Biosemiotics: a new understanding of life

The "biomolecular humanities"? New challenges and perspectives

Biomolecular humanities is a developing transdisciplinary research area in which we see natural sciences and humanities increasingly integrated and conceived of as data production and scientific discovery entities on an equal basis. This umbrella term allows us to think generatively about how humanities and natural sciences are providing study material, methodologies, theoretical conceptualizations, analytical results, and synergetic interpretations together, for and about each other.

Kidney development and regeneration: An introduction to this volume in Current Topics in Developmental Biology

Mechanistic studies of renal development arguably began 70 years ago, in 1955 when Clifford Grobstein identified an inductive interaction between ureteric bud and metanephric mesenchyme. As an introduction to a special volume of Current Topics in Developmental Biology, this review looks back over the decades since Grobstein's paper to ask how well we have now answered the mechanistic questions raised in his 'pre-molecular' age, and to highlight new questions that have emerged from an increasing understanding of how kidneys develop. I consider that some old questions, such as lineage, have been answered fairly comprehensively. Some questions such as the nature of inductive signalling have become much more complicated, as a notion of 'the signal' has been replaced by hundreds, or possibly thousands, of communications that coordinate renal development. Some old questions, particularly about morphogenesis, remain open. Others, such as metabolism, were ignored for decades but are now being studied again, very profitably. New topics, such as stem cell behaviour, self-organization, epigenetics and congenital abnormalities, join work on the old ones. We have undoubtedly learned much over the last 70 years but, strangely perhaps, the number of questions still to be answered now seems much larger than it did in decades long past.

The concepts of code biology

Today there are two dominant paradigms in Biology: the idea that 'Life is Chemistry' and the idea that 'Life is Chemistry plus Information'. There is also a third paradigm, the idea that 'Life is Chemistry, Information and Meaning' but today this is a minority view, despite the fact that meaning is produced by codes and there is ample experimental evidence that hundreds of codes exist in living systems. This is because that evidence has not yet reached the university books, but what exists in nature is bound to exist, one day, also in our books and at that point the codes will become an integral part of biology. This paper is a brief description of the key concepts of that third paradigm that has become known as Code Biology.

Natural languages and RNA virus evolution

Information concepts from physics, mathematics and computer science support many areas of research in biology. Their focus is on objective information, which provides correlations and patterns related to objects, processes, marks and signals. In these approaches only the quantitative aspects of the meaning of the information is relevant. In other areas of biology, 'meaningful information', which is subjective in nature, relies on the physiology of the organism's sensory organs and on the interpretation of the perceived signals, which is then translated into action, even if this is only mental (in brained animals). Information is involved, in terms of both amount and quality. Here we contextualize and review the main theories that deal with 'meaningful-information' at a molecular level from different areas of natural language research, namely biosemiotics, code-biology, biocommunication and biohermeneutics. As this information mediates between the organism and its environment, we emphasize how such theories compare with the neo-Darwinian treatment of genetic information, and how they project onto the rapid evolution of RNA viruses.

Self-Improvising Memory: A Perspective on Memories as Agential, Dynamically Reinterpreting Cognitive Glue

Many studies on memory emphasize the material substrate and mechanisms by which data can be stored and reliably read out. Here, I focus on complementary aspects: the need for agents to dynamically reinterpret and modify memories to suit their ever-changing selves and environment. Using examples from developmental biology, evolution, and synthetic bioengineering, in addition to neuroscience, I propose that a perspective on memory as preserving salience, not fidelity, is applicable to many phenomena on scales from cells to societies. Continuous commitment to creative, adaptive confabulation, from the molecular to the behavioral levels, is the answer to the persistence paradox as it applies to individuals and whole lineages. I also speculate that a substrate-independent, processual view of life and mind suggests that memories, as patterns in the excitable medium of cognitive systems, could be seen as active agents in the sense-making process. I explore a view of life as a diverse set of embodied perspectives-nested agents who interpret each other's and their own past messages and actions as best as they can (polycomputation). This synthesis suggests unifying symmetries across scales and disciplines, which is of relevance to research programs in Diverse Intelligence and the engineering of novel embodied minds.

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.

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.

