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. (shrink)

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. (shrink)

The emergence of organic, metabolic, cognitive and cultural codes points us to the need for a new kind of explanatory causality, and a different kind of bio-logic— one dependent on, but different from, the deterministic logic derived from mechanical causality, and one which can account for the increase in semiotic freedom which is evident in the biological hierarchy. Building upon previous work (Bruni 2003), in this article I provide a stipulative definition of semiotic freedom and its relation to causality in (...) biological and cognitive systems. To do so, I will first discuss the close relation that triadic causality and semiotic freedom have to the notions of teleology and emergence, and how the latter two are interrelated in living systems. I pinpoint some of the reservations that these notions have encountered in the history of science (including evolutionary biology and cognitive science), but stress also their necessity in the study of any given biological and cognitive system. I draw a distinction between horizontal and vertical emergence in order to arrive at a notion of ‘second order emergence’ that affords us a more viable definition of semiotic freedom. I will then attempt to show that all of these concepts are of paramount importance when we come to study processes of sensing, perception andcognition at any level of a living system. Accordingly, these ideas are part of a framework-in-development to research the scale of thresholds of semiotic freedom, by assuming a top-down approach i.e., by starting from the highest levels of semiotic freedom and cognitive processes, and exploring how those processes disaggregate into lesser degrees of freedom. I thus hope to bridge the gap between those levels from above. (shrink)

In this introductory article to the special issue on Multi-level semiosis we attempt to stage the background for qualifying the notion of “multi-levelness” when considering communication processes and semiosis in all life forms, i.e. from the cellular to the organismic level. While structures are organized hierarchically, communication processes require a kind of processual organization that may be better described as being heterarchical. Theoretically, the challenge arises in the temporal domain, that is, in the developmental and evolutionary dimension of dynamic semiotic (...) processes. We discuss the importance of this fundamental difference in order to explain how levels, domains and orders of magnitude, on the one hand, and synchronic and diachronic processes, on the other, contribute to the overall organization of every living being. To account for such multi-level organization, semiotic freedom is assumed to be a scalar property that endows living systems at different levels and domains with the capacity to ponder selectively the overall structural coherence and functional compatibility of their heterarchical processing, which is increasingly less conditioned by the underlying molecular determinism. (shrink)

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. (shrink)

The emergence of organic, metabolic, cognitive and cultural codes points us to the need for a new kind of explanatory causality, and a different kind of bio-logic— one dependent on, but different from, the deterministic logic derived from mechanical causality, and one which can account for the increase in semiotic freedom which is evident in the biological hierarchy. Building upon previous work (Bruni 2003), in this article I provide a stipulative definition of semiotic freedom and its relation to causality in (...) biological and cognitive systems. To do so, I will first discuss the close relation that triadic causality and semiotic freedom have to the notions of teleology and emergence, and how the latter two are interrelated in living systems. I pinpoint some of the reservations that these notions have encountered in the history of science (including evolutionary biology and cognitive science), but stress also their necessity in the study of any given biological and cognitive system. I draw a distinction between horizontal and vertical emergence in order to arrive at a notion of ‘second order emergence’ that affords us a more viable definition of semiotic freedom. I will then attempt to show that all of these concepts are of paramount importance when we come to study processes of sensing, perception andcognition at any level of a living system. Accordingly, these ideas are part of a framework-in-development to research the scale of thresholds of semiotic freedom, by assuming a top-down approach i.e., by starting from the highest levels of semiotic freedom and cognitive processes, and exploring how those processes disaggregate into lesser degrees of freedom. I thus hope to bridge the gap between those levels from above. (shrink)

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. (shrink)

