Making Science Accessible: A Semiotics of Scientific Communication

This article serves as a demonstration of how certain models of literary analysis, used to theorize and analyze fiction and narrative, can also be applied to scientific communication in such a manner as to promote the accessibility of science to the general public and a greater awareness of the methodology used in making scientific discovery. The approach of this article is based on the assumption that the principles of structuralism and semiotics can provide plausible explanations for the divide between the reception of science and literature. We provide a semiotic analysis of a scientific article that has had significant impact in the field of molecular biology with profound medical implications. Furthermore, we show how the structural and semiotic characteristics of literary texts are also evident in the scientific papers, and we address how these characteristics can be applied to scientific prose in order to propose a model of scientific communication that reaches the public. By applying this theoretical framework to the analysis of both scientific and literary communication, we establish parallels between primary scientific texts and literary prose.     

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.     

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.     

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.     

Where Did Information Go? Reflections on the Logical Status of Information in a Cybernetic and Semiotic Perspective

This article explores the usefulness of interdisciplinarity as method of enquiry by proposing an investigation of the concept of information in the light of semiotics. This is because, as Kull, Deacon, Emmeche, Hoffmeyer and Stjernfelt state, information is an implicitly semiotic term (Biological Theory 4(2):167–173, 2009: 169), but the logical relation between semiosis and information has not been sufficiently clarified yet. Across the history of cybernetics, the concept of information undergoes an uneven development; that is, information is an ‘objective’ entity in first order cybernetics, and becomes a ‘subjective’ entity in second order cybernetics. This contradiction relegates the status of information to that of a ‘true’ or ‘false’ formal logic problem. The present study proposes that a solution to this contradiction can be found in Deely’s reconfiguration of Peirce’s ‘object’ (as found in his triadic model of semiosis) into ‘thing’ and ‘object’ (Deely 1981). This ontology allows one to argue that information is neither ‘true’ nor ‘false’, and to suggest that, when considered in light of its workability, information can be both true and false, and as such it constitutes an organism’s purely objective reality (Deely 2009b). It is stated that in the process of building such a reality, information is ‘motivated’ by environmental, physiological, emotional (including past feelings and expectations) constraints which are, in turn, framed by observership. Information is therefore found in the irreducible cybersemiotic process that links at once all these conditions and that is simultaneously constrained by them. The integration of cybernetics’ and semiotics’ understanding of information shows that history is the analytical principle that grants scientific rigour to interdisciplinary investigations. As such, in any attempt to clarify its epistemological stance (e.g. the semiotic aspect of information), it is argued that biosemiotics does not need only to acknowledge semiotics (as it does), but also cybernetics in its interdisciplinary heritage.     

Visual Saliency Models for Text Detection in Real World

This paper evaluates the degree of saliency of texts in natural scenes using visual saliency models. A large scale scene image database with pixel level ground truth is created for this purpose. Using this scene image database and five state-of-the-art models, visual saliency maps that represent the degree of saliency of the objects are calculated. The receiver operating characteristic curve is employed in order to evaluate the saliency of scene texts, which is calculated by visual saliency models. A visualization of the distribution of scene texts and non-texts in the space constructed by three kinds of saliency maps, which are calculated using Itti''s visual saliency model with intensity, color and orientation features, is given. This visualization of distribution indicates that text characters are more salient than their non-text neighbors, and can be captured from the background. Therefore, scene texts can be extracted from the scene images. With this in mind, a new visual saliency architecture, named hierarchical visual saliency model, is proposed. Hierarchical visual saliency model is based on Itti''s model and consists of two stages. In the first stage, Itti''s model is used to calculate the saliency map, and Otsu''s global thresholding algorithm is applied to extract the salient region that we are interested in. In the second stage, Itti''s model is applied to the salient region to calculate the final saliency map. An experimental evaluation demonstrates that the proposed model outperforms Itti''s model in terms of captured scene texts.     

