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VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

4. Cellular Holobiont Symbiogenesis

Gordon, Daniel, et al. Hierarchical Self-Organization of Cytoskeletal Active Networks. Physical Biology. 9/2, 2012. A “cytoskeleton” is the internal framework of a cell, composed of actin filaments and microtubules. Ben Gurion University of the Negev researchers testify to the exemplary presence of self-arranging dynamics as they scale into micro and macro cellular realms.

The structural reorganization of the actin cytoskeleton is facilitated through the action of motor proteins that crosslink the actin filaments and transport them relative to each other. Here, we present a combined experimental-computational study that probes the dynamic evolution of mixtures of actin filaments and clusters of myosin motors. While on small spatial and temporal scales the system behaves in a very noisy manner, on larger scales it evolves into several well distinct patterns such as bundles, asters and networks. These patterns are characterized by junctions with high connectivity, whose formation is possible due to the organization of the motors in 'oligoclusters' (intermediate-size aggregates). The simulations reveal that the self-organization process proceeds through a series of hierarchical steps, starting from local microscopic moves and ranging up to the macroscopic large scales where the steady-state structures are formed. (Abstract)

Guerrero, Ricardo and Mercedes Berlanga. From the Cell to the Ecosystem: The Physiological Evolution of Symbiosis. Evolutionary Biology. Online November, 2015. In this 2015 “Synthesis Paper,” University of Barcelona biologists trace nature’s pervasive mutualities across this wide expanse. Life’s origin is seen as a “biopoiesis,” from the Greek word for poetry, which then proceeds by virtue of autopoietic, holobiont “obligate coevolved partnerships” and “interdependent cooperative functional-metabolic interactions.” These effective propensities recur everywhere as microbial mats exemplify.

Hanczyc, Martin, et al. Experimental Models of Primitive Cellular Compartments. Science. 302/618, 2003. Whereof a persistent, natural tendency to form encapsulated, bounded protocells is identified, but, excuse me, life is not a ‘machine.’

The bilayer membranes that surround all present-day cells and act as boundaries are thought to have originated in the spontaneous self-assembly of amphiphilic molecules into membrane vesicles. (618) These experiments constitute a proof-of-principle demonstration that vesicle growth and division can result from simple physico-chemical forces, without any complex biochemical machinery. (621)

Harold, Franklin. Molecules into Cells: Specifying Spatial Architecture. Microbiology and Molecular Biology Reviews. 69/4, 2005. The University of Washington microbiologist joins a growing movement to liberate organic form and development from a dogmatic 20th century genetic fixation. Rather, an array of non-genetic forces from innate dynamics to environmental constraints provides an “epigenetic” guidance. A number of recent papers noted on the website, such as by Albert, Mameli, Newman, Muller, Keller, Van Speybroeck, Levin, and Ma’ayan, describe an oriented, iterative emergence of development and evolution.

This exercise provides fresh support for a holistic point of view that diverges significantly from the opinions held, at least conventionally, by many molecular scientists. Spatial organization is not written out in the genetic blueprint; it emerges epigenetically from the interplay of genetically specified molecules, by way of a hierarchy of self-organizing processes, constrained by heritable structures, membranes in particular. (545) The hierarchy of order envisages a nested succession of stages, beginning with the translation of genetic information into functional proteins….If (cellular) unity can be discerned, it revolves around the kinds of processes that progressively build up structures, organization, and global form. The word to conjure with nowadays is self-organization. (545)

The spatial organization of cells, including the arrangement of cytoplasmic constituents and the cells’ global form, is not explicitly spelled out in the genome. Genes specify only the primary sequences of macromolecules, portions of which are indeed relevant to the localization of those molecules in space. But cell architecture, for the most part, arises epigenetically from the interactions of numerous gene products. Many of these interactions can be well described as instances of molecular self-organization, either self-assembly or dynamic self-construction. (559) Spatial order is not encoded anywhere at all but emerges from the interactions of the cell’s molecular building blocks; it arises by self-organization, like the specifications of a termite mound or the unique jumble of streets in my home town of Seattle. And the propagation of order down the generations depends not on a codebook but on history repeating itself: the same building blocks, released into the same constraining context, will reproduce the same structure time and again. (559)

Harold, Franklin. The Way of the Cell. Oxford: Oxford University Press, 2001. A biochemist’s tour of the origins, evolution, symbiotic assembly, and autopoietic functions of cellularity. These insights are based on a unique blend of theories of thermodynamics, self-organization, and natural selection. But Harold remains a “materialist” and holds that life is due to “peculiar” complex systems which channel energy and information.

