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

2. Microbial Colonies

Sher, Daniel, et al. Quantitative principles of microbial metabolism shared across scales.. . . Nature Microbiology., 2024. By this year, our Earthuman collective studies of life’s prokaryotic foundation now enables Boston University and MIT researchers to discern common, recurrent characteristics across its multifaceted film-like assemblies. See also Recent advances in deep learning and language models for studying the microbiome by Binghao Yan, et al. arXiv:2409.10579 for a concurrent survey.

A metabolism is the complex network of chemical reactions within every cell and organism, maintaining life and mediating ecosystems. Here we highlight principles that exhibit commonalities across scales, which could help achieve an integrated perspective on microbial life. The mechanisms underlying these flows, such as enzyme–substrate interactions, often are represented by equations like those that characterize cells and resources or predators and prey. We propose that these formal similarities reflect shared principles and discuss how their investigation may contribute to a common language for studying microbial metabolism across scales.

Shis, David, et al. Dynamics of Bacterial Gene Regulatory Networks. Annual Reviews of Biophysics. 47/447, 2018. Rice University bioscientists press on with revolutionary noticea of how ubiquitous interconnective topologies grace and serve all manner of organisms. A typical section is Mathematical and Computational Modeling of Biochemical Networks. Circa 2018, such articles can display an holistic sequence across natural scales, herein from protons to proteins, bacteria, colonies, microbiome organisms, and onto ecologies. A grand iterative progression is just now being completed by our worldwise collaborations. See also Gerstein 2018 in Annual Review of Biomedical Data Science for another example.

The ability of bacterial cells to adjust their gene expression program in response to environmental perturbation is often critical for their survival. Recent experimental advances allowing us to quantitatively record gene expression dynamics in single cells and in populations coupled with mathematical modeling enable mechanistic understanding on how these responses are shaped by the underlying regulatory networks. Here, we review how the combination of local and global factors affect dynamical responses of gene regulatory networks. Our goal is to discuss the general principles that allow extrapolation from a few model bacteria to less understood microbes. (Abstract)

Shishkov, Olga and Orit Peleg. Social Insects and Beyond: The Physics of Soft, Dense Invertebrate Aggregations. arXiv:2206.11129. Since circa 2010 when this “active matter” milieu came into being (see its Ecosmos section) University of Colorado biobehavioral researchers here achieve a thorough review to date. A novel advance is an ability to perceive these many dynamic animate, and inorganic occasions as exemplary manifestation of deep physical phenomena such as phase transitions. See also Bacterial Active Matter by Igor Aranson in Reports on Progress in Physics (85/7, 2022) for similar work. A number of current surmises become notably apparent. Once again, an independent mathematic domain seems to be in generative effect at each and every instance from mold blobs to urban areas. In regard, an emergent 21st century worldwise sapience in these 2020s can thus finally accomplish a whole scale vista of a universal genesis as it may reach it’s vital self-recognition.

Aggregation is a common behavior by which organisms arrange into cohesive groups. Whether airborne (honey bee clusters), ground dwellers (army ant bridges), or in water (sludge worm blobs), these collectives serve vital functions, Here we survey a variety of insects, arthropods, and worms as active soft matte . A group can be much larger than its members yet exist as a coherent entity. We discuss how novel aggregation physics can add to insights from ecological and physiological considerations as entities exchange information, energy, and matter as if a super-organism. With this work, we seek to scope out the inherent collective physics of dense living aggregations. (OS excerpt)

Analogies between the formation of aggregations of invertebrates to phase separation of non-living particles reveal unique properties of living aggregations. Wild-type C. elegans worms align through collisions with one another to aggregate into a nematic (oriented) phase. The process by which sludge worms water assemble into a blob is similar to polymer phase separation. These examples highlight the similarities and differences between living aggregations and non-living materials. (11)

Bacteria colonize diverse habitats and play a significant role in the oxygen, carbon, and nitrogen cycles. Suspensions of motile bacteria provide a good model of active matter as a broad class of non-equilibrium systems converting energy from the environment into motion. Concentrated suspensions, often termed active fluids, exhibit complex collective behavior such as turbulent-like swarming. The paper discusses microbial motilities from a deep physics viewpoint by way of experiments, main theories, and how visco-elasticity, liquid crystallinity, and confinement effect collective behaviors. (Aronson excerpt)

Sirota-Madi, Alexandra, et al. Genome Sequence of the Pattern Forming Paenibacillus vortex Bacterium Reveals Potential for Thriving in Complex Environments. BMC Genomics. 11/710, 2011. A premier international team of sixteen research microbiologists, led by Eshel Ben Jacob of Tel Aviv University, provide an extensive report on the colonial intricacy and real cognitive facility of this candidate microbe. As a Scientific American news item “The Smartest Bacteria on Earth” (June 2011) notes, these networked communities exhibit a remarkable degree of social intelligence by which to survive and prosper in varied environments. A collective swarm intelligence is persistently evident. With a long bibliography, the article stands as a decade long consummation of these studies of bacterial groupings. As such, they can be appreciated as a prime, microcosmic example of complex, dynamic self-organization, a cooperative pattern and process which is iteratively repeated across life’s nested emergence.

Accomplishing such intricate cooperative ventures requires sophisticated cell-cell communication. Communicating with each other, bacteria exchange information regarding population size, a myriad of individual environmental measurements at different locations, their internal states and their phenotypic and epigenetic adjustments. The bacteria collectively sense the environment and execute distributed information processing to glean and assess relevant information. Next, the bacteria respond accordingly, by reshaping the colony while redistributing tasks and cell differentiations, and turning on defense and offense mechanisms, thus achieving better adaptability to heterogeneous environments. Such collective, decentralized, adaptive decision making is a form of swarm intelligence, a term originally derived from cybernetics but applicable to some aspects of colonial organisms including ants, birds, humans and bacteria. (4)

The P. vortex species is marked by its complex spatial organization of the colony, with the bacteria forming different patterns to better cope with the environment. Pattern-formation and self-organization in microbial systems is an intriguing phenomenon that might also provide insights into the evolutionary development of the concerted action of cells in higher organisms. Therefore, sequencing of the P. vortex genome paves the way to understanding of regulatory processes involved in cell-cell communication and colonial patterning and more generally, to understanding of cooperative bacterial response to changing environmental conditions. (11-12)

Stanley-Wall, Nicola, et al. A Snapshot of the Extraordinary World of Social Microbiology. Journal of Molecular Biology. 427/23, 2015. An introduction to a special issue on Cooperative Behavior in Microbial Communities. Typical papers are How Myxobacteria Cooperate, The Evolution of Aggregative Multicellularity and Cell-Cell Communication in the Dictyostelia, and Bacterial Networks in Cells and Communities, see Abstract below.

Research on the bacterial regulatory networks is currently experiencing a true revival, driven by advances in methodology and by emergence of novel concepts. The biannual conference Bacterial Networks (BacNet15) held in May 2015, in Sant Feliu de Guíxols, Spain, covered progress in the studies of regulatory networks that control bacterial physiology, cell biology, stress responses, metabolism, collective behavior and evolution. It demonstrated how interdisciplinary approaches that combine molecular biology and biochemistry with the latest microscopy developments, whole cell (-omics) approaches and mathematical modeling can help understand design principles relevant in microbiology. It further showed how current biotechnology and medical microbiology could profit from our knowledge of and ability to engineer regulatory networks of bacteria. (Abstract)

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).

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