Finding or Creating a Living Organism? Past and Future Thought Experiments in Astrobiology Applied to Artificial Intelligence

This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms-definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution-to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. A novel definition of consciousness is developed which describes mental objects both with and without communicable properties, and this helps to clarify how consciousness in machines may be studied as an emergent process related to choice functions in systems. A perspective on how quantization, acting on nucleic acids, sets up natural limits to system behavior is offered as a partial address to the problem of biogenesis.

The major evolutionary transitions and codes of life

Major evolutionary transitions as well as the evolution of codes of life are key elements in macroevolution which are characterized by increase in complexity Major evolutionary transitions ensues by a transition in individuality and by the evolution of a novel mode of using, transmitting or storing information. Here is where codes of life enter the picture: they are arbitrary mappings between different (mostly) molecular species. This flexibility allows information to be employed in a variety of ways, which can fuel evolutionary innovation. The collation of the list of major evolutionary transitions and the list of codes of life show a clear pattern: codes evolved prior to a major evolutionary transition and then played roles in the transition and/or in the transformation of the new individual. The evolution of a new code of life is in itself not a major evolutionary transition but allow major evolutionary transitions to happen. This could help us to identify new organic codes.

Biosemiotics comprehension of PrP code and prion disease

Prions or PrP^Sc (prion protein, Scrapie isoform) are proteins with an aberrant three-dimensional conformation that present the ability to alter the three-dimensional structure of natively folded PrP^C (prion protein, cellular isoform) inducing its abnormal folding, giving raise to neurological diseases known as Transmissible spongiforms encephalopathies (TSEs) or prion diseases. In this work, through a biosemiotic study, we will analyze the molecular code of meanings that are known in the molecular pathway of PrP^C and how it is altered in prion diseases. This biosemiotic code presents a socio-semiotic correlate in organisms that could be unraveled with the ultimate goal of understanding the code of signs that mediates the process. Finally, we will study recent works that indicate possible relationships in the code between prion proteins and other proteins such as the tau protein and alpha-synuclein to evaluate if it is possible that there is a semiotic expansion of the PrP code and prion diseases in the meaning recently expounded by Prusiner, winner of the Nobel Prize for describing these unusual pathological processes.

Discerning Meaning and Producing Information: Semiosis in Knowing the Past

This article explores how the meaning of information related to things, people, events, and processes in the past is discerned and interpreted to satisfy some current purpose. Starting from the premise that Information about the Past results from a cognitive construction, it considers factors that affect the probability of success in producing Information about the Past. The article analyzes the process, components, and products of learning about the past, building on Constructed Past Theory and applying concepts from semiotics. It identifies characteristic ways in which things in the past are misinterpreted.

Complex Temporal Biology: Towards A Unified Multi-Scale Approach to Predict the Flow of Information

Two hallmarks of biological processes are complexity and time. While complexity can have many meanings, in this paper we propose an explicit link to the flow of time and how it is experienced by the organism. While the flow of time is rooted in constraints of fundamental physics, understanding the operation of biological systems in terms of processual flow and tempo is more elusive. Fortunately, the convergence of new computational and methodological perspectives will provide a means to transform complicated, nonlinear paths between related phenomena at different time scales into dynamic four-dimensional perspectives. According to the complex temporal biology approach, information flow between time scales of multiple lengths is a transformational process that acts to regulate life's complexity. Interactions between temporal intervals of differing magnitude and otherwise loosely-related mechanisms can be understood as inter-timescale information flow. We further propose that informational flow between time scales is the glue that binds the multiple vertical layers of biocomplexity, as well as yielding surprising outcomes ranging from complex behaviors to the persistence of lineages. Building a foundation of rules based on common interactions between orders of time and common experiential contexts would help to reintegrate biology. Emerging methodologies such as state-of-the-art imaging, visualization techniques, and computational data analysis can help us uncover these interactions. In conclusion, we propose educational and community-level changes that would better enable our vision.

