Search

Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935). These works became a bibliographical rarity. A complete English translation of "Theoretical Biology" is an important task for the future. [ABSTRACT FROM AUTHOR]

Ervin Bauer (1890–1938) was the first to build a general molecular-based biological theory. He defined the basic principles of theoretical biology from a thermodynamic perspective, focusing on the capacity of biological systems to produce and support the state of sustainable non-equilibrium. His central work "Theoretical Biology" (1935) was written long before modern advances in molecular biology, genetics, and information theory. Ervin Bauer and his wife Stefánia were executed in Stalin's Great Terror. This paper presents a brief introduction to Ervin Bauer's life and includes his short biography. [ABSTRACT FROM AUTHOR]

Ervin Bauer was the only biologist who recognized that the best way to develop theoretical biology on an equal footing with theoretical physics was to follow the method that has ensured the great successes of modern theoretical physics: the general method of science. Following this method, he succeeded to find the universal principle of biology. From this principle he managed to derive all the basic equations of biology, that of metabolism, reproduction, growth, responsiveness and successfully explained all the fundamental phenomena of life. In this paper, I introduce Bauer's theoretical biology and discuss whether he understood it within the framework of the modern physical worldview, or in a broader framework. I point out that the theoretical biology of Ervin Bauer is the first to go beyond the physical worldview, to establish a deeper, biological worldview, and thus to represent a major advance in our understanding of the nature of life, with a significance even greater than that of the Copernican turn. Clarifying the difference between the living and the non-living, it is important to consider the difference between machines and living organisms. It is well known that machines are the manifestations of a dual control; globally, their behavior is controlled by their given structure, while locally, their behavior is governed by the physical laws. Based on Bauer's theoretical biology, it is pointed out that living organisms manifest a three-level causality; the 'additional', biological level corresponds to the autonomous, time-dependent control of their structures. [ABSTRACT FROM AUTHOR]

A range of studies published in the last few decades promotes the cognitive aspects of life: all organisms, from bacteria to mammals, are capable of sensing/perception, decision-making, problem-solving, learning, and other cognitive functions, including sentience and consciousness. In this paper I present a scientific and philosophical synthesis of these studies, leading to an integrated view of cognitive biology. This view is expressed through the four principles applicable to all living systems: (1) sentience and consciousness, (2) autopoiesis, (3) free energy principle and relational biology, and (4) cognitive repertoire. The principles are circular, and they reinforce themselves. The circularity is not rigid, meaning that hierarchical and heterarchical shifts are widespread in the biosphere. The above principles emerged at the dawn of life, with the first cells, bacteria and archaea. All biogenic forms and functions that emerged since then can be traced to the first cells – indivisible units of biological agency. Following these principles, I developed the concept of biocivilisations to explain various forms of social intelligence in different kingdoms of life. The term biociviloisations draws on the human interpretation of the concept of civilisation, which searches for non-human equivalents of communication, engineering, science, medicine, art, and agriculture, in all kingdoms of life by applying the principles of cognitive biology. Potential avenues for testing the concept of biocivilisations are highlighted. [ABSTRACT FROM AUTHOR]

This paper lays the foundations for an investigation of aesthetics in the light of the theories proposed in the field of Code Biology. Starting from the research objectives that aesthetics has set since its origins, a comparison is made with those aesthetic theories that have been most concerned with the sensory approach to the environment, with the attempt to unite human sciences and the main biological discoveries. Thanks to the scientifically grounded insights offered by Code Biology, we will first outline the field of interest of aesthetics and its foundations, and then delineate certain boundaries – such as those between sensations and perceptions, the aesthetic process and the work of art – that characterise such a field of research. Particular attention will be paid to locating the aesthetic process within the more general cognitive processes, i.e. the three cognitive macrosystems that enable the modelling of the world. [ABSTRACT FROM AUTHOR]

Abstract Tree trunks and other cylindrical objects, where aggregated insects live, represent a very specific world for predator-prey interactions, which must differ from the situation on a 2D plane. In the present paper, in order to gain a better understanding of the specificity of predator-prey interaction in a cylindrical space, we applied a theoretical approach. Here we introduce a numerical model that allows us to test the effect of different interaction properties between predator and aggregated prey on the plane (2D) and on a cylinder (3D), taking into consideration different abilities of predators to visually detect the prey in these two types of space. The main aim was to test these interactions in an environment, which more realistically reproduces the conditions where aggregated insects usually live. We showed that the aggregation in conjunction with a specific environment may bring additional advantages for the prey. When one prey subgroup aggregates on the other side of the tree trunk and becomes invisible behind the horizon of events for the predator, the subgroup will survive with an extremely high probability. After all, the predator moving along one side of the tree will finally loose the major group completely. [ABSTRACT FROM AUTHOR]

