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

3. Cellular Self-Organization and Holobiont Symbiogenesis

Giorgi, Franco, et al. The Egg as a Semiotic Gateway to Reproduction. Biosemiotics. Online September, 2013. Giorgi, University of Pisa, Luis Emilio Bruni, Aalborg University, Denmark, and Louis Goldberg, SUNY Buffalo, propose that an “oogenesis” oriented development from egg to I may best be understood by way of information conveyances in dual textually semiotic digital and analog modes.

The egg behaves as a prospective cell sustaining the developmental processes of the future embryo. In biosemiotic terms, this apparent teleonomic behaviour can be accounted for without referring to the exclusive causal role played by its genetic makeup. We envision two different processes that are uniquely found in the oocyte: (1) the first involves the mechanisms by which large amounts of mRNA accumulate in the ooplasm to establish the embryo axes prior to fertilization; (2) the second involves transfer of an excess of maternally supplied ribosomes to the oocyte to provide the future embryo with newly synthesized proteins. In this paper, we argue that the information required to sustain embryonic development is not due to any physical properties of the zygotic DNA and the maternal mRNAs, but to their spatially and temporally ordered relationship in the zygote’s internal space. (Abstract)

The oocyte itself is a topologically closed system since it is a cell bounded by a plasma membrane. The existence of such a boundary makes it possible for the oocyte to build up an internal organized ooplasm with an autoreferential character and to refer to the mother’s body as another entity occupying its external environment. This situation stems directly from the necessity to distinguish the content to be described, and eventually to be constructed as the internal organized structure of the oocyte, from its surroundings: a clear distinction between what could be defined as selfhood and everything else that is to be experienced as otherness. It follows that self-description is a pre-condition for the system to undergo self-replication. Self-description and self-replication are thus two key processes that together allow the oocyte to constitute a new emerging individuality distinct from the mother’s body and to maintain unaltered the species’ heritage from generation to generation. (2)

In conclusion, we have claimed a unique status for the oocyte. The single cell carries within it the digitalized memory of the history of the species in the form of a haploid chromosome set and the analogically organized ooplasm in the form of differentially distributed transcripts. Following fertilization, it is the interaction between the zygotic nuclei and the maternally generated transcripts that allows the developmental potential of the embryo to be fully unfolded, even though the structural organization of the ooplasm involves more than just their topological distribution. Many additional hierarchical levels constrain the context-dependent interpretations on local contingencies, as they gradually unfold from these prime interactions. (7)

Gontier, Nathalie. How Symbiosis, Horizontal Gene Transfer, and Virolution Call for an Extended Synthesis. http://aaas.confex.com/aaas/2013/webprogram/Session5780.html.. An AAAS session at the February 2013 Boston annual meeting, organized by the University of Lisbon philosopher. Speakers include Douglas Zook, “Symbiosis as a Driving Force of Evolution,” Frederic Bouchard “How Research on Symbiosis Should Transform Our Understanding of Adaption,” and Gontier on “Importance of Horizontal Evolution for the Sociocultural Sciences.” See also on this site a parallel session “How Macro-Evolutionary Studies Call for an Extended Synthesis.”

Comparative (meta)genomics have made us realize that horizontal evolutionary phenomena have been vastly underestimated. The serial endosymbiogenetic theory has proven the symbiogenetic origin of mitochondria and plastids. Symbiosis studies further prove that symbiotic unions continue to be relevant to understand evolution. Symbiotic unions can become transmitted vertically, from parent to offspring, through means other than germ-line transmission. Abundant evidence also exists for horizontal or lateral gene transfer in microorganisms. And evidence is piling up that lateral gene transfer also occurs abundantly in eukaryotic organisms. Gene sequencing techniques further prove that viruses also contribute to the evolution of life. They may have played a crucial role in the development of the genetic code, and viral genes are abundantly present in non-coding DNA regions that used to be designated as “junk DNA.” Such horizontal evolutionary phenomena pose major challenges to the Modern Synthesis, which makes a clear distinction between ontogeny and phylogeny, emphasizes germ-line transmission, and defines speciation as a splitting or “branching off” process. Horizontal evolutionary studies have consequences for how we define units of evolution, and biological individuals, how we draw the tree of life, and how we conceptualize speciation. (Session Abstract)

Gontier, Nathalie. Universal Symbiogenesis: An Alternative to Universal Selectionist Accounts of Evolution. Symbiosis. 44/1-3, 2007. A paper presented at the 5th International Symbiosis Society Congress in Vienna by the Vrije Universiteit Brussel research philosopher that begins with a good review of the Darwinian prevalence of selective winnowing alone. But as many writers aver, this view is an inadequate explanation that needs to be complemented and advanced by prior, innate affinities for mutual assembly. Examples are then offered across the strata from prokaryotes and viruses to cultures and languages to reveal how ubiquitous in nature this cooperative “hybridization” effect is. See also Nathalie's chapter Introducing Universal Symbiogenesis in Special Sciences and the Unity of Science, Olga Pombo, et al, eds. (Springer, 2012).

The process of symbiogenesis need not be confined to either the microcosm or the origin of eukaryotic beings. On the contrary, just as natural selection today is being universalized by evolutionary biologists and evolutionary epistemologists, symbiogenesis can be universalized as well. It will be argued that in its universalized form, symbiogenesis can provide: (1) a general tool to examine various forms of interaction between different biological organisms (regular symbiogenesis, hybridization, virus-host interactions), and (2) new metaphors for extra-biological fields such as cosmology, the cultural sciences, and language. Universal symbiogenesis can thus complement universal selectionist accounts of evolution. (167)

Definition: Universal symbiogenesis is the process whereby new entities are introduced because of the interactions between (different) previously independently existing entities. These interactions encompass horizontal mergings and the new entities that emerge because of this are called symbionts. (174-175)

Gontier, Nathalie, ed. Reticulate Evolution. Berlin: Springer, 2015. “Reticulate” is meant to represent nature’s pervasive symbiogenesis by way of networks geometries. A lead chapter is Symbiosis – Evolution’s Co-Author by Douglas Zook, a colleague of the late Lynn Margulis. The University of Lisbon editor goes on to include horizontal gene transfer as another instance. A typical entry is Can We Understand Evolution Without Symbiogenesis? by Francisco Carrapico.

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)

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