Life's organization between matter and form: Neo-Aristotelian approaches and biosemiotics

In this paper, I discuss the neo-Aristotelian approaches, which usually reinterpret Aristotle's ideas on form and/or borrow the notion of formal cause without engaging with the broader implications of Aristotle's metaphysics. In opposition to these approaches, I claim that biosemiotics can propose an alternative view on life's form. Specifically, I examine the proposals to replace the formal cause with gene-centrism, functionalism, and structuralism. After critically addressing these approaches, I discuss the problems of reconciling Aristotelianism with the modern view of life's organization. I claim that the notion of the final cause proposes a cosmological hierarchy and that this is the main problem with applying the formal cause to biology. An alternative categorization of conceptualizing life's form involves (1) the processual identity, (2) relational property clusters, and (3) context-dependent transmission of representational units. The third category points to a semiotic basis of the form of life. In this context, I offer to readjust the focus of the problem of matter-form duality by pointing out that form is primarily an issue of the subject-object relation. Biosemiotics helps to understand the constructive role of symbolic representation in living systems, which is crucial to extend the analysis of the form from cognitive representations to external phenomena. Emergence of subjectivity and perspectivity of interactions are key elements to bridge the form and actual processes within a non-hylomorphic account. To demonstrate transitions from the physical influence of shapes to the organic recognition of forms, I address the biological studies on the synchronization of coincidental inputs and enzyme specificity.

The Semiotic Paradigm in Psychology. A Mature Weltanschauung for the Definition of Semiotic Mind

The author discusses the relevance of the semiotic perspective for the psychological studies in order to deal with some critical issues. In the view of the author, the presumed weakness of psychology, its difficult to be acknowledged among hard sciences, and the lack of worldwide acceptance of its constructs cannot be solved by an evolutionary perspective that risk to cut off many relevant features of living beings and human beings as well. The core of the issue remains untouched. Assuming a wide semiotic paradigm, the mind can be considered a situated, recursive and contextual process of sensemaking engaged in articulating a flow of signs. The process of semiotic mediation is a crucial point at stake: the use of signs is not only to refer/point something or to communicate a message in coded forms, but it is to create models of world in order to think, to act and to share experiences. By a wide range of semiotic processes (iconic, indexical, symbolic), each living specie create its own world. Continuities and discontinuities with humang beings are presented and discussed.

Following Schrödinger's Code: A Personal Journey

On a wintery afternoon over 60 years ago, I was browsing the Baker Library stacks at Dartmouth College and stumbled across a small book with an arresting title: What Is Life? [Schrödinger, E. What is Life? The physical aspect of the living cell and mind. Cambridge: Cambridge University Press, 1944]. This small volume contained numerous concepts that would transform the future of the biological sciences, giving rise to new fields, dogmas, approaches, and debates. Here, I present the core concepts of Schrödinger’s book, the influence they have had on biology, and the influence they may continue to have on the cognitive neurosciences.

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.

Hierarchical pattern formation during amphibian limb regeneration

In 1901 T.H. Morgan proposed in "Regeneration" that pattern formation in amphibian limb regeneration is a stepwise process. Since, biologist have continued to piece together the molecular components of this process to better understand the "patterning code" responsible for regenerate formation. Within this context, several different models have been proposed; however, all are based on one of two underlying hypotheses. The first is the "morphogen hypothesis" that dictates that pattern emerges from localized expression of signaling molecules, which produce differing position-specific cellular responses in receptive cells depending on the intensity of the signal. The second hypothesis is that cells in the remaining tissues retain memory of their patterning information, and use this information to generate new cells with the missing positional identities. A growing body of evidence supports the possibility that these two mechanisms are not mutually exclusive. Here, we propose our theory of hierarchical pattern formation, which consists of 4 basic steps. The first is the existence of cells with positional memory. The second is the communication of positional information through cell-cell interactions in a regeneration-permissive environment. The third step is the induction of molecular signaling centers. And the last step is the interpretation of these signals by specialized cell types to ultimately restore the limb in its entirety. Biological codes are intertwined throughout this model, and we will discuss their multiple roles and mechanisms.

Waste as scats: For an organizational engagement with waste

This article coins the term ‘scatolic’ to suggest a new way for organizations to think about and engage with waste. Scatolic engagement draws on Reno’s analogy of waste as scats and of scats as signs for enabling interspecies communication. This analogy stresses the impossibility for waste producers to dissociate themselves from their waste and emphasizes the contingent, multiple, and transient value of waste. Correspondingly, the article suggests that organizations grow a semiotic competence at reading waste and develop a sense of responsibility for materials. Adopting a scatolic approach to waste is featured as a way for organizations to deal with waste in the Anthropocene.

