A formal model of the processes of digestion in a hypothetical cell is developed and discussed as a case study of how the threefold logic of Peircean semiotics works within Rosen’s paradigm of relational ontology. The formal model is used to demonstrate several fundamental differences between a relational description of biological processes and a mechanistic description. The formal model produces a logic of embodied generalization that is mediated and determined by the cell through its interactions with the environment. Specifically, the (...) synchronization of the functions of pattern recognition and semantic attribution results in an open and adaptive learning system that is stabilized by a hermeneutical circle. The relational principles of biosemiotics demonstrated through this case study are applicable to other biological systems, as well as to the relational ontology of systems theory, artificial intelligence systems, and relativistic quantum theory. (shrink)

According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little to say about how mechanisms relate to the organism in which they reside. A key feature of organisms, emphasized by the autonomy tradition, is that organisms maintain themselves. To do this, they rely on mechanisms. But mechanisms must be controlled so that they produce the phenomena for which they are responsible when and in the manner needed by the organism. To account for how (...) they are controlled, we characterize mechanisms as sets of constraints on the flow of free energy. Some constraints are flexible and can be acted on by other mechanisms, control mechanisms, that utilize information procured from the organism and its environment to alter the flexible constraints in other mechanisms so that they produce phenomena appropriate to the circumstances. We further show that control mechanisms in living organisms are organized heterarchically—control is carried out primarily by local controllers that integrate information they acquire as well as that which they procure from other control mechanisms. The result is not a hierarchy of control but an integrated network of control mechanisms that has been crafted over the course of evolution. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

This chapter draws on insights from non-equilibrium thermodynamics to demonstrate the ontological inadequacy of the machine conception of the organism. The thermodynamic character of living systems underlies the importance of metabolism and calls for the adoption of a processual view, exemplified by the Heraclitean metaphor of the stream of life. This alternative conception is explored in its various historical formulations and the extent to which it captures the nature of living systems is examined. Following this, the chapter considers the metaphysical (...) implications of reconceptualizing the organism from complex machine to flowing stream. What do we learn when we reject the mechanical and embrace the processual? Three key lessons for biological ontology are identified. The first is that activity is a necessary condition for existence. The second is that persistence is grounded in the continuous self-maintenance of form. And the third is that order does not entail design. (shrink)

Living systems employ several mechanisms and behaviors to achieve robustness and maintain themselves under changing internal and external conditions. Regulation stands out from them as a specific form of higher-order control, exerted over the basic regime responsible for the production and maintenance of the organism, and provides the system with the capacity to act on its own constitutive dynamics. It consists in the capability to selectively shift between different available regimes of self-production and self-maintenance in response to specific signals and (...) perturbations, due to the action of a dedicated subsystem which is operationally distinct from the regulated ones. The role of regulation, however, is not exhausted by its contribution to maintain a living system’s viability. While enhancing robustness, regulatory mechanisms play a fundamental role in the realization of an autonomous biological organization. Specifically, they are at the basis of the remarkable integration of biological systems, insofar as they coordinate and modulate the activity of distinct functional subsystems. Moreover, by implementing complex and hierarchically organized control architectures, they allow for an increase in structural and organizational complexity while minimizing fragility. Finally, they endow living systems, from their most basic unicellular instances, with the capability to control their own internal dynamics to adaptively respond to specific features of their interaction with the environment, thus providing the basis for the emergence of minimal forms of cognition. (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)

According to David Chalmers, the hard problem of consciousness consists of explaining how and why qualitative experience arises from physical states. Moreover, Chalmers argues that materialist and reductive explanations of mentality are incapable of addressing the hard problem. In this chapter, I suggest that Chalmers’ hard problem can be usefully distinguished into a ‘how question’ and ‘why question,’ and I argue that evolutionary biology has the resources to address the question of why qualitative experience arises from brain states. From this (...) perspective, I discuss the different kinds of evolutionary explanations (e.g., adaptationist, exaptationist, spandrel) that can explain the origins of the qualitative aspects of various conscious states. This argument is intended to clarify which parts of Chalmers’ hard problem are amenable to scientific analysis. (shrink)

