The recent literature on causality has seen the introduction of several distinctions within causality, which are thought to be important for understanding the widespread scientific practice of focusing causal explanations on a subset of the factors that are causally relevant for a phenomenon. Concepts used to draw such distinctions include, among others, stability, specificity, proportionality, or actual-difference making. In this contribution, I propose a new distinction that picks out an explanatorily salient class of causes in biological systems. Some select (...) causes in complex biological systems, I argue, have the property of enabling coherent causal control of these systems. Examples of such control variables include hormones and other signaling molecules, e.g., TOR (target of rapamycin), morphogens or the products of homeotic selector genes in embryonic pattern formation. I propose an analysis of this notion based on concepts borrowed from causal graph theory. (shrink)

Understanding causation in social-ecological systems (SES) is indispensable for promoting sustainable outcomes. However, the study of such causal relations is challenging because they are often complex and intertwined, and their analysis involves diverse disciplines. Although there is agreement that no single research approach (RA) can comprehensively explain SES phenomena, there is a lack of ability to deal with this diversity. Underlying this diversity and the challenge of dealing with it are different causal reasonings that are rarely explicit. (...) Awareness of hidden assumptions is essential for understanding how the causal reasoning of an RA is constituted, and for promoting the integration, translation, or juxtaposition of different RAs. We identify the following elements as particularly relevant for understanding causal reasoning: methods, frameworks and theories, accounts of causation, analytical focus, and causal notions. We begin with the idea that one of these elements typically figures as an entry point to an RA. This entry point is particularly important because it generates a path dependence that orients causal reasoning. In a subsequent step, when an approach is applied, causal reasoning concretizes as a result of a particular constellation of the remaining elements. We come to these insights by studying the application of four different RAs to the same social-ecological case (the collapse of Baltic cod stocks in the 1980s). On the basis of our findings we developed a guide for the analysis of causal reasoning by raising awareness of the assumptions, key elements, and the relations between these key elements for a given RA. The guide can be used to elicit the causal reasoning of RAs, facilitate interdisciplinary collaboration, and support disclosure of ethical/political dimensions that underlie management/governance interventions that are formulated on the basis of causal findings of research studies. (shrink)

Crossing the road within the traffic system is an example of an action human agents perform successfully day-to-day in complex systems. How do they perform such successful actions given that the behaviour of complex systems is often difficult to predict? The contemporary literature contains two contrasting approaches to the epistemology of complex systems: an analytic and a post-modern approach. We argue that neither approach adequately accounts for how successful action is possible in complex (...) systems. Agents regularly perform successful actions without obeying (explicit or implicit) algorithmic rules (as the analytic approach suggests) and without an existential leap to action (as the post-modern approach suggests). We offer an alternative: A common-sense pragmatist epistemology, one that focuses on the kind of actions making up most agents’ successful moment-to-moment actions in complex systems. Successful actions obtain when agents apply ceteris paribus rules-of-thumb during predictive and decisional practices while achieving some desired goal. (shrink)

Scientists depend on complex computational systems that are often ineliminably opaque, to the detriment of our ability to give scientific explanations and detect artifacts. Some philosophers have s...

In this paper I suggest that several problems in the study of emotion depend on a lack of adequate analytical tools, in particular on the tendency of viewing the organism as a modular and hierarchical system whose activity is mainly constituted by strictly sequential causal events. I argue that theories and models based on this view are inadequate to account for the complex reciprocal influences of the many ingredients that constitute emotions. Cognitive processes, feelings and bodily states are so (...) subtly intertwined that it is not possible to determine which one "comes first" in a causal chain. The dynamical systems approach in cognitive science, I suggest, provides a more appropriate framework for the study of emotion. In particular, the notion of circular causation and collective action help depict the organism as a self-organising system in which emotion emerges as a function of its global activity. Among others, this dynamical perspective allows revising the popular notion of appraisal in a way that can dissolve some of the questions that have taunted emotion theorists thus far. (shrink)

