The major evolutionary transitions and codes of life

Codes across (life)sciences

The concept of "code" connotes different meanings, intentions, and formalizations. From mathematics and computer sciences to psychology and culture, the term becomes less formal, more diverse, and sometimes appears ambiguous. In biology a growing number of codes ignite a debate about their role in evolution, biocomplexity, and agency, to name just a few. Here, a transdisciplinary group of code scientists attempts to capture the big picture of code research across their fields of interest. In this cross-sectional overview commonalities emerge that may pave the way towards a unified theory of life-based-on-codes. Codes underly cellular processes, perception, cognition, and communication. From ecosystems to human language, codes influence how individuals behave in groups, memorize, learn, and take part in cultural practices. Emotions like aggression, fear, anger, frustration, are important motivators of behaviour modulating mutual communication and sculpting individual experience. The inheritance of experience in form of innate release mechanisms, stereotyped behaviour, or archetypes may have phylogenetic and ontogenetic roots that rely on codes and impact our conscious decision making. Unconsciously, even our dreams draw on codes. In the future, conflation of different coding systems, e.g., from synthetic biology and generative artificial intelligence, will merge biological codes with machine logic and computer language to promote next-level transhumanism. Codes emerge as a currency converter between systems of life and between different scientific disciplines.

Reflexive neural circuits and the origin of language and music codes

Conscious activity is grounded in the reflexive self-awareness in sense perception, through which the codes signifying sensual perceptive events operate and constrain human behavior. These codes grow via the creative generation of hypertextual statements. We apply the model of Vladimir Lefebvre (Lefebvre, V.A., 1987, J. Soc. Biol. Struct. 10, 129-175) to reveal the underlying structures on which the perception and creative development of language and music codes are based. According to this model, the reflexive structure of conscious subject is grounded in three thermodynamic cycles united by the control of the basic functional cycle by the second one, and resulting in the internal action that it turn is perceived by the third cycle evaluating this action. In this arrangement, the generative language structures are formed and the frequencies of sounds that form musical phrases and patterns are selected. We discuss the participation of certain neural brain structures and the establishment of reflexive neural circuits in the ad hoc transformation of perceptive signals, and show the similarities between the processes of perception and of biological self-maintenance and morphogenesis. We trace the peculiarities of the temporal encoding of emotions in music and musical creativity, as well as the principles of sharing musical information between the performing and the perceiving individuals.

The tri-flow adaptiveness of codes in major evolutionary transitions

Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.

The calculus of codes - From entropy, complexity, and information to life

Exploring the core components that define living systems and their operational mechanisms within emerging biological entities is a complex endeavor. In the realm of biological systems literature, the terms matter, energy, information, complexity, and entropy are frequently referenced. However, possessing these concepts alone does not guarantee a comprehensive understanding or the ability to reconstruct the intricate nature of life. This study aims to illuminate the trajectory of these organic attributes, presenting a theoretical framework that delves into the integrated role of these concepts in biology. We assert that Code Biology serves as a pivotal steppingstone for unraveling the mechanisms underlying life. Biological codes (BCs) emerge not only from the interplay of matter and energy but also from Information. Contrary to deriving information from the former elements, we propose that information holds its place as a fundamental physical aspect. Consequently, we propose a continuum perspective called Calculus of Fundamentals involving three fundamentals: Matter, Energy, and Information, to depict the dynamics of BCs. To achieve this, we emphasize the necessity of studying Entropy and Complexity as integral organic descriptors. This perspective also facilitates the introduction of a mathematical theoretical framework that aids in comprehending continuous changes, the driving dynamics of biological fundamentals. We posit that Energy, Matter, and Information constitute the essential building blocks of living systems, and their interactions are governed by Entropy and Complexity analyses, redefined as biological descriptors. This interdisciplinary perspective of Code Biology sheds light on the intricate interplay between the controversial phenomenon of life and advances the idea of constructing a theory rooted in information as an organic fundamental.

Macroevolution, differentiation trees, and the growth of coding systems

An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.

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.