In the philosophy of science, we can consider debates about the nature of non-causal explanations in general (e.g. Reutlinger, Saatsi 2018; Lange 2017) and then especially those in the life sciences (e.g. Huneman, 2018; Kostić 2020). These debates are accompanied by the development of a new mechanism that is becoming the major response to the nature of scientific explanation in the life sciences (e.g. Craver, Darden 2013; Craver 2006); and also by the development of a design explanation (e.g. Eck, Mennes 2016) that represents a modern variant of a functional explanation. In this paper, we will methodically: 1. evaluate the plurality of explanatory strategies in contemporary science (chapter 2). 2. describe the mechanical philosophy and mechanistic explanation (Glennan 2016; Craver, Darden 2013, etc.) (chapter 3). 3. explicate the role of mechanisms in code biology (Barbieri 2015, 2002, etc.) and its relation to the new mechanism (chapter 4). 4. fulfill the main goal of the paper – to apply mechanistic explanations in code biology (Barbieri 2019, etc.) and to apply their suitability for this scientific domain (chapter 5). [ABSTRACT FROM AUTHOR]

In this paper, it is argued that Jakob von Uexküll’s “search image” notion, the original version of this notion within ethology, is still of use. A search image, in Uexküll’s sense, is an imagined object that an organism has in mind when it searches for something. Uexküll’s conception of the search image is useful both for understanding the theoretical context of contemporary notions of search images, and with an eye to envisioning possible future developments of the idea. Uexküll’s classical notion differs from contemporary versions in that it has a wider application, and is therefore of greater relevance to theoretical biology and cognitive science. It constituted an integral part of his ground-breaking Umwelt theory, stressing the fundamental plasticity of the Umwelt, the subjective lifeworld of an animal or human subject. In a contemporary development of Umwelt theory, expressed by the tripartite Umwelt model , the search image notion represents a key connection between the directly experienced core Umwelt and the mediated Umwelt. However, the key function that schemata have in cognitive processes is also the starting point for mistakes in perception. This article details both the constructive function search images have in animal and human perception, and the mismatches in perception they can lead to. It also explains how the existence of search images can help explain puzzles concerning subjective and neural time in contemporary cognitive science. [ABSTRACT FROM AUTHOR]

This paper presents an alternative to Autopoietic Enactivism in the form of a Code Biology-informed account on human sense-making. It demonstrates the possibility of avoiding a dualism between, on the one hand, the autonomy of individual sense-makers and, on the other, the heteronomy of social facts. This is possible because code biological principles are pertinent to different levels of biological and non-biological organization and cut across the organismic self—non-self border. Analytically, one can maintain the overall integrity of an agent as a separable unit of (inter)action while also avoiding an autonomy-heteronomy divide. We therefore emphasise the constitutive role of codified relations that, while irreducible to operational closure, connect the sense-making agent's social interactions to those of other agents. The move grants a central, constitutive role to external norms (or, heteronomy) as altering the internal, embodied integrity of an autonomous agent. Drawing on the case of prosthetics use in amputees, we show that successful integration of a prothesis cannot be reduced to the substitution of a missing limb. Rather, it demands experienced bodily wholeness on the part of the agent which can only be achieved by attuning and adapting to use of a prosthesis while also internalizing social norms and values. It is concluded that many aspects of the living actualize codified relations which incorporate both heteronomous and autonomous traits. [ABSTRACT FROM AUTHOR]

Abstract: At first glance, biology and computer science are diametrically opposed sciences. Biology deals with carbon based life forms shaped by evolution and natural selection. Computer Science deals with electronic machines designed by engineers and guided by mathematical algorithms. In this brief paper, we review biologically inspired computing. We discuss several models of computation which have arisen from various biological studies. We show what these have in common, and conjecture how biology can still suggest answers and models for the next generation of computing problems. We discuss computation and argue that these biologically inspired models do not extend the theoretical limits on computation. We suggest that, in practice, biological models may give more succinct representations of various problems, and we mention a few cases in which biological models have proved useful. We also discuss the reciprocal impact of computer science on biology and cite a few significant contributions to biological science. [Copyright &y& Elsevier]

As a clinical psychologist, I observe stereotyped formulas of behavior in action every day in the consulting room, despite differences in age, race, or culture; they present themselves as codified rules or typical modes of behavior in archetypical situations. Such circumstances coincide with what C.G. Jung defended: the existence of archetypes stored in an inherited/phylogenetic repository, which he called the collective unconscious – somewhat similar to the notion of an ethogram , as shown by ethology. Psychologists can use a perspective to facilitate understanding the phenomenon: the code biology perspective (Barbieri 2014). This approach can help us recognize how these phenomenological events have an ontological reality based not only on the existence of organic information but also on the existence of organic meaning. We are not a tabula rasa (Wilson 2000): despite the explosive diversification of the brain and the emergence of conscience and intentionality, we observe the conservation of basic instincts and emotions (Ekman 2004 ; Damasio 2010) not only in humans but in all mammals and other living beings; we refer to the neural activity on which the discrimination behavior is based, i.e., the neural codes. The conservation of these fundamental set-of-rules or conventions suggests that one or more neural codes have been highly conserved and serves as an interpretive basis for what happens to the living being who owns them (Barbieri 2003). Thus, archetypes' phenomenological reality can be understood not as something metaphorical but as an ontological (phylogenetic) fact (Goodwyn 2019). Furthermore, epigenetic regulation theories present the possibility that the biomolecular process incorporates elements of the context where it takes place; something fundamental to understand our concept – the archetype presents itself as the mnesic remnant of the behavioral history of individuals who preceded us on the evolutionary scale. In short: brains are optimized for processing ethologically relevant sensory signals (Clemens et al., 2015). From the perspective of the corporeal mind (Searle 2002), in this paper, we will show the parallels between code biology and the concept of the archetype, as Jung defended it and as it appears in clinical practice. [ABSTRACT FROM AUTHOR]