Should we think of our universe as law-governed and “clockwork”-like or as disorderly and “soup”-like? Alternatively, should we consciously and intentionally synthesize these two extreme pictures? More concretely, how deterministic are the postulated causes and how rigid are the modeled properties of the best statistical methodologies used in the biological and behavioral sciences? The charge of this entry is to explore thinking about causation in the temporal evolution of biological and behavioral systems. Regression analysis and path analysis are (...) simply explicated with reference to a thought experiment of painting three universes (clockwork, soup, and conscious) useful for imagining our actual universe. Attention to historical, structural, and mechanistic explanatory perspectives broadens the palette of methodologies available for analyzing determinism in, and explanation of, biological and behavioral systems. Each justified methodology provides a partial perspective on complex reality. Is a total explanation of any system ever possible, and what would it require? (shrink)

Emergence is typically discussed in the context of mental properties or the properties of the natural sciences, and accounts of emergence within these contexts tend to look a certain way. The emergent property is taken to emerge instantaneously out of, or to be proximately caused by, complex interaction of colocated entities. Here, however, I focus on the properties instantiated by the elements of certain systems discussed in social ontology, such as being a five-dollar bill or a pawn-movement, and (...) I suggest that these properties emerge in a distinctive way. They emerge in part because of a system that is far beyond and typically before the object that instantiates them. I characterize how emergence occurs in these cases, juxtaposing it with how emergence is typically discussed. I then consider whether their emergence is best framed as weak or strong as these notions are characterized in the literature, and I reveal what debates are central to answering this question. Though I will not resolve these debates, I do show a collection of views that would vindicate these properties as strongly emergent and downwardly causing. (shrink)

The systems studied in the special sciences are often said to be causally autonomous, in the sense that their higher-level properties have causal powers that are independent of the causal powers of their more basic physical properties. This view was espoused by the British emergentists, who claimed that systems achieving a certain level of organizational complexity have distinctive causal powers that emerge from their constituent elements but do not derive from them. More recently, non-reductive physicalists have espoused a (...) similar view about the causal autonomy of special-science properties. They argue that since these properties can typically have multiple physical realizations, they are not identical to physical properties, and further they possess causal powers that differ from those of their physical realisers. Despite the orthodoxy of this view, it is hard to find a clear exposition of its meaning or a defence of it in terms of a well-motivated account of causation. In this paper, we aim to address this gap in the literature by clarifying what is implied by the doctrine of the causal autonomy of special-science properties and by defending the doctrine using a prominent theory of causation from the philosophy of science. (shrink)

Consciousness has been the bone of contention for philosophers throughout centuries. Indian philosophy largely adopted lived experience as the starting point for its explorations of consciousness. For this reason, from the very beginning, experience was an integral way of grasping consciousness, whose validity as a tool was considered self-evident. Thus, in Indian philosophy, the question was not to move from the brain to mind but to understand experience of an individual and how such an experience is determined through mental structures (...) (and secondarily, the preoccupation with the brain and its relation to the mind). In contrast, cognitive science (the study of mind and cognition through 1 interdisciplinary methods, with emphasis on computational methods) found its debates soaked in discussion which primarily involved the brain and mind. Experience was not considered a primary source of information and its validity had to be established to consider it a source of information of mind. With the rise of physicalism and realization that mental states are correlative to brain states, the body was virtually neglected from involvement in understanding the mind and the attempts to reduce mind to the brain were rampant. The inability to explain subjective experience of an individual through neuroscientific findings alone has urged philosophers to explore other ways of understanding the ontology of mind. Over the last few years, embodied cognition and enactive approach have brought back the body as a central participant in this debate, providing fertile grounds to explain the relation of brain, body and mind. This paper proposes that we understand the brain as a complex system from which the mind emerges. This emergence is marked by the development of novel property of self-consciousness in human beings. The mind is a process which is embedded throughout the body and thus, the body acts as an actualizing medium for the individual. Thus, the brain is a necessary condition for the mind to be while the mind is embedded throughout the body. The brain and mind are in reciprocal causal relationship with one another, as is the body and environment with one another. In this paper, embodied cognition is understood through principles of Merleau Ponty's idea of embodiment, than through Andy Clark and Francis Varela's alone. (shrink)

