There is renewed interest in questions of ontology in various fields, as there has been in biosemiotics. But for umwelt theory, ontology needs to be approached in particular ways, in order to avoid it from being yet another “philosophy of access”, part and parcel of the epistemology-ontology dyad, where “ontology” is the leftover of epistemology, or any sort of subjective constitution of things. The article engages in philosophical considerations about what kinds of assumptions and preliminary considerations should be made for (...) a semiosic ontology that was multiple, relational, and irreducible, with the principle goal being to engage with some terminological issues at the meeting point of ontology and umwelt theory. Ontography is proposed as a name for a low-key descriptive engagement with non-human umwelts considered as “worldings”, and maieutics as a particular attitude, or ethos, for the practical situation of direct inaccessibility of nonhuman umwelts. Parallels are drawn with the ontological turn in anthropology, which has also successfully engaged with alterity. A comparative study of umwelts should consider the ontological self-determination of the nonhuman other. (shrink)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that biology as a discipline (...) employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (shrink)

An overview of the issues and chapters in the book.

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. (shrink)

Insights into the nondual relationship of organism and environment and their processual nature have resulted in numerous efforts at understanding human behavior and motivation from a holistic and contextual perspective. Meadian social theory, cultural historical activity theory (CHAT), ecological psychology, and some interpretations of complexity theory persist in relating human activity to the wider and more scientifically valid view that a process metaphysics suggests. I would like to articulate a concept from ecological psychology – that of the affordance, and relate (...) it to aspects of phenomenology and neuroscience such that interpretations of the self, cognition, and the brain are understood as similar to interpretations of molar behaviors exhibited in social processes. Experience with meditation as a method of joining normal reflective consciousness with ‘awareness’ is described and suggested as a useful tool in coming to better understand the nondual nature of the body. (shrink)

The notion of computation has changed the world more than any previous expressions of knowledge. However, as know-how in its particular algorithmic embodiment, computation is closed to meaning. Therefore, computer-based data processing can only mimic life’s creative aspects, without being creative itself. AI’s current record of accomplishments shows that it automates tasks associated with intelligence, without being intelligent itself. Mistaking the abstract for the concrete has led to the religion of “everything is an output of computation”—even the humankind that conceived (...) the computer. The hypostatized role of computers explains the increased dependence on them. The convergence machine called deep learning is only the most recent form through which the deterministic theology of the machine claims more than what it actually is: extremely effective data processing. A proper understanding of complexity, as well as the need to distinguish between the reactive nature of the artificial and the anticipatory nature of the living are suggested as practical responses to the challenges posed by machine theology. (shrink)

Modern science originated in Western Europe, but its astonishing successes have forced every other civilization in the world to acknowledge and embrace its achievements. It is at the core of modernity and of the globalization of civilization. Consequently, efforts to show that non-Western traditions of thought should be taken seriously within the paradigm of science itself will inevitably provoke skepticism. However, science itself is riven not only by major problems and rival research programs, but by different conceptions about what is (...) science and what are its goals. These have generated such confusion, even within such advanced fields of science as physics, that more and more scientists are examining non-Western traditions of thought to provide a sufficiently broad perspective to overcome this confusion, to identify the core problems within science and to redefine it and its goals. This special edition brings into focus such work in a historical-epistemological perspective. (shrink)

The idea about this special issue came from a paper published as an updated and upridged version of an older memorial lecture given by Brian D. Josephson and Michael Conrad at the Gujarat Vidyapith University in Ahmedabad, India on March 2, 1984. The title of this paper was “Uniting Eastern Philosophy and Western Science” (1992). We thought that this topic deserves to be revisited after 25 years to demonstrate to the scientific community which new insights and achievements were attained in (...) this fairly broad field during this period. (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

