A systematic theory of naturalism, bridging metaphysics and the science of complexity and emergence.

ABSTRACT. This paper contemplates Organicism and its relation with molecular and evolutionary biology. We explore whether twentieth-first century biology is returning to positions held at the beginning of the twentieth century and then abandoned. The guiding line is a history of theoretical biology in which we distinguish three periods: 1. The 20s-30s, and the Theoretical Biology Club (Needham, Woodger, and Waddington, among others); 2. An intermediate period in the 60s-70s, in which, in spite of the eclosion of the molecular and (...) evolutionary biologies, there is some recovery of organicist positions, and 3. The present post-genomic situation, which is demanding a systemic approach. (shrink)

One general principle in the construction of classification schemes is that of grouping phenomena to be classified according to their shared origin in evolution or history (phylogenesis). In general schemes, this idea has been applied by several classificationists in identifying a series of integrative levels, each originated from the previous ones, and using them as the main classes. In special schemes, common origin is a key principle in many domains: examples are given from the classification of climates, of organisms, and (...) of musical instruments. Experience from these domains, however, suggests that using common origin alone, as done in cladistic taxonomy, can produce weird results, like having birds as a subclass of reptiles; while the most satisfying classifications use a well balanced mix of common origin and similarity. It is discussed how this could be applied to the development of a general classification of phenomena in an emergentist perspective, and how the resulting classification tree could be structured. Charles Bennett's notion of logical depth appears to be a promising conceptual tool for this purpose. (shrink)

In evolutionary biology and ecology, ontological and epistemological perspectives based on the replicator and the interactor have become the background that makes it possible to transcend traditional biological levels of organization and to achieve a unified view of evolution in which replication and interaction are fundamental operating processes. Using the transactional perspective proposed originally by John Dewey and Arthur Fisher Bentley, a new ontological and methodological category is proposed here: the transactor. The transactional perspective, based on the concept of the (...) transactor, bridges the dichotomy between organisms and environment that characterizes the interactional perspective on evolution and provides epistemological support for the emergentist, systemic view of evolutionary and developmental processes. (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 concept of hierarchical organization is commonplace in science. Subatomic particles compose atoms, which compose molecules; cells compose tissues, which compose organs, which compose organisms; etc. Hierarchical organization is particularly prominent in ecology, a field of research explicitly arranged around levels of ecological organization. The concept of levels of organization is also central to a variety of debates in philosophy of science. Yet many difficulties plague the concept of discrete hierarchical levels. In this paper, we show how these difficulties undermine (...) various implications ascribed to hierarchical organization, and we suggest the concept of scale as a promising alternative to levels. Investigating causal processes at different scales offers a way to retain a notion of quasi-levels that avoids the difficulties inherent in the classic concept of hierarchical levels of organization. Throughout, our focus is on ecology, but the results generalize to other invocations of hierarchy in science and philosophy of science. (shrink)

The classical holism-reductionism debate, which has been of major importance to the development of ecological theory and methodology, is an epistemological patchwork. At any moment, there is a risk of it slipping into an incoherent, chaotic Tower of Babel. Yet philosophy, like the sciences, requires that words and their correlative concepts be used rigorously and univocally. The prevalent use of everyday language in the holism-reductionism issue may give a false impression regarding its underlying clarity and coherence. In reality, the conceptual (...) categories underlying the debate have yet to be accurately defined and consistently used. There is a need to map out a clear conceptual, logical and epistemological framework. To this end, we propose a minimalist epistemological foundation. The issue is easier to grasp if we keep in mind that holism generally represents the ontological background of emergentism, but does not necessarily coincide with it. We therefore speak in very loose terms of the “holism-reductionism” debate, although it would really be better characterised by the terms emergentism and reductionism. The confrontation between these antagonistic paradigms unfolds at various semantic and operational levels. In definitional terms, there is not just emergentism and reductionism, but various kinds of emergentisms and reductionisms. (shrink)

Radboud Universiteit Nijmegen, 06 september 2010.

