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

2. Microbial Colonies

Ben-Jacob, Eshel. Bacterial Self-organization. Philosophical Transactions of the Royal Society of London A. 361/1283, 2003. Ben-Jacob further articulates how the busy microbes provide an exemplary expression of complex emergence at work. What is notable is that at this elementary phase, both for evolution and living systems, the incentive to organize into larger groups actually enhances the welfare of its members, a good example early on of creative union. In an Epilogue he goes on to suggest that cognitive processes are a similar case of self-generated, cooperative freedom.

The ‘smart’ bacteria have ‘realized’ (over evolution) that increasing informative communication between individuals results in increased freedom and cooperation of the individuals. (1285)

Ben-Jacob, Eshel. Bacterial Wisdom, Godel’s Theorem and Creative Genomic Webs. Physica A. 248/57, 1998. Tel Aviv University biologist Ben-Jacob is a pioneer in applying complexity principles to the microbial realm. The “complex colonial patterning as an example of adaptive self-organization” is seen to possess self-reference, information, and a modicum of awareness. As an assembly of microbes interact with “mutual dependence” through a common “language,” they give rise to a distinct communal “self.”

My proposed solution to the above paradox (Darwinism vs. Vitalism) leads to a new evolutionary picture where progress is not the result of successful accumulation of mistakes in replication of the genetic code, but is rather the outcome of designed creative processes. (58)

Ben-Jacob, Eshel. Learning from Bacteria about Natural Information Processing. Annals of the New York Academy of Science. Vol. 1178, 2009. In the edition Natural Genetic Engineering and Natural Genome Editing, an exemplary paper from the Tel Aviv University biophysicist upon how well microbial colonies imbue and epitomize complex, self-organizing, modular networks. By these reciprocities they achieve a modicum of social intelligence that displays a distributed, neural-like cognition and collective decision making, indeed a colonial “super-brain.”

Ben-Jacob, Eshel, et al. Bacterial Survival Strategies Suggest Rethinking Cancer Cooperativity. Trends in Microbiology. 20/9, 2012. Biophysicists Ben-Jacob, Tel-Aviv University, Herbert Levine, Rice University, and Donald Coffey, Johns Hopkins School of Medicine, each a noted authority, make a strong case for affinities between microbial collectives and cancerous cells, based on recent findings. As this section documents, bacterial communities are often seen as iconic self-organizing complex adaptive systems, with an especial knack for intelligent responses. Since tumors are likewise perceived as “smart social cells,” they might be treatable in similar ways to the design of drugs for bacterial and viral infections. A companion post is “How Brainless Slime Molds Redefine Intelligence” by Ferris Jabr (2012 herein)

Despite decades of a much improved understanding of cancer biology, we are still baffled by questions regarding the deadliest traits of malignancy: metastatic colonization, dormancy and relapse, and the rapid evolution of multiple drug and immune resistance. New ideas are needed to resolve these critical issues. Relying on finding and demonstrating parallels between collective behavior capabilities of cancer cells and that of bacteria, we suggest communal behaviors of bacteria as a valuable model system for new perspectives and research directions. Understanding the ways in which bacteria thrive in competitive habitats and their cooperative strategies for surviving extreme stress can shed light on cooperativity in tumorigenesis and portray tumors as societies of smart communicating cells. (Abstract)

Ben-Jacob, Eshel, et al. Cooperative Self-Organization of Microorganisms. Advances in Physics. 49/4, 2000. A book-length article on how bacteria occur not as isolated particles but survive and flourish in spontaneous communities formed by communication networks. These researchers believe that such dynamic, fractal-like assemblies imply common, underlying principles.

Only during the last decade has a satisfying answer started to emerge. Exciting new developments in the understanding of pattern determination in condensed matter systems offer the promise that a unified theoretical framework is possible. (397)

Boedicker, James and Kenneth Nealson. Microbial Communication via Quorum Sensing. IEEE Transactions on Molecular, Biological and Multi-Scale Communications. 1/4, 2015. A University of Southern California physicist and a biologist finesse appreciations of how bacteria survive and flourish in quite democratic associations.