Constructivist biosemiotics foundations imply the first-person basis of cognition. CBF are developed by the biology of cognition, relational biology, enactive approach, ecology of mind, second order cybernetics, genetic epistemology, gestalt, ecological perception and affordances, and active inference by minimization of free energy. CBF reject the idea of an objective independent reality to be represented by information processing in order to be the fittest. CBF assumes that perception is the behavioral configuration of an object and objects are tokens for eigen-behaviors. Cognition (...) takes place in the organism-environment structural coupling during the ontogeny and phylogeny of all biological unities including unicellular organisms. Therefore, if exogenous DNA particles are just tokens for the cell signalling eigen-behaviors, if there is no ‘information’ in the DNA sequence, how can we explain that the same virus or trans- sequence is associated with a similar phenotype? We call this ‘exogenomic problem’. With this basic example, but sufficiently generic to the whole biological world, we agree respectively with Autopoiesis, -system, and Gaia theory: i) ‘Information, code and meaning’ in the DNA sequence belong to the domain of the observer’s description. ii) Genetic ‘information’ is not a program or algorithmic software in DNA sequence. Rather it is a microphysical observable mode of eigen-behaviors in biological unities. iii) The transfer and acquisition of DNA particles is a biospheric phenomenon that maintains its homeorhesis, symbiotic and biosemiotic entailment. Based on the theoretical and experimental results of these theories, it is concluded that genetic ‘information’ is not a genomic sequence, nor any kind of information, but for the cell DNA must embody physical forcing. Genetic characters are the effects and not the cause of phenotype and DNA particles do not ‘use or manipulate’ cellular metabolism. Rather, any cellular configuration change that occurred before or during DNA perturbation is determined on the basis of the cellular standpoint. (shrink)

Attempts to ‘naturalize’ phenomenology challenge both traditional phenomenology and traditional approaches to cognitive science. They challenge Edmund Husserl’s rejection of naturalism and his attempt to establish phenomenology as a foundational transcendental discipline, and they challenge efforts to explain cognition through mainstream science. While appearing to be a retreat from the bold claims made for phenomenology, it is really its triumph. Naturalized phenomenology is spearheading a successful challenge to the heritage of Cartesian dualism. This converges with the reaction against Cartesian thought (...) within science itself. Descartes divided the universe between res cogitans, thinking substances, and res extensa, the mechanical world. The latter won with Newton and we have, in most of objective science since, literally lost our mind, hence our humanity. Despite Darwin, biologists remain children of Newton, and dream of a grand theory that is epistemologically complete and would allow lawful entailment of the evolution of the biosphere. This dream is no longer tenable. We now have to recognize that science and scientists are within and part of the world we are striving to comprehend, as proponents of endophysics have argued, and that physics, biology and mathematics have to be reconceived accordingly. Interpreting quantum mechanics from this perspective is shown to both illuminate conscious experience and reveal new paths for its further development. In biology we must now justify the use of the word “function”. As we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws “entail” evolution. The dream of a grand theory fails. In place of entailing laws, a post-entailing law explanatory framework is proposed in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, Adjacent Possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of Adjacent Possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world, becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws. (shrink)

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive (...) tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics. (shrink)

In this paper we will demonstrate that a computational system can meet the criteria for autonomy laid down by classical enactivism. The two criteria that we will focus on are operational closure and structural determinism, and we will show that both can be applied to a basic example of a physically instantiated Turing machine. We will also address the question of precariousness, and briefly suggest that a precarious Turing machine could be designed. Our aim in this paper is to challenge (...) the assumption that computational systems are necessarily heteronomous systems, to try and motivate in enactivism a more nuanced and less rigid conception of computational systems, and to demonstrate to computational theorists that they might find some interesting material within the enactivist tradition, despite its historical hostility towards computationalism. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended to a Łukasiewicz–Moisil (...) Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

