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

2. Microbial Colonies

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.

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)

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)

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