The term “Complex Systems Biology” was introduced a few years ago [Kaneko, 2006] and, although not yet of widespread use, it seems particularly well suited to indicate an approach to biology which is well rooted in complex systems science. Although broad generalizations are always dangerous, it is safe to state that mainstream biology has been largely dominated by a gene-centric view in the last decades, due to the success of molecular biology. So the one gene - (...) one trait approch, which has often proved to be effective, has been extended to cover even complex traits. This simplifying view has been appropriately criticized, and the movement called systems biology has taken off. Systems biology [Noble, 2006] emphasizes the presence of several feedback loops in biological systems, which severely limit the range of validity of explanations based upon linear causal chains (e.g. gene → behaviour). Mathematical modelling is one the favourite tools of systems biologists to analyze the possible effects of competing negative and positive feedback loops which can be observed at several levels (from molecules to organelles, cells, tissues, organs, organisms, ecosystems). Systems biology is by now a well-established field, as it can be inferred by the rapid growth in number of conferences and journals devoted to it, as well as by the existence of several grants and funded projects.Systems biology is mainly focused upon the description of specific biological items, like for example specific organisms, or specific organs in a class of animals, or specific genetic-metabolic circuits. It therefore leaves open the issue of the search for general principles of biological organization, which apply to all living beings or to at least to broad classes. We know indeed that there are some principles of this kind, biological evolution being the most famous one. The theory of cellular organization also qualifies as a general principle. But the main focus of biological research has been that of studying specific cases, with some reluctance to accept (and perhaps a limited interest for) broad generalizations. This may however change, and this is indeed the challenge of complex systems biology: looking for general principles in biological systems, in the spirit of complex systems science which searches for similar features and behaviours in various kinds of systems. The hope to find such general principles appears well founded, and I will show in Section 2 that there are indeed data which provide support to this claim. Besides data, there are also general ideas and models concerning the way in which biological systems work. The strategy, in this case, is that of introducing simplified models of biological organisms or processes, and to look for their generic properties: this term, borrowed from statistical physics, is used for those properties which are shared by a wide class of systems. In order to model these properties, the most effective approach has been so far that of using ensembles of systems, where each member can be different from another one, and to look for those properties which are widespread. This approach was introduced many years ago [Kauffman, 1971] in modelling gene regulatory networks. At that time one had very few information about the way in which the expression of a given gene affects that of other genes, apart from the fact that this influence is real and can be studied in few selected cases (like e.g. the lactose metabolism in E. coli). Today, after many years of triumphs of molecular biology, much more has been discovered, however the possibility of describing a complete map of gene-gene interactions in a moderately complex organism is still out of reach. Therefore the goal of fully describing a network of interacting genes in a real organism could not be (and still cannot be) achieved. But a different approach has proven very fruitful, that of asking what are the typical properties of such a set of interacting genes. Making some plausible hypotheses and introducing some simplifying assumptions, Kauffman was able to address some important problems. In particular, he drew attention to the fact that a dynamical system of interacting genes displays selforganizing properties which explain some key aspects of life, most notably the existence of a limited number of cellular types in every multicellular organism (these numbers are of the order of a few hundreds, while the number of theoretically possible types, absent interactions, would be much much larger than the number of protons in the universe). In section 3 I will describe the ensemble based approach in the context of gene regulatory networks, and I will show that it can describe some important experimental data. Finally, in section 4 I will discuss some methodological aspects. (shrink)