If complexity is a necessary but not sufficient premise for the existence and expression of the living, anticipation is the distinguishing characteristic of what is alive. Anticipation is at work even at levels of existence where we cannot refer to intelligence. The prospect of artificially generating aesthetic artifacts and ethical constructs of relevance to a world in which the natural and the artificial are coexistent cannot be subsumed as yet another product of scientific and technological advancement. Beyond the artificial, the (...) synthetic conjures the understanding of aesthetics and ethics no longer from the perspective of the How? type of question, but rather the Why? Given the current infatuation with synthetic biology (i.e., making life from non-life), there is a practical consequence to such considerations. Synthetic life, as any other form of life, implies the possibility of evolution. Anticipation, which is the underlying factor of evolution, is thus expected. At the level of human existence, anticipation is expressed, for instance (but not exclusively), in aesthetic forms and ethical values. This translates, in turn, into an argument for the role aesthetics and ethics play in the process. Consequently, to qualify as life, the synthesis of the physical and the living will have to efficiently handle ambiguity. Current computational facilities, regardless of their nature or performance, operate exclusively in the semiotic domain of the well defined non-ambiguous. (shrink)

The collection Virtual Mathematics: the logic of difference brings together a range of new philosophical engagements with mathematics, using the work of French philosopher Gilles Deleuze as its focus. Deleuze’s engagements with mathematics rely upon the construction of alternative lineages in the history of mathematics in order to reconfigure particular philosophical problems and to develop new concepts. These alternative conceptual histories also challenge some of the self-imposed limits of the discipline of mathematics, and suggest the possibility of forging new connections (...) between philosophy and more recent developments in mathematics. This component of Deleuze’s work has, to date, been rather neglected by commentators working in the field of Deleuze studies. One of the aims of this collection is to address this critical deficit by providing a philosophical presentation of Deleuze’s relation to mathematics; one that is adequate to his project of constructing a philosophy of difference and to the exploration of some of its applications. This project developed as a result of encounters with an increasing number of researchers who have been working on the mathematical aspects of Deleuze’s work and the key role that these play in his philosophy. By bringing this work together for the first time, this collection makes an important contribution to the emerging body of work that endeavours to explore the broad range of Deleuze’s philosophy. (shrink)

This paper compares the two known logical forms of hierarchy, both of which have been used in models of natural phenomena, including the biological. I contrast their general properties, internal formal relations, modes of growth (emergence) in applications to the natural world, criteria for applying them, the complexities that they embody, their dynamical relations in applied models, and their informational relations and semiotic aspects.

The ecological approach to perception-action is unlike the standard approach in several respects. It takes the animal-in-its-environment as the proper scale for the theory and analysis of perception-action, it eschews symbol based accounts of perception-action, it promotes self-organization as the theory-constitutive metaphor for perception-action, and it employs self-referring, non-predicative definitions in explaining perception-action. The present article details the complexity issues confronted by the ecological approach in terms suggested by Rosen and introduces non-well-founded set theory as a potentially useful tool for (...) expressing them. The issues and the tool are brought to focus in the concept of affordance that is the basis for explanation of prospective control of action in the ecological approach. (shrink)

Algebraic/topological descriptions of living processes are indispensable to the understanding of both biological and cognitive functions. This paper presents a fundamental algebraic description of living/cognitive processes and exposes its inherent ambiguity. Since ambiguity is forbidden to computation, no computational description can lend insight to inherently ambiguous processes. The impredicativity of these models is not a flaw, but is, rather, their strength. It enables us to reason with ambiguous mathematical representations of ambiguous natural processes. The noncomputability of these structures means computerized (...) simulacra of them are uninformative of their key properties. This leads to the question of how we should reason about them. That question is answered in this paper by presenting an example of such reasoning, the demonstration of a topological strategy for understanding how the fundamental structure can form itself from within itself. (shrink)

This is the editorial to the special edition of Progress in Biophysics and Molecular Biology on the role engagement with Eastern traditions of thought could play in the advancement of science generally and biology and the science of mind in particular.

