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Genes, Information, Semiosis
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... ¿Puede ser la semiosis pensada y explicada como un sistema? Esas son precisamente el tipo de preguntas que se formulan El-Hani et al. (2009) en su propuesta sobre la emergencia de la semiosis, propuesta que recuperaré a continuación, dada su importancia para la explicación sobre las condiciones iniciales de la emergencia de la significación en sistemas semióticos y comunicativos. un aCerCamiento multiniVel de la emergenCia de la semiosis Al estudiar algunos procesos involucrados en el sistema de información genética, El-Hani et al. (2009) plantean un caso de estudio que consiste en considerar a la semiosis en los sistemas celulares, como involucrando relaciones en diversos niveles. ...
... Para los autores (El Hani et al., 2009), pese a que el debate sobre la emergencia cesó por algún tiempo, ya a mediados de los años noventa el debate se había reactivado por su constante uso en campos como las ciencias cognitivas, la biología evolutiva, en las teorías de la autoorganización, la filosofía de la mente, en las teorías de sistemas dinámicos y, de manera mucho más puntual, en los campos basados en la simulación computacional como la vida artificial, la robótica cognitiva y la etología sintética. Si bien en muchas de ellas el uso del concepto todavía es impreciso o simplemente vago, lo cierto es que el debate ya se había recuperado a inicios del siglo xxi. ...
... Tomando como base el trabajo de Stephan (1998), El-Hani et al. (2009 consideran que una primera acepción del concepto de emergencia supone asociarla a la "creación de nuevas propiedades" (p. 148). ...
En este trabajo analizo el proceso de la emergencia de la semiosis desde el punto de vista de la semiótica con la intención de explorar las implicaciones que podría tener para el campo de estudios de la comunicación respecto a la extensión de sus fronteras antropocéntricas. La investigación se encuentra fundamentada en la semiótica peirceana y en la cibersemiótica, una teoría transdisciplinar de la comunicación, la cognición, la información y la significación.
... The choice of lower, focal, or higher levels depends on the research goals, on the researcher's interests (observer). According to the authors (El-Hani et al., 2009). ...
... For the authors (El-Hani et al., 2009), although the debate on the emergence ceased for some time, by the mid-1990s the debate had been reactivated by its constant use in fields such as cognitive sciences, evolutionary biology, in self-organization theories, philosophy of mind, in dynamic systems theories and, much more specifically, in fields based on computational simulation such as artificial life, cognitive robotics, and synthetic ethology. Despite that in many of those fields, the use of the concept is still imprecise or simply vague, the truth is that the debate had already recovered at the beginning of the 21st century. ...
... 149). Fourth, since El-Hani et al. (2009) consider the idea of a hierarchy of levels of existence, then it is necessary to ask, "how should we describe levels in semiotic systems and, moreover, how do these levels relate to the emergence of semiosis?" (p. ...
In this paper, I analyze the process of semiosis emergence from the semiotic point of view to clarify the implications it may have for the field of communication studies regarding the extension of its anthropocentric boundaries. The research is based on Peirce's semiotics and the theoretical framework of cybersemiotics, a transdisciplinary theory of communication, cognition, information, and signification.
... For instance, it has been argued by a number of theorists that Shannon's notion of information is inadequate to understand biotic processes (Logan 2012;Perrett and Longo 2016), while Brier (2008) argued that it is inadequate to understand either biotic or cultural processes. Through a careful study of the problems in characterizing the functioning of genes through syntactic, semantic, and pragmatic theories of information, and the superior potential of Peirce's notion of information as semiosis for accounting for epigenesis, El-Hani et al. (2008) argued for the potential fruitfulness and thereby provided a good defence biosemiotics utilizing Peirce's philosophy as a viable research program (p.222). In doing so, they still argued convincingly that 'we don't have an established notion of biological information up to this point' (p.222). ...
... Utilizing Peirce's mature philosophy, biosemioticians influenced by Peirce treated information as the process of informing the interpretant, which could be developing the form of an organism or the mind of a person. Information from this perspective can only be understood in terms of the triadic nature of semiosis as a process, and in fact, as El-Hani et al. (2008) argued, is semiosis. With semiosis, the sign, the object and the interpretant cannot be identified except as components of this triadic process, and this is why the conception of information as self-subsistent, atomic 'bits' as characterized by the information scientists and those who have embraced their work, must be seen as defective. ...
