Endless forms of endless formation - The morphogenesis of organisms and scientific objects

The present article proceeds from the premises that living forms and abstract formalization come into being by similar mechanisms (e.g., random variation, selection, conventions) and have similar properties (e.g., semiosis, stasis and complexity). These convergences justify the comparative analysis of form's development, evolution and action in both fields. Here we shall focus on the notion of "endless forms" advanced by Darwin's seminal work in evolutionary biology "On The Origin of Species" to discuss the various ways in which it relates to biological formation. I shall explore the idea of "infinitude of evolved forms" through the lens of the five connotations of the word "endless" provided by the Merriam-Webster Thesaurus dictionary, which are: perpetual; incomputable; manifold; unfinished; steady. From each synonym chosen, a new iteration of dictionary search was made to produce a list of terms that are used in the reviewed literature to describe biological morphogenetic features, which are respectively: reproducible, unpredictable, additive, undetermined, the end of their own formation. In conclusion, I propose a tentative mapping between each of these five connotations and the biological processes at work in their making, which are, respectively: 1) copying organic information; coding organic signs; manufacturing organic meaning 2) natural variation, natural selection, natural conventions; 3) multilevel organization, differentiation/development, complexity; 4) ambiguity, degeneracy, semiotic thresholds; 5) homeostasis, autopoiesis, codepoiesis. The processes discussed here gained salience as developments, additions, or nuances to Darwin's original theory. It must be noted that, even though the discussion is mainly framed by Code Biology as a source of conceptualization, inputs from a wide range of theoretical perspectives will be given emphasis when suitable.

Code biology and aesthetics

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.

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).

Revisiting Carl Jung's archetype theory a psychobiological approach

This paper delves into the concept of archetypes, universal patterns of behavior and cognition, and proposes a novel tripartite model distinguishing between structural, regulatory, and representational archetypes. Drawing on insights from code biology, neuroscience, genetics, and epigenetics, the model provides a nuanced framework for understanding archetypes and their role in shaping cognition and behavior. The paper also explores the interplay between these elements to express representational archetypes. Furthermore, it addresses the informational capacity of the genome and its influence on post-natal development and the psyche. The paper concludes by discussing the future trajectory of psychology, emphasizing the need for an integrative approach that combines our understanding of social constructs with insights into our inherent organizational propensities or archetypes. This exploration holds the potential to advance our understanding of the human condition.

The principle "like begets like" in algebra-matrix genetics and code biology

The article is devoted to analysis of emergent properties of the system of binary oppositions in the genetic code ensemble. The epochal model of the double helix of DNA by Watson and Crick showed that the multiple reproduction of genetic information on DNA strands uses the ancient principle "like begets like" based on the simple complementarity in pairs of nucleobases. Each of these pairs is built on the binary opposition "purine-pyrimidine". But the system of DNA n-plet alphabets and genetic coding is much richer in types of binary oppositions, which also have some coding meanings related to this principle. The article contains the results of the application of the author's "method of hierarchy binary stochastics" (HBS-method) to the analysis of the quasi-stochastic organization of binary sequences of hydrogen bonds in genomic single-stranded DNAs. This analysis revealed hidden probability rules related to dichotomous fractal-like probability trees. The relationship between inherited bodily dichotomies in living organisms and the discovered probability dichotomies in information sequences of genomic DNAs is discussed. The encoding properties of molecular binary oppositions in the DNA nucleotide system allows the algorithmic construction of (2n∗2n)-matrices of probabilities of n-plets in these binary sequences, which are matrix representations of 2n-dimensional hyperbolic numbers. Connections of these multidimensional numbers with some inherited physiological phenomena and deep neural networks are noted. A unified algebra-numeric certification of the DNAs of genomes and genes - based on these multidimensional numerical systems - is proposed.