We argue that constructive approaches in epistemology and systems science, which are focused on normativity, knowledge, and communication of organisms and emphasize the primacy of activity, self-construction, and niche-construction in the cognitive agents, fit naturally to the both methodology and theory of biosemiotics. In particular, constructive view was already present in the works of the major precursors of biosemiotics: von Uexküll and Bateson, and to some extent Peirce. Biosemiotics has a chance to function as a mediating field in the theoretical (...) integration of semiotics with its construction-related sister disciplines (e.g., second order cybernetics, autopoiesis, constructivism, enactivism, and interactivism) because of its explicit assumption of the semiotic nature of life and agency and its objectified “first person” view to biosemiotic agents, the view that nevertheless avoids the agnostic attitude towards reality. (shrink)

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and (M, R) systems—participate in a (...) hylomorphist pattern of thinking which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined. (shrink)

In his attempt to find cognitive traits that set humans apart from nonhuman primates with respect to tool use, Vaesen overlooks the primacy of the environment toward the use of which behavior evolves. The occurrence of a particular behavior is a result of how that behavior has evolved in a complex and changing environment selected by a unique population.

This paper seeks to understand machine cognition. The nature of machine cognition has been shrouded in incomprehensibility. We have often encountered familiar arguments in cognitive science that human cognition is still faintly understood. This paper will argue that machine cognition is far less understood than even human cognition despite the fact that a lot about computer architecture and computational operations is known. Even if there have been putative claims about the transparency of the notion of machine computations, these claims do (...) not hold out in unraveling machine cognition, let alone machine consciousness (if there is any such thing). The nature and form of machine cognition remains further confused also because of attempts to explain human cognition in terms of computation and to model/simulate (aspects of) human cognitive processing in machines. Given that these problems in characterizing machine cognition persist, a view of machine cognition that aims to avoid these problems is outlined. The argument that is advanced is that something becomes a computation in machines only when a human interprets it, which is a kind of semiotic causation. From this it follows that a computing machine is not engaged in a computation unless a human interprets what it is doing; instead, it is engaged in machine cognition, which is defined as a member or subset of the set of all possible mappings of inputs to outputs. The human interpretation, which is a semiotic process, gives meaning to what a machine does, and then what it does becomes a computation. (shrink)

ABSTRACT: With a view to suggesting the possible relevance of Aristotelian thought to current notions of complexity and self-organization, studies Aristotlenard cells, and the theories of Schneider, Kay, and D. Sagan.

I comment on the preceding essays in this current thematic issue of Axiomathes , essays that discuss my 2009 book More Than Life Itself: A Synthetic Continuation in Relation Biology.

This essay is an attempt to construct an artificial dialog loosely modeled after that sought by Robert Maynard Hutchins who was a significant influence on many of us including and especially Robert Rosen. The dialog is needed to counter the deep and devastating effects of Cartesian reductionism on today’s world. The success of such a dialog is made more probable thanks to the recent book by A. Louie. This book makes a rigorous basis for a new paradigm, the one pioneered (...) by the late Robert Rosen. If we are to make such a paradigm shift happen, it has to be in the spirit of the dialog. The relationship between science, economics, technology and politics has to be openly recognized and dealt with. The message that Rosen sent to us has to be told outside small select circles of devotees. The situation has even been described by some as resembling a cult. This is no way for universal truths like these to be seen. The essay examines why this present situation has happened and identifies the systemic nature of the problem in terms of Rosen’s concepts about systems. The dialog involves works by George Lakoff, W. Brian Arthur, N. Katherine Hayles, Robert Reich and Dorion Sagan. These scholars each have their own approach to identifying the nature of the interacting systems that involve human activity and the importance of identifying levels of abstraction in analyzing systems. Pooling their insights into different facets of a complex system is very useful in constructing a model of the self referential system that humans and their technology have shaped. The role of the human component in the whole earth system is the goal of the analysis. The impact of the Cartesian reductionist paradigm on science and the related aspects of human activity are examined to establish an explanation for the isolation of Rosen’s paradigm. The possible way to proceed is examined in the conclusion. (shrink)

This talk, delivered at De l''autopoièse à la neurophénoménologie: un hommage à Francisco Varela; from autopoiesis to neurophenomenology: a tribute to Francisco Varela, June 18–20, at the Sorbonne in Paris, explicates several links between Varela''s neurophenomenology and his biological concept of autopoiesis.

