Philosophy in Reality: Scientific Discovery and Logical Recovery

Coupling and biological free-energy transduction processes as a bridge between physics and life: Molecular-level instantiation of Ervin Bauer's pioneering concepts in biological thermodynamics

The nonequilibrium coupled processes of oxidation and ATP synthesis in the biological process of oxidative phosphorylation (OXPHOS) are fundamental to all life on our planet. These steady-state energy transduction processes ‒ coupled by proton and anion/counter-cation concentration gradients in the OXPHOS pathway ‒ generate ∼95 % of the ATP requirement of aerobic systems for cellular function. The rapid energy cycling and homeostasis of metabolites involved in this coupling are shown to be responsible for maintenance and regulation of stable nonequilibrium states, the latter first postulated in pioneering biothermodynamics work by Ervin Bauer between 1920 and 1935. How exactly does this occur? This is shown to be answered by molecular considerations arising from Nath's torsional mechanism of ATP synthesis and two-ion theory of energy coupling developed in 25 years of research work on the subject. A fresh analysis of the biological thermodynamics of coupling that goes beyond the previous work of Stucki and others and shows how the system functions at the molecular level has been carried out. Thermodynamic parameters, such as the overall degree of coupling, q of the coupled system are evaluated for the state 4 to state 3 transition in animal mitochondria with succinate as substrate. The actual or operative P to O ratio, the efficiency of the coupled reactions, η, and the Gibbs energy dissipation, Φ have been calculated and shown to be in good agreement with experimental data. Novel mechanistic insights arising from the above have been discussed. A fourth law/principle of thermodynamics is formulated for a sub-class of physical and biological systems. The critical importance of constraints and time-varying boundary conditions for function and regulation is discussed in detail. Dynamic internal structural changes essential for torsional energy storage within the γ-subunit in a single molecule of the FOF1-ATP synthase and its transduction have been highlighted. These results provide a molecular-level instantiation of Ervin Bauer's pioneering concepts in biological thermodynamics.

Toward the Relational Formulation of Biological Thermodynamics

Classical thermodynamics employs the state of thermodynamic equilibrium, characterized by maximal disorder of the constituent particles, as the reference frame from which the Second Law is formulated and the definition of entropy is derived. Non-equilibrium thermodynamics analyzes the fluxes of matter and energy that are generated in the course of the general tendency to achieve equilibrium. The systems described by classical and non-equilibrium thermodynamics may be heuristically useful within certain limits, but epistemologically, they have fundamental problems in the application to autopoietic living systems. We discuss here the paradigm defined as a relational biological thermodynamics. The standard to which this refers relates to the biological function operating within the context of particular environment and not to the abstract state of thermodynamic equilibrium. This is defined as the stable non-equilibrium state, following Ervin Bauer. Similar to physics, where abandoning the absolute space-time resulted in the application of non-Euclidean geometry, relational biological thermodynamics leads to revealing the basic iterative structures that are formed as a consequence of the search for an optimal coordinate system by living organisms to maintain stable non-equilibrium. Through this search, the developing system achieves the condition of maximization of its power via synergistic effects.

On Semiotics Perspectives of Computational Thinking: Unravelling the “Pamphlet” Approach, a Case Study

Computational thinking (CT) is in the midst of an ongoing debate about its scope and definitions. There is a trend away from a “traditional” computer science-inspired agenda towards a focus on universal competences for today’s labor market. However—and this is the motivation behind the research—the shift described is just an unconscious attempt to reveal the immanent nature of CT as an evolving semiotic phenomenon. The aim of this study is to explore directions and perspectives for the further development of CT and related methodological design approaches. As a research strategy, this article utilizes a case study on the presented set of resources dedicated to CT early education and reveals it in terms of multimodal discourse analysis. As a result, a landscape of future CT trends is presented, uncovering CT from a multimodal semiotic perspective. This article discusses various issues related to CT and its multimodal semiotics nature, perspectives on the design of CT-related resources and additional educational issues such as the perspectives on instructional approaches for CT teaching. We conclude that CT as a social phenomenon is in the process of an evolutionary transformation of its constitutive structure in the direction of further revealing its agentive semiotic nature.

Mathematics in biological reality: The emergence of natural computation in living systems

Mathematics is a powerful tool to express the computable part of the reality of the physical world. For living systems, mathematical relations emerge internally as an abstracting capacity in the course of development and adaptation to the external world. All living systems possess internal coding structures which represent their embedded description. They are anticipatory in the sense that the embedded description generates deterministic model of their behavior. If the model does not provide a correct result, they can evolve through the acquisition of new statements inside the embedded description that overcome limitations of the existing model. The newly generated statements acquire meaning in and from the changing environment. The growth of complexity, being a consequence of the internal active adaptation to externality performed by the systems, increases the amount of external work and generates the observed patterns of spatiotemporal structures of evolving systems. In living systems, the symbolic memory constraints are dynamic processes in themselves, co-evolving with the other components of biological systems. Separation of the symbolic memory and the dynamic laws (defined as the epistemic cut), required for self-replication of biological systems, forms the basis for their onto-epistemic relation to reality. In this regard, living systems possess their own internal abstracting capacity and invent mathematics. The digital structure of the genetic code is a manifestation of this mathematics.

The emergence of a fractal structure of formal logic via the spatiotemporal reflexive self-identification

In this paper, we aim to analyze the structure of formal logic in relation to its emergence as a universal tool for understanding and description of reality. There are some extended variations of logic that treat time and/or space (e.g. temporal logic), however in general, formal logic is regarded as universal. This universality makes formal logic neither spatial nor temporal. Nevertheless, the emergence of formal logic takes place in time and space and its operation is characterized by the simultaneous temporal and spatial features. We realize these aspects of formal logic along the line of the previously developed model of the Double Homunculus (Sawa K., Igamberdiev A.U., 2016, BioSystems 144, 1-7) which can be seen as an emergence of logic. A diagrammatic representation of this concept reveals fractal structures. At the same time, we present actual logical connectives on these fractal figures with the transformations over time and space. This can provide the basis for understanding the relationships between time, space, and logic.