“Freedom” is a phenomenon in the natural world. This phenomenon—and indirectly the question of free will—is explored using a variety of systems-theoretic ideas. It is argued that freedom can emerge only in systems that are partially determined and partially random, and that freedom is a matter of degree. The paper considers types of freedom and their conditions of possibility in simple living systems and in complex living systems that have modeling subsystems. In simple living systems, types of freedom include independence (...) from fixed materiality, internal rather than external determination, activeness that is unblocked and holistic, and the capacity to choose or alter environmental constraint. In complex living systems, there is freedom in satisfaction of lower level needs that allows higher potentials to be realized. Several types of freedom also manifest in the modeling subsystems of these complex systems: in the transcending of automatism in subjective experience, in reason as instrument for passion yet also in reason ruling over passion, in independence from informational colonization by the environment, and in mobility of attention. Considering the wide range of freedoms in simple and complex living systems allows a panoramic view of this diverse and important natural phenomenon. (shrink)

Existing accounts of mechanistic causation are not suited for understanding causation in biological and neural mechanisms because they do not have the resources to capture the unique causal structure of control heterarchies. In this paper, we provide a new account on which the causal powers of mechanisms are grounded by time-dependent, variable constraints. Constraints can also serve as a key bridge concept between the mechanistic approach to explanation and underappreciated work in theoretical biology that sheds light on how biological systems (...) channel energy to actively respond to the environment in adaptive ways, perform work, and fulfill the requirements to maintain themselves far from equilibrium. We show how the framework applies to several concrete examples of control in simple organisms as well as the nervous system of complex organisms. (shrink)

The present work is a comment of a recent paper by Fortin and coauthors in which the authors propose the introduction of Bohmian mechanics in the philosophy of chemistry and the use of standard quantum mechanics as a mere instrument of prediction. This way would allow overcoming the obstacles found in linking molecular chemistry and quantum mechanics. Starting from some remarks on the orbital concept, we highlight and discuss some general issues that need to be taken into account when two (...) scientific theories coexist within the same investigation field, i.e. SQM and BM. (shrink)

A notion of delegated causality is introduced here. This subtle kind of causality is dual to interventional causality. Delegated causality elucidates the causal role of dynamical systems at the “edge of chaos”, explicates evident cases of downward causation, and relates emergent phenomena to Gödel’s incompleteness theorem. Apparently rich implications are noticed in biology and Chinese philosophy. The perspective of delegated causality supports cognitive interpretations of self-organization and evolution.

The notion of feedback has been exploited with considerable success in scientific and technological fields as well as in the sciences of man and society. Its use in philosophical, cultural and educational contexts, however, is still rather meagre, even if some notable attempts can be found in the literature. This paper shows that the feedback concept can help learn and understand some classical philosophical theories. In particular, attention focuses on Fichte’s doctrine of science, usually presented in obscure terms following its (...) inventor’s style, and on the vulgate version of Hegel’s dialectic. Also a classic problem of linguistics concerning the meaning of sentences in partially unknown languages is interpreted with the aid of feedback diagrams. Even if the analysis is only qualitative, it is believed that it may serve as a useful tool for thought for both students and researchers. (shrink)

Biosemiotics argues that “sign” and “meaning” are two essential concepts for the explanation of life. Peircean biosemiotics, founded by Tomas Sebeok from Peirce’s semiotics and Jacob von Uexkül’s studies on animal communication, today makes up the mainstream of this discipline. Marcello Barbieri has developed an alternative account of meaning in biology based on the concept of code. Barbieri rejects Peircean biosemiotics on the grounds that this discipline opens the door to nonscientific approaches to biology through its use of the concept (...) of “interpretation.” In this article, it is noted that Barbieri does not adequately distinguish among Peirce’s semiotics, Peircean biosemiotics, and “interpretation-based” biosemiotics. Two key arguments of Barbieri are criticized: his limited view of science and his rejection of “interpretation-based” biosemiotics. My argument is based on tools taken from a different approach: Robert Rosen’s relational biology. Instead of “signs” and “meanings,” the study begins in this case from the “components” and “functions” of the organism. Rosen pursues a new definition of a law of nature, introduces the anticipatory nature of organisms, and defines the living being as a system closed to efficient cause. It is shown that Code Biosemiotics and Peircean biosemiotics can share a common field of study. Additionally, some proposals are suggested to carry out a reading of Rosen’s biology as a biosemiotic theory. (shrink)

To confine scientific narrative to only material and mechanical causes is to ensure incomplete and at times contrived descriptions of phenomena. In the life sciences, and particularly in the field of ecology, causality takes on qualitatively distinct forms at different hierarchical levels. The notion of formal cause provides for entirely natural and quantitative explanations of ecosystem behavior.