This article compares the methodologies of two types of sciences (according to J. Locke) — semiotics, and physics — and attempts thereby to characterise the semiotic and non-semiotic approaches to the description of ecosystems. The principal difference between the physical and semiotic sciences is that there exists just a single physical reality that is studied by physics via repetitiveness, whereas there are many semiotic realities that are studied as unique individuals. Seventeen complementary definitions of the semiosphere are listed, among them, (...) semiosphere defined as the space of qualitative (incommensurable) diversity. It is stated that, paradoxically, diversity, being a creation of communication, can also be destroyed due to excessive communication. (shrink)

The paper presents the most general aspects of scientific modeling and shows that social systems naturally include different belief systems. Belief systems differ in a variety of respects, most notably in the selection of suitable qualities to encode and the internal structure of the observables. The following results emerge from the analysis: conflict is explained by showing that different models encode different qualities, which implies that they model different realities; explicitly connecting models to the realities that they encode makes it (...) possible to clarify the relations among models; by understanding that social systems are complex one knows that there is no chance of developing a maximal model of the system; the distinction among different levels of depth implicitly includes a strategy for inducing change; identity-preserving models are among the most difficult to modify; since models do not customarily generate internal signals of error, strategies with which to determine when models are out of synch with their situations are especially valuable; changing the form of power from a zero sum game to a positive sum game helps transform the nature of conflicts. (shrink)

Juri Lotman wrote, in Russian, a book Непредсказуемые механизмы культуры — the unpredictable mechanisms of culture. Its English translator, Brian Baer, preferred to translate the title as The Unpredictable Workings of Culture . He had a reason for this — many scholars tend to refuse the term ‘mechanism’ for the phenomena of meaning-making. However, there exist quite clear cultural differences in this opinion. For instance in Russian, ‘mechanisms’ are understood so broadly that there is no question to use the term (...) for purely mental creations; the case is similar in German, in Estonian, and in several other languages. It seems that the applicability of this term to culture is correlated with the usage of the term ‘science’. In Russian, in German, and in Estonian, the humanities are sciences , while the English-language tradition tends to separate the humanities from the sciences. However, the latter h .. (shrink)

In his recent book Reinventing the Sacred, renowned biologist and systems theorist Stuart Kauffman offers an avenue for the revival of the sacred and for reconciling sacredness with a robust scientific outlook. According to Kauffman, God is a human cultural invention, and he urges us to reinvent the sacred as the ceaseless creativity in nature. I argue that Kauffman's proposal suffers from a major shortcoming, namely, being at odds with the nature, and content, of authentic experiences of the sacred, experiences (...) which point invariably in the direction of a reality which transcends human imagination and capacity for cultural innovation. Correspondingly, I point in the direction of an alternative approach to the revival of the sacred rooted in what I call the path of direct spiritual awareness. I argue that, while being in better accord with the phenomenology of religious experience, this realist alternative to Kauffman's constructivism also avoids the unpleasant symptoms which often accompany traditional theism, namely, dogmatism, irrationalism, and incompatibility with a scientifically minded metaphysics. (shrink)

(No abstract is available for this citation).

When we deal with complex things, like human subjects or organizations, we deal with identity – that which makes a person or an organization what it is and distinguishes him/her/it from other persons or organizations, a kind of “self”. Our identity determines how we think about and interact with others. It will be argued in this chapter that the self is constituted relationally. Moreover, when we are in the realm of the self, we are always already in the realm of (...) engaging with and mediating differences – the realm of ethics. The position which will be developed argues that approaching identity as a complex system allows us to resist thinking of identity as an easily identifiable and static entity. Identity is always being constituted within a complex and contingent world, where we have to make choices based on contingent values rather than on universal knowledge or the outcome of rational calculations. As a result, we have to keep in mind that our daily practices always already have an ethical component, and our decisions need to be continually evaluated and re-evaluated in the light of our (and others’) varying identities. (shrink)

