Code biology and the problem of emergence

Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics

Biological systems operate toward the maximization of their self-maintenance and adaptability. This is achieved through the establishment of robust self-maintaining configurations acting as attractors resistant to external and internal perturbations. Ervin Bauer (1890-1938) was the first who formulated this essential thermodynamic constraint in the operation of biological systems, which he defined as the stable non-equilibrium state. The latter appears as the basic attractor relative to which biological organization is established. The stable non-equilibrium state represents a generalized cell energy status corresponding to efficient spatiotemporal organization of the fluxes of matter and energy and constantly reproducing the conditions of self-maintenance of metabolism and controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles. This state is realized in the autopoietic structures having closed loops of causation based on the operation of biological codes. The principle of thermodynamic buffering determines the conditions for optimization of the fluxes of load and consumption in metabolism establishing the conditions of metabolic stable non-equilibrium. In developing and evolving biological systems, the principle of stable non-equilibrium is transformed into the principle of increasing external work, which is grounded in the hyper-restorative non-equilibrium dynamics. Bauer's concept of the stable non-equilibrium state puts thermodynamics into the frames of the internal biological causality governing self-maintenance and development of living systems. It can be defined as a relational theory of biological thermodynamics since the standard to which it refers represents the actual biological function rather than the abstract state of thermodynamic equilibrium.

Turing and von Neumann machines: Completing the new mechanism

Turing (1937) introduces a model of code that is followed by other pioneers of computing machines (such as Flowers 1983, Eckert, Mauchly, Brainerd 1945 and others). One of them is John von Neumann, who defines the concept of optimal code in the context of the conception of EDVAC. He later uses it to build on in his theoretical considerations of the universal constructor (von Neumann 1966). Von Neumann (1963) further presents one of the first neural network models, in relation to the work of McCulloch and Pitts (1943), for both theoretical purposes (von Neumann probe) and practical applications (computer architecture of EDVAC). The aim of this paper is (1) to describe the differences between Turing's and von Neumann's conceptualizations of code and the mechanical computing model. Between von Neumann's abstract technical conception (von Neumann 1963 and 1966) and Turing's more concrete biochemical conception (Turing 1952). Furthermore, (2) we want to answer the question why these influential models of mechanisms (predominantly in computer science) have so far been ignored by philosophers of the new mechanism (Machamer, Darden, Craver 2000, Glennan 2017). We will show that these classical models of machines are not only compatible with the new mechanism, but moreover complement it, since they represent a completely separate type of model of mechanism, alongside producing, maintaining and underlying (Zámečník 2021). The final (3) and main goal of our paper will be an attempt to relate von Neumann's and Turing's notion of mechanism to Barbieri's notion of extended mechanism (Barbieri 2015).

Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution

Organismal evolution displays complex dynamics in phase and scale which seem to trend towards increasing biocomplexity and diversity. For over a century, such amazing dynamics have been cleverly explained by the apparently straightforward mechanism of natural selection: all diversification, including speciation, results from the gradual accumulation of small beneficial or near-neutral alterations over long timescales. However, although this has been widely accepted, natural selection makes a crucial assumption that has not yet been validated. Specifically, the informational relationship between small microevolutionary alterations and large macroevolutionary changes in natural selection is unclear. To address the macroevolution-microevolution relationship, it is crucial to incorporate the concept of organic codes and particularly the "karyotype code" which defines macroevolutionary changes. This concept piece examines the karyotype from the perspective of two-phased evolution and four key components of information management. It offers insight into how the karyotype creates and preserves information that defines the scale and phase of macroevolution and, by extension, microevolution. We briefly describe the relationship between the karyotype code, the genetic code, and other organic codes in the context of generating evolutionary novelties in macroevolution and imposing constraints on them as biological routines in microevolution. Our analyses suggest that karyotype coding preserves many organic codes by providing system-level inheritance, and similar analyses are needed to classify and prioritize a large number of different organic codes based on the phases and scales of evolution. Finally, the importance of natural information self-creation is briefly discussed, leading to a call to integrate information and time into the relationship between matter and energy.