Kampis proposes the study of chaotic itinerancy, pointing out its significance in domains of cognitive science and philosophy. He has discovered in the concept of chaotic itinerancy the possibility for a new dynamical approach that elucidates mental states with a physical basis. This approach may therefore provide the means to go beyond the connectionist approach. In accordance with his theory, I here highlight three issues regarding chaotic itinerancy: transitory dynamics, diversity, and self-modifying system.

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)

I examine the abstraction/representation theory of computation put forward by Horsman et al., connecting it to the broader notion of modeling, and in particular, model-based explanation, as considered by Rosen. I argue that the ‘representational entities’ it depends on cannot themselves be computational, and that, in particular, their representational capacities cannot be realized by computational means, and must remain explanatorily opaque to them. I then propose that representation might be realized by subjective experience, through being the bearer of the structure (...) of abstract objects that are represented. (shrink)

The commentators expressed concerns regarding the relevance and value of non-computational non-symbolic explanations of cognitive performance. But what counts as an “explanation” depends on the pre-theoretical assumptions behind the scenes of empirical science regarding the kinds of variables and relationships that are sought out in the first place, and some of the present disagreements stem from incommensurate assumptions. Traditional cognitive science presumes cognition to be a decomposable system of components interacting according to computational rules to generate cognitive performances (i.e., component-dominant (...) dynamics). We assign primacy to interaction-dominant dynamics among components. Though either choice can be a good guess before the fact, the primacy of interactions is now supported by much recent empirical work in cognitive science. Consequently, in the main, the commentators have failed so far to address the growing evidence corroborating the theory-driven predictions of complexity science. (shrink)

This article addresses the issue of objectivism vs constructivism in two areas,biology and cognitive science, which areintermediate between the natural sciences suchas physics (where objectivism is dominant) andthe human and social sciences (whereconstructivism is widespread). The issues inbiology and in cognitive science are intimatelyrelated; in each of these twin areas, the objectivism vs constructivism issue isinterestingly and rather evenly balanced; as aresult, this issue engenders two contrastingparadigms, each of which has substantialspecific scientific content. The neo-Darwinianparadigm in biology is closely resonant (...) withthe classical cognitivist paradigm in cognitivescience, and both of them are intrinsicallyobjectivist. The organismic paradigm inbiology, based on the concept of autopoiesis,is consonant with the paradigm of enaction incognitive science; the latter paradigms are bothprofoundly constructivist.In cognitive science, the objectivism vsconstructivism issue is internal to thescientific field itself and reflexivity isinescapable. At this level, strong ontologicalobjectivism is self-contradictory and thereforeuntenable. Radical constructivism isself-coherent; but it also rehabilitatesa weak form of objectivism as a pragmaticallyviable alternative. In conclusion, there is aneven-handed reciprocity between objectivistand constructivist perspectives. Finally, thearticle examines the consequences of thisconclusion for fields other than cognitivescience: biology; physics and the naturalsciences; and the human and social sciences. (shrink)

There is a famous passage in chapter six of James’ Principles of Psychology whose import, many believe, deals a devastating blow to the explanatory aspirations of panpsychism. In the present paper I take a close look at James’ argument, as well as at the claim that it underlies a powerful critique of panpsychism. Apart from the fact that the argument was never aimed at panpsychism as such, I show that it rests on highly problematic assumptions which, if followed to their (...) logical consequences, are just as inedible to contemporary critics of panpsychism as they are to its present-day supporters. Hence, a naïve employment of the argument, as a critique leveled by physicalists against panpsychism, is counterproductive and even self-defeating. After examining the metaphysical shortcomings undermining James’ position , I conclude with some reflections on what needs to be done in order to obtain a better perspective regarding the explanatory prospects of panpsychism as an alternative approach to mainstream physicalism in the study of conscious phenomena. (shrink)

Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False. . ???aop.label???. doi: 10.1080/09515089.2013.804045.