Delectable Creatures and the Fundamental Reality of Metaphor: Biosemiotics and Animal Mind

This article argues that organisms, defined by a semi-permeable membrane or skin separating organism from environment, are (must be) semiotically alert responders to environments (both Innenwelt and Umwelt). As organisms and environments complexify over time, so, necessarily, does semiotic responsiveness, or ‘semiotic freedom’. In complex environments, semiotic responsiveness necessitates increasing plasticity of discernment, or discrimination. Such judgements, in other words, involve interpretations. The latter, in effect, consist of translations of a range of sign relations which, like metaphor, are based on transfers (carryings over) of meanings or expressions from one semiotic ‘site’ to another. The article argues that what humans describe as ‘metaphor’ (and believe is something which only pertains to human speech and mind and, in essence, is ‘not real’) is, in fact, fundamental to all semiotic and biosemiotic sign processes in all living things. The article first argues that metaphor and mind are immanent in all life, and are evolutionary, and, thus, that animals certainly do have minds. Following Heidegger and then Agamben, the article continues by asking about the place of animal mind in humans, and concludes that, as a kind of ‘night science’, ‘humananimal’ mind is central to the semiotics of Peircean abduction.     

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.     

Introduction to the Special Issue <Emphasis Type="Italic">Semiotics of Perception</Emphasis> Being in the World of the Living—Semiotic Perspectives

This special issue on the semiotics of perception originates from two workshops arranged in Tartu, Estonia, in February 2009. We are located at the junction of nature and culture, and of semiotics and phenomenology. Can they be reconciled? More particularly, can subfields such as biosemiotics and ecophenomenology be mutually enriching? The authors of the current special issue believe that they can. Semiotic study of life and the living can emerge as properly informed only if it is capable of incorporating observations made in natural science, philosophy and cultural studies. The semiotic study of nature entails an experiential turn in the study of life processes. Perception is—or should be—at the heart of the life sciences.     

Live sequence charts to model medical information

ABSTRACT: BACKGROUND: Medical records accumulate data concerning patient health and the natural history of disease progression. However, methods to mine information systematically in a form other than an electronic health record are not yet available. The purpose of this study was to develop an object modeling technique as a first step towards a formal database of medical records. METHOD: Live Sequence Charts (LSC) were used to formalize the narrative text obtained during a patient interview. LSCs utilize a visual scenario-based programming language to build object models. LSC extends the classical language of UML message sequence charts (MSC), predominantly through addition of modalities and providing executable semantics. Interobject scenarios were defined to specify natural history event interactions and different scenarios in the narrative text. Result A simulated medical record was specified into LSC formalism by translating the text into an object model that comprised a set of entities and events. The entities described the participating components (i.e., doctor, patient and record) and the events described the interactions between elements. A conceptual model is presented to illustrate the approach. An object model was generated from data extracted from an actual new patient interview, where the individual was eventually diagnosed as suffering from Chronic Fatigue Syndrome (CFS). This yielded a preliminary formal designated vocabulary for CFS development that provided a basis for future formalism of these records. CONCLUSIONS: Translation of medical records into object models created the basis for a formal database of the patient narrative that temporally depicts the events preceding disease, the diagnosis and treatment approach. The LSCs object model of the medical narrative provided an intuitive, visual representation of the natural history of the patient's disease.     

The Forbidden Signs

While the field of semiotics has been active since it was started by Peirce, it appears like the last decade has been especially productive with a number of important new concepts being developed within the biosemiotics community. The novel concept of the Semiotic scaffold by Hoffmeyer is an important addition that offers insight into the hardware requirements for bio-semiosis. As any type of semiosis must be dependent upon Semiotic scaffolds, I recently argued that the process of semiosis has to be divided into two separate processes of sign establishment and sign interpretation, and that misalignment between the two processes result in faulty sign interpretation and over-signification. Such faulty signs were forbidden in the sign classification system of Peirce, so I defined them as forbidden signs. Here I present an analysis of the forbidden sign categories with examples from Occult semiotics. I also show that biological semiosis offers examples of forbidden signs, where the faulty interpretation of signs may lead to decimation of whole evolutionary lines of organisms. A new concept of Evolutionary memory which is applicable to both human and biological semiosis is explained as the combination of two processes; one leading to diversity generation within semiotic scaffolds followed by a second process of decimation of faulty signs during selection in specific learning environments. The analysis suggests that forbidden signs are always used as early stages in the iterative sign establishment process during semiosis.     

