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

2. Microbial Colonies

Strassmann, Joan and David Queller. Altruism among Amoebas. Natural History. September, 2007. These single cell microbes actually prosper in communities that form by a vicarious interplay of cooperation and cheating. The genetic basis of the ‘kin selection’ activity involved is just becoming discernible. The authors are Rice University biologists whose copious work in Social Evolution can be accessed at: www.ruf.rice.edu/~evolve/joan_david.html.

Tero, Atsushi, et al. Rules for Biologically Inspired Adaptive Network Design. Science. 327/439, 2010. Along with a news note “Amoeba-Inspired Network Design” in the same issue, how such microbial colonies can be seen as exemplars of self-organizing systems, which are being found to recur throughout nature’s ascendant nest, especially for viable human societies. All of which it is said seems to spring from an independent, universal mathematical source.

Wakeford, Tom. Liaisons of Life. New York: Wiley, 2001. A biologist and science writer lauds the new appreciation of symbiotic associations in microbial realms which are leavening the Darwinian emphasis on competition and conflict.

Wang, Weijia, et al. The Impact of Individual Perceptual and Cognitive Factors on Collective States in a Fish School Model.. PLOS Computational Biology. March, 2022. University of Toulouse and Beijing Normal University researchers including Guy Theraulaz quantify how interactive behaviors become altogether coordinated for both member and group benefit. See also Global Dynamics of Microbial Communities Emerge from Local Interactions Rules by Simon Van Vliet, et al (Canada, Switzerland) in the same issue. We can once again note that in these papers, cases, and across the site, a definitive pattern and process can be seen in independent, recurrent effect. Phenotype-like communal entities over many scales arise from and are guided by an independent, universal, genotypic source code. But into 2022, these diverse entries in an open Public Library of Science are by researchers aware of work in their field, but still sans any sense of a novel Earthuman faculty learning on her/his own, nor of any phenomenal ecosmic universe reality they manifestly arise from.

Waters, Christopher and Bonnie Bassler. Quorum Sensing: Cell-to-Cell Communication in Bacteria. Annual Review of Cell and Developmental Biology. 21/319, 2005. Prokaryotic microbes are seen to act as multi-cellular organisms as they communicate via chemical signal molecules. In so doing, hormone-like agents are constantly produced, released, and detected in response to changing environments, which then result in an overall favorable behavior. Compare with the same phenomena found in honey bee swarms as reported by Seeley, et al.

West, Stuart, at al. The Social Lives of Microbes. Annual Review of Ecology, Evolution, and Systematics. 38/53, 2007. From the Universities of Edinburgh, Nottingham, and Oxford, another report on the epochal shift from discrete amoeba long taught in schools to an appreciation of their true, viable communal essence.

Our understanding of the social lives of microbes has been revolutionized over the past 20 years. It used to be assumed that bacteria and other microorganisms lived relatively independent unicellular lives, without the cooperative behaviors that have provoked so much interest in mammals, birds, and insects. However, a rapidly expanding body of research has completely overturned this idea, showing that microbes indulge in a variety of social behaviors involving complex systems of cooperation, communication, and synchronization.

West, Stuart, et al. Social Evolution Theory for Microorganisms. Nature Reviews Microbiology. 4/8, 2007. A research program is described to see if propensities to advantageously cooperate which pervade groups of organisms can also be recognized in the microbial behaviors of dispersal, nutrient acquisition, biofilm formation, and quorum sensing. The tacit assumption is that they similarly do. In this regard see a follow up report: Diggle, S., et al. Cooperation and Conflict in Quorum-Sensing Bacterial Populations (Nature. 450/411, 2007), and also Frank, Steven. All of Life is Social (Current Biology. 17/16, 2007).

Witzany, Gunther, ed. Biocommunication in Soil Microorganisms. New York: Springer, 2011. After 2009 and 2010 overviews noted in Emergent Genetic Information, in this edited volume the Austrian biophilosopher and many colleagues consider how chemical semiotic sensing across intracellular, intercellular, and trans-kingdom stages between microbes aids their viable assemblies. By way of Springer’s advanced website, on the main book page one can click on a Read Online button to access the table of contents and abstracts for each chapter.

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context-dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular biocommunication between soil microorganisms. This includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (Synopsis)

Woese, Carl. A New Biology for a New Century. Microbiology and Molecular Biology Reviews. 68/2, 2004. The bacterial, archaeal and eukaryotic kingdoms began in a “pre-Darwinian,” RNA world of horizontal gene transfer within a continuum of modular, semiautonomous, “subcellular” groupings.

The community of primitive evolving biological entities as a whole as well as the surrounding field of cosmopolitan genes participates in a collective reticulate (network) evolution. (182)

Wong, Gerard, et al. Roadmap Concepts in the Physical Biology of Bacterial Biofilms. Physical Biology. 18/051501, 2021. Some 40 micorbiologists from every continent including Bonnie Bassler post considerations of 18 aspects from The Role of bacterial flagella in surface sensing and Gliding mobility of social bacterium to Membrane vesicles and bacterial signaling and Self-organized collective motion in bacterial communities. Each segment comes with its own expert and to do summary.

Bacterial biofilms are communities that exist as aggregates which can adhere to surfaces or be free-standing. This complex, social organization pervades the physiology and behaviors of microbes. Such biofilms are more than the sum of their parts: single-cells have a complex relation to collective community behavior, in a manner perhaps cognate to atomic physics and condensed matter physics. In this roadmap, we highlight the work of scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions exemplify how well physics and biology can be combined to achieve a new synthesis. (Abstract excerpt)

Xavier, Joao and Kevin Foster. Cooperation and Conflict in Microbial Biofilms. Proceedings of the National Academy of Sciences. 104/876, 2006. From the Center for Systems Biology at Harvard University, that bacterial colonies are not benignly communal but are found to occur and succeed by competitions such as between the quality of polymer production. By this view, microbes are similar to animal groupings.

Yusufaly, Tahir and James Boedicker. Mapping Quorum Sensing onto Neural Networks to Understand Collective Decision Making in Heterogeneous Microbial Communities. arXiv:1703.01353. University of Southern California biophysicists achieve further quantifications of how bacteria flourish by way of chemical communications. Of note is a use of neural net dynamics to gain better insights, which is another avail of this generic natural system. See also Spatial Dispersal of Bacterial Colonies induces a dynamical transition for Local to Global Quorum Sensing by the authors in Physical Review E (94/062410, 2016).

Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. Understanding these interactions is a prerequisite for deciphering the consequences of crosstalk in real ecosystems, where multiple AIs are regularly present in the same environment. As a step towards this goal, we map crosstalk in a heterogeneous community of variant QS strains onto an artificial neural network model. This formulation allows us to systematically analyze how crosstalk regulates the community's capacity for flexible decision making. (Abstract excerpt)

In summary, we have demonstrated a novel approach to compressing chemical details into simplified, generalizable neural network models, in order to study communication in complex real-world microbial ecosystems. The unexpected relationship between intercellular signaling dynamics and neural networks promises to be a valuable new theoretical tool for future studies of communication in heterogeneous microbial communities, with implications for both the basic science of microbial ecology and evolution, and also for synthetic biology efforts to engineer novel emergent behaviors in artificial multicellular consortia. (7)

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