Functional decomposition is an important goal in the life sciences, and is central to mechanistic explanation and explanatory reduction. A growing literature in philosophy of science, however, has challenged decomposition-based notions of explanation. ‘Holists’ posit that complex systems exhibit context-sensitivity, dynamic interaction, and network dependence, and that these properties undermine decomposition. They then infer from the failure of decomposition to the failure of mechanistic explanation and reduction. I argue that complexity, so construed, is only incompatible with one notion (...) of decomposition, which I call ‘atomism’, and not with decomposition writ large. Atomism posits that function ascriptions must be made to parts with minimal reference to the surrounding system. Complexity does indeed falsify atomism, but I contend that there is a weaker, ‘contextualist’ notion of decomposition that is fully compatible with the properties that holists cite. Contextualism suggests that the function of parts can shift with external context, and that interactions with other parts might help determine their context-appropriate functions. This still admits of functional decomposition within a given context. I will give examples based on the notion of oscillatory multiplexing in systems neuroscience. If contextualism is feasible, then holist inferences are faulty—one cannot infer from the presence of complexity to the failure of decomposition, mechanism, and reductionism. (shrink)

Museums lose their conceptual complexity and polysemy under conditions of war, forced confrontation, and struggles for survival, which may lead to a loss of diversity in the long run. Parametric General Systems analysis allows us to consider a museum as a system and to explore substratum, structural, and conceptual types of simplicity and complexity. Such qualitative analysis makes it possible to move the discussion from the ideological and value sphere to the field of rational and science-based justification. This justification, (...) in turn, illustrates why it is important to maintain complex interpretations in Ukrainian museums during the current war. (shrink)

Comprehensive when it was published in 1990, this guide brought together information on the broad spectrum of education and research opportunities then available in the sciences of complexity. Its purpose was to make these kinds of investigations more accessible by providing information on programs, institutions, organizations, and literature where one can learn about their principles, methods, and applications. The guide was intended to help interested students and educators locate the various academic fields, departments, institutes, and programs that offer education in (...) systems thinking and complex systems research. The guide also served professionals who are already involved in the systems sciences as a directory to general activity in what are otherwise widely separate fields. By browsing the guide one can get a snapshot of where education and research in systems science was happening at the time in both North America and Europe. The landscape has since massively changed so its value is mostly historical. (shrink)

Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems (MACS). While taking the emergence of properties seriously, the notion of MACS enables at the same time the design (or “meta-design”) of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the (...) self-organized systems studied in the field of Artificial Life, the specificity of MACS essentially lies in the close relation between their emergent properties and functional properties. Second, we argue that to be a MACS a system does not need to display more than weak emergent properties. Third, since the notion of weak emergence is based on the possibility of simulation, whether computational or mechanistic via machines, we see MACS as good candidates to help design artificial self-architected systems (such as robotic swarms) but also harness and redesign living ones (such as synthetic bacterial films). (shrink)

In this article, network science is discussed from a methodological perspective, and two central theses are defended. The first is that network science exploits the very properties that make a system complex. Rather than using idealization techniques to strip those properties away, as is standard practice in other areas of science, network science brings them to the fore, and uses them to furnish new forms of explanation. The second thesis is that network representations are particularly helpful in explaining the (...) properties of non-decomposable systems. Where part-whole decomposition is not possible, network science provides a much-needed alternative method of compressing information about the behavior of complex systems, and does so without succumbing to problems associated with combinatorial explosion. The article concludes with a comparison between the uses of network representation analyzed in the main discussion, and an entirely distinct use of network representation that has recently been discussed in connection with mechanistic modeling. (shrink)

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what (...) the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems. (shrink)

A common strategy for simplifying complex systems involves partitioning them into subsystems whose behaviors are roughly independent of one another at shorter timescales. Dynamic causal models clarify how doing so reveals a system’s nonequilibrium causal relationships. Here I use these models to elucidate the idealizations and abstractions involved in representing a system at a timescale. The models reveal that key features of causal representations—such as which variables are exogenous—may vary with the timescale at which a system is considered. (...) This has implications for debates regarding which systems can be represented causally. (shrink)