The concept of information and its relation to biosemiotics is a major area of contention among biosemioticians. Biosemioticians influenced by von Uexküll, Sebeok, Bateson and Peirce are critical of the way the concept as developed in information science has been applied to biology, while others believe that for biosemiotics to gain acceptance it will have to embrace information science and distance biosemiotics from Peirce’s philosophical work. Here I will defend the influence of Peirce on biosemiotics, arguing that information science and biosemiotics as these were originally formulated are radically opposed research traditions. Failure to appreciate this will undermine the challenge of biosemiotics and other anti-reductionist traditions to mainstream science with its reductionist ambition to explain everything through physics. However, for this challenge to be successful, it will be necessary to respond to criticisms of Peircian ideas, jettisoning ideas that are no longer defensible and integrating ideas allied to his anti-reductionist agenda. Here I will argue that the natural philosophy of Gilbert Simondon, offering a searching critique of the application of the new concept of information and cybernetics to the life and human sciences, provides the means to defend and advance Peirce’s core ideas and thereby defend post-reductionist biosemiotics.
In this chapter we will discuss the biosemiotic view of evolution. In order to understand the role that sign action may play in the evolution of organisms, we attempt to provide an explanation encompassing an overview of what biosemiotics does, how its concepts play out in a naturalistic view of organisms, and what dimension these concepts open in regard to functional explanations in biology. The semiotic view of evolution is informed by the consideration that meaning-making is an essential feature of organisms with a causal role in behavior and evolution both at the individual level and in long time scales. Biosemiotic theory tries to uncover how exactly meaning-making builds and is built upon networks of relevance for organisms that act as markers for behavior, which is in turn inherited and an active participant in the long-term changes of organisms.
Approaches to Biosemiotics is the first issue in the Biosocial World collection, and contains a series of articles on what biosemiotics does, how it does it and what its long-term objectives may be. As a more specialized discipline in the boundaries of linguistics, the biosociology, the philosophy of biology and the sciences, we hope to offer a point of entry into the world of biosemiotics through articles that deal with general topics from within the field. Our aim is, thus, to contribute to the biosemiotic landscape by opening a door to its recurring themes, problems and descriptions.
Intended as a branch of synthetic biology, xenobiology aims to design and build non-standard life forms, that is to constructively venture into biological otherness. According to this creative and speculative character, it challenges the principles of synthetic biology itself, which is tied to a fundamentally reductionist approach. Xenobiology does not treat life as a closed code, but rather as a field of ontological innovation; in this sense, it evokes a biosemiotic paradigm that accounts for sense-making and non-anthropomorphic interactions.
Xenobiology, however, can also be intended as the “divergent” and most speculative part of astrobiology, namely as a theory of contact with extra-terrestrial life. According to this second meaning, it searches for and speculates on alien biologies. Building on these two meanings, the paper aims to outline a semiotic theory of otherness, or ‘xenosemiotics’, that shifts the focus from communication to morphogenetic information.
This book invites readers to embark on a journey into the world of agency encompassing humans, other organisms, cells, intracellular molecular agents, colonies, populations, ecological systems, and artificial autonomous systems. We combine mechanistic and non-mechanistic approaches in the analysis of the function and evolution of organisms, their subagents, and multi-organism systems, and in this way offer a theoretical platform for integrating biosemiotics with both natural science and the humanities/social sciences. Agents are autonomous systems that incorporate knowledge on how to make sense of their environment and use it to achieve their goals. The functions of all agents are supported by mechanisms at the lowest level; however, the explanatory power of mechanistic analysis is not sufficient for complex agents. Non-mechanistic methods rely on the goal-directedness of agents whose dynamics follow self-stabilized dynamic attractors. The properties of attractors depend on stable or slowly changing factors, and such dependencies can be interpreted as sign relations if they are adaptive in nature. Agents can replace or redirect mechanisms on demand in order to preserve their functions; for performing higher-level semiotic functions, mechanisms are thus only means. We assume that mechanism and semiosis are not mutually exclusive, and that simple agents can interpret signs mechanistically. This assumption allows us to extend semiotic analysis to all agents, including ribosomes in cells, computers, and robots. This book challenges established traditions in natural science and the humanities/social sciences: semiotics no longer appears as restricted to humans and rational thinking, and biology is no longer limited to rely exclusively on mechanistic reasoning.