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 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 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. (shrink)

Principles of constructivism are used here to explore how organisms develop tools, subagents, scaffolds, signs, and adaptations. Here I discuss reasons why organisms have composite nature and include diverse subagents that interact in partially cooperating and partially conflicting ways. Such modularity is necessary for efficient and robust functionality, including mutual construction and adaptability at various time scales. Subagents interact via material and semiotic relations, some of which force or prescribe actions of partners. Other interactions, which I call “guiding”, do not (...) have immediate effects and do not disrupt the evolution and learning capacity of partner agents. However, they modify the extent of learning and evolutionary possibilities of partners via establishment of scaffolds and constraints. As a result, subagents construct reciprocal scaffolding for each other to rebalance their communal evolution and learning. As an example, I discuss guiding interactions between the body and mind of animals, where the pain system adjusts mind-based learning to the physical and physiological constraints of the body. Reciprocal effects of mind and behaviors on the development and evolution of the body includes the effects of Lamarck and Baldwin. (shrink)

In this short contribution we explore the historical roots of recent synthetic approaches in biology and try to assess their real potential, as well as identify future hurdles or the reasons behind some of the main difficulties they currently face. We suggest that part of these difficulties might not be just the result of our present lack of adequate technical skills or understanding, but could spring directly from the nature of the biological phenomenon itself. In particular, if life is conceived (...) as autonomy in open-ended evolution, which would help to explain the highly complex and dynamic organization of the simplest known organisms (i.e., genetically-instructed cellular metabolisms), external synthetic implementations of such systems, or interventions on them, are bound to interfere with some of their characteristic transformation processes, both at the ontogenetic and phylogenetic scales. In any case, this will prove very revealing and productive, technologically and scientifically speaking, since the knowledge gathered from those implementations/interventions will be extremely valuable in establishing our capacities and limitations to fully comprehend, utilize, and expand the living domain as we know it today. (shrink)

In this paper we review and argue for the relevance of the concept of open-ended evolution in biological theory. Defining it as a process in which a set of chemical systems bring about an unlimited variety of equivalent systems that are not subject to any pre-determined upper bound of organizational complexity, we explain why only a special type of self-constructing, autonomous systems can actually implement it. We further argue that this capacity derives from the ‘dynamic decoupling’ (in its minimal or (...) most basic sense: the phenotype–genotype decoupling) by means of which a radically new way of material organization (minimal living organization) is achieved, allowing for the long-term sustenance of systems whose individual-metabolic and collective-historical pathways become thereafter deeply intertwined. (shrink)

Our aim in the present paper is to approach the nature of life from the perspective of autonomy, showing that this perspective can be helpful for overcoming the traditional Cartesian gap between the physical and cognitive domains. We first argue that, although the phenomenon of life manifests itself as highly complex and multidimensional, requiring various levels of description, individual organisms constitute the core of this multifarious phenomenology. Thereafter, our discussion focuses on the nature of the organization of individual living entities, (...) proposing autonomy as the main concept to grasp it. In the second part of the article we show how autonomy is also fundamental to explaining major evolutionary transitions, in an attempt to rethink evolution from the point of view of the organizational structure of the entities/organisms involved. This gives further support to the idea of autonomy not only as a key to understanding life in general but also the complex expressions of it that we observe on our planet. Finally, we suggest a possible general principle that underlies those evolutionary transitions, which allow for the open-ended redefinition of autonomous systems: namely, the relative dynamic decoupling that must be articulated among distinct parts, modules or modes of operation in these systems. (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)

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)

Kinetic models using enzyme kinetics are developed for the three ways that Louie proved that Rosen’s minimal (M-R)-System can be closed to efficient cause; i.e., how the “replication” component can itself be entailed from within the system. The kinetic models are developed using the techniques of network thermodynamics. As a demonstration, each model is simulated using a SPICE circuit simulator using arbitrarily chosen rate constants. The models are built from SPICE sub-circuits representing the key terms in the chemical rate equations. (...) The models include the addition of an ad hoc semi-permeable membrane so the system can achieve steady state fluxes and also to illustrate the need for all the efficient cause agents to be continually replaced. Comments are made about exactly what is being simulated. (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)