In this chapter we examine the relation between mechanisms and laws/counterfactuals by revisiting the main notions of mechanism found in the literature. We distinguish between two different conceptions of ‘mechanism’: mechanisms-of underlie or constitute a causal process; mechanisms-for are complex systems that function so as to produce a certain behavior. According to some mechanists, a mechanism fulfills both of these roles simultaneously. The main argument of the chapter is that there is an asymmetrical dependence between both kinds of (...) mechanisms and laws/counterfactuals: while some laws and counterfactuals must be taken as primitive (non-mechanistic) facts of the world, all mechanisms depend on laws/counterfactuals. (shrink)

Today a change is imperative in approaching global problems: what is needed is not arm-twisting and power politics, but searching for ways of co-evolution in the complex social and geopolitical systems of the world. The modern theory of self-organization of complex systems provides us with an understanding of the possible forms of coexistence of heterogeneous social and geopolitical structures at different stages of development regarding the different paths of their sustainable co-evolutionary development. The theory argues that (...) the evolutionary channel to the observed increasing complexity is extremely narrow and only certain discrete spectra of relatively stable self-maintained structures are feasible in complex systems. There exists a restricted set of ways of assembling a complex evolutionary whole from diverse parts. The law of nonlinear synthesis of complex structures reads: the integration of structures in more complex ones occurs due to the establishment of a common tempo of their evolution. On the basis of the theory, we can see not only desirable but also attainable futures. (shrink)

In the last 20 years, a stream of research emerged under the label of „complex problem solving“ (CPS). This research was intended to describe the way people deal with complex, dynamic, and intransparent situations. Complex computer-simulated scenarios were as stimulus material in psychological experiments. This line of research lead to subtle insights into the way how people deal with complexity and uncertainty. Besides these knowledge-rich, realistic, intransparent, complex, dynamic scenarios with many variables, a second line of (...) research used more simple, knowledge-lean scenarios with a low number of variables („minimal complex systems“, MCS) that have been proposed recently in problem-solving research for the purpose of educational assessment. In both cases, the idea behind the use of microworlds is to increase validity of problem solving tasks by presenting interactive environments that can be explored and controlled by participants while pursuing certain action goals. The main argument presented here is: both types of systems - CPS and MCS – can only be dealt with successfully if causal dependencies between input and output variables are identified and used for system control. System knowledge is necessary for control and intervention. But CPS and MCS differ in their way of how causal dependencies are identified and how the mental model is constructed; therefore, they cannot be compared directly to each other with respect to the cognitive processes that are necessary for solving the tasks. Knowledge-poor MCS tasks address only a small fraction of the cognitive processes and structures needed for knowledge-rich CPS situations. (shrink)

In this paper, we will explore the relation between molecular structure and functions displayed by biochemical molecules in complex physiological processes by using tools from the philosophy of science and the philosophy of scientific practice. We will argue that biochemical functions are weakly emergent from molecular structure by using an account of weak. In order to explore this thesis, we will consider the role of vitamin B12 in contributing to the process of erythropoiesis. The structure of the paper is (...) the following: First, we will consider biochemical functions and why they cannot be easily reduced to their chemical realisers. We will suggest weak emergence as an alternative while also accounting for the relevance of the context, in our case, systemic and organisational. The paper will conclude by considering (1) how the usage of tools from the philosophy of science, such as weak emergence, can aid our understanding of the relations between the components of complex phenomena, such as erythropoiesis, and (2) how the philosophy of scientific practice sheds light on the explanatory role of processes that are dynamically stabilised and the different levels of organisation implied. (shrink)