This paper explores the similarities between the conceptual structure of quantum theory and relational biology as developed within the Rashevsky-Rosen-Louie school of theoretical biology. With this aim, generalized quantum theory and the abstract formalism of (M,R)-systems are briefly presented. In particular, the notion of organizational invariance and relational identity are formalized mathematically and a particular example is given. Several quantum-like attributes of Rosen’s complex systems such as complementarity and nonseparability are discussed. Taken together, this work emphasizes the possible role of (...) self-referentiality and impredicativity in quantum theory. (shrink)

A novel conceptual framework is introduced for the Complexity Levels Theory in a Categorical Ontology of Space and Time. This conceptual and formal construction is intended for ontological studies of Emergent Biosystems, Super-complex Dynamics, Evolution and Human Consciousness. A claim is defended concerning the universal representation of an item’s essence in categorical terms. As an essential example, relational structures of living organisms are well represented by applying the important categorical concept of natural transformations to biomolecular reactions and relational structures that (...) emerge from the latter in living systems. Thus, several relational theories of living systems can be represented by natural transformations of organismic, relational structures. The ascent of man and other living organisms through adaptation, is viewed in novel categorical terms, such as variable biogroupoid representations of evolving species. Such precise but flexible evolutionary concepts will allow the further development of the unifying theme of local-to-global approaches to highly complex systems in order to represent novel patterns of relations that emerge in super- and ultra-complex systems in terms of compositions of local procedures. Solutions to such local-to-global problems in highly complex systems with ‘broken symmetry’ might be possible to be reached with the help of higher homotopy theorems in algebraic topology such as the generalized van Kampen theorems (HHvKT). Categories of many-valued, Łukasiewicz-Moisil (LM) logic algebras provide useful concepts for representing the intrinsic dynamic ‘asymmetry’ of genetic networks in organismic development and evolution, as well as to derive novel results for (non-commutative) Quantum Logics. Furthermore, as recently pointed out by Baianu and Poli (Theory and applications of ontology, vol 1. Springer, Berlin, in press), LM-logic algebras may also provide the appropriate framework for future developments of the ontological theory of levels with its complex/entangled/intertwined ramifications in psychology, sociology and ecology. As shown in the preceding two papers in this issue, a paradigm shift towards non-commutative, or non-Abelian, theories of highly complex dynamics—which is presently unfolding in physics, mathematics, life and cognitive sciences—may be implemented through realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. (shrink)

The social sciences and humanities are fragmented into specialized areas, each with their own parlance and procedures. This hinders information sharing and the growth of a coherent body of knowledge. Modeling and simulation can be the scientific lingua franca, or shared technical language, that can unite, integrate, and relate relevant parts of these diverse disciplines.Models are well established in the scientific community as mediators, contributors, and enablers of scientific knowledge. We propose a potentially revolutionary linkage between social sciences, humanities and (...) computer simulation, forging what we call “human simulation.” We explore three facets of human simulation, namely: the simulation of humans, the design of simulations for human use, and simulations that include humans as well as simulated agents among the actors. We describe the potential of human simulation using several illuminating examples. We also discuss computational, epistemological, and hermeneutical challenges constraining the use of human simulation. (shrink)

Model organisms are a living form of scientific models. Despite the widespread use of model organisms in scientific research, the actual representational relationship between model organisms and their target species is often poorly characterized in the context of cross-species research. Many model organisms do not represent the target species adequately, let alone accurately. This is partly due to the complex and emergent life phenomena in the organism, and partly due to the fact that a model organism is always taken to (...) represent a broad range of diverse organisms. More often than not, model organisms are taken as a reference point for an extrapolation to be made to the unknown characteristics of other species. I propose to view model organisms as analogue simulators which represent the emergent phenomenon in the context of cross-species research. A model organism represents a wide range of species by simulating their molecular microstates which underlie various emergent phenomena. I show that although model organisms represent the target species inadequately at many levels of complexity, they have epistemic values as a simulator in virtue of which the emergent phenomenon can be modeled dynamically, a virtue that is hardly attainable by non-dynamic models. (shrink)

Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for treating diseases such as cancers, is (...) pointed out. The roles played by multiple metastable states in the “continuous uphill flow of Life” supported through internal bioenergetic processes that are coupled to essential inflows are also discussed in relation to dynamic realizations of (M,R)-systems. Furthermore, the roles played by the underlying, many-valued, quantum logics and symbolic computations for ultra-complex biological systems are also briefly discussed. (shrink)

The phenomenological calculus is a relational paradigm for complex systems, closely related in substance and spirit to Robert Rosen’s own approach. Its mathematical language is multilinear algebra. The epistemological exploration continues in this paper, with the expansion of the phenomenological calculus into the realm of anisotropy.

Morphological EvoDevo is a field of biological inquiry in which explicit relations between evolutionary patterns and growth or morphogenetic processes are made. Historically, morphological EvoDevo results from the coming together of several traditions, notably Naturphilosophie, embryology, the study of heterochrony, and developmental constraints. A special feature binding different approaches to morphological EvoDevo is the use of formalisms and mathematical models. Here we will introduce anatomical network analysis, a new approach centered on connectivity patterns formed by anatomical parts, with its own (...) concepts and tools specifically designed for the study of morphological EvoDevo questions. Riedl’s concept of burden is tightly related to the use of anatomical networks, providing a nexus between the evolutionary patterns and the structural constraints that shape them. (shrink)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism – different understandings (...) of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

This paper examines the biosemiotic approach to the study of life processes by fashioning a series of questions that any worthwhile semiotic study of life should ask. These questions can be understood simultaneously as: (1) questions that distinguish a semiotic biology from a non-semiotic (i.e., reductionist–physicalist) one; (2) questions that any student in biosemiotics should ask when doing a case study; and (3) still currently unanswered questions of biosemiotics. In addition, some examples of previously undertaken biosemiotic case studies are examined (...) so as to suggest a broad picture of how such a biosemiotic approach to biology might be done. (shrink)

Francisco Varela’s work is a monumental achievement in 20th century biological and biophilosophical thought. After his early collaboration in neo-cybernetics with Humberto Maturana (“autopoiesis”), Varela made fundamental contributions to immunology (“network theory”), Artificial Life (“cellular automata”), cognitive science (“enaction”), philosophy of mind (“neurophenomenology”), brain studies (“the brainweb”), and East- West dialogue (the Mind and Life conferences). In the course of his career, Varela influenced many important collaborators and interlocutors, formed a generation of excellent students, and touched the lives of many (...) with the intensity of his mind, the sharpness of his wit, and the strength of his spirit. In this essay, I will trace some of the key turning points in his thought, with special focus on the concept of emergence, which was always central to his work, and on questions of politics, which operate at the margins of his thought. I will divide Varela’s work into three periods – autopoiesis, enaction, and radical embodiment – each of which is marked by a guiding concept; a specific.. (shrink)

Fundamental properties of N-valued logics are compared and eleven theorems are presented for their Logic Algebras, including Łukasiewicz–Moisil Logic Algebras represented in terms of categories and functors. For example, the Fundamental Logic Adjunction Theorem allows one to transfer certain universal, or global, properties of the Category of Boolean Algebras,, (which are well-understood) to the more general category \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\cal L}$$\end{document}Mn of Łukasiewicz–Moisil Algebras. Furthermore, the relationships of LMn-algebras to other many-valued logical structures, (...) such as the n-valued Post, MV and Heyting logic algebras, are investigated and several pertinent theorems are derived. Applications of Łukasiewicz–Moisil Algebras to biological problems, such as nonlinear dynamics of genetic networks – that were previously reported – are also briefly noted here, and finally, probabilities are precisely defined over LMn-algebras with an eye to immediate, possible applications in biostatistics. (shrink)