The term ‘information’ is used extensively in biology, cognitive science and the philosophy of consciousness in relation to the concepts of ‘meaning’ and ‘causation’. While ‘information’ is a term that serves a useful purpose in specific disciplines, there is much to the concept that is problematic. Part 1 is a critique of the stance that information is an independently existing entity. On this view, and in biological contexts, systems transmit, acquire, assimilate, decode and manipulate it, and in so doing, generate (...) meaning. I provide a detailed proposal in Part 2 that supports the claim that it is the dynamic form of a system that qualifies the informational nature of meaningful interactive engagement, that is, that information is dependent on dynamic form rather than that it exists independently. In Part 3, I reflect on the importance of the distinction between the independent and dependent stances by looking specifically at the implications for how we might better interpret causation and emergence. (shrink)

Anticipatory acts or predictive behavior are prerequisites for living organisms to sustain their survival when escaping from a predator, catching prey, or schooling. For example, catching prey requires that the predator perform some procedures that are equivalent to estimating the directional movement of the prey, its speed and its distance relative to the predator. Underlying these procedures is time experience, which does not adhere to man-made mechanical clocks. Living organisms keep time based on the local activities of each participant and (...) form ecological clocks together. The timekeeping of ecological clocks has been called E-series time, which is interactive in character and consists of mutual alignment of timing that is co-adjusted to each other’s movements and rhythms. A main objective of our current work is to illustrate how E-series time is used for flows of anticipatory acts. To explain such predictive moves and their efforts based on how the perspective of the immediate future affects the present, we resort to the organismic activity of revising the preceding acts in retrospect and semiotic scaffolding that extends beyond simple linear causality. Special attention is paid to the construction of the notion of retrocausal scaffolding, which is a series of dialogical punctuations or mutual coordination of rhythms for the joint production of the present moment of now. Retrocausal scaffolding is synonymous with negotiated anticipation, which is a semiotic/communicative account of revising the preceding acts in the present moment. (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)

The current assumptions of knowledge acquisition brought about the crisis in the reproducibility of experiments. A complementary perspective should account for the specific causality characteristic of life by integrating past, present, and future. A “second Cartesian revolution,” informed by and in awareness of anticipatory processes, should result in scientific methods that transcend the theology of determinism and reductionism. In our days, science, itself an expression of anticipatory activity, makes possible alternative understandings of reality and its dynamics. For this purpose, the (...) study advances G-complexity for defining and comparing decidable and undecidable knowledge. AI and related computational expressions of knowledge could benefit from the awareness of what distinguishes the dynamics of life from any other expressions of change. (shrink)

This paper argues that biological organisation can be legitimately conceived of as an intrinsically teleological causal regime. The core of the argument consists in establishing a connection between organisation and teleology through the concept of self-determination: biological organisation determines itself in the sense that the effects of its activity contribute to determine its own conditions of existence. We suggest that not any kind of circular regime realises self-determination, which should be specifically understood as self-constraint: in biological systems, in particular, self-constraint (...) takes the form of closure, i.e. a network of mutually dependent constitutive constraints. We then explore the occurrence of intrinsic teleology in the biological domain and beyond. On the one hand, the organisational account might possibly concede that supra-organismal biological systems could realise closure, and hence be teleological. On the other hand, the realisation of closure beyond the biological realm appears to be highly unlikely. In turn, the occurrence of simpler forms of self-determination remains a controversial issue, in particular with respect to the case of self-organising dissipative systems. (shrink)

In this paper, we advocate the idea that an adequate explanation of biological systems requires appealing to organizational closure as an emergent causal regime. We first develop a theoretical justification of emergence in terms of relatedness, by arguing that configurations, because of the relatedness among their constituents, possess ontologically irreducible properties, providing them with distinctive causal powers. We then focus on those emergent causal powers exerted as constraints, and we claim that biological systems crucially differ from other natural systems in (...) that they realize a closure of constraints, i.e. a second-order emergent regime of causation such that the constituents, each of them acting as a constraint, realize a mutual dependence among them, and are collectively able to self-maintain. Lastly, we claim that closure can be justifiably taken as an emergent regime of causation, without admitting that it inherently involves whole-parts causation, which would require to commit to stronger ontological and epistemological assumptions. (shrink)

Entry of the Encyclopedia of Systems Biology.