Contemporary complexity theory has been instrumental in providing novel rigorous definitions for some classic philosophical concepts, including emergence. In an attempt to provide an account of emergence that is consistent with complexity and dynamical systems theory, several authors have turned to the notion of constraints on state transitions. Drawing on complexity theory directly, this paper builds on those accounts, further developing the constraint-based interpretation of emergence and arguing that such accounts recover many of the features of more traditional accounts. (...) We show that the constraint-based account of emergence also leads naturally into a meaningful definition of self-organization, another concept that has received increasing attention recently. Along the way, we distinguish between order and organization, two concepts which are frequently conflated. Finally, we consider possibilities for future research in the philosophy of complex systems, as well as applications of the distinctions made in this paper. (shrink)

Abstract: The use of evolutionary explanations to account for proximate phenomena has been labeled by various authors as an explanatory error, the so-called phylogeny fallacy. In this paper, this fallacy will be analyzed in the context of teleosemantics. I will discuss whether teleosemantics projects that rely on the Selected-Effect Theory of Functions (i.e., mainstream teleosemantics) generally commit the fallacy. To frame the discussion, I will present two desiderata that, as argued here, every teleosemantic project must fulfill. The actuality desideratum, motivated (...) by Brentano’s problem, demands for a proximate analysis of the properties that make a system intentional. The historical desideratum, on the other hand, says that a teleological view of intentionality requires a historical dimension in order to understand the causal basis of teleological explanations. While I give some reasons why mainstream teleosemantics might be implicated in the phylogeny fallacy, my main argument aims to highlight an explanatory gap in mainstream teleosemantics: the population perspective on teleofunctions is inadequate to explain the proximate properties of intentional systems. In other words, the account of the historical desideratum in population-evolutionary terms prevents an adequate solution to the actuality desideratum. This is related to two central goals of teleosemantics: The goal of explaining content determination by recourse to natural selection processes makes it impossible to solve another goal of teleosemantics, the so-called problem of representational status. I analyze this situation and argue that inherited information (sometimes interpreted in a teleosemantic sense) plays the role of closing the gap. This leads teleosemantics into a complex situation: in order to close the gap, it must commit the fallacy. At the end of the article, I propose an alternative to fulfill both desiderata, motivated by an evo-devo perspective. I state that lineage explanations have the property of providing historical explanations based on proximate causes. (shrink)

Research on moral judgment is refueling public interest in an old debate concerning the general foundation of morals. Are moral judgments based on reason or on feeling? Recent research in moral psychology and neuroscience concludes that moral judgments occur rapidly, automatically, and largely without the aid of inference. Such findings are utilized to criticize moral theories that require deliberation to precede moral judgment as its cause. The main targets of this criticism are the moral theories of Piaget and Kohlberg, but (...) Kant's moral philosophy is also criticized for this failing. This essay defends Kant from this charge by clarifying the role of deliberation in his moral theory and by demonstrating that, for Kant, moral judgment invokes a self-organizing system that has the capacity to rapidly determine the moral permissibility of any desired purpose - real or imagined. Further support for Kant's moral theory is gleaned from recent work on self-organization in the brain. (shrink)

