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

5. Multicellular Fauna and Flora Organisms

Mao, Yanlan and Jeremy Green. Systems Morphodynamics. Philosophical Transactions of the Royal Society B. 372/20160505, 2017. An introduction by British biologists to an issue with this suggested title to represent current integral understandings of how organisms and evolutions form and flourish in concert.

Marijuan, Pedro, et al. On Eukaryotic Intelligence: Signaling System’s Guidance in the Evolution of Multicellular Organization. Biosystems. Online July, 2013. Zaragosa, Spain, systems biologists continue with colleagues to seek a better understanding of these cellular domains and emergent transitions via their constant informational and semiotic communication processes. As a result, a relative, waxing presence of cognitive qualities can be posited even at these rudimentary stages. With all this going on, it is still curious that “machinery” terms are often used, which for this reason is said to be ‘blind’ to what it is doing. So there remains a urgent natural philosophy to notice and clarify, see for example Daniel Nicholson’s “Organisms ≠ Machines” (2013) above.

In all biological systems, from prokaryotes to eukaryotes – and rather astoundingly even within neuronal synapses themselves – signaling is tightly coupled with gene transcription and protein synthesis. Theoretically, is there any fundamental link between signaling systems and the basic eukaryotic organization/evolution towards increased complexity? An immediate rationale is that the transcriptional machinery, being ‘blind,’ needs massive signaling guidance in order to deploy the adequate genetic circuits, so to fabricate and put into cellular milieu the adequate RNA and protein agents. Thus, signaling means the topological governance of the transcriptional regulatory network, the decision of what parts should activated or should be inhibited, particularly throughout the very fast changes in second messenger concentrations. (15)

From an informational point of view, the cell’s self-constructing machinery may be seen as a realization of von Neumann’s theory of self-constructing machines, which mandates separation between the inner description of the system and its production structure. (16) Biological evolution means two basic characteristics: self-production and communication with the environment. Both aspects are irremediably linked within the basic cell-engine of eukaryotic complexity, and the knowledge on both has increased dramatically during last decades. It is in this sense that an informational updating of venerable “cellular theory” seem possible and necessary. (16) A new informational approach to the self-production and communications processes of living cells, to the informational organization of both prokaryotic and eukaryotic “intelligences,” looks feasible. Many different strands have to be put together, from open systems, to self-organization, to informational architectures of molecular encoding self-production, problem-solving engines, signaling guidance, but it looks a plausible task not far from several of yesteryear: artificial life, natural computing, synthetic life, or bioinformation. (16)

Michod, Richard and Denis Roze. Transitions in Individuality. Proceedings of the Royal Society of London B. 264/853, 1997. Noted more elsewhere, biologist Michod’s University of Arizona group contributes to the growing perception of a nested evolutionary scale of integral entities.

The evolution of multicellular organisms is the premier example of the integration of lower levels into a single, higher level individual….We provide an explicit two-locus genetic framework for understanding this transition in terms of the increase of cooperation among cells and the regulation of conflict within the emerging organism. (853)

Mietke, Alexander, et al. Self-Organized Shape Dynamics of Active Surfaces. Proceedings of the National Academy of Sciences. 116/1, 2019. We recall a decade ago when self-organization as a formative force in cellular development was rarely mentioned or factored in. Here MPI Physics of Complex Systems and Technical University of Dresden theorists add to its inherent contribution to physiological function and somatic vitality. May it also be said that some 65 years after WW II, a global human phenomenon can rise Phoenix-like to learn about cosmic life’s self-verification, and to so offset a looming WW III, achieve our common Earthwise understanding and affirmation.