Levels of reality reflect one kind of complexity, which can be modeled using a specification hierarchy. Levels emerged during the Big Bang, as physical degrees of freedom became increasingly fixed as the expanding universe developed, and new degrees of freedom associated with higher levels opened up locally, requiring new descriptive semantics. History became embodied in higher level entities, which are increasingly individuated, aggregate patterns of lower level entities. Development is an epigenetic trajectory from vaguer to more definite and individuated embodiment, (...) punctuated by the emergence of new integrative levels. It is constrained by being subsumed by lower levels (e.g., physical dynamics) and may be guided by structural attractors as well as by internally stored information (e.g., genes) in the higher levels. I conjecture, on a thermodynamic basis, that the number of levels that become manifest in an expanding universe depends upon its rate of expansion. (shrink)

How should biological behaviour be modelled? A relatively new approach is to investigate problems in neuroethology by building physical robot models of biological sensorimotor systems. The explication and justification of this approach are here placed within a framework for describing and comparing models in the behavioural and biological sciences. First, simulation models – the representation of a hypothesis about a target system – are distinguished from several other relationships also termed “modelling” in discussions of scientific explanation. Seven dimensions on which (...) simulation models can differ are defined and distinctions between them discussed: 1. Relevance: whether the model tests and generates hypotheses applicable to biology. 2. Level: the elemental units of the model in the hierarchy from atoms to societies. 3. Generality: the range of biological systems the model can represent. 4. Abstraction: the complexity, relative to the target, or amount of detail included in the model. 5. Structural accuracy: how well the model represents the actual mechanisms underlying the behaviour. 6. Performance match: to what extent the model behaviour matches the target behaviour. 7. Medium: the physical basis by which the model is implemented. No specific position in the space of models thus defined is the only correct one, but a good modelling methodology should be explicit about its position and the justification for that position. It is argued that in building robot models biological relevance is more effective than loose biological inspiration; multiple levels can be integrated; that generality cannot be assumed but might emerge from studying specific instances; abstraction is better done by simplification than idealisation; accuracy can be approached through iterations of complete systems; that the model should be able to match and predict target behaviour; and that a physical medium can have significant advantages. These arguments reflect the view that biological behaviour needs to be studied and modelled in context, that is, in terms of the real problems faced by real animals in real environments. Key Words: animal behaviour; levels; models; neuroethology; realism; robotics; simulation. (shrink)

The dominant position in Philosophy of Science contends that downward causation is an illusion. Instead, we argue that downward causation doesn’t introduce vicious circles either in physics or in biology. We also question the metaphysical claim that “physical facts fix all the facts.” Downward causation does not imply any contradiction if we reject the assumption of the completeness and the causal closure of the physical world that this assertion contains. We provide an argument for rejecting this assumption. Furthermore, this allows (...) us to reconsider the concept of diachronic emergence. (shrink)

In this paper I present a historiography of the recent emergence of philosophy of chemistry. Special attention is given to the interest in this domain in Eastern Europe before the collapse of the USSR. It is shown that the initial neglect of the philosophy of chemistry is due to the unanimous view in philosophy and philosophy of science that only physics is a proper science (to put in Kant's words). More recently, due to the common though incorrect assumption that chemistry (...) can in principle be reduced to physics, the neglect continued, even when interest in sciences such as biology and psychology entered more strongly in philosophy of science. It is concluded that chemistry is an autonomous science and is perhaps a more typical science than physics. (shrink)

Metaphor influences the construction of biological models and theories and the analysis of its use can reveal important tools of thought. Some aspects of biological organisation are investigated through the analysis of metaphors associated with treating biosystems as a kind of text. In particular, the use of glue and verbs is considered. Some of the reasons why glue is important in the construction of hierarchies are pursued in the light of specific examples, and some of the conceptual links between glue (...) in biology and other domains is discussed. Verbs are shown to be important in the construction of networks. Some of the relations between glue, verb and text are considered and the text metaphor is placed within a much broader context of ideas associated with form, relation and system. The paper concludes with comments on the nature of biological information and the need for extending or better understanding the verbal vocabulary. (shrink)

