The Origins and Evolution of Animal Identity

The Darwinian synthesis focuses on speciation as the leading edge of evolution. But species are poor candidates for natural kinds because they are always susceptible to giving rise to something new. Physicalist evolutionary developmental biology presents an alternative scenario in which broad differences between organismal types were ontologically and temporally prior to subtypes and species-level variants. The cell masses that first developed into the metazoans, or animals, for example, arose from unicellular antecedents by a set of molecular innovations that constituted the embryos of these organisms as an unprecedented form of matter – liquid and liquid crystalline tissues – and thus a natural kind. This novel material embodied a set of morphogenetic processes and motifs that laid the basis for subsequent animal evolution. With the addition of other molecular functionalities simple “basal” metazoan body plans (sponges, placozoans) engendered more complex diploblasts (cnidarians, ctenophores) and bilaterian triploblasts (arthropods, chordates, mollusks, and so forth). Self-organizing patterning processes arising within these integrated communities of cells produced segments, appendages, patterned skeletons and organs. Bioelectrical scaffolding effects and the standardizing effects of development from an egg transformed phylotypic forms into canalized, integrated individuals that exist in the biosphere as “natural purposes,” causes and effects of themselves

The Origins and Evolution of Animal Identity

The Darwinian synthesis focuses on speciation as the leading edge of evolution. But species are poor candidates for bearers of well-defined biological identity because they are always susceptible to giving rise to something new. Physicalist evolutionary developmental biology presents an alternative scenario in which broad differences between organismal types were ontologically and temporally prior to subtypes and species-level variants. The cell masses that first developed into the metazoans, or animals, for example, arose from unicellular antecedents by a set of molecular innovations that constituted the embryos of these organisms as an unprecedented form of matter – liquid and liquid crystalline tissues – and thus a natural kind. This novel material embodied a set of morphogenetic processes and motifs that laid the basis for subsequent animal evolution. With the addition of other molecular functionalities simple “basal” metazoan body plans (sponges, placozoans) engendered more complex diploblasts (cnidarians, ctenophores) and bilaterian triploblasts (arthropods, chordates, mollusks, and so forth). Self-organizing patterning processes arising within these integrated communities of cells produced segments, appendages, patterned skeletons and organs. Bioelectrical scaffolding effects and the standardizing effects of development from an egg transformed phylotypic forms into canalized, integrated individuals that exist in the biosphere as “natural purposes,” causes and effects of themselves

The Origins and Evolution of Animal Identity

The Darwinian synthesis focuses on speciation as the leading edge of evolution. But species are poor candidates for bearers of well-defined biological identity because they are always susceptible to giving rise to something new. Physicalist evolutionary developmental biology presents an alternative scenario in which broad differences between organismal types were ontologically and temporally prior to subtypes and species-level variants. The cell masses that first developed into the metazoans, or animals, for example, arose from unicellular antecedents by a set of molecular innovations that constituted the embryos of these organisms as an unprecedented form of matter – liquid and liquid crystalline tissues – and thus a natural kind. This novel material embodied a set of morphogenetic processes and motifs that laid the basis for subsequent animal evolution. With the addition of other molecular functionalities simple “basal” metazoan body plans (sponges, placozoans) engendered more complex diploblasts (cnidarians, ctenophores) and bilaterian triploblasts (arthropods, chordates, mollusks, and so forth). Self-organizing patterning processes arising within these integrated communities of cells produced segments, appendages, patterned skeletons and organs. Bioelectrical scaffolding effects and the standardizing effects of development from an egg transformed phylotypic forms into canalized, integrated individuals that exist in the biosphere as “natural purposes,” causes and effects of themselves

Cell differentiation: what have we learned in 50 years?

I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network (MGRN) model, in light of newer knowledge of mechanisms of gene regulation in the metazoans (animals). The two models continue to inform hypotheses and computational studies of differentiation of lineage-adjacent cell types. However, their shared notion (based on bacterial regulatory systems) of gene switches and networks built from them, have constrained progress in understanding the dynamics and evolution of differentiation. Recent work has described unique write-read-rewrite chromatin-based expression encoding in eukaryotes, as well metazoan-specific processes of gene activation and silencing in condensed-phase, enhancer-recruiting regulatory hubs, employing disordered proteins, including transcription factors, with context-dependent identities. These findings suggest an evolutionary scenario in which the origination of differentiation in animals, rather than depending exclusively on adaptive natural selection, emerged as a consequence of a type of multicellularity in which the novel metazoan gene regulatory apparatus was readily mobilized to amplify and exaggerate inherent cell functions of unicellular ancestors. The plausibility of this hypothesis is illustrated by the evolution of the developmental role of Grainyhead-like in the formation of epithelium