Let us start by some general definitions of the concept of complexity. We take a complex system to be one composed by a large number of parts, and whose properties are not fully explained by an understanding of its components parts. Studies of complex systems recognized the importance of “wholeness”, defined as problems of organization (and of regulation), phenomena non resolvable into local events, dynamics interactions in the difference of behaviour of parts when isolated or in higher (...) configuration, etc., in short, systems of various orders (or levels) not understandable by investigation of their respective parts in isolation. In a complex system it is essential to distinguish between ‘global’ and ‘local’ properties. Theoretical physicists in the last two decades have discovered that the collective behaviour of a macro-system, i.e. a system composed of many objects, does not change qualitatively when the behaviour of single components are modified slightly. Conversely, it has been also found that the behaviour of single components does change when the overall behaviour of the system is modified. There are many universal classes which describe the collective behaviour of the system, and each class has its own characteristics; the universal classes do not change when we perturb the system. The most interesting and rewarding work consists in finding these universal classes and in spelling out their properties. This conception has been followed in studies done in the last twenty years on second order phase transitions. The objective, which has been mostly achieved, was to classify all possible types of phase transitions in different universality classes and to compute the parameters that control the behaviour of the system near the transition (or critical or bifurcation) point as a function of the universality class. This point of view is not very different from the one expressed by Thom in the introduction of Structural Stability and Morphogenesis (1975). It differs from Thom’s program because there is no a priori idea of the mathematical framework which should be used. Indeed Thom considers only a restricted class of models (ordinary differential equations in low dimensional spaces) while we do not have any prejudice regarding which models should be accepted. One of the most interesting and surprising results obtained by studying complex systems is the possibility of classifying the configurations of the system taxonomically. It is well-known that a well founded taxonomy is possible only if the objects we want to classify have some unique properties, i.e. species may be introduced in an objective way only if it is impossible to go continuously from one specie to another; in a more mathematical language, we say that objects must have the property of ultrametricity. More precisely, it was discovered that there are conditions under which a class of complex systems may only exist in configurations that have the ultrametricity property and consequently they can be classified in a hierarchical way. Indeed, it has been found that only this ultrametricity property is shared by the near-optimal solutions of many optimization problems of complex functions, i.e. corrugated landscapes in Kauffman’s language. These results are derived from the study of spin glass model, but they have wider implications. It is possible that the kind of structures that arise in these cases is present in many other apparently unrelated problems. Before to go on with our considerations, we have to pick in mind two main complementary ideas about complexity. (i) According to the prevalent and usual point of view, the essence of complex systems lies in the emergence of complex structures from the non-linear interaction of many simple elements that obey simple rules. Typically, these rules consist of 0–1 alternatives selected in response to the input received, as in many prototypes like cellular automata, Boolean networks, spin systems, etc. Quite intricate patterns and structures can occur in such systems. However, what can be also said is that these are toy systems, and the systems occurring in reality rather consist of elements that individually are quite complex themselves. (ii) So, this bring a new aspect that seems essential and indispensable to the emergence and functioning of complex systems, namely the coordination of individual agents or elements that themselves are complex at their own scale of operation. This coordination dramatically reduces the degree of freedom of those participating agents. Even the constituents of molecules, i.e. the atoms, are rather complicated conglomerations of subatomic particles, perhaps ultimately excitations of patterns of superstrings. Genes, the elementary biochemical coding units, are very complex macromolecular strings, as are the metabolic units, the proteins. Neurons, the basic elements of cognitive networks, themselves are cells. In those mentioned and in other complex systems, it is an important feature that the potential complexity of the behaviour of the individual agents gets dramatically simplified through the global interactions within the system. The individual degrees of freedom are drastically reduced, or, in a more formal terminology, the factual space of the system is much smaller than the product of the state space of the individual elements. That is one key aspect. The other one is that on this basis, that is utilizing the coordination between the activities of its members, the system then becomes able to develop and express a coherent structure at a higher level, that is, an emergent behaviour (and emergent properties) that transcends what each element is individually capable of. (shrink)

I present three reasons why philosophers of science should be more concerned about violations of causal faithfulness (CF). In complex evolved systems, mechanisms for maintaining various equilibrium states are highly likely to violate CF. Even when such systems do not precisely violate CF, they may nevertheless generate precisely the same problems for inferring causal structure from probabilistic relationships in data as do genuine CF-violations. Thus, potential CF-violations are particularly germane to experimental science when we rely on probabilistic (...) information to uncover the DAG, rather than already knowing the DAG from which we could predict the right experiments to ‘catch out’ the hidden causal relationships. (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)