Sign is a semiotic
tool, whose form
is meaningful for certain agents. Agents use signs to regulate their activities, communicate with others, and accumulate knowledge in the form
of heredity, memory
, perception
, representation
, and cognition. Sign processes, collectively known as semiosis, vary in their complexity and function
, and their types roughly fall in line with the hierarchy of agents. Actions of agents are always sign-mediated, and draw on some form
of experience
, which is also sign-mediated. The main difference between signs and agents is that the role of signs is to signify to agents, whereas the role of agents is to interpret signs and act accordingly. In a system hierarchy, agents are above signs because agents perform interpretation
and create or reshape sign relations. We integrate the concept
of semiosis with the notion of information in the sense
of Gregory Bateson. Two aspects of signs are distinguished: a sign process has a material side and is space-time specific. A sign relation is a type of sign process that is embodied and encoded in an agent
. Agents use sign relations to control material processes, and thereby have some powers to change matter. The second half of the chapter presents an overview of two basic levels of semiosis: (1) protosemiosis is a mechanistic processing of signals inside living cells, where objects are not perceived; (2) eusemiosis constitutes a ‘minimal mind’ that supports perception
and recognition (categorization
) of objects.
This introductory chapter delineates a general historical, philosophical, and scientific framework for the individual studies collected in this book. It emphasizes how the biosemiotic paradigm and related approaches in biology—especially current evolutionary thought—contribute to an epistemological pluralism that allows for a more productive dialogue between natural sciences, on the one hand, and social sciences and humanities, on the other hand, ultimately pointing out to the artificial character of this long-standing traditional duality. For this purpose, we first outline some essential philosophical and historical elements presupposed in the paradigm shifts that marked the life sciences in the nineteenth and twentieth centuries. Next, an overview of the fundamental connections between biological sciences, phenomenology, and biosemiotics is presented.
After Thomas Sebeok’s proposal of global semiotics in the 70s, an attempt to move beyond anthroposemiotics to the realm of zoosemiotics, phytosemiotics, endosemiotics, and, ultimately, to the all-encompassing realm of biosemiotics was made. Semiotics was then established as a serious candidate as the transdisciplinary base of science and humanities –particularly from the triadic and pragmaticist semiotic proposal of C. S. Peirce. However, the semiotic attempt to explain the fundamental aspects of living systems from the standpoint of meaning production and reproduction demonstrate that in order to explain the meaning-making process in living organisms a systemic, biological, cybernetic and informational approach was also needed. The integrative visions have discovered some basic similarities among these theoretical perspectives from which it has been possible to recognize complementarities among them. At the same time, it also made possible to identify variations at the very bottom of each approach, which resulted in a complex task of theoretical integration. Thus, in order to uncover these tensions and complementarities, I will focus my attention in the process of communication in an attempt to move from cybernetics to semiotics and further on to cybersemiotics considering some aspects of biosemiotics, first and second-order cybernetics, Peircean semiotics, and information theory. The goal of this chapter is to overcome the problem of defining the limits and boundaries of communication as a physical, biological, and social phenomena and its nature as an academic field by proposing communication as a transdisciplinary concept from the point of view of cybersemiotics (Vidales, Commun Soc 30:45–67, 2017b), from which it is also possible to address the process of communication, explained in what Brier (Cogn Semiotics 4:28–63, 2009) considers to be the levels of cybersemiotics, and the consequences it may have for the explanation of meaning-making processes in living systems.
We describe four series of experiments to study the emergence of inherently meaningful communicationby synthetic evolution in a population of artificial agents, which are controlled either by finite state machines or by neural net- works. We found that the agents can evolve the ability to use single symbols and, to a limited extent, pairs of symbols exhibiting rudimentary syntax. We show that the communication system evolved by the population can be studied in its own right as an evolving emergent phenomenon, and that the emergent communication systems exhibit some of the richness of natural communica- tion.
Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biolo-gists as basically 'the carriers of hereditary information.' Nevertheless, a number of researchers consider such talk as inadequate and 'just metaphor-ical,' thus expressing a skepticism about the use of the term 'information' and its derivatives in biology as a natural science. First, because the mean-ing of that term in biology is not as precise as it is, for instance, in the mathematical theory of communication. Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved. Biosemiotics, a field that at-tempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology. From the perspective of Peircean biosemiotics, we develop here an account of genes as signs, including a detailed analysis of two fundamental processes in the genetic information system (transcription and protein synthesis) that have not been made so far in this field of research. Furthermore, we propose here an account of information based on Peircean semiotics and apply it to our analysis of transcription and protein synthesis.
