Luis Emilio Bruni

CELLULAR SEMIOTICS AND SIGNAL TRANSDUCTION

Semiosis, the processes of production, communication and interpretation of signs – coding and de-coding – takes place within and between organisms. The term “endosemiosis” refers to the processes of interpretation and sign transmission inside an organism (as opposed to “exosemiosis”, which refers to the processes of sign interpretation and transmission between organisms of the same or different species). In Biosemiotics it is customary to recognise the cell as the most elementary integration unit for semiosis. Therefore intra and intercellular communication constitute the departure point for the study of endosemiotics In contemporary molecular and cell biology, signal transduction research has remarkably contributed to a major paradigm shift in biology in which biology is now seen as a “science of sensing”. Once we recognise that sensing is one of the necessary properties of life, we cannot do without considering semiotic logic in order to construct our understanding of living phenomena. Given the central integrating role of signal transduction in physiological and ecological studies, this chapter outlines its semiotic implications.The multi-modality and modularity of signal molecules and relative “infrastructure” components poses one of the central problems for understanding metabolic codes: the occurrence of different instances of “cross-talk”, “redundancy” and “categorial sensing” at different hierarchical levels. The term “categorial sensing” captures very well the essence of the “outstanding question(s)” in signal transduction; i.e., how specificity is determined, how ubiquitous signals or messengers convey specific information, how undesired cross-talk is avoided, how redundancy integrates the system. This chapter proposes a basic conceptual toolbox for interpreting empirical data that deals with such puzzling phenomena from a biosemiotic perspective

Hierarchical Categorical Perception in Sensing and Cognitive Processes

This article considers categorical perception (CP) as a crucial process involved in all sort of communication throughout the biological hierarchy, i.e. in all of biosemiosis. Until now, there has been consideration of CP exclusively within the functional cycle of perception–cognition–action and it has not been considered the possibility to extend this kind of phenomena to the mere physiological level. To generalise the notion of CP in this sense, I have proposed to distinguish between categorical perception (CP) and categorical sensing (CS) in order to extend the CP framework to all communication processes in living systems, including intracellular, intercellular, metabolic, physiological, cognitive and ecological levels. The main idea is to provide an account that considers the heterarchical embeddedness of many instances of CP and CS. This will take me to relate the hierarchical nature of categorical sensing and perception with the equally hierarchical issues of the “binding problem”, “triadic causality”, the “emergent interpretant” and the increasing semiotic freedom observed in biological and cognitive systems.

Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents.

Towards a heterarchical approach to biology and cognition.

In this article we challenge the pervasive notion of hierarchy in biological and cognitive systems and delineate the basis for a complementary heterarchical approach starting from the seminal ideas of Warren McCullock and Gregory Bateson. We intend these considerations as a contribution to the different scientific disciplines working towards a multilevel integrative perspective of biological and cognitive processes, such as systems and integrative biology and neuroscience, social and cultural neuroscience, social signal transduction and psychoneuroimmunology, for instance. We argue that structures and substrates are by necessity organized hierarchically, while communication processes - and their embeddedness - are rather organized heterarchically. Before getting into the implications of the heterarchical approach and its congeniality with the semiotic perspective to biology and cognition, we introduce a set of notions and concepts in order to advance a framework that considers the heterarchical embeddedness of different layers of physiological, behavioral, affective, cognitive, technological and socio-cultural levels implicit in networks of interacting minds, considering the dynamic complementarity of bottom-up and top-down causal links. This should contribute to account for the integration, interpretation and response to complex aggregates of information at different levels of organization in a developmental context. We illustrate the dialectical nature of embedded heterarchical processes by addressing the simultaneity and circularity of cognition and volition, and how such dialectics can be present in primitive instances of proto-cognition and proto-volition, giving rise to our claim that subjectivity and semiotic freedom are scalar properties. We collate the framework with recent empirical systemic approaches to biology and integrative neuroscience, and conclude with a reflection on its implications to the understanding of the emergence of pathological conditions in multi-level semiotic systems.

Narrative Intelligibility and Closure in Interactive Systems

In this article we define various aspects, or parameters, of interactive narrative systems and present them as a framework that can help authors, creators and designers to conceive, analyze, or prioritize the narrative goals of a given system. We start by defining the Author-Audience distance (AAD), which in turn can be seen as a function of Narrative Intelligibility. AAD can also be influenced by the intended or unintended level of abstractedness or didascalicity (i.e. figurativeness) of a given narrative. We define narrative intelligibility in complementarity with the related notion of Narrative Closure. We also make a distinction between the goals of the system and the goals of the narrative that it mediates, and consider the proposed parameters at two interrelated levels of analysis: the system level and the embedded narrative level, as the normative values and goals of these two levels should not be taken for granted.