When dealing with biological communication and information, unifying concepts are necessary in order to couple the different “codes” that are being inductively “cracked” and defined at different emergent and “deemergent” levels of the biological hierarchy. In this paper I compare the type of biological information implied by genetic information with that implied in the concept of “quorum sensing” (which refers to a prokaryotic cell-to-cell communication system) in order to explore if such integration is being achieved. I use the Lux operon (...) paradigm and the Vibrio fischeri – Euprymna scolopes symbiotic partnership to exemplify the emergence of informational contexts along the biological hierarchy (from molecules to ecologies). I suggest that the biosemiotic epistemological framework can play an integrative role to overcome the limits of dyadic mechanistic descriptions when relating the different emergent levels. I also emphasise that the realisation ofbiology as being a “science of sensing” and the new importance that is being ascribed to the “context” in experimental biology corroborate past claims ofbiosemioticians about a shift from a focus on information (as a material agent of causality) towards a focus on the world of signification. (shrink)

Receptor oligomerization plays a key role in maintaining genome stability and restricting protein mutagenesis. When properly folded, protein monomers assemble as oligomeric receptors and interact with environmental ligands. In a gene-centered view, the ligand specificity expressed by these receptors is assumed to be causally predetermined by the cell genome. However, this mechanism does not fully explain how differentiated cells have come to express specific receptor repertoires and which combinatorial codes have been explored to activate their associated signaling pathways. It is (...) our contention that the plasma membrane acts as the locus where several contextual cues may be integrated. As such it allows the semiotic selection of those receptor configurations that provide cells with the minimum essential requirements for agency. The occurrence of protein misfolding makes it impossible for receptor monomers to assemble along the membrane and to sustain meaningful relationships with environmental ligands. How could a cell lineage deal with these loss-of-function mutations during evolution and restrain gene redundancy accordingly? In this paper, we will be arguing that the easiest way for bacteria clones to accomplish this goal is by getting rid of cells expressing mutated receptor proteins. The mechanism sustaining this cell selection is also occurring in many somatic tissues and its function is currently believed to counteract in vivo protein mutagenesis. Our discussion will be mainly focused on the significance and semiotic nature of the interplay between membrane receptors and the epigenetic control of gene expression, as mediated by the control of mismatched repairing and protein folding mechanisms. (shrink)

During the recent decades, a global culrural-institutional network has gradually grown lip to project, implement, and use an enormous technological web that is supposed to observe, monitor, communicate, inventory, and assess our environment and its biodiversity in order to implement sustainable management models. The majority of "knowledge tools" that have been incorporated in the mainstream of this "techno-web" are amply based on a combination of mechanistic biology, genetic reductionism, economical determinism and neo-Darwinian cultural and biological perspectives. These approaches leave aside (...) many of the qualitative and relational aspects that can only be grasped by considering the semiotic networks operative in complex ecological and cultural systems. In this paper, it is suggested that a biosemiotic approach to ecology may prove useful for the modelling process which in turn will allow the construction of meaningful monitoring systems. It is aJso advanced that it may as well serve to better integrate our understanding and monitoring of ecosystems into the cultural process of searching for (human) sustainability. (shrink)

During the recent decades, a global culrural-institutional network has gradually grown lip to project, implement, and use an enormous technological web that is supposed to observe, monitor, communicate, inventory, and assess our environment and its biodiversity in order to implement sustainable management models. The majority of "knowledge tools" that have been incorporated in the mainstream of this "techno-web" are amply based on a combination of mechanistic biology, genetic reductionism, economical determinism and neo-Darwinian cultural and biological perspectives. These approaches leave aside (...) many of the qualitative and relational aspects that can only be grasped by considering the semiotic networks operative in complex ecological and cultural systems. In this paper, it is suggested that a biosemiotic approach to ecology may prove useful for the modelling process which in turn will allow the construction of meaningful monitoring systems. It is aJso advanced that it may as well serve to better integrate our understanding and monitoring of ecosystems into the cultural process of searching for (human) sustainability. (shrink)

Background: Electroconvulsive therapy is one of the most effective treatments for major depressive disorder. Recently, there has been increasing attention to evaluate the effect of ECT on resting-state functional magnetic resonance imaging. This study aims to compare rs-fMRI of depressive disorder patients with healthy participants, investigate whether pre-ECT dynamic functional network connectivity network estimated from patients rs-fMRI is associated with an eventual ECT outcome, and explore the effect of ECT on brain network states.Method: Resting-state functional magnetic resonance imaging data were (...) collected from 119 patients with depression or depressive disorder, and 61 healthy participants, with an age mean of 52.25 years old. The pre-ECT and post-ECT Hamilton Depression Rating Scale were 25.59 ± 6.14 and 11.48 ± 9.07, respectively. Twenty-four independent components from default mode and cognitive control network were extracted, using group-independent component analysis from pre-ECT and post-ECT rs-fMRI. Then, the sliding window approach was used to estimate the pre-and post-ECT dFNC of each subject. Next, k-means clustering was separately applied to pre-ECT dFNC and post-ECT dFNC to assess three distinct states from each participant. We calculated the amount of time each subject spends in each state, which is called “occupancy rate” or OCR. Next, we compared OCR values between HC and DEP participants. We also calculated the partial correlation between pre-ECT OCRs and HDRS change while controlling for age, gender, and site. Finally, we evaluated the effectiveness of ECT by comparing pre- and post-ECT OCR of DEP and HC participants.Results: The main findings include depressive disorder patients had significantly lower OCR values than the HC group in state 2, where connectivity between cognitive control network and default mode network was relatively higher than other states, Pre-ECT OCR of state, with more negative connectivity between CCN and DMN components, is linked with the HDRS changes. This means that those DEP patients who spent less time in this state showed more HDRS change, and The post-ECT OCR analysis suggested that ECT increased the amount of time DEP patients spent in state 2.Conclusion: Our finding suggests that dynamic functional network connectivity features, estimated from CCN and DMN, show promise as a predictive biomarker of the ECT outcome of DEP patients. Also, this study identifies a possible underlying mechanism associated with the ECT effect on DEP patients. (shrink)

Germ cells are cross-roads of development and evolution. They define the origin of every new generation and, at the same time, represent the biological end-product of any mature organism. Germ cells are endowed with the following capacities: to store a self-descriptive program, to accumulate a protein-synthesizing machinery, and to incorporate enough nourishment to sustain embryonic development. To accomplish this goal, germ cells do not simply unfold a pre-determined program or realize a sole instructive role. On the contrary, due to the (...) complexity of their cytoarchitecture and the nature of the soma-to-germ interactions, they are heavily involved in processes of sign recognition and meaningful tissue exploration. At each stage of their inward migration, germ plasma membranes act as semiotic interfaces allowing cells to interact with the surrounding extracellular milieu and experience the compatibility of selected developmental sequences. The question of which signaling pathways are activated at each developmental stage does not result from a strictly predetermined program instructing germ cell stemness. Rather, each developmental sequence is an open-ended semiotic relationship explored and gradually defined during evolution by the context-dependency of specific cell-to-cell interactions. In this way, any structural and functional novelty that has emerged in the course of germ cell interactions may be interpreted as an exaptation fixed in the species genome in response to specific environmental constraints. (shrink)

The egg behaves as a prospective cell sustaining the developmental processes of the future embryo. In biosemiotic terms, this apparent teleonomic behaviour can be accounted for without referring to the exclusive causal role played by its genetic makeup. We envision two different processes that are uniquely found in the oocyte: (1) the first involves the mechanisms by which large amounts of mRNA accumulate in the ooplasm to establish the embryo axes prior to fertilization; (2) the second involves transfer of an (...) excess of maternally supplied ribosomes to the oocyte to provide the future embryo with newly synthesized proteins. In this paper, we argue that the information required to sustain embryonic development is not due to any physical properties of the zygotic DNA and the maternal mRNAs, but to their spatially and temporally ordered relationship in the zygote’s internal space. (shrink)