Causality in Biological Transmission: Forces and Energies

Transmission is a basic process in biology that can be analyzed in accordance with information theory. A sender or transmitter located in a particular patch of space is the source of the transmitted object, the message. A receiver patch interacts to receive the message. The "messages" that are transmitted between patches (eventually located in different hierarchical biological levels) are "meaningful" biological entities (biosemiotics). cis-acting transmission occurs when unenclosed patches acting as emitter and receiver entities of the same hierarchical level are linked (frequently by a vehicle) across an unfit space; trans-acting transmission occurs between biological individuals of different hierarchical levels, embedded within a close external common limit. To understand the causal frame of transmission events, we analyze the ultimate, but most importantly also the proximate, causes of transmission. These include the repelling, centrifugal "forces" influencing the transmission (emigration) and the attractive, centripetal "energies" involved in the reception (immigration). As transmission is a key process in evolution, creating both genetic-embedded complexity-diversity (trans-acting transmission, as introgression), and exposure to novel and alternative patches-environments (cis-acting transmission, as migration), the causal frame of transmission shows the cis-evolutionary and trans-evolutionary dimensions of evolution.

The bioelectric code: An ancient computational medium for dynamic control of growth and form

What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering.

Viral tRNA Mimicry from a Biocommunicative Perspective

RNA viruses have very small genomes which limits the functions they can encode. One of the strategies employed by these viruses is to mimic key factors of the host cell so they can take advantage of the interactions and activities these factors typically participate in. The viral RNA genome itself was first observed to mimic cellular tRNA over 40 years ago. Since then researchers have confirmed that distinct families of RNA viruses are accessible to a battery of cellular factors involved in tRNA-related activities. Recently, potential tRNA-like structures have been detected within the sequences of a 100 mRNAs taken from human cells, one of these being the host defense interferon-alpha mRNA; these are then additional to the examples found in bacterial and yeast mRNAs. The mimetic relationship between tRNA, cellular mRNA, and viral RNA is the central focus of two considerations described below. These are subsequently used as a preface for a final hypothesis drawing on concepts relating to mimicry from the social sciences and humanities, such as power relations and creativity. Firstly, the presence of tRNA-like structures in mRNAs indicates that the viral tRNA-like signal could be mimicking tRNA-like elements that are contextualized by the specific carrier mRNAs, rather than, or in addition to, the tRNA itself, which would significantly increase the number of potential semiotic relations mediated by the viral signals. Secondly, and in particular, mimicking a host defense mRNA could be considered a potential new viral strategy for survival. Finally, we propose that mRNA's mimicry of tRNA could be indicative of an ancestral intracellular conflict in which species of mRNAs invaded the cell, but from within. As the meaning of the mimetic signal depends on the context, in this case, the conflict that arises when the viral signal enters the cell can change the meaning of the mRNAs' internal tRNA-like signals, from their current significance to that they had in the distant past.

Transmission as a basic process in microbial biology. Lwoff Award Prize Lecture

Transmission is a basic process in biology and evolution, as it communicates different biological entities within and across hierarchical levels (from genes to holobionts) both in time and space. Vertical descent, replication, is transmission of information across generations (in the time dimension), and horizontal descent is transmission of information across compartments (in the space dimension). Transmission is essentially a communication process that can be studied by analogy of the classic information theory, based on 'emitters', 'messages' and 'receivers'. The analogy can be easily extended to the triad 'emigration', 'migration' and 'immigration'. A number of causes (forces) determine the emission, and another set of causes (energies) assures the reception. The message in fact is essentially constituted by 'meaningful' biological entities. A DNA sequence, a cell and a population have a semiotic dimension, are 'signs' that are eventually recognized (decoded) and integrated by receiver biological entities. In cis-acting or unenclosed transmission, the emitters and receivers correspond to separated entities of the same hierarchical level; in trans-acting or embedded transmission, the information flows between different, but frequently nested, hierarchical levels. The result (as in introgressive events) is constantly producing innovation and feeding natural selection, influencing also the evolution of transmission processes. This review is based on the concepts presented at the André Lwoff Award Lecture in the FEMS Microbiology Congress in Maastricht in 2015.