Steps to a Semiotics of Being

The following points, which represent a path to a semiotics of being, are pertinent to various sub-fields at the conjunction of semiotics of nature (biosemiotics, ecosemiotics, zoosemiotics) and semiotics of culture—semioethics and existential semiotics included. 1) Semiotics of being entails inquiry at all levels of biological organization, albeit, wherever there are individuals, with emphasis on the living qua individuals (integrated biological individualism). 2) An Umwelt is the public aspect (cf. the Innenwelt, the private aspect) of a phenomenal/experienced world that is organism-specific (rather than species-specific) and ultimately refers to an existential realm. 3) Existential universals at work on Earth include seeking out the edible, dwelling in a medium, holding a phenomenal world (possibly an Umwelt) and being endowed with life, and consequently being mortal. 4) Human Umwelten include speechless Umwelten, spoken Umwelten and alphabetic Umwelten. 5) An Uexküllian phenomenology—stating that semiotic states represent the general class to which all mental/cognitive states belong—can draw on the works of the phenomenologists David Abram and Ted Toadvine (The notion of semiotic states is treated in Tønnessen 2009a: 62–63. For an introduction to eco-phenomenology, see Brown and Toadvine (eds.) 2003). 6) A task for such a phenomenology is to portray the natural history of the phenomenal world. 7) An imperative task in our contemporary world of faltering biological diversity is that of Umwelt mapping, i.e. a mapping of ontological niches. 8) The ecological crisis is an ontological crisis with historical roots in humankind’s domestication of animals and plants, which can be taken as archetypical for our attempted planet-scale taming of the wild. 9) The process of globalization is expressed by correlated trends of depletion of semiotic diversity and semiotic diversification. 10) Semiotic economy is a field which task it is to map the human ontological niche insofar as its semiotic relations are of an economic nature. All ten points will be commented (explicitly or implicitly) in due time.     

Modeling of Muscle Force at Varied Joint Angles of the Human Arm and Estimation of Gripping Force Using Surface EMG

This paper aims to determine the force required for holding the objects by human hand. A static analysis is performed on mathematical models to obtain holding force considering lower arm as class three lever and by varying the joint angles. Three mathematical models are discussed to quantify the force required to hold any object, for different weight of the object and the joint angles. A noninvasive experimentation using surface electromyogram was performed to determine the forces required by human hand for the same objects used in the mathematical modeling. Twenty-one male subjects participated in this test and were asked to hold different objects. EMG signals were recorded and converted into grip force in Newton. The EMG to Force conversion was accomplished by the equation derived from the Hills model. The experimentation revealed that subjects in the age group of 20-50 years generated more grip force as compared to those above the age of fifty years. The values of muscle force obtained from the experimentation are optimum values which depend upon the nature of the gripping habits subjects are used to. Whereas, in the case of mathematical models yielded maximum force required to sustain the weight placed on the hand considering it as a mechanical system. The study revealed an average gripping force of 85 Newton required to hold the objects weighing between 0.015 kg to 1.18 kg used in the experimentation. The mathematical model resulted in an average of 162 Newton muscle force to hold the object having similar weights.     

Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words

Mathematical models of the generation of genetic texts appeared simultaneously with the first sequencing DNA. They are used to establish functional and evolutionary relations between genetic texts, to predict the number and distribution of specific sites in a sequence and to identify "meaningful" words. The present paper deals with two problems: 1) The significance of deviations from the mean statistical characteristics in a genetic text. Anyone who has addressed himself to the statistical analysis of sequenced DNA is familiar with the question: what deviations from the expected frequencies of occurrence of particular words testify to the "biological" significance of those words? We propose a formula for the variance of the number of word's occurrences in the text, with allowance for word overlaps, making it possible to assess the significance of the deviations from the expected statistical characteristics. 2) A new method for predicting the frequencies of occurrence of particular words in a genetic text using the statistical characteristics of "spaced" L-grams. The method can be used for predicting the number of restriction sites in human DNA and in planning experiments on the physical mapping and sequencing of the human genome.     

What Does it Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics

This paper presents a critical analysis of code-semiotics, which we see as the latest attempt to create paradigmatic foundation for solving the question of the emergence of life and consciousness. We view code semiotics as a an attempt to revise the empirical scientific Darwinian paradigm, and to go beyond the complex systems, emergence, self-organization, and informational paradigms, and also the selfish gene theory of Dawkins and the Peircean pragmaticist semiotic theory built on the simultaneous types of evolution. As such it is a new and bold attempt to use semiotics to solve the problems created by the evolutionary paradigm’s commitment to produce a theory of how to connect the two sides of the Cartesian dualistic view of physical reality and consciousness in a consistent way.     