Biologically motivated computing seeks to transfer ideas from the biosciences to computer science. In seeking to make transfers it is helpful to be able to appreciate the metaphors which people use. This is because metaphors provide the context through which analogies and similes are made and by which many scientific models are constructed. As such, it is important for any rapidly evolving domain of knowledge to have developments accounted for in these terms. This paper seeks to provide one overview of (...) the process of modelling and shows how it can be used to account for a variety of biologically motivated computational models. Certain key ideas are identified in the subsequent analysis of biological sources, notably, systemic metaphors. Three important aspects of biological thinking are then considered in the light of computer science applications: biological organization, the cell, and models of evolution. The analysis throughout the paper is descriptive rather than formalized so that a large variety of potential applications may be considered. (shrink)

The holism-reductionism debate, one of the classic subjects of study in the philosopy of science, is currently at the heart of epistemological concerns in ecology. Yet the division between holism and reductionism does not always stand out clearly in this field. In particular, almost all work in ecosystem ecology and landscape ecology presents itself as holistic and emergentist. Nonetheless, the operational approaches used rely on conventional reductionist methodology.From an emergentist epistemological perspective, a set of general 'transactional' principles inspired by the (...) work of J. Dewey and J.K. Feibleman are proposed in an effort to develop a coherent ontological and methodological semantics. (shrink)

A long-standing problem in understanding goal-directed systems has been the insufficiency of mechanistic explanations to make sense of them. This paper offers a solution to this problem. It begins by observing the limitations of mechanistic decompositions when it comes to understanding physical fields. We argue that introducing the field concept, as it has been developed in field theory, alongside mechanisms is able to provide an account of goal directedness in the sciences.

Emergence can be described as a relationship between entities at different levels of organization, that looks especially puzzling at the transitions between the major levels of matter, life, cognition and culture. Indeed, each major level is dependent on the lower one not just for its constituents, but in some more formal way. A passage by François Jacob suggests that all such evolutionary transitions are associated with the appearance of some form of memory–genetic, neural or linguistic respectively. This implies that they (...) have an informational nature. Based on this idea, we propose a general model of informational systems understood as combinations of modules taken from a limited inventory. Some informational systems are “semantic” models, that is reproduce features of their environment. Among these, some are also “informed”, that is have a pattern derived from a memory subsystem. The levels and components of informed systems can be listed to provide a general framework for knowledge organization, of relevance in both philosophical ontology and applied information services. (shrink)

Following its initial development in the 1920’s and 1930’s, by mid-century the concept of “levels of organization” began to disperse throughout the life science textbook literature. Among other early textbooks that first applied the levels concept, Eugene P. Odum’s usage of the notion in his textbook series Fundamentals of Ecology (and his later series Ecology) stands out due to the marked emphasis placed on the concept as a foundational, erotetically-oriented organizing principle. In this paper, I examine Odum’s efforts toward advocating (...) the levels concept in ecology in light of the concept’s wider uptake in biology around that time. (shrink)

This edited collection highlights the valuable ontological and creative insights gathered from anticipation studies, which orients itself to the future in order to recreate the present. The gathered essays engage with many writers from speculative metaphysics to poetic philosophy, ancient writing systems to the fringes of pataphysics. The book situates itself as a creative intervention in and with various thinkers, designers, artists, scientists and poets to offer insight into ways of anticipating. It brings together philosophical practices for which creativity is (...) both a fundamental area of consideration and a mode of working, a characterization of recent Continental Philosophy which takes a departure from traditional futures studies thinking. This book will be of interest to scholars and research in futures studies, anticipation, philosophy, creative practice and theories about creative practice, as well as the intersections between philosophy, creativity and business. (shrink)

In this book, William Brant inquires how violence is reduced. Social causes of violence are exposed. War, sexual domination, leadership, propagandizing and comedy are investigated. Legal systems are explored as reducers and implementers of violence and threats.