The Origins and Evolution of Animal Identity

The Darwinian synthesis focuses on speciation as the leading edge of evolution. But species are poor candidates for natural kinds because they are always susceptible to giving rise to something new. Physicalist evolutionary developmental biology presents an alternative scenario in which broad differences between organismal types were ontologically and temporally prior to subtypes and species-level variants. The cell masses that first developed into the metazoans, or animals, for example, arose from unicellular antecedents by a set of molecular innovations that constituted the embryos of these organisms as an unprecedented form of matter – liquid and liquid crystalline tissues – and thus a natural kind. This novel material embodied a set of morphogenetic processes and motifs that laid the basis for subsequent animal evolution. With the addition of other molecular functionalities simple “basal” metazoan body plans (sponges, placozoans) engendered more complex diploblasts (cnidarians, ctenophores) and bilaterian triploblasts (arthropods, chordates, mollusks, and so forth). Self-organizing patterning processes arising within these integrated communities of cells produced segments, appendages, patterned skeletons and organs. Bioelectrical scaffolding effects and the standardizing effects of development from an egg transformed phylotypic forms into canalized, integrated individuals that exist in the biosphere as “natural purposes,” causes and effects of themselves

Form, function, mind: what doesn't compute (and what might)

The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, dynamicism is similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life

Before programs: The physical origination of multicellular forms

ABSTRACT By examining the formative role of physical processes in modern-day developmental systems, we infer that although such determinants are subject to constraints and rarely act in a “pure ” fashion, they are identical to processes generic to all viscoelastic, chemically excitable media, non-living as well as living. The processes considered are free diffusion, immiscible liquid behavior, oscillation and multistability of chemical state, reaction-diffusion coupling and mecha-nochemical responsivity. We suggest that such processes had freer reign at early stages in the history of multicellular life, when less evolution had occurred of genetic mechanisms for stabilization and entrenchment of functionally successful morphologies. From this we devise a hypothetical scenario for pattern formation and morphogenesis in the earliest metazoa. We show that the expected morphologies that would arise during this relatively unconstrained “physical” stage of evolution correspond to the hollow, multilayered and segmented morphotypes seen in the gastrulation stage embryos of modern-day metazoa as well as in Ediacaran fossil deposits of ~600 Ma. We suggest several ways in which organisms that were originally formed by predomi-nantly physical mechanisms could have evolved genetic mechanisms to perpetuate their mor-phologies

Continuous macroscopic limit of a discrete stochastic model for interaction of living cells

In the development of multiscale biological models it is crucial to establish a connection between discrete microscopic or mesoscopic stochastic models and macroscopic continuous descriptions based on cellular density. In this paper a continuous limit of a two-dimensional Cellular Potts Model (CPM) with excluded volume is derived, describing cells moving in a medium and reacting to each other through both direct contact and long range chemotaxis. The continuous macroscopic model is obtained as a Fokker-Planck equation describing evolution of the cell probability density function. All coefficients of the general macroscopic model are derived from parameters of the CPM and a very good agreement is demonstrated between CPM Monte Carlo simulations and numerical solution of the macroscopic model. It is also shown that in the absence of contact cell-cell interactions, the obtained model reduces to the classical macroscopic Keller-Segel model. General multiscale approach is demonstrated by simulating spongy bone formation from loosely packed mesenchyme via the intramembranous route suggesting that self-organizing physical mechanisms can account for this developmental process.Comment: 4 pages, 3 figure

The brown adipocyte differentiation pathway in birds: An evolutionary road not taken

Background Thermogenic brown adipose tissue has never been described in birds or other non-mammalian vertebrates. Brown adipocytes in mammals are distinguished from the more common white fat adipocytes by having numerous small lipid droplets rather than a single large one, elevated numbers of mitochondria, and mitochondrial expression of the nuclear gene UCP1, the uncoupler of oxidative phosphorylation responsible for non-shivering thermogenesis. Results We have identified in vitro inductive conditions in which mesenchymal cells isolated from the embryonic chicken limb bud differentiate into avian brown adipocyte-like cells (ABALCs) with the morphological and many of the biochemical properties of terminally differentiated brown adipocytes. Avian, and as we show here, lizard species lack the gene for UCP1, although it is present in amphibian and fish species. While ABALCs are therefore not functional brown adipocytes, they are generated by a developmental pathway virtually identical to brown fat differentiation in mammals: both the common adipogenic transcription factor peroxisome proliferator-activated receptor-γ (PPARγ), and a coactivator of that factor specific to brown fat differentiation in mammals, PGC1α, are elevated in expression, as are mitochondrial volume and DNA. Furthermore, ABALCs induction resulted in strong transcription from a transfected mouse UCP1 promoter. Conclusion These findings strongly suggest that the brown fat differentiation pathway evolved in a common ancestor of birds and mammals and its thermogenicity was lost in the avian lineage, with the degradation of UCP1, after it separated from the mammalian lineage. Since this event occurred no later than the saurian ancestor of birds and lizards, an implication of this is that dinosaurs had neither UCP1 nor canonically thermogenic brown fat.Nadejda V Mezentseva, Jaliya S Kumaratilake and Stuart A Newma