Morphogenesis, the emergence of shape and form in biological systems, is a process that is fundamentally mechanochemical: Shape changes of material are driven by active mechanical forces that are generated by chemical processes, which in turn can be affected by the deformations and flows that occur. We provide a framework that integrates these interactions between the geometry of deforming materials and active processes in them by introducing the shape dynamics of self-organized active surfaces. We show that the tight coupling between surface mechanics and active processes gives rise to the spontaneous formation of nontrivial shapes, shape oscillations, and directed peristaltic motion. Our simple yet general description lays the foundation to explore the regulatory role of shape in morphogenetic processes. (Significance)

Minelli, Alessandro. Perspectives in Animal Phylogeny. Oxford: Oxford University Press, 2009. The University of Padova zoologist writes a well-reviewed survey of the leading conceptual edges of evolutionary biology. A summary highlights these findings and next steps: metazoan life forms unto a general hierarchical scale; organism development proceeds via local dynamic modules; we need move beyond an adultocentric focus; and an acknowledgement of how pervasive convergence is.

Read the other way around, we can take as the (admittedly, somewhat idealized) default state of living matter a condition of everlasting dynamics which, in multicellular organisms, easily translates into unlimited growth and fractal-like iteration of developmental patterning. (243)

Minelli, Alessandro. The Development of Animal Form. Cambridge: Cambridge University Press, 2003. A significant volume about rethinking how organisms grow to relative maturity. Rather than occurring along a fixed path legislated by a molecular program, many epigenetic forces are in play which builds in a stochastic flexibility. In this way developmental biology can affect the evolution of life, which can inform a reintegration of these disciplines. A further consequence is an expansion of focus from either the DNA or adult form of an organism to its entire life cycle.

Moen, Daniel, et al. Evolutionary Conservatism and Convergence Both Lead to Striking Similarity in Ecology, Morphology and Performance across Continents in Frogs. Proceeding of the Royal Society B. 280/20132156, 2013. Life scientists Moen and John Wiens, SUNY Stony Brook, and Duncan Irschick, University of Massachusetts, Amherst, achieve a uniquely comprehensive study that includes all these title aspects at once. As a result, a substantial affirmation can be made of nature’s seemingly innate propensity to repeat common patterns and behaviors everywhere across for life’s disparate yet oriented development and radiation.

Many clades contain ecologically and phenotypically similar species across continents, yet the processes generating this similarity are largely unstudied, leaving fundamental questions unanswered. Is similarity in morphology and performance across assemblages caused by evolutionary convergence or by biogeographic dispersal of evolutionarily conserved ecotypes? Does convergence to new ecological conditions erase evidence of past adaptation? Here, we analyse ecology, morphology and performance in frog assemblages from three continents (Asia, Australia and South America), assessing the importance of dispersal and convergent evolution in explaining similarity across regions.

We find three striking results. First, species using the same microhabitat type are highly similar in morphology and performance across both clades and continents. Second, some species on different continents owe their similarity to dispersal and evolutionary conservatism (rather than evolutionary convergence), even over vast temporal and spatial scales. Third, in one case, an ecologically specialized ancestor radiated into diverse ecotypes that have converged with those on other continents, largely erasing traces of past adaptation to their ancestral ecology. Overall, our study highlights the roles of both evolutionary conservatism and convergence in explaining similarity in species traits over large spatial and temporal scales and demonstrates a statistical framework for addressing these questions in other systems. (Abstract)

Many species are ecologically and morphologically similar to species in similar biomes on other continents. This pattern of among-continent similarity in species traits occurs across many ecological guilds, clades and biomes (e.g. placental and marsupial mammals, Mediterranean-climate plants and desert lizards. However, the ecological and evolutionary processes underlying this similarity are not well understood, and thus many fundamental questions in ecology and evolutionary biology remain unresolved. (1)

Naranjo-Ortiz, Miguel and Toni Gabaldon. Fungal Evolution: Cellular, Genomic and Metabolic Complexity. Biological Reviews. April, 2020. As the life sciences proceed apace to record the anatomic presence of networks everywhere, here Barcelona Institute of Science and Technology geneticists explore in detail how these prolific microorganisms can be an exemplary way to study this interlinked and communicative phenomena. Within a sense of a transitional emergence from nucleotides and prokaryotes to mobile, varigated organisms, the fungi family do indeed provide an iconic, valuable model.