This article summarizes the question of finding effective solutions to ensure the excellence of modern business through the introduction of managerial innovations. The main purpose of the study is to improve the theoretical and methodological approach to the implementation of managerial innovations in the system of modern business solutions. Systematization of literature sources and approaches to solving the problem of improving business management through the introduction of managerial innovations indicates the widespread use of methodological approaches and methods of managerial innovation, (...) but much management issues to ensure business excellence, justification of new opportunities for its development remain unnoticed. The urgency of solving this scientific problem is that in conditions of growing uncertainty and risk, accelerating the transformation of business, the importance of ensuring its perfection in the long term economic development of Ukraine is growing. The methodological tools of research methods were a system of methods used to obtain the final results of the study: generalization and comparative analysis – to clarify the essence of the concept of «managerial innovation»; abstract-logical – to reveal the relationship between the use of information and communication technologies, business excellence and implementation of management innovations; system-analytical – in developing a model of business excellence based on the use of modern information and communication technologies. The object of research is the industrial enterprises of the modern economy of Ukraine, because they are the basis of economic formation, a source of replenishment of the country budget and form the export orientation of business. The article presents the results of abstract-logical analysis of the blocks of business excellence, which showed that at the present stage of its development, the introduction of managerial innovations should be associated with the digital transformation of business. The results of the system-analytical analysis are presented, which are the basis for the development of an economic model for business excellence. The results of the study can be useful for business structures (and in particular, business units of the industrial complex of Ukraine), which seek to increase the efficiency of decision-making in today's digital business transformation. (shrink)

Being supposedly the ground for an exchange system that does not depend on central, top-down regulation, cryptocurrencies increasingly need new algorithmic and policy-driven rules to maintain their trustworthiness and capacity to exhibit empirically supported growth. The present paper offers a conceptual and philosophical discussion on whether and how cryptosystems could be able to generate resilient development in a way that is coherent with a non-reductionist view of positive economics. As proposed, a plausible way to understand them can be achieved considering (...) their complexity and their concrete, local features, which have to be grasped both in terms of formal and material specificity. (shrink)

ABSTRACT The individual-community relationship has always been one of the most fundamental topics of social sciences. In sociology, this is known as the micro-macro relationship while in economics it refers to the processes, through which, individual actions lead to macroeconomic phenomena. Based on philosophical discourse and systems theory, many sociologists even use the term "emergence" in their understanding of micro-macro relationship, which refers to collective phenomena that are created by the cooperation of individuals, but cannot be reduced to individual (...) actions. "Emergence" theories attempt to explain the nature of society as a complex system by examining how individuals and their relationships lead to the creation of integrated and macro-social phenomena such as markets, educational systems, cultural beliefs, and shared social practices. As a prelude to activity, every researcher has to answer the question from the methodological point of view, how is it possible to study the behavior of social groups and how can we gain knowledge about the laws related to social groups? Anyone who deals with humanities and social sciences or any reality and phenomenon that affects human beings, inevitably deals with the reality that is emerging. In fact, emergence occurs when one level of reality emerges radically from another level. Examples of emergent levels of reality include how the mind emerges from the body; or the way society emerges from human beings. Therefore, when there is an emerging factor, different scientific disciplines should be used, because it is inevitable to talk about social affairs, psychology and neurobiology, as well as physical and even chemical. -/- INTRODUCTION Since its beginning in the 19th century, sociology has faced the fundamental question of what a social phenomena stands for? At a glance, sociologists deal with the study of social groups, collective behavior, institutions, social structures, social networks, and social dynamics, and ultimately all such phenomena are composed of individuals. Therefore, social phenomena seem to have no independent ontological status, and in this case, sociology is ultimately about reducible individuals. Different approaches about the micro-macro relationship, using the concept of "emergence", argue that although collective phenomena are created by individuals, they cannot be reduced to individual action. The term "emergence" is used to distinguish "emergent results" from " Procedural results". Results are called Procedural that can only be calculated by adding or subtracting the causes that act together. On the contrary, they are emergent outcomes that are qualitatively novel compared to the causes from which they originