The major transitions of life from a network perspective

Phase transitions in evolutionary dynamics

Sharp changes in state, such as transitions from survival to extinction, are hallmarks of evolutionary dynamics in biological systems. These transitions can be explored using the techniques of statistical physics and the physics of nonlinear and complex systems. For example, a survival-to-extinction transition can be characterized as a non-equilibrium phase transition to an absorbing state. Here, we review the literature on phase transitions in evolutionary dynamics. We discuss directed percolation transitions in cellular automata and evolutionary models, and models that diverge from the directed percolation universality class. We explore in detail an example of an absorbing phase transition in an agent-based model of evolutionary dynamics, including previously unpublished data demonstrating similarity to, but also divergence from, directed percolation, as well as evidence for phase transition behavior at multiple levels of the model system's evolutionary structure. We discuss phase transition models of the error catastrophe in RNA virus dynamics and phase transition models for transition from chemistry to biochemistry, i.e., the origin of life. We conclude with a review of phase transition dynamics in models of natural selection, discuss the possible role of phase transitions in unraveling fundamental unresolved questions regarding multilevel selection and the major evolutionary transitions, and assess the future outlook for phase transitions in the investigation of evolutionary dynamics.

Reactive Oxygen, Nitrogen, and Sulfur Species (RONSS) as a Metabolic Cluster for Signaling and Biostimulation of Plants: An Overview

This review highlights the relationship between the metabolism of reactive oxygen species (ROS), reactive nitrogen species (RNS), and H₂S-reactive sulfur species (RSS). These three metabolic pathways, collectively termed reactive oxygen, nitrogen, and sulfur species (RONSS), constitute a conglomerate of reactions that function as an energy dissipation mechanism, in addition to allowing environmental signals to be transduced into cellular information. This information, in the form of proteins with posttranslational modifications or signaling metabolites derived from RONSS, serves as an inducer of many processes for redoxtasis and metabolic adjustment to the changing environmental conditions to which plants are subjected. Although it is thought that the role of reactive chemical species was originally energy dissipation, during evolution they seem to form a cluster of RONSS that, in addition to dissipating excess excitation potential or reducing potential, also fulfils essential signaling functions that play a vital role in the stress acclimation of plants. Signaling occurs by synthesizing many biomolecules that modify the activity of transcription factors and through modifications in thiol groups of enzymes. The result is a series of adjustments in plants' gene expression, biochemistry, and physiology. Therefore, we present an overview of the synthesis and functions of the RONSS, considering the importance and implications in agronomic management, particularly on the biostimulation of crops.

Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow

As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses.

Are the somatic mutation and tissue organization field theories of carcinogenesis incompatible?

Two drastically different approaches to understanding the forces driving carcinogenesis have crystallized through years of research. These are the somatic mutation theory (SMT) and the tissue organization field theory (TOFT). The essence of SMT is that cancer is derived from a single somatic cell that has successively accumulated multiple DNA mutations, and that those mutations occur on genes which control cell proliferation and cell cycle. Thus, according to SMT, neoplastic lesions are the results of DNA-level events. Conversely, according to TOFT, carcinogenesis is primarily a problem of tissue organization: carcinogenic agents destroy the normal tissue architecture thus disrupting cell-to-cell signaling and compromising genomic integrity. Hence, in TOFT the DNA mutations are the effect, and not the cause, of the tissue-level events. Cardinal importance of successful resolution of the TOFT versus SMT controversy dwells in the fact that, according to SMT, cancer is a unidirectional and mostly irreversible disease; whereas, according to TOFT, it is curable and reversible. In this paper, our goal is to outline a plausible scenario in which TOFT and SMT can be reconciled using the framework and concepts of the self-organized criticality (SOC), the principle proven to be extremely fruitful in a wide range of disciplines pertaining to natural phenomena, to biological communities, to large-scale social developments, to technological networks, and to many other subjects of research.

Field-Control, Phase-Transitions, and Life's Emergence

Instances of critical-like characteristics in living systems at each organizational level (bio-molecules to ecosystems) as well as the spontaneous emergence of computation (Langton), do suggest the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics - lacking the "soft-matter" response properties of today's complex bio-molecules - have dissipated energy from primordial reactions (eventually reducing CO(2)) in a controlled manner for their "ordering"? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the "functional-takeover" of a soft magnetic scaffold by organics (c.f. Cairns-Smith's "crystal-scaffold"). A field-controlled structure offers a mechanism for boot-strapping - bottom-up assembly with top-down control: its super-paramagnetic colloidal components obey reversible dynamics, but its dissipation of magnetic (H)-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic dipolar network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically oriented system (trimming the phase-space via sterically coupled organics) toward a series of phase-transitions with appropriate organic replacements "taking-over" its functions. Where available, experiments are cited in support of these speculations and for designing appropriate tests.