Receptor Oligomerization as a Process Modulating Cellular Semiotics

The majority of G protein-coupled receptors (GPCRs) self-assemble in the form dimeric/oligomeric complexes along the plasma membrane. Due to the molecular interactions they participate, GPCRs can potentially provide the framework for discriminating a wide variety of intercellular signals, as based on some kind of combinatorial receptor codes. GPCRs can in fact transduce signals from the external milieu by modifying the activity of such intracellular proteins as adenylyl cyclases, phospholipases and ion channels via interactions with specific G-proteins. However, in spite of the number of cell functions they can actually control, both GPCRs and their associated signal transduction pathways are extremely well conserved, for only a few alleles with null or minor functional alterations have so far been found. This would seem to suggest that, beside a mechanism for DNA repairing, there must be another level of quality control that may help maintaining GPCRs rather stable throughout evolution. We propose here receptor oligomerization to be a basic molecular mechanism controlling GPCRs redundancy in many different cell types, and the plasma membrane as the first hierarchical cell structure at which selective categorical sensing may occur. Categorical sensing can be seen as the cellular capacity for identifying and ordering complex patterns of mixed signals out of a contextual matrix, i.e., the recognition of meaningful patterns out of ubiquitous signals. In this context, redundancy and degeneracy may appear as the required feature to integrate the cell system into functional units of progressively higher hierarchical levels.

Are olfactory receptors really olfactive

Any living organism interacts with and responds specifically to environmental molecules by expressing specific olfactory receptors. In this paper, this specificity will be first examined in causal terms with particular emphasis on the mechanisms controlling olfactory gene expression, cell-to-cell interactions and odor-decoding processes. However, this type of explanation does not entirely justify the role olfactory receptors have played during evolution, since they are also expressed ectopically in different organs and/or tissues. Homologous olfactory genes have in fact been found in such diverse cells and/or organs as spermatozoa, testis and kidney where they are assumed to act as chemotactic sensors or renin modulators. To justify their functional diversity, homologous olfactory receptors are assumed to share the same basic role: that of conferring a self-identity to cells or tissues under varying environmental conditions. By adopting this standpoint, the functional attribution as olfactory or chemotactic sensors to these receptors should not be seen either as a cause conditioning receptor gene expression, or as a final effect resulting from genetically predetermined programs, but as a direct consequence of the environmental conditions olfactory receptor genes have explored during evolution. The association of odorant patterns with specific environmental or contextual situations makes their relationship semiotically triadic, due to the emergence of an interpretant capable of perceiving odorants as meaningful signs out of a noisy background. This perspective highlights the importance of odorant-receptor relationships as respect to the properties of the interacting partners. It is our contention that only when taken together can these different explanatory strategies provide a realistic account of how olfactory receptor genes have been structurally and functionally modified during evolution.

Authoring for Engagement in Plot-Based Interactive Dramatic Experiences for Learning

When developing interactive storytelling applications, most authors have to choose between providing the interacting subjects with either a pre-determined and plot-based narrative structure or a loose arrangement of events, which maintains the freedom of interactivity while sacrificing the author’s control over communicating a theme. To address this problem, this paper contributes a method for organizing narrative events in a free-roaming virtual environment. The Interactive Dramatic Experience Model (IDEM) retains the freedom of navigation while maintaining the possibility to construct various coherent narratives that enable the theme to be communicated. This may be of particular relevance when using digital, interactive, and representational technologies in the mediation of ethically relevant and socially responsible themes. In order to explore the use of the IDEM, we have developed and evaluated the “First Person Victim” application. This interactive experiential storytelling scenario is intended as a tool for teaching about the negative consequences of war.

First Person Victim: Developing a 3D Interactive Dramatic Experience

Interactive Drama in 3D worlds has great potential for communicating serious themes, however it can become challenging to organize the content in such a way that the theme is communicated clearly while maintaining the feeling of free spatial navigation in the 3D world. In order to address this problem, and to propose a way to structure content, we have developed the Interactive Dramatic Experience Model, which attempts to organize narrative events in a 3D world while keeping the freedom of spatial interactivity. In order to exemplify this model, we have chosen to oppose the classic genre of violent interactive shooter experiences by allowing the participants to experience the feeling of being a victim of war. An evaluation of the implementation indicated that participants experienced free spatial interaction, while still being able to acquire an understanding of the theme being mediated.

Heterarchical Semiosis: From Signal Transduction to Narrative Intelligibility

This chapter intends to offer a framework for contributing to bridge the gap between biosemiotics, cognitive semiotics, and, eventually, cultural semiotics. The discussion about semiotic thresholds and the hierarchical organization of semiotic processes in nature is instrumental to this bridge. Therefore, as a starting point I review and compare four different models of hierarchical organization of semiosis implying different semiotic thresholds. The current debate seems to put too much exclusive emphasis on evolutionary issues at the cost of paying little attention to the developmental questions in synchronous embedded semiotic processes, which are the focus of the present work. It is argued that a sound description of such processes needs to challenge a view that adheres to a strictly hierarchical organization, being preferable to opt for a heterarchical approach. What is important to map in these models of hierarchies is the continuity and/or the causal links of the increasing semiotic freedom from the lowest to the higher levels, which is then what determines not only the (evolutionary) transitions from proto-intentionality and subjectivity to the full-blown versions but also the heterarchical embeddedness of these levels which are by necessity manifested in simultaneity.