viruses, Archaea, protists, plants, and fungi. These new data are demanding a reexamination of the very concepts of what constitutes a genome, a population, an environment, and an organism. Similarly, features once considered exceptional such as symbiosis, are now recognized as likely the rule, and novel models for research are emerging across biology. As a consequence, the New Synthesis of the 1930s and beyond must be reconsidered in terms of three areas in which it has proven weakest: symbiosis, development, and microbiology. (3234)

Menon, Shakti, et al. Information Integration and Collective Motility in Phototactic Cyanobacteria. PLoS Computational Biology. April, 2020. Institute of Mathematical Sciences, Tamil Nadu, India researchers describe how bacterial groupings can be seen to exhibit and be modeled by active matter phenomena. In regard, quorum sensing is interpreted to proceed by way of integrating relevant information. Altogether another manifestation of universal principles and formations.

Microbial colonies in the wild often consist of large groups of heterogeneous cells that coordinate and integrate information across multiple spatio-temporal scales. We describe a computational model for the collective behavior of phototaxis in the cyanobacterium Synechocystis that move in response to light. The results suggest that tracking individual cyanobacteria may provide a way to determine their mode of information integration. Our model allows us to address the emergent nature of this class of collective bacterial motion, linking individual cell response to the large scale dynamics of the colony. (Summary)

Molina, Nacho and Erik van Nimwegen. Scaling Laws in Functional Genome Content Across Prokaryotic Clades and Lifestyles. Trends in Genetics. 25/6, 2009. University of Basel information biologists report finding constant, nested patterns throughout all manner of microbial, and microcellular life forms, quite suggestive of a universal generative source. (See also Beslin, G., et al “Scaling Laws in Bacterial Genomes” in BioSystems (102/1, 2010).

For high-level functional categories that are represented in almost all prokaryotic genomes, the numbers of genes in these categories scale as power-laws in the total number of genes. We present a comprehensive analysis of the variation in these scaling laws across prokaryotic clades and lifestyles. For the large majority of functional categories, including transcription regulators, the inferred scaling laws are statistically indistinguishable across clades and lifestyles, supporting the simple hypothesis that these scaling laws are universally shared by all prokaryotes. (243)

These results support the idea that the origins of the scaling laws must lie in fundamental physical and/or evolutionary principles. At this point it is still unclear whether the scaling laws originate mainly from physico-chemical constraints that apply to all prokaryotes or whether they are an inherent feature of the evolutionary dynamics. (247)

Nayfach, Stephen, et al. A Genomic Catalog of Earth’s Microbiomes. Nature Biotechnology. 39/4, 2021. A 35 member international team with affiliations such as the Integrated Microbial Genomes Data Consortium and Genomes from Earth’s Microbiomes report current progress as our EarthWise sapience proceeds to retro-quantify all the living systems that brought our presence to be here.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering Earth’s continents and oceans, including human and animal hosts, and natural agricultural soils, so to capture microbial, metabolic and functional domains This comprehensive catalog includes 52,515 metagenomes for 12,556 species-level taxonomic units spanning 135 phyla. This resource highlights the value of genome-centric approaches for sequencing microorganisms that affect ecosystem processes. (Abstract excerpt)

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