The question of how phenotypic and genomic complexity are related and shaped through evolution is a central to animal and plant biology. Recently, fungi have emerged as an alternative system of much value because they present a broad and diverse range of phenotypic traits and many different shapes. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout their evolution. Similarly, fungal genomes have a diverse architecture with rapid changes in genome organization. We explore how the interplay of cellular, genomic and metabolic traits mediates the emergence of complex phenotypes. (Abstract)

Fungus compose a group of spore-producing organisms feeding on organic matter, including molds, yeast, mushrooms, and toadstools.

Newman, Stuart, et al. The Vertebrate Limb: An Evolving Complex of Self-Organizing Systems. Progress in Biophysics and Molecular Biology. 137/12, 2018. In a special issue on Biological Challenges in Morphogenesis, SN, New York Medical College, Tilmann Glimm, Western Washington University and Ramray Bhat, Indian Institute of Science describe the latest verifications which reveal how life draws on the same homologous formations in kind across the animal kingdoms from insects and birds to our human selves. See also Some Caveats to Mathematical Modeling in Biology by Scott Gilbert and The Extracellular Matrix as a Driving Force by Marta Linde-Medina and Ralph Marcucio.

Nicholson, Daniel. Organisms ≠ Machines. Studies in the History and Philosophy of Biological and Biomedical Sciences. 44/4, 2013. With these sciences burdened by a centuries old ruling metaphor of life defined and described by mechanistic terms, a Cohn Institute, Tel Aviv University, philosopher explains and calls for a much overdue corrective. How obvious the error when a comparison is as clearly drawn as this. Machines are externally made, passive, can be taken apart, with no vitality of their own. Organisms have an intrinsic, motive purpose, holistic by way of interdependent cellular organs, and so on. In our midst of a cosmic Copernican revolution from dead to alive, this negative conflation that tacitly controls and constrains scientific mindsets is in much need of resolve. For a contrast see, e.g., Marijuan, et al (2013) on ‘blind’ cellular machinery, or Marchetti, et al (2013) about the lively physics of “active matter.”

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (Abstract)

Nicholson, Jeremy, et al. The Challenges of Modeling Mammalian Biocomplexity. Nature Biotechnology. 22/10, 2004. From a special issue on Systems Biology, a case is made that complex organisms such as human beings ought to be appreciated as “superorganisms” composed on many types of functional microbes. By this approach, better methods of drug design and prescription can be achieved.

Highly complex animals such as humans can be considered ‘superorganisms’ with an internal ecosystem of diverse symbiotic macrobiota and parasites that have interactive metabolic processes. (1268)

Niklas, Karl and Stuart Newman. The Origins of Multicellular Organisms. Evolution & Development. 15/1, 2013. The Cornell University plant biologist and New York Medical College cell biologist provide a current update of the persistent course of unicellular life to form more complex creatures in similar self-organized, symbiotic ways as they became whole entities.

Multicellularity has evolved in several eukaryotic lineages leading to plants, fungi, and animals. Theoretically, in each case, this involved (1) cell-to-cell adhesion with an alignment-of-fitness among cells, (2) cell-to-cell communication, cooperation, and specialization with an export-of-fitness to a multicellular organism, and (3) in some cases, a transition from “simple” to “complex” multicellularity. When mapped onto a matrix of morphologies based on developmental and physical rules for plants, these three phases help to identify a “unicellular   colonial   filamentous (unbranched   branched)   pseudoparenchymatous    parenchymatous” morphological transformation series that is consistent with trends observed within each of the three major plant clades. In contrast, a more direct “unicellular   colonial or siphonous    parenchymatous” series is observed in fungal and animal lineages. In these contexts, we discuss the roles played by the cooptation, expansion, and subsequent diversification of ancestral genomic toolkits and patterning modules during the evolution of multicellularity. (Summary)

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