Composite Agency: Semiotics of Modularity and Guiding Interactions

Principles of constructivism are used here to explore how organisms develop tools, subagents, scaffolds, signs, and adaptations. Here I discuss reasons why organisms have composite nature and include diverse subagents that interact in partially cooperating and partially conflicting ways. Such modularity is necessary for efficient and robust functionality, including mutual construction and adaptability at various time scales. Subagents interact via material and semiotic relations, some of which force or prescribe actions of partners. Other interactions, which I call "guiding", do not have immediate effects and do not disrupt the evolution and learning capacity of partner agents. However, they modify the extent of learning and evolutionary possibilities of partners via establishment of scaffolds and constraints. As a result, subagents construct reciprocal scaffolding for each other to rebalance their communal evolution and learning. As an example, I discuss guiding interactions between the body and mind of animals, where the pain system adjusts mind-based learning to the physical and physiological constraints of the body. Reciprocal effects of mind and behaviors on the development and evolution of the body includes the effects of Lamarck and Baldwin.

Evolutionary biosemiotics and multilevel construction networks

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism (in a broad sense) to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components (i.e., agents, scaffolds, signs, and resources) that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents.

'Genetic Coding' Reconsidered: An Analysis of Actual Usage

This article reconsiders the theoretical role of the genetic code. By drawing on published and unpublished sources from the 1950s, I analyse how the code metaphor was actually employed by the scientists who first promoted its use. The analysis shows that the term 'code' picked out mechanism sketches, consisting of more or less detailed descriptions of ordinary molecular components, processes, and structural properties of the mechanism of protein synthesis. The sketches provided how-possibly explanations for the ordering of amino acids by nucleic acids (the 'coding problem'). I argue that employing the code metaphor was justified in virtue of its descriptive-denotational and explanatory roles, and because it highlighted a similarity with conventional codes that was particularly salient at the time. 1 Introduction2 Coding Schemes in the 1950s   2.1 The research problem: Determining amino acid sequences  2.2 The solution: Mapping schemes or 'codes'3 The Code Metaphor Played Descriptive and Explanatory Roles4 The Abstractness of Codes and the Expendability of the Code Metaphor5 The Role of Arbitrariness6 Conclusions.

Evolution of natural agents: preservation, advance, and emergence of functional information

Biological evolution is often viewed narrowly as a change of morphology or allele frequency in a sequence of generations. Here I pursue an alternative informational concept of evolution, as preservation, advance, and emergence of functional information in natural agents. Functional information is a network of signs (e.g., memory, transient messengers, and external signs) that are used by agents to preserve and regulate their functions. Functional information is preserved in evolution via complex interplay of copying and construction processes: the digital components are copied, whereas interpreting subagents together with scaffolds, tools, and resources, are constructed. Some of these processes are simple and invariant, whereas others are complex and contextual. Advance of functional information includes improvement and modification of already existing functions. Although the genome information may change passively and randomly, the interpretation is active and guided by the logic of agent behavior and embryonic development. Emergence of new functions is based on the reinterpretation of already existing information, when old tools, resources, and control algorithms are adopted for novel functions. Evolution of functional information progressed from protosemiosis, where signs correspond directly to actions, to eusemiosis, where agents associate signs with objects. Language is the most advanced form of eusemiosis, where the knowledge of objects and models is communicated between agents.

An Informational Study of the Evolution of Codes and of Emerging Concepts in Populations of Agents

We consider the problem of the evolution of a code within a structured population of agents. The agents try to maximize their information about their environment by acquiring information from the outputs of other agents in the population. A naive use of information-theoretic methods would assume that every agent knows how to interpret the information offered by other agents. However, this assumes that it knows which other agents it observes, and thus which code they use. In our model, however, we wish to preclude that: It is not clear which other agents an agent is observing, and the resulting usable information is therefore influenced by the universality of the code used and by which agents an agent is listening to. We further investigate whether an agent that does not directly perceive the environment can distinguish states by observing other agents' outputs. For this purpose, we consider a population of different types of agents talking about different concepts, and try to extract new ones by considering their outputs only.