Abstract: Monte Carlo methods have received much attention recently in the literature of phylogenetic tree construction. However, they often suffer from two difficulties, the curse of dimensionality and the local-trap problem. The former one is due to that the number of possible phylogenetic trees increases at a super-exponential rate as the number of taxa increases. The latter one is due to that the phylogenetic tree has often a rugged energy landscape. In this paper, we propose a new phylogenetic tree construction method, which attempts to alleviate these two difficulties simultaneously by making use of the sequential structure of phylogenetic trees in conjunction with stochastic approximation Monte Carlo (SAMC) simulations. The use of the sequential structure of the problem provides substantial help to reduce the curse of dimensionality in simulations, and SAMC effectively prevents the system from getting trapped in local energy minima. The new method is compared with a variety of existing Bayesian and non-Bayesian methods on simulated and real datasets. Numerical results are in favor of the new method in terms of quality of the resulting phylogenetic trees. [Copyright &y& Elsevier]

Abstract: In this paper we consider networks of evolutionary processors with splicing rules and permitting context (NEPPS) as language generating and computational devices. Such a network consists of several processors placed on the nodes of a virtual graph and are able to perform splicing (which is a biologically motivated operation) on the words present in that node, according to the splicing rules present there. Before applying the splicing operation on words, we check for the presence of certain symbols (permitting context) in the strings on which the rule is applied. Each node is associated with an input and output filter. When the filters are based on random context conditions, one gets the computational power of Turing machines with networks of size two. We also show how these networks can be used to solve NP-complete problems in linear time. [Copyright &y& Elsevier]

Abstract: Membrane systems are purely abstract computational models afar inspired by biological cells, their membranes, and their biochemistry. The inherently parallel nature of membrane systems makes them obviously highly inefficient to execute on a sequential von Neumann computer architecture and in addition, programming a membrane system is often a painstakingly difficult undertaking. The main goal of this paper is to provide some key elements for bringing membrane systems from the abstract model closer to a genuine, novel, and unconventional in silico computer architecture. In particular, we will address the mechanisms of self-configuration and self-replication on a macroscopic level and will discuss some general issues related to genuine hardware realizations on the microscopic level. [Copyright &y& Elsevier]

Abstract: In this paper we develop a theory to describe stochastic influences on the fate of new species with non-linear growth rates in evolutionary processes. We develop a theoretical framework based on notions of species, network, innovation, competition, survival and fitness. We introduce a stochastic picture describing the role of fluctuations in the survival of new species in non-linear systems. In particular we consider the fate of new species with non-linear growth. As an application of the general model framework we consider the fate of ‘rare species’ in early biological evolution. We show that hypercycle systems do not represent the end of the evolutionary process as they may evolve further in small niches. This has implications for different types of applications ranging from biological systems on one level to socio-technological systems on a more metaphoric level. [Copyright &y& Elsevier]

Abstract: The structure of a system influences its adaptability. An important result of adaptability theory is that subsystem independence increases adaptability [Conrad, M., 1983. Adaptability. Plenum Press, New York]. Adaptability is essential in systems that face an uncertain environment such as biological systems and organizations. Modern organizations are the product of human design. And so it is their structure and the effect that it has on their adaptability. In this paper we explore the potential effects of computer-based information processing on the adaptability of organizations. The integration of computer-based processes into the dynamics of the functions they support and the effect it has on subsystem independence are especially relevant to our analysis. [Copyright &y& Elsevier]

Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two aspects of SET. First, using the concept of "universal symbiogenesis", developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent "viral eukaryogenesis" hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory. [ABSTRACT FROM AUTHOR]

Church's Thesis is a metamathematical hypothesis that says the concepts of effective calculability and computability are coextensive. It is reasonable to consider everything that happens in the material world to be 'effective'. If Church's Thesis were true in the natural world, then it would mean that all material processes could be expressed in purely syntactic terms. A corollary in relational biology is that a living system must have noncomputable models. Thus the existence of living systems implies that Church's Thesis is false as a physical proposition. The paper begins with a review of the tenets of relational biology, which is the standpoint from which this exposition on the Foundations of Mathematics and Theoretical Biology is composed. [ABSTRACT FROM AUTHOR]