Reflexive structure of the conscious subject and the origin of language codes

The code paradigm in biological and social sciences arises to Aristotle. For conscious activity, Aristotle introduced the notion of reflexive self-awareness in sense perception. This reflexive process generates the codes that signify sensual perceptive events and constrain human behavior. Coding systems grow via the generation of hypertextual statements reflecting new meanings in the process defined by Marcello Barbieri as a codepoiesis. It results in the establishment of higher-level codes (metacodes) forming the semiotic screen that has a nature of the set of perceived objects internalized by the conscious subject in encoding the symbolic actions. The characteristic feature of the semiotic screen consists in its property of being shared between the communicating agents. A sufficient complexity of nervous system, through the appearance of mirror neurons that are fired both when a subject executes certain action and when he observes another subject performing a similar action, represents a prerequisite for the emergence of reflexive codes in evolution. The codes appearing as a result of reflexive awareness and establishing different sociotypes, span from the symbolic systems of art and music through the common language to the formal language of logic and mathematics. Social dynamics is based on the implementation of reflexive coding activity and results in the growth and decay of social systems and civilizations.

Nothing in evolution makes sense except in the light of code biology

This article highlights the potential contribution of biological codes to the course and dynamics of evolution. The concept of organic codes, developed by Marcello Barbieri, has fundamentally changed our view of how living systems function. The notion that molecular interactions built on adaptors that arbitrarily link molecules from different "worlds" in a conventional, i.e., rule-based way, departs significantly from the law-based constraints imposed on livening things by physical and chemical mechanisms. In other words, living and non-living things behave like rules and laws, respectively, but this important distinction is rarely considered in current evolutionary theory. The many known codes allow quantification of codes that relate to a cell, or comparisons between different biological systems and may pave the way to a quantitative and empirical research agenda in code biology. A starting point for such an endeavour is the introduction of a simple dichotomous classification of structural and regulatory codes. This classification can be used as a tool to analyse and quantify key organising principles of the living world, such as modularity, hierarchy, and robustness, based on organic codes. The implications for evolutionary research are related to the unique dynamics of codes, or ´Eigendynamics´ (self-momentum) and how they determine the behaviour of biological systems from within, whereas physical constraints are imposed mainly from without. A speculation on the drivers of macroevolution in light of codes is followed by the conclusion that a meaningful and comprehensive understanding of evolution depends including codes into the equation of life.

Ensuring wholeness: Using Code Biology to overcome the autonomy-heteronomy divide

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.

The modularity codes

The hypothesis presented here is that codes as described by Marcello Barbieri are the fundamental principle behind biological modularity. Modularity has been studied in different life science disciplines, especially in the fields of evolution and development, as well as in network biology, yet there is still no consensus on how modularity evolved itself. Modularity is basically the functional integrity of multiple molecular players involved in a common process. Codes as defined by Barbieri describe a tripartite relation involving an adapter molecule connecting two other independent types of molecules to each other in an arbitrary, but semantic manner. This form of interaction goes beyond predictable mere physical or chemical one-to-one interactions and always relates three molecules to each other. A code of three topologically related molecules interacting in a defined order may be considered a minimal module on its own, but when one regards a set of multiple, overlapping tripartite, coded interactions, this paves the way towards logically and functionally consistent coherence of multiple participants of a certain, modular process. A theoretical outline of how to identify and describe such modular structures is given.

The lower threshold as a unifying principle between Code Biology and Biosemiotics

Whether we emphasize the notion of 'sign' or the notion of 'code', either way the main interest of biosemiotics and Code Biology is the same, and we argue that the idea of the lower threshold is what still unifies these two groups. Code Biology concentrates on the notion of code: living organisms are defined as code-users or code-makers, and so it may be called the 'lower coding threshold' in this case. The semiotic threshold on the other hand is a concept without a specific definition. There are many possible ways of understanding this term. In order to maintain the lower threshold as the unifying concept between Code Biology and biosemiotics, it is important to be very clear about where this threshold is located and how it is defined. We focus on establishing the lower semiotic threshold at protein biosynthesis, and we propose basing the semiotic understanding of the lowest life forms on the following criteria: arbitrariness, representation, repetition, historicity and self-replication. We also offer that this definition of the lower threshold need not include the notion of interpretation, in the hope that this newly specified common principle of the lower threshold be accepted as a way forward in the conversation between Code Biology and biosemiotics.

Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology

According to the founders of quantum mechanics and quantum biology P. Jordan and E. Schrödinger, the main difference between living and inanimate objects is the dictatorial influence of genetic molecules on the whole living organism. Code biology can make a valuable contribution to understanding this dictatorial influence of genetic molecules whose ensemble is endowed with many interconnected alphabets and codes. The paper is devoted to probability rules of nucleotide sequences of single-stranded DNA in eukaryotic and prokaryotic genomes. These rules are connected with n-plets alphabets of DNA whose nucleotide sequences are considered as bunches of many parallel texts written in interconnected n-plets alphabets. The rules draw attention to genomic phenomena of special tetragroupings of n-plets and new genomic symmetries. A generalization of the second Chargaff's rule is described. They show the existence of long-range coherence in genomic DNA sequences and reveal new connections of structural features of genomic sequences with formalisms of quantum mechanics and quantum informatics. The author supposes that the received results are related to the known vibration-resonance theory of G. Frohlich about long-range coherence in biological systems, that is, about collective quantum effects there. The possible influence of the described genetiс probability phenomena on the genetically inherited physiological structures is noted and discussed.

Archetypes and code biology

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.

Causal and non-causal explanations in code biology

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).

On the context-sensitive grammar of the genetic code

We address the possibilities of the semiotic description of the genetic information as a dual and self-replicative system of correspondence between its biochemical substance and semiotic form of organization. Combining the principles of contextual dependence and arbitrariness of sign leads to the conclusion that the genetic code's primary elements (nucleotides) can be considered not as biochemical constants but as semiotic or, more precisely, grammatical variables. We suggest describing the genetic code as a language, consisting of 1) units of the alphabet; 2) a vocabulary that includes meaningful items and the rules of correspondence between units of different levels; 3) context-sensitive grammar - a system of rules for the formation of units based on abstract grammatical categories.

Code biology and the problem of emergence

It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the 'conventional' nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen's paradox of how a complex code could originate, I will argue that along with Barbieri's efforts to account for the origins of life based on the ribosome and then to account for the refined codes through a process of ambiguity reduction, something more is required. Barbieri has not provided an adequate account of emergence, or the basis for providing such an account. I will argue that Stanley Salthe has clarified to some extent the nature of emergence by conceptualizing it as the interpolation of new enabling constraints. Clearly, codes can be seen as enabling constraints. How this actually happens, though, is still not explained. Stuart Kauffman has grappled with this issue and shown that it radically challenges the assumptions of mainstream science going back to Newton. He has attempted to reintroduce real possibilities or potentialities into his ontology, and argued that radically new developments in nature are associated with realizing adjacent possibles. This is still not adequate. What is also involved, I will suggest, utilizing concepts developed by the French natural philosopher Gilbert Simondon, is 'transduction' as part of 'ontogenesis' of individuals in a process of 'individuation', that is, the emergence of 'individuals' from preindividual fields or milieux.

Life and living beings under the perspective of organic macrocodes

A powerful and concise concept of life is crucial for studies aiming to understand the characteristics that emerged from an inorganic world. Among biologists, the most accepted argument define life under a top-down strategy by looking into the shared characteristics observed in all cellular organisms. This is often made highlighting (i) autonomy and (ii) evolutionary capacity as fundamental characteristics observed in all cellular organisms. Along the present work, we assume the framework of code biology considering that biology started with the emergence of the first organic code by self-organization. We reinforces that the conceptual structure of life should be reallocated from the ontology class of Matter to its sister class of Process. Along the emergence and early evolution of biological systems, biological codes changed from open systems of "naked" molecules (at the progenote era), to close, encapsulated systems (at the organismic era). Living beings appeared at the very moment when nucleic acids with coding properties became encapsulated. This led to the origin of viruses and, then, to the origin of cells. In this context, we propose that the single character that makes a clear distinction between the abiotic and the biotic world is the capacity to process organic codes. Thus, life appears with the self-assembly of a genetic code and evolves by the emergence of other overlapping codes. Once life has been clearly conceptualized, we go further to conceptualize organisms, parents, lineages, and species in terms of code biology.