Virus is a Signal for the Host Cell

Currently, the concept of the cell as a society or an ecosystem of molecular elements is gaining increasing acceptance. The basic idea arose in the 19th century, from the surmise that there is not just a single unit underlying an individual's appearance, but a plurality of entities with both collaborative and conflicting relationships. The following hypothesis is based around this model. The incompatible activities taking place between different original elements, which were subsumed into the first cell and could not be eliminated, had to be controlled very closely. Similarly, a strong level of control had to be developed over many cellular elements after the cell changed its genome to DNA. We assume that at least some of those original RNA agents and other biomolecules which carry incompatibilities and risks, are retained within current cells, although they are now under strict control. A virus functions as a signal informing these repressed cellular RNAs and other elements of ancient origin how to restore suppressed degrees of molecular freedom, favoring pre-existing molecular affinities and activities, re-establishing ancient molecular webs of interactions, and giving fragments of ancient coded information (mostly in the form of RNA structural motifs) the opportunity to be re-expressed. Collectively, these newly activated mechanisms lead to different possibilities for pathological cell states. All these processes are opposed by cell-control mechanisms. Thus, in this new scenario, the battle is considered intracellular rather than between the virus and the cell. And so the virus is treated as the signal that precipitates the cell's change from a latent to an active pathological state.

The Natural Emergence of (Bio)Semiosic Phenomena

Biological organisms appear to have agency, goals, and meaningful behaviour. One possibility is that this is mere appearance, where such properties are not real, but only 'as if' consequences of the physiological structure of organisms. Another possibility is that these properties are real, as emerging from the organism's structure and from how the organism interacts with its environment. Here I will discuss a recent theory showing that the latter position is most likely correct, and argue that the theory is largely consistent with the basics of the field of biosemiotics. The theory can be represented as a triad that resembles the semiotic triad proposed by Peirce, which connects a sign with its object through a process of interpretation. In the theory presented, the sign is an internalized version of fitness (i.e., expected reproductive rate) which refers to the true fitness through a feedback loop that in effect produces interpretation. The feedback loop entangles deterministic and stochastic forms of causation in such a way that genuine agency, goal-directedness, and their associated meaning emerge. It produces a strong form of emergence not reducible to its constituents. The result is that novel phenomena arise that are real and necessary components for a complete understanding of living organisms.

Protosemiosis: agency with reduced representation capacity

Life has semiotic nature; and as life forms differ in their complexity, functionality, and adaptability, we assume that forms of semiosis also vary accordingly. Here we propose a criterion to distinguish between the primitive kind of semiosis, which we call "protosemiosis" (following Prodi) from the advanced kind of semiosis, or "eusemiosis". In protosemiosis, agents associate signs directly with actions without considering objects, whereas in eusemiosis, agents associate signs with objects and only then possibly with actions. Protosemiosis started from the origin of life, and eusemiosis started when evolving agents acquired the ability to track and classify objects. Eusemiosis is qualitatively different from protosemiosis because it can not be reduced to a small number of specific signaling pathways. Proto-signs can be classified into proto-icons that signal via single specific interaction, proto-indexes that combine several functions, and proto-symbols that are processed by a universal subagent equipped with a set of heritable adapters. Prefix "proto" is used here to characterize signs at the protosemiotic level. Although objects are not recognized by protosemiotic agents, they can be reliably reconstructed by human observers. In summary, protosemiosis is a primitive kind of semiosis that supports "know-how" without "know-what". Without studying protosemiosis, the biosemiotics theory would be incomplete.

Redundancy of the genetic code enables translational pausing

The codon redundancy (“degeneracy”) found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PI_o) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.

A general framework of persistence strategies for biological systems helps explain domains of life

The nature and cause of the division of organisms in superkingdoms is not fully understood. Assuming that environment shapes physiology, here we construct a novel theoretical framework that helps identify general patterns of organism persistence. This framework is based on Jacob von Uexküll's organism-centric view of the environment and James G. Miller's view of organisms as matter-energy-information processing molecular machines. Three concepts describe an organism's environmental niche: scope, umwelt, and gap. Scope denotes the entirety of environmental events and conditions to which the organism is exposed during its lifetime. Umwelt encompasses an organism's perception of these events. The gap is the organism's blind spot, the scope that is not covered by umwelt. These concepts bring organisms of different complexity to a common ecological denominator. Ecological and physiological data suggest organisms persist using three strategies: flexibility, robustness, and economy. All organisms use umwelt information to flexibly adapt to environmental change. They implement robustness against environmental perturbations within the gap generally through redundancy and reliability of internal constituents. Both flexibility and robustness improve survival. However, they also incur metabolic matter-energy processing costs, which otherwise could have been used for growth and reproduction. Lineages evolve unique tradeoff solutions among strategies in the space of what we call "a persistence triangle." Protein domain architecture and other evidence support the preferential use of flexibility and robustness properties. Archaea and Bacteria gravitate toward the triangle's economy vertex, with Archaea biased toward robustness. Eukarya trade economy for survivability. Protista occupy a saddle manifold separating akaryotes from multicellular organisms. Plants and the more flexible Fungi share an economic stratum, and Metazoa are locked in a positive feedback loop toward flexibility.