Toward a Bio-Organon: A model of interdependence between energy, information and knowledge in living systems

What is an organism? In the absence of a fundamental biological definition, what constitutes a living organism, whether it is a unicellular microbe, a multicellular being or a multi-organismal society, remains an open question. New models of living systems are needed to address the scale of this question, with implications for the relationship between humanity and planetary ecology. Here we develop a generic model of an organism that can be applied across multiple scales and through major evolutionary transitions to form a toolkit, or bio-organon, for theoretical studies of planetary-wide physiology. The tool identifies the following core organismic principles that cut across spatial scale: (1) evolvability through self-knowledge, (2) entanglement between energy and information, and (3) extrasomatic "technology" to scaffold increases in spatial scale. Living systems are generally defined by their ability to self-sustain against entropic forces of degradation. Life "knows" how to survive from the inside, not from its genetic code alone, but by utilizing this code through dynamically embodied and functionally specialized flows of information and energy. That is, entangled metabolic and communication networks bring encoded knowledge to life in order to sustain life. However, knowledge is itself evolved and is evolving. The functional coupling between knowledge, energy and information has ancient origins, enabling the original, cellular "biotechnology," and cumulative evolutionary creativity in biochemical products and forms. Cellular biotechnology also enabled the nesting of specialized cells into multicellular organisms. This nested organismal hierarchy can be extended further, suggesting that an organism of organisms, or a human "superorganism," is not only possible, but in keeping with evolutionary trends.

Sudden bio-mathematical self-similarity and the uniqueness of human mass societies: from T-patterns and T-strings to T-societies

With the explosive growth of human knowledge especially in the twenteeth century with even greater facilitation of access to knowledge, the world of even relatively recent great thinkers becomes daunting as seen from a modern viewpoint. Recently, humans ignored the existence of the complex intracellular world of cell organs, giant information molecules such as DNA, societies of specialized worker molecules (proteins), and generally the surprising nanoscale world visible to humanity since only a few decades ago. Moreover, computational power and video technology were inaccessible to all scientists from, for example, Aristotle to Freud, so new views and ideas seem to be expected about phenomena at all scales including nano and human. Some have arrived very recently. Thus urgently needed knowledge about the biology of animal and human behavior received the first Nobel Prize as late as 1973, in Physiology and Medicine, shared by Karl von Frisch, Konrad Lorenz, and Niko Tinbergen. Lorenz's Nobel lecture was entitled "Analogy as a Source of Knowledge" which did not mention self-analogy (self-similarity) as none of the species studied were part of others and knowledge of the nanoscale phenomena at the heart of this article had barely become available. The views and empirical findings presented in this article depend on such recent intracellular nanoscale insights and the development of a set of mathematical patterns, called T-system, of which only two are considered, the self-similar (i.e., parts having a structure similar to the whole) T-pattern and the derived T-string, a T-patterned material string (here, polymer or text). Specially developed algorithms implemented in the THEME^TM software for T-pattern detection and analysis (TPA) allowed the detection of interaction T-patterns in humans, animals, and brain neuronal networks, showing self-similarity between animal interaction patterns and neuronal interaction patterns in their brains. TPA of DNA and text also showed unique self-similarity between modern human literate mass societies and the protein societies of their body cells, both with Giant Extra-Individual Purely Informational T-strings (GEIPIT; genomes or textomes) defining the behavioral potentials of their specialized citizens. This kind of society is here called T-society and only exists in humans and proteins, while the self-similarity between them only exists in human T-societies.

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.

Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: Gene expression of bees performing grooming behavior

Introduction

Social organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restrain the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry.

Methods

A bidirectional breeding program to select honey bee colonies with low and high V. destructor population growth (LVG and HVG, respectively) was conducted. Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: 'light groomers' and 'intense groomers'. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified.

Results

Four odorant-binding proteins and a gustatory receptor were identified as differentially expressed genes. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the LVG line showed lower levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1/DWV-B), and Deformed wing virus-A (DWV-A) compared to bees of the HVG line. The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways.

Discussion

These results provide new insights on the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic assisted selection to improve breeding programs.