On the origin of mental representations

The symbol grounding problem raises its head in the fields of the philosophy of AI, philosophy of psychology and philosophy of cognitive sciences. The solution to the symbol grounding problem must account for the genesis of mental representations in the world. It has to offer a strategy for grounding mental representations in the objective domain. Orthodox representationalist theories do not provide a satisfactory reply to the symbol grounding problem. On the other hand, there are embodied-enactivist approaches that dissolve the problem but only at the cost of representations and internal phenomenal states. The code model of biosemiotics provides a biologically viable (i.e., mechanistic) venue for developing a new solution to the problem. For the same reason, it could reconcile representationalism to the embodied approach.

Semiotic realms: Codes, language, mind. A psychoanalytic perspective

Exploring continuity from organic codes and natural signals to cultural sign and symbol systems, this paper is undergirded conceptually by a semiotic tree depicting an ascending hierarchy of semiotic forms. Originating in underground roots from a medley of organic codes, the human use of codified meanings surfaces in the trunk, (in Latin Caudex or Codex), our simplest semiotic instrument. Ascending branches represent natural and man-made signals, and indicative and denotative signs, rising to more complex fully symbolic abstract forms in various sign systems. Each level corresponds to a different mental organization, determining the quality and nature of subjective experience and knowledge, epistemology and information being closely tied to semiotic and semantic factors. The psychoanalytic method focuses on unconscious phenomena descending interpretively below the limen of linguistic consciousness generating a semantic field that exposes multiple levels and kinds of meanings. This positions us optimally to observe different semiotic organizations, a multi-coded spectrum of human enacted and mediated meanings that is best systemized along developmental lines (Aragno, 1997/,2016). Freud's decoding the grammar of dreams enables the linguistic interpretation of condensed and displaced pictographic representations of a deeply unconscious 'Primary Process' semantic bridging biological and psychological processes that are ongoing throughout life. A multilayered model of mind reframes theoretical understanding around epigenetic and morphological principles that are applicable to phylogenetic and ontogenetic development. From this revised meta-theoretical base, this paper illustrates how language absorbs and often serves deep unconscious functions, as well as, conversely, elevating abstract cognition and conscious articulation. A bio-semiotic multiple-code model of mind is based on progressive stages in the development of symbolization, a cerebral faculty unique to our species, distinguishing us from all other animals, without which we could neither speak nor conceive of "Mind" at all. Conscious 'mind' emerges through a signifying act, assigning a name to a 'person' or 'thing' that can be represented within, in its absence. This simple concept has far reaching cognitive/psychological consequences impacting on all aspects of experience and knowledge.

The evolutionary dynamics of language

The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits. (i) It makes a bridge to neurobiological models of the brain that have also adopted an evolutionary dynamics point of view, thus opening a new horizon for studying how human brains achieve the remarkably complex competence for language. And (ii) it suggests a new foundation for studying cultural language change as an evolutionary dynamics process. The paper sketches this novel perspective, provides references to empirical data and computational experiments, and points to open problems.

How prokaryotes 'encode' their environment: Systemic tools for organizing the information flow

An important issue related to code biology concerns the cell's informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows. The analysis here of the simplest cells will involve two basic aspects. On the one side, the molecular apparatuses of the prokaryotic signaling system, with all its variety of environmental signals and component pathways (which have been called 1-2-3 Component Systems), including the role of a few second messengers which have been pointed out in bacteria too. And in the other side, the gene transcription system as depending not only on signaling inputs but also on a diversity of factors. Amidst the continuum of energy, matter, and information flows, there seems to be evidence for signaling codes, mostly established around the arrangement of life-cycle stages, in large metabolic changes, or in the relationships with conspecifics (quorum sensing) and within microbial ecosystems. Additionally, and considering the complexity growth of signaling systems from prokaryotes to eukaryotes, four avenues or "roots" for the advancement of such complexity would come out. A comparative will be established in between the signaling strategies and organization of both kinds of cellular systems. Finally, a new characterization of "informational architectures" will be proposed in order to explain the coding spectrum of both prokaryotic and eukaryotic signaling systems. Among other evolutionary aspects, cellular strategies for the construction of novel functional codes via the intermixing of informational architectures could be related to the persistence of retro-elements with obvious viral ancestry.