Chemical communication enables microbes to probe local cell density and coordinate collective behavior through a process known as quorum sensing (QS). In QS, microbes produce and detect small molecule signals, and the expression levels of many genes change in response to these signals. QS signals, known as autoinducers, potentially accumulate around the cell and relay information about environmental conditions, transport dynamics, and the number and identity of microbial neighbors. In this paper, we focus on the history of QS, the variety of molecular networks used by microbes to achieve QS, modeling approaches, and applications of QS control. (Abstract)

Bown, J. L., et al. Evidence for Emergent Behavior in the Community-Scale Dynamics of a Fungal Microcosm. Proceedings of the Royal Society of London B. 266/1947, 1999. How cooperative agents are at work everywhere give rise to higher-level organizations.

Brown, Samuel and Rufus Johnstone. Cooperation in the Dark: Signalling and Collective Action in Quorum-Sensing Bacteria. Proceedings of the Royal Society of London B. 268/961, 2001. A pervasive dialogue amongst microbes goes on in order to insure community survival in changing environments.

Bublitz, DeAnna, et al. Peptidoglycan Production by an Insect-Bacterial Mosaic. Cell. 179/1, 2019. We cite this entry by eleven Caltech, University of Montana, and University of Sheffield, UK scientists including John McCutcheon for its recognition of how much endosymbiotic structures and processes are in primary effect. A notice Cell Bacteria Mergers Offer Clues to How Organelles Evolved by Vivane Callier in Quanta Magazine (October 3, 2019) cites an import of this work.

Canzian, Luca, et al. A Dynamic Network Formation Model for Understanding Bacterial Self-Organization into Micro-Colonies. IEEE Transactions on Molecular, Biological and Multi-Scale Communications. 1/1, 2015. UCLA bioengineers explain how microbes persistently form vital, adaptable communal groupings in varying environments. The general intent is to employ such understandings to achieve a “synthetic microbiology” for everyone’s betterment.

We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. Micro-colonies represent the first social step towards the formation of structured multicellular communities known as bacterial biofilms, which protect the bacteria against antimicrobials. In our model, bacteria can form links in the form of intercellular adhesins (such as polysaccharides) to collaborate in the production of resources that are fundamental to protect them against antimicrobials. We rigorously characterize some of the key properties of the network evolution depending on the parameters of the system. In particular, we derive the parameters under which it is guaranteed that all bacteria will join micro- colonies and the parameters under which it is guaranteed that some bacteria will not join micro-colonies. Importantly, our study does not only characterize the properties of networks emerging in equilibrium, but it also provides important insights on how the network dynamically evolves and on how the formation history impacts the emerging networks in equilibrium. (Abstract)

Cavalier-Smith, Thomas, et al. Introduction: How and When did Microbes Change the World? Philosophical Transactions of the Royal Society B. 361/843, 2006. This volume contains many papers from a Discussion Meeting on Major Steps in Cell Evolution: Palaeontological, Molecular and Cellular Evidence of their Timing and Global Effects.

Cepelewicz, Jordana. Bacterial Complexity Revises Ideas About ‘Which Came First?’. Quanta. Online June 12, 2019. A science writer conducts a wide survey of microbiologists such as Arash Komeili, Damien Devos, Michael Rout, Mark Field, Kate Adamala (see her lab page), Joel Dacks, and Anthony Poole about revolutionary rethinkings in this field about the appearance, composition and import of prokaryotic and eukaryotic microbial cells. With a main reference to Ectosymbiotic Bacteria at the Origin of Magnetoreception in a Marine Protist by Caroline Monteil, et al in Nature Microbiology (4/1088, 2019), once more a formative symbiosis is in effect everywhere.

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