Me,Myself, and Semiotic Function: Finding the “I” in Biology

This essay argues that stable, heritable, habituated semiotics on one scale of life allows for opportunism, origination, and the solving of novel problems on others. This is grounded in how interpretation is neither caused nor determined by its object, such that success at interpretation simply cannot be defined by any comparison between an interpretation and its object. Rather, an interpretation is a reciprocated incorporation of a living thing and its environment, and successful if it furthers the living, interpreting thing. By applying biosemiotic theory to seemingly disparate studies of parasitic infections (Jaroslav Flegr), autonomic nervous systems (Stephen Porges), and social change (Charles Tilly) as well as the classical pragmatic notion that biology, psychology and sociology are disparate approaches to the singular, radically continuous, and perennial question of who (or what) am I (Dewey, James, Mead). I argue that the distinction (e.g.,) between voluntary and autonomic behavior is but a ghost of older dualisms, the pseudo-contradictions of matter v. mind, body v. soul, but also self v. not self. Moreover, all such pseudo-contradictions (individual v. social, sensation v. response, parasite v. host, and etc.) are resolved as scale thick, self-similar examples of semiotic transaction wherein degeneration or habituation on one scale of life allows for generative or novel interaction on another.     

A database method for automated map interpretation in protein crystallography.

A significant portion of new protein structures contain folds that are related to those seen before. During the development of a computer program that can accurately position, in electron density maps, large protein domains with large structural deviations, it became apparent that the redundancy in protein folds could be used in a non trivial manner during a protein structure determination. As a result a computational procedure, Database Assisted Density Interpretation (DADI), was developed and tested to aid in the building of models in protein crystallography and to assist in interpreting electron density maps. The initial tests of the DADI procedure using a small database of protein domains are described. The philosophy is to first work with entire domains then with the secondary structure elements of these domains and finally with individual residues of the secondary structure elements via Monte Carlo, "chopping" and "clipping" procedures, respectively. The first test case was a traceable 3.2 A multiple isomorphous replacement with anomalous scattering (MIRAS) electron density map of a human topoisomerase I-DNA complex. The second test case uses poor electron density for the third domain of the diphtheria toxin repressor resulting from a molecular replacement solution with the first two domains. Despite the fact that a fairly small database was employed in these test cases, the DADI procedure was able to find a large portion of the protein backbone with very few errors. In the first case nearly 45% of the backbone and more than 80% of the secondary structure was placed automatically. In the second test case nearly 50% of the third domain was automatically detected. A particular encouraging result was that in both cases more than 75% of the beta sheet secondary structure was found automatically by the DADI procedure. Clearly, the procedures employed are promising avenues to exploit the current explosion of protein structures for the determination of future structures. Proteins 1999;36:526-541.     

Taking the Relational Turn: Biosemiotics and Some New Trends in Biology

A cluster of similar trends emerging in separate fields of science and philosophy points to new opportunities to apply biosemiotic ideas as tools for conceptual integration in theoretical biology. I characterize these developments as the outcome of a “relational turn” in these disciplines. They signal a shift of attention away from objects and things and towards relational structures and processes. Increasingly sophisticated research technologies of molecular biology have generated an enormous quantity of experimental data, sparking a need for relational approaches that could help to find recurrent patterns in the mass of data. Earlier conceptions of relational biology and cybernetics, once deemed too abstract and speculative, are now resurrected and applied by means of new computational and simulation tools. I think this receptivity should be extended to incorporate nets of semiotic relations as heuristic guides for discerning global patterns of interactions in living systems. In this article I review aspects of systems biology and new directions in evolutionary theory, focusing on the role of circular and downward causation in relational structures and dynamical networks. I also indicate promising avenues of integration of some ideas of biosemiotics with those emerging from these new currents in biology. Relational developments in biology bear a telling similarity to a parallel relational turn presently manifest in the philosophy of science, rooted in the philosophy of physics and mathematics and in different varieties of structural and informational realism. The recognition of the relational nature of reality within these disciplines entails a tacit repudiation of nominalistic biases in science that have hindered the reception of semitiotic conceptions in biology. In previous investigations I explored connections between two kinds of relational structures: the networks of self-referential circular loops that appear pervasively in living systems, and the triadic relational structures that Peircean semiotics places at the basis of all semiotic transactions. Current relational views in the sciences seem oblivious to the difference between dyadic and triadic relations. Incorporating this essential distinction from biosemiotics into other fields could be a first step in seizing the opportunities opened by the relational turn for a renewal of biology and of natural philosophy in general, across disciplinary boundaries.