Multi-Level Semiosis: a Paradigm of Emergent Innovation

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.     

The semiotics of control and modeling relations in complex systems

We provide a conceptual analysis of ideas and principles from the systems theory discourse which underlie Pattee's semantic or semiotic closure, which is itself foundational for a school of theoretical biology derived from systems theory and cybernetics, and is now being related to biological semiotics and explicated in the relational biological school of Rashevsky and Rosen. Atomic control systems and models are described as the canonical forms of semiotic organization, sharing measurement relations, but differing topologically in that control systems are circularly and models linearly related to their environments. Computation in control systems is introduced, motivating hierarchical decomposition, hybrid modeling and control systems, and anticipatory or model-based control. The semiotic relations in complex control systems are described in terms of relational constraints, and rules and laws are distinguished as contingent and necessary functional entailments, respectively. Finally, selection as a meta-level of constraint is introduced as the necessary condition for semantic relations in control systems and models.     

Signs of the Self: An Exploration in Semiotic Anthropology

Peirce's general theory of signs, or semiotic, as he called it, yields a theory of the self that sees it both as the object and the subject of semiotic systems. From this viewpoint, the locus, unity, and continuity of the self will be found in the systems of signs that constitute the dialogues between utterers and interpreters of the signs. Personal identity, in this theory, is also a social and cultural identity and is not confined to the individual organism. Peirce's anti-Cartesianism, which denies intuitive and introspective knowledge of the self, derived that knowledge from the fallible inferences we all make from the observations of external facts, including the signs of the self. This laid the foundation for a semiotic psychology as well as for a semiotic anthropology. [self, semiotic anthropology, personal identity, C. S. Peirce]     

Towards an ecosystem semiotics: Some basic aspects for a new research programme

The paper argues that ecosystem should be recognized as semiotic systems and that it is necessary to carry out studies of the ongoing semiotic processes in addition to traditional ecosystem research. It is suggested that interpretation of ecosystems within such a semiotic framework is of utmost importance and essential if we want to fully understand the complexity issue and how complex behaviour comes about at this level of biological hierarchy. This area—called ecosystem semiotics—is suggested to become a new direction of study dedicated to this understanding.As a consequence of the ontic character of ecosystem complexity, studies on the importance of semiotic processes can only be synthesized through modelling efforts. Hitherto, this type of process with a few exceptions has been neglected or at best only implicitly integrated and accounted for in ecosystem models. In the future, ecosystem models will need to integrate this type of behaviour in order to get full insight into the causal mechanisms behind the emergence of their complex behaviour. In addition, the concept of exergy in its classical form derived by Evans is suggested as a platform to integrate thermodynamic information of the systems as a complexity measure. The thermodynamic information may be split into parts that causally originate in the ontic existence of various ecosystem elements. Ecosystem semiotics is thought to considerably increase the thermodynamic efficiency of the ecosystem, leading to an increase in thermodynamic information and for instance ascendancy that would not have existed if it was not emerging from the semiotic processes.In other words, by incorporating semiotics, we add a “metaphysical” layer to our models, which may be referred to as the semiotype of the system. The semiotype acts as downward causation on the lower layers of interactions and allows for modification and adaptations of existing genotype or phenotype possibilities that would not be possible without the existence of semiosis and cognitive processes.     

Autocatalysis, information and coding

Autocatalytic self-construction in macromolecular systems requires the existence of a reflexive relationship between structural components and the functional operations they perform to synthesise themselves. The possibility of reflexivity depends on formal, semiotic features of the catalytic structure–function relationship, that is, the embedding of catalytic functions in the space of polymeric structures. Reflexivity is a semiotic property of some genetic sequences. Such sequences may serve as the basis for the evolution of coding as a result of autocatalytic self-organisation in a population of assignment catalysts. Autocatalytic selection is a mechanism whereby matter becomes differentiated in primitive biochemical systems. In the case of coding self-organisation, it corresponds to the creation of symbolic information. Prions are present-day entities whose replication through autocatalysis reflects aspects of biological semiotics less obvious than genetic coding.     

一种基于chirp编码的高帧速率超声成像方法

在医学超声成像系统中,帧速率由每帧图像的扫查发射次数所决定.同时发射多条波束可以提高图像的帧速率,但是这会带来不同波束间相互干扰的问题,形成伪像.本文基于编码激励的原理,提出了一种新的高帧速率成像方法.该方法通过发射一组线性频率调制编码信号,有效的降低了波束间的互扰.可以在不影响图像质量的情况下,成倍的提高图像的帧速率.     

Vision without Frames: A Semiotic Paradigm of Event Based Computer Vision

Conventional imagers and almost all vision processes use and rely on theories that are based on the principle of static image-frames. A frame is a 2D matrix that represents the spatial locations of intensities of a scene projected on the imager. The notion of a frame itself is so embedded in machine vision, that it is usually taken for granted that this is how biological systems store light information. This paper presents a biosinpired event-based image formation principle, which output data rely on an asynchronous acquisition process. The generated information is stored in temporal volumes, which size and information depend only on the dynamic content of observed scenes. Practical analysis of such information will shows that the processing of visual information can only be based on a semiotic process. The paper also provides a general definition of the notion of visual features as the interpretation of signs according to different possible readings of the codified visual signal.     

Semiotic Mechanisms Underlying Niche Construction

The explanatory value of niche construction can be strengthened by firm footing in semiotic theory. Anthropologists have a unique perspective on the integration of such diverse approaches to human action and evolutionary processes. Here, we seek to open a dialogue between anthropology and biosemiotics. The overarching aim of this paper is to demonstrate that niche construction, including the underlying mechanism of reciprocal causation, is a semiotic process relating to biological development (sensu stricto) as well as cognitive development and cultural change. In making this argument we emphasize the semiotic mechanisms underlying the niche concept. We argue that the “niche” in ecology and evolutionary biology can be consistent with the Umwelt of Jakob von Uexkull. Following John Deely we therefore suggest that investigations into the organism—environment interface constituting niche construction should emphasize the semiotic basis of experience. Peircean signs are pervasive and allow for flexible interpretations of phenomena in relation to the perceptual and cognitive capacities of the behaving organism, which is particularly pertinent for understanding the relation of proximate/ultimate selective forces as co-productive (i.e., reciprocal). Additionally, theoretical work by Kinji Imanishi on the evolution of daily life and Gregory Bateson’s relational view of evolution both support the linkage between proximate and ultimate evolutionary processes of causation necessitated by the niche construction perspective. We will then apply this theoretical framework to two specific examples: 1) hominin evolution, including uniquely human cultural behaviors with niche constructive implications; and 2) the multispecies and anthropocentric niche of human-dog coevolution from which complex cognitive capacities and semiotic relationships emerged. The intended outcome of this paper is the establishment of concrete semiotic mechanisms and theory underlying niche constructive behavior which can then be applied to a broad spectrum of organisms to contextualize the reciprocal relation between proximate and ultimate drivers of behavior.     

Intrinsic Multi-Scale Dynamic Behaviors of Complex Financial Systems

The empirical mode decomposition is applied to analyze the intrinsic multi-scale dynamic behaviors of complex financial systems. In this approach, the time series of the price returns of each stock is decomposed into a small number of intrinsic mode functions, which represent the price motion from high frequency to low frequency. These intrinsic mode functions are then grouped into three modes, i.e., the fast mode, medium mode and slow mode. The probability distribution of returns and auto-correlation of volatilities for the fast and medium modes exhibit similar behaviors as those of the full time series, i.e., these characteristics are rather robust in multi time scale. However, the cross-correlation between individual stocks and the return-volatility correlation are time scale dependent. The structure of business sectors is mainly governed by the fast mode when returns are sampled at a couple of days, while by the medium mode when returns are sampled at dozens of days. More importantly, the leverage and anti-leverage effects are dominated by the medium mode.     

The effects of Tubulin denaturation on the characterization of its polymerization behavior

We report here upon a simulation study examining the effect of a dynamic mode of tubulin denaturation upon the kinetic and thermodynamic characterisation of the polymer formed for two idealized models of a tubulin polymerization reaction: (i) an irreversibly polymerizing system; and (ii) a reversibly polymerizing system. The effects of each denaturation mode upon the two model systems behavior are highlighted by interpretation of the data in terms of the classical Oosawa reversible condensation polymerization model. We reveal here findings which suggest that the measurement strategy in concert with Tubulin's instability over the time course of the experiment may bias the results obtained so as to make an irreversible system's behavior conform to the equilibrium model or alternatively distort the results obtained from a truly reversible system to produce values of the critical concentration quite seriously in error. It was also found that Tubulin denaturation may seriously distort parameter estimates gained from a kinetic characterization of the system (e.g. nucleus size and growth rate constant).     

Three Types of Semiosis

The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different types of signs and has led to the distinction between iconic, indexical and symbolic semiosis. In all these cases, however, semiosis has been defined by the Peirce model, i.e., by the idea that the basic structure is a triad of ‘sign, object and interpretant’, and that interpretation is an essential component of semiosis. This model is undoubtedly applicable to animals, since it was precisely the discovery that animals are capable of interpretation that allowed Thomas Sebeok to conclude that they are also capable of semiosis. Unfortunately, however, it is not clear how far the Peirce model can be extended beyond the animal kingdom, and we already know that we cannot apply it to the cell. The rules of the genetic code have been virtually the same in all living systems and in all environments ever since the origin of life, which clearly shows that they do not depend on interpretation. Luckily, it has been pointed out that semiosis is not necessarily based on interpretation and can be defined exclusively in terms of coding. According to the ‘code model’, a semiotic system is made of signs, meanings and coding rules, all produced by the same codemaker, and in this form it is immediately applicable to the cell. The code model, furthermore, allows us to recognize the existence of many organic codes in living systems, and to divide them into two main types that here are referred to as manufacturing semiosis and signalling semiosis. The genetic code and the splicing codes, for example, take part in processes that actually manufacture biological objects, whereas signal transduction codes and compartment codes organize existing objects into functioning supramolecular structures. The organic codes of single cells appeared in the first three billion years of the history of life and were involved either in manufacturing semiosis or in signalling semiosis. With the origin of animals, however, a third type of semiosis came into being, a type that can be referred to as interpretive semiosis because it became closely involved with interpretation. We realize in this way that the contribution of semiosis to life was far greater than that predicted by the Peirce model, where semiosis is always a means of interpreting the world. Life is essentially about three things: (1) it is about manufacturing objects, (2) it is about organizing objects into functioning systems, and (3) it is about interpreting the world. The idea that these are all semiotic processes, tells us that life depends on semiosis much more deeply and extensively than we thought. We realize in this way that there are three distinct types of semiosis in Nature, and that they gave very different contributions to the origin and the evolution of life.     

Regulated gene expression in Staphylococcus aureus for identifying conditional lethal phenotypes and antibiotic mode of action

Selectively regulating gene expression in bacteria has provided an important tool for studying gene function. However, well-regulated gene control systems have been restricted primarily for use in laboratory non-pathogenic strains of bacteria (e.g. Escherichia coli, Bacillus subtilis). The development of analogous systems for use in bacterial pathogens such as Staphylococcus aureus would significantly enhance our ability to examine the contribution of any given gene product to pathogen growth and viability. In this report, we adapt, examine and compare three regulated gene expression systems in S. aureus, which had previously been used in B. subtilis. We demonstrate that all three systems function and exhibit titratable induction, together covering a dynamic range of gene expression of approximately 3000-fold. This dynamic range correlates well with the physiological expression levels of cellular proteins. Importantly, we show that one of these systems, the Spac system, is particularly useful for examining gene essentiality and creating specific conditional lethal phenotypes. Moreover, we find that titration of selective target gene products using this system allows direct demonstration of antibiotic mode of action.     

Implementation of a field programmable gate array based transcranial Doppler ultrasound system using pulse compression techniques

A field programmable gate array (FPGA) based hardware platform that is used to implement a digital, multi-gate pulsed Doppler ultrasound system for transcranial Doppler (TCD) use is described. The Doppler audio signal is extracted from the digitised radio-frequency signal by matched filtering and suitable sampling. The system was configured to acquire Doppler signals from 16 depth locations and to display Doppler signal power versus depth as well as a sonogram from a user specified depth. The signal-to-noise performance of the system was comparable with that of a commercially available TCD unit for equivalent pulse repetition frequency and sample volume settings.The flexibility of the platform was used to demonstrate the feasibility of using coded transducer excitation and pulse compression techniques to improve axial resolution compared to a non-coded implementation. The axial resolution improvement was demonstrated using a flow phantom and measured using a vibrating wire phantom. The measured resolutions were 9.1 and 2.4 mm for the conventional and coded implementations, respectively. The reduction in signal-to-noise ratio of approximately 5 dB associated with the configuration using coded excitation was attributable to the frequency response characteristics of the transducer rather than the processing technique used. This work demonstrates both the flexibility associated with an FPGA implementation of a Doppler ultrasound system and the potential for coded excitation to improve axial resolution in TCD systems.     

reflection of stimulus orientation in reactions of visual cortex neurons

A mathematical model of neuronal target structure with spatial anisotropy of lateral inhibition is discussed. The positions of the neuronal target to oriented sensory stimuli are investigated by computer simulation. It is suggested that visual stimuli orientation is coded in the late phase of dynamic responses of cortical neurons. This idea is in agreement with the data obtained in experiments on guinea pig visual cortex neurons.     

On Meaning: A Biosemiotic Approach

A life form and its environment constitute an essential unit, a microcosm. This microcosm is sustained by a privileged dialectic relationship in which the embedded agent- an entity endowed with a particular physical architecture- and its specific environment, coupled, mutually influence each other. Identical principles rule both the basic forms of semiotic organisation and the upper forms. When we distinguish these two levels of semiotic structuring we are distinguishing the semiotic relations that involve a stimulus-response relationship, which is dyadic in nature, from those that involve a more complex relationship where the capacity of symbolically encoding allows organisms to go beyond the immediacy of sensory awareness. However in all instances of semiotic structuring, there is the presence of a living system that evolves in an environment individuating and assigning a value to typical environmental features. Acknowledging this fact is crucial: the inquiry into how elemental life forms interact with their environments leads to the identification of the fundamental role played by the physical architecture of the agent and sheds light on the semiotic process that is common to all life forms, ultimately highlighting the very nature of meaning and reality.     

Becoming a Sign: The Mimic’s Activity in Biological Mimicry

From a semiotic perspective biological mimicry can be described as a tripartite system with a double structure that consists of ecological relations between species and semiotic relations of sign. In this article the focus is on the mimic who is the individual benefiting from its resemblance to the cues or signals of other species or to the environment. In establishing the mimetic resemblance the question of mimic’s activity becomes crucial, and the activity can range from the fixed bodily patterns to fully dynamic behavioural displays. The mimic’s activity can be targeted at two other participants of the mimicry system—either at the model or at the receiver. The first possibility is quite common in camouflage and there are several possibilities for mimic’s activity to occur: selecting a resting place or habitat based on conformity with the environment, changing body coloration to correspond to the surrounding environment, covering oneself with particles of the soil. In its activity aimed at the model, the mimic develops a strong semiotic connection with its specific perceptual environment or part of it and obtains a representational character. In the second possibility the activity of a mimetic organism is aimed at the receiver who is confused by the resemblance, and between the two participants an active communicative interaction is established. Such type of mimicry can be exemplified by abstract threat displays found in various groups of animals, for instance a toad’s upright posture as a response to the presence of a snake. From the semiotic viewpoint it can be interpreted as the motive of fear in the predator’s Umwelt being entered into the mimic’s subjective world and manifested in its behaviour. The mimetic organism ends up in an ambiguous position, where it needs to pretend to be something other than it is. In the final part of the article it is argued that the mimetic sign is basically a false designator as the mimic’s activity to become a sign is aimed at a specific type of signs. Rather than signifying belonging to its own species or group, a mimetic sign indicates that its carrier belongs to the type of some other species. The tension between the form and behaviour of mimetic organisms arises from the discrepancy between the type of organism that it essentially is and the type of organism that the mimetic sign it carries imposes on it.     

A Biosemiotic Approach to the Problem of Structure and Agency

A human being is the simultaneous composite of several different levels of being, from atomic and subatomic to the level of complex social interaction, and these levels are nested within the individual hierarchically (lower levels giving rise to higher levels, etc.). One of the most important and influential approaches developed in the history of science has been that of systems theory and systemic thinking, in which the different levels of the hierarchy, and the interactions between those levels, are considered simultaneously. Although this model provides a comprehensive view of biological being, the transition from one level to the other is not well defined in it. Uexküll and Pauli (Advances: Journal of the Institute for 417 the Advancement of Health 3:158–174, 1986) suggested that semiosis is the translator of the events from one level to the other. From a psychological point of view, a myriad of semiotic events happen inside an individual, and it has been suggested that among other semiotic events, inner speech plays an important role in mediating personal agency. Dialogical theories of the self, Jungian psychology and hypnosis research evidence show that there is a semiotic multiplicity in human agency and consciousness, and that these multiple streams are all converge to a central semiotic singularity. I argue in this paper that by taking a biosemiotic point of view, human ‘agency’ may be defined as the ability of an individual to direct the incoming and internal streams of semioses and the ability to create an integrative and superordinate new stream of semiosis in addition to the upwardly and downwardly component ones, and how such a view might open a new door for research into the concept of human ‘personality’ and ‘agency’.     

Semiotics and the Technique of Empathy

The subject of this research is one of the basic units of the psychotechnical theory of psychotherapy developed by the author, “immediate experience–empathy.” The structure of empathy is analyzed as a therapist's communicative act. This structure includes a number of elements—an operator of understanding, a mode of experiencing, a sign of experiencing, and so forth. The possibilities for modifying empathic responses and the functions of these modifications in the psychotherapeutic process are considered. Special attention is given to semiotic and expressive aspects of empathy.     

Towards an Evolutionary Biosemiotics: Semiotic Selection and Semiotic Co-option

In biosemiotics, living beings are not conceived of as the passive result of anonymous selection pressures acted upon through the course of evolution. Rather, organisms are considered active participants that influence, shape and re-shape other organisms, the surrounding environment, and eventually also their own constitutional and functional integrity. The traditional Darwinian division between natural and sexual selection seems insufficient to encompass the richness of these processes, particularly in light of recent knowledge on communicational processes in the realm of life. Here, we introduce the concepts of semiotic selection and semiotic co-option which in part represent a reinterpretation of classical biological terms and, at the same time, keep explanations sensitive to semiosic processes taking place in living nature. We introduce the term ‘semiotic selection’ to emphasize the fact that actions of different semiotic subjects (selectors) will produce qualitatively different selection pressures. Thereafter, ‘semiotic co-option’ explains how semiotic selection may shape appearance in animals through remodelling existing forms and relations. Considering the event of co-option followed by the process of semiotic selection enables us to describe the evolution of semantic organs.