Since Darwin it is widely accepted that natural selection (NS) is the most important mechanism to explain how biological organisms—in their amazing variety—evolve and, therefore, also how the complexity of certain natural systems can increase over time, creating ever new functions or functional structures/relationships. Nevertheless, the way in which NS is conceived within Darwinian Theory already requires an open, wide enough, functional domain where selective forces may act. And, as the present paper will try to show, this becomes even more (...) evident if one looks into the problem of origins. If there was a time when NS was not operating (as it is quite reasonable to assume), where did that initial functional diversity, necessary to trigger off the process, come from? Self-organization processes may be part of the answer, as many authors have claimed in recent years, but surely not the complete one. We will argue here that a special type of self-maintaining organization, arising from the interplay among a set of different endogenously produced constraints (pre-enzymatic catalysts and primitive compartments included), is required for the appearance of functional diversity in the first place. Starting from that point, NS can progressively lead to new (and, at times, also more complex) organizations that, in turn, provide wider functional variety to be selected for, enlarging in this way the range of action and consequences of the mechanism of NS, in a kind of mutually enhancing effect. (shrink)

This review of John Russon's Human Experience: Philosophy, Neurosis, and the Elements of Everyday Life focuses on Russon's position that experience is open (having a developmental, situated and dynamic, rather than fixed, structure) and figured (having a structure inseparable from forms of bodily function), and that mind is something learned in the process of working out experience as figured and open. These themes are drawn together in relation to recent scientific discussions (e.g., of bodily dynamics, mirror neurons, robotic systems and (...) thermodynamics), to show how Russon's view challenges deep philosophical assumptions in prevailing accounts of mind, body and experience. (shrink)

Husserlian variation, Bergsonian intuition and Peircean abduction are contrasted as methodological responses to the traditional philosophical problem of deriving knowledge of universals from singulars. Each method implies a correspondingly different view of the generation of the variations from which knowledge is derived. To make sense of the latter differences, and to distinguish the different sorts of variation sought by philosophers and scientists, a distinction between extensive, intensive, and abductive-intensive variation is introduced. The link between philosophical method and the generation of (...) variation is used to illuminate different philosophical conceptions of nature and nature's relation to meaning and sense. (shrink)

We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a (...) set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology. (shrink)

The Anthropocene crisis is frequently described as the rarefaction of resources or resources per capita. However, both energy and minerals correspond to fundamentally conserved quantities from the perspective of physics. A specific concept is required to understand the rarefaction of available resources. This concept, entropy, pertains to energy and matter configurations and not just to their sheer amount. However, the physics concept of entropy is insufficient to understand biological and social organizations. Biological phenomena display both historicity and systemic properties. A (...) biological organization, the ability of a specific living being to last over time, results from history, expresses itself by systemic properties, and may require generating novelties The concept of anti-entropy stems from the combination of these features. We propose that Anthropocene changes disrupt biological organizations by randomizing them, that is, decreasing anti-entropy. Moreover, second-order disruptions correspond to the decline of the ability to produce functional novelties, that is, to produce anti-entropy. (shrink)

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)

The purpose of this paper is to present a general mechanistic framework for analyzing causal representational claims, and offer a way to distinguish genuinely representational explanations from those that invoke representations for honorific purposes. It is usually agreed that rats are capable of navigation because they maintain a cognitive map of their environment. Exactly how and why their neural states give rise to mental representations is a matter of an ongoing debate. I will show that anticipatory mechanisms involved in rats’ (...) evaluation of possible routes give rise to satisfaction conditions of contents, and this is why they are representationally relevant for explaining and predicting rats’ behavior. I argue that a naturalistic account of satisfaction conditions of contents answers the most important objections of antirepresentationalists. (shrink)

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)