Helikar, Tomas, et al. The Cell Collective: Toward an Open and Collaborative Approach to Systems Biology. BMC Systems Biology. 6/96, 2012. In a paper akin to Karr, et al below, a team of ten University of Nebraska mathematicians and physicians propose an open source “Cell Collective Knowledge Base, Bio-Logic Builder, and Large-Scale Dynamical Models.” By these qualities, it is expected to facilitate an electronic cross sharing, as if an instant worldwide cognitive research activity.

Background Despite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic study of biochemical pathways requires computer modeling. Due to the complexity of cells, it is not feasible for one person or group to model the cell in its entirety. Conclusions The Cell Collective is a web-based platform that enables laboratory scientists from across the globe to collaboratively build large-scale models of various biological processes, and simulate/analyze them in real time. In this manuscript, we show examples of its application to a large-scale model of signal transduction.

Hird, Myra. The Origins of Sociable Life. London: Palgrave Macmillan, 2009. The Queen’s University, Ontario, National Scholar of micro and macro organisms, writes a postmodern manifesto for an expanded evolutionary synthesis by way of the recognition and inclusion of symbiotic assemblies. In regard then, these vast, robust microbial realms might be availed as archetypal exemplars and guidance for more viable, coherent, sensitive organic societies.

Howard, Martin and Karsten Kruse. Cellular Organization by Self-Organization. Journal of Cell Biology. 168/4, 2005. Since cells are composed of many dynamically interacting elements or components, they exemplify the self-organizing behavior of complex systems. Another example of this formative natural agency at work.

We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new insights into the mechanisms of self-organization in bacterial cells and indicate how these ideas may be applicable to more complex structure formation in eukaryotic cells. (533)

Igamberdiev, Abir, et al, eds. Symbiogenesis and Progressive Evolution. Biosystems. April, 2021. is a special collection edited by AI, Richard Gordon, and George Mikhailovsky which into the 2020s seeks to report frontier insights and evidence that nature’s constant preference for a mutual convergent synthesis of diverse members is in primary procreative effect everywhere. We note in this issue From Empedocles to Symbiogenetics: Lynn Margulis's Revolutionary Influence on Evolutionary Biology by Dorion Sagan and Symbiogenesis as a Driving Force of Evolution: The Legacy of Boris Kozo-Polyansky by Vladimir Agafonov, et al, Serial Endosymbiosis Theory: From Biology to Astronomy and Back to the Origin of Life by Predrag Slijepcevic (search) and Archaeal Origins of Eckaryotic Cells by Frantisek Baluska and Sherrie Lyons.

Symbiogenesis played a crucial role in the origin of eukaryotic cells and onto life’s emergence. It led to a complexification of coding systems as a result of merging individual genomes of prokaryotic cells. This issue will explore the role of horizontal gene transfer and symbiogenesis onto complex multicellular organisms. The papers herein will seek to understand the role of symbiogenesis in the evolutionary process and suggest computational models to describe the emergence of complex biological systems. The issue is dedicated to the founders of the concept of symbiogenesis Boris Kozo-Polyansky (1890-1957) and Lynn Margulis (1938-2011), the former chief editor of BioSystems, who proved this concept and introduced it into the mainstream of evolutionary theory. (Issue Introduction excerpt)

Karr, Jonathan, et al. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell. 150/2, 2012. Nine Stanford University and Craig Venter Institute computational biophysicists illuminate the presence of a mathematical domain that in addition to familiar metabolic, microbial components graces and enhances a cell’s relational interactive development.

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery. (Abstract)

Kiers, Toby and Stuart West. Evolving New Organisms Via Symbiosis. Science. 348/392, 2015. Vrije Universiteit, Amsterdam, and Oxford University, zoologists proceed to integrate the well accepted fact that cellular creatures arose by way of mutual reciprocities with the popular major evolutionary transition scale of relative individualities, within which such symbiotic ways become even more valid.

Kooijman, S., et al. Quantitative Steps in Symbiogenesis and the Evolution of Homeostasis. Biological Reviews. 78/3, 2003. A dynamic energy budget (DEB) model is proposed for the reciprocal endosybiotic process.

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