Molecular codes in biological and chemical reaction networks

Shannon’s theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process “meaningful” information from those that do not. Here, we present a formal method to assess a system’s semantic capacity by analyzing a reaction network’s capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems posses different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

Biphasic patterns of diversification and the emergence of modules

The intricate molecular and cellular structure of organisms converts energy to work, which builds and maintains structure. Evolving structure implements modules, in which parts are tightly linked. Each module performs characteristic functions. In this work we propose that a module can emerge through two phases of diversification of parts. Early in the first phase of this biphasic pattern, the parts have weak linkage-they interact weakly and associate variously. The parts diversify and compete. Under selection for performance, interactions among the parts increasingly constrain their structure and associations. As many variants are eliminated, parts self-organize into modules with tight linkage. Linkage may increase in response to exogenous stresses as well as endogenous processes. In the second phase of diversification, variants of the module and its functions evolve and become new parts for a new cycle of generation of higher-level modules. This linkage hypothesis can interpret biphasic patterns in the diversification of protein domain structure, RNA and protein shapes, and networks in metabolism, codes, and embryos, and can explain hierarchical levels of structural organization that are widespread in biology.

Is life unique?

Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity-heat agitation and the cause-and-effect determinism of nature's orderliness-cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.

Cells as semantic systems

BACKGROUND

We consider cells as biological systems that process information by means of molecular codes. Many studies analyze cellular information processing exclusively in syntactic terms (e.g., by measuring Shannon entropy of sets of macromolecules), and abstract completely from semantic aspects that are related to the meaning of molecular information.

METHODS

This mini-review focuses on semantic aspects of molecular information, particularly on codes that organize the semantic dimension of molecular information. First, a general conceptual framework for describing molecular information is proposed. Second, some examples of molecular codes are presented. Third, a mathematical approach that makes the identification of molecular codes in reaction networks possible, is developed.

RESULTS

By combining a systematic conceptual framework for describing molecular information and a mathematical approach to identify molecular codes, it is possible to give a formally consistent and empirically adequate model of the code-based semantics of molecular information in cells.

GENERAL SIGNIFICANCE

Research on the semantics of molecular information is of great importance particularly to systems biology since molecular codes embedded in systems of interrelated codes govern main traits of cells. Describing cells as semantic systems may thus trigger new experiments and generate new insights into the fundamental processes of cellular information processing. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

Communication theory and multicellular biology

In this Perspective, we propose that communication theory--a field of mathematics concerned with the problems of signal transmission, reception and processing--provides a new quantitative lens for investigating multicellular biology, ancient and modern. What underpins the cohesive organisation and collective behaviour of multicellular ecosystems such as microbial colonies and communities (microbiomes) and multicellular organisms such as plants and animals, whether built of simple tissue layers (sponges) or of complex differentiated cells arranged in tissues and organs (members of the 35 or so phyla of the subkingdom Metazoa)? How do mammalian tissues and organs develop, maintain their architecture, become subverted in disease, and decline with age? How did single-celled organisms coalesce to produce many-celled forms that evolved and diversified into the varied multicellular organisms in existence today? Some answers can be found in the blueprints or recipes encoded in (epi)genomes, yet others lie in the generic physical properties of biological matter such as the ability of cell aggregates to attain a certain complexity in size, shape, and pattern. We suggest that Lasswell's maxim "Who says what to whom in what channel with what effect" provides a foundation for understanding not only the emergence and evolution of multicellularity, but also the assembly and sculpting of multicellular ecosystems and many-celled structures, whether of natural or human-engineered origin. We explore how the abstraction of communication theory as an organising principle for multicellular biology could be realised. We highlight the inherent ability of communication theory to be blind to molecular and/or genetic mechanisms. We describe selected applications that analyse the physics of communication and use energy efficiency as a central tenet. Whilst communication theory has and could contribute to understanding a myriad of problems in biology, investigations of multicellular biology could, in turn, lead to advances in communication theory, especially in the still immature field of network information theory.

The capabilities of chaos and complexity

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization?