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

2. Microbial Colonies

Hulse, Brad, et al. A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection. eLife. October, 2021. A nine person team at the Janelia Research Campus, Howard Hughes Medical Institute, Virginia, report and discuss novel abilities to sequence the neural architecture of such a minimal insect entity. Thus our collaborative neuroscience is able to reconstruct ever deeper origins from whence this worldwise Earthuman acumen arose. Once more a true genesis uniVerse reveals itself as a grand learning process, which seems potentially on the way to its own vital acknowledge.

Flexible behaviors over long timescales are thought to engage neural networks in deep brain regions, which are often difficult to study. In insects, recurrent circuit dynamics in a brain region called the central complex enable directed locomotion, sleep, and context- and experience-dependent spatial navigation. We describe the first complete electron-microscopy-based connectome of the Drosophila CX. We also identified numerous pathways that may facilitate the selection of CX-driven behavioral patterns by their internal state. Our results provide a comprehensive brainscape mapping by which to understand network dynamics underlying sleep, flexible navigation, and state-dependent action selection. (Abstract excerpt)

Hussa, Elizabeth and Heidi Goodrich-Blair. It Takes a Village: Ecological and Fitness Impacts of Multipartite Mutualism. Annual Review of Microbiology. 67/161, 2013. University of Wisconsin bacteriologists further appreciate life’s natural propensity from prokaryotes to primates to form viable groupings sustained by symbiotic reciprocities of component members and a bounded organic whole. Typical benefits are niche adaptation and survival defense. Aka “multipartite interdependence,” the abstract term is another version of “competitive coherence” by Vic Norris, et al, Pierre Teilhard de Chardin’s “creative union,” traditional African “ubuntu,” many others. While critics complain that such mutually based societies may tend to communal control, in natural practice, as Teilhard stressed, more social support actually enhances personal liberty.

Microbial symbioses, in which microbes have either positive (mutualistic) or negative (parasitic) impacts on host fitness, are integral to all aspects of biology, from ecology to human health. In many well-studied cases, microbial symbiosis is characterized by a specialized association between a host and a specific microbe that provides it with one or more beneficial functions, such as novel metabolic pathways or defense against pathogens. Even in relatively simple associations, symbiont-derived benefits can be context dependent and influenced by other host-associated or environmental microbes. Furthermore, naturally occurring symbioses are typically complex, in which multiple symbionts exhibit coordinated, competing, or independent influences on host physiology, or in which individual symbionts affect multiple interacting hosts. Here we describe research on the mechanisms and consequences of multipartite symbioses, including consortia in which multiple organisms interact with the host and one another, and on conditional mutualists whose impact on the host depends on additional interacting organisms. (Abstract)

Jabr, Ferris. How Brainless Slime Molds Redefine Intelligence. www.nature.com/news/how-brainless-slime-molds-redefine-intelligence-1.11811. Online November 2012, a news report on a segment from the NOVA and Scientific American TV program “What are Animals Thinking?” These single-cell amoeba are found to be capable in communal unison to remember, make decisions, plan for change. As a result, they seem to possess innate propensities for cognitive abilities.

Something scientists have come to understand is that slime molds are much smarter than they look. One species in particular, the SpongeBob SquarePants – yellow Physarum polycephalum, can solve mazes, mimic the layout of man-made transportation networks and choose the healthiest food from a diverse menu—and all this without a brain or nervous system. "Slime molds are redefining what you need to have to qualify as intelligent” says Chris Reid of the University of Sydney.

Joint, Ian, et al. Bacterial Conversations: Talking, Listening and Eavesdropping. Philosophical Transactions of the Royal Society B. 362/1115, 2007. An introduction to an issue on the prevalence of microbial communication, known as quorum sensing, by which bacteria persist not as separate isolates but in viable colonial biofilms and populations.

Kacar, Betul. Foundations for reconstructing early microbial life.. arXiv:2406.09354. A University of Wisconsin bacteriologist proposes that a better comprehension of how this primal prokaryotic stage originally managed to survive and thrive as a guide to our present climate stresses.

For more than 3.5 billion years, life had extreme environmental conditions which include shifts from oxygen-less to over-oxygenated atmospheres and cycling between hothouse Earth and glaciations. Meanwhile, the planet evolved from a long microbial stage to plants and animals. Many cellular attributes evolved which collectively define our biosphere and now concern our human fate. In regard, a new disciplinary synthesis is needed to learn how microbes survived an ever changing globe over deep time. This review describes an emerging area in microbiology and evolutionary synthetic biology so to reconstruct the earliest microbial innovations.

Kacar, Betul. Reconstructing Early Microbial Life.. Annual Review of Microbiology. August, 2024. In this comprehensive status paper, a University of Wisconsin bacteriologist (search) describes the latest views about life’s prokaryotic biosphere from its ancient, foundational onset all the way to our human microbiomes and beyond to a new phase of a beneficial makeover.