Philosophers and social scientists of diverse orientations have sug-gested that the pragmatics of semiosis is germane to a dynamic account of meaning as process. Semiosis, the central focus of C. S. Peirce's pragmatic philosophy, may hold a key to perennial problems regarding meaning. Indeed, Peirce's thought should be deemed seminal when placed within the cognitive sciences, especially with respect to his concept of the sign. According to Peirce's pragmatic model, semiosis is a triadic, time-bound, context-sensitive, interpreter-dependent, materially extended dynamic process. Semiosis in-volves inter-relatedness and inter-action between signs, their objects, acts and events in the world, and the semiotic agents who are in the process of making and taking them. Pragmatism 2 , in its original formulation, can be defined as a theory of meaning. 3 At first developed by C. S. Peirce, in the 1870s, in the am-bience of a series of informal meeting under the guise of the Meta-1 Also: We haved decided to use the more general term 'pragmatism', instead of the more specific, Peircean based term, 'pragmaticism', since our discussion includes 'pragmatic' philosophers other than Peirce. 3 We write 'original formulation' in order to differentiate between the strain of pragmatism that will be the focus of this inquiry and the more recent strain, often going by the name of 'neopragmatism', among the most notable proponents of which are Richard Rorty (1979; 1982) and Donald Davidson (1984).
We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broads classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components within the system cannot be predicted, even in principle, from the behavior of the systems parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature.
The tradition of pragmatism has, especially since Dewey, been characterized by a commitment to nonreductive naturalism. The notion of emergence, popular in the early decades of the twentieth century and currently re-emerging as a central concept in metaphysics and the philosophy of mind, may be useful in explicating that commitment. The present paper discusses the issue of the reality of emergent properties, drawing particular attention to a pragmatic way of approaching this issue. The reality of emergents can be defended as a pragmatically-useful ontological commitment; hence, pragmatism can be employed as a tool in the debate over the structure and reality of emergence. This strategy of justifying ontological commitments is examined through historical and systematic discussions of the pragmatist tradition. It turns out, among other things, that while classical pragmatists did not specify any technical notion of emergence in the contemporary sense, their non-reductively naturalist views are relevant to the more recent emergence discussions -- especially because they rejected the metaphysical realism typical of today’s ontologically-oriented emergence theories.
The mentalist mind-brain model is defended against weaknesses alleged by L. R. Vandervert (see record
1992-11849-001). It is argued that the perceived failings are based mostly on misinterpretation of mentalism and emergent interaction. Foundational concepts of the mentalist view are compared with those of the new cognitive paradigm in psychology. A changed "emergent interactionist" form of causation is posited that combines traditional microdeterminism with emergent "top-down" control. This emergent form of causation has wide application to causal explanation in general and is hypothesized to be the key common precursor for the consciousness (cognitive) revolution and subsequent boom in new worldviews, "systems thinking," emerging new paradigms, and other transformative developments of the 1970s and 1980s. (PsycINFO Database Record (c) 2012 APA, all rights reserved)
Organicism (materialistic holism) has provided the philosophical underpinnings for embryology since the time of Kant. It had influenced the founders of developmental mechanics, and the importance of organicism to embryology was explicitly recognized by such figures as O. Hertwig, H. Spemann, R. Harrison, A. M. Dalq, J. Needham, and C. H. Waddington. Many of the principles of organicism remain in contemporary developmental biology, but they are rarely defined as such. A combination of genetic reductionism and the adoption of holism by unscientific communities has led to the devaluation of organicism as a fruitful heuristic for research. This essay attempts to define organicism, provide a brief history of its importance to experimental embryology, outline some sociologically based reasons for its decline, and document its value in contemporary developmental biology. Based on principles or organicism, developmental biology should become a science of emerging complexity. However, this does mean that some of us will have to learn calculus. © 2000 Wiley-Liss, Inc.
This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the covariation between residues in folded proteins. We also review applications to molecular sequence and structure analysis, and introduce new tools in the characterization of resistance mutations, and in drug design.
Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different fields of biological research.
John Maynard Smith has defended against philosophical criticism the view that developmental biology is the study of the expression of information encoded in the genes by natural selection. However, like other naturalistic concepts of information, this 'teleosemantic' information applies to many non-genetic factors in development. Maynard Smith also fails to show that developmental biology is concerned with teleosemantic information. Some other ways to support Maynard Smith's conclusion are considered. It is argued that on any definition of information the view that development is the expression of genetic information is misleading. Some reasons for the popularity of that view are suggested.