For more than 3.5 billion years, life experienced environmental extremes on Earth such as shifts to oxygenated atmospheres, hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. Earth evolved from only microbial life to the plants and animals that are familiar today. However, the incorporation of molecular genetics, population biology, and evolutionary biology approaches into the study of Precambrian biota remains a significant challenge. This review synthesizes our current knowledge of early microbial life and describes a frontier area that integrates microbiology, paleobiology, and evolutionary synthetic biology to reconstruct ancient biological innovations. (Abstract)

Kolter, Roberto and Peter Greenberg. The Superficial Life of Microbes. Nature. 441/300, 2006. A news report on the realization that the bacterial realm, especially surface biofilms, ought to be rightly understood as communal in kind.

Koonin, Eugene and Yuri Wolf. Genomics of Bacteria and Archaea: the Emerging Dynamic View of the Prokaryotic World. Nucleic Acids Research. 36/21, 2008. National Center for Biotechnology Information, NIH, scientists explore the major rethinking of this microbial realm now in process. But how might we imagine in a Natural Genesis, that such a typical paper, in its linguistic exercise, is itself genetic in kind as the cosmic and molecular code lately emerges to reflective human recognition and continuance?

However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution,….A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution. (6688)

The paradox of today’s state of the art is that, despite the tremendous progress—but also owing to these advances—the emerging complexity of the prokaryotic world is currently beyond our grasp. We have no adequate language, in terms of theory or tools, to describe the workings and histories of the genomic network. Developing such a language is the major challenge for the next stage in the evolution of prokaryotic genomics. (6713)

Kreimer, Anat, et al. The Evolution of Modularity in Bacterial Metabolic Networks. Proceedings of the National Academy of Sciences. 105/6976, 2008. As exemplified by this subject realm, complex adaptive systems at every evolutionary stage repetitively exhibit the feature of forming semi-autonomous functional modules. (See also Luis Amaral PNAS 105/6795, 2008)

Here we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species. (6976)

Kundu, Parag, et al. Our Gut Microbiome: The Evolving Inner Self. Cell. 171/7, 2017. In a synoptic paper, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore metabolic scientists and Weizmann Institute of Science, Israel immunologists cover life’s course from pre-natal to neonatal, childhood, puberty, onto adult stages and older ages. In much detail, aspects such as nutrition, mobility, medicines, life style are considered within the dynamical human microbiome.

The “holobiont” concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality. (Abstract)

Without symbiosis, life on earth as we see it today would not exist. Symbiosis between microbes and simple one-cell organisms have been assumed to be essential for the subsequent expansion of multicellular eukaryotes, as well as for the diversification of species. Moreover, any given human cell carries remnants of prokaryotes in the form of mitochondria and organelles, without which we cannot sustain life. (1481)

Lan, Ganhui and Yuhai Tu. Information Processing in Bacteria: Memory, Computation, and Statistical Physics. Reports on Progress in Physics. 79/5, 2016. As the quotes cite, George Washington University and IBM Watson Research Center biophysicists find sophisticated behaviors in microbial activities, which they then proceed to link to a dynamic physical basis.

In this review, we describe some of the recent work in developing a quantitative predictive model of bacterial chemotaxis, which can be considered as the hydrogen atom of systems biology. Using statistical physics approaches, such as the Ising model and Langevin equation, we study how bacteria, such as E. coli, sense and amplify external signals, how they keep a working memory of the stimuli, and how they use these data to compute the chemical gradient. In particular, we will describe how E. coli cells avoid cross-talk in a heterogeneous receptor cluster to keep a ligand-specific memory. We will also study the thermodynamic costs of adaptation for cells to maintain an accurate memory. The statistical physics based approach described here should be useful in understanding design principles for cellular biochemical circuits in general. (Abstract)

Biological systems need to sense and process information from their environment in order to make decisions vital for their survival and growth. Like a computer, a cell not only needs to take the input information, it also has the ability to store information (memory) and to use the memory together with the input to compute an output (decision) that will enhance its survival and/or growth. In this review, we use the simple E. coli chemotaxis signaling system as an example to demonstrate the ability of a cell to maintain an accurate memory and to compute. In a loose sense, the E. coli chemotaxis pathway can be considered as a probabilistic Turing machine. (15)

Lau, Maggie, et al. An Oligotrophic Deep-subsurface Community Dependent on Syntrophy is Dominated by Sulfur-driven Autotrophic Denitrifiers. Proceedings of the National Academy of Sciences. 113/E7927, 2016. A 23 member international team reports for the first time the presence of bacterial organisms in these extreme, internal environs. Along with biochemistries, their success is seen as due to uniquely viable metabolic networks. The project merited a later notice in PNAS (114/788, 2017) as Bacteria Work Together to Survive Earth’s Depths.

Microorganisms are known to live in the deep subsurface, kilometers below the photic zone, but the community-wide metabolic networks and trophic structures (the organization of their energy and nutritional hierarchy) remain poorly understood. We show that an active subsurface lithoautotrophic microbial ecosystem (SLiME) under oligotrophic condition exists. Taxonomically and metabolically diverse microorganisms are supported, with sulfur-driven autotrophic denitrifiers predominating in the community. Denitrification is a highly active process in the deep subsurface that evaded recognition in the past. This study highlights the critical role of metabolic cooperation, via syntrophy between subsurface microbial groups, for the survival of the whole community under the oligotrophic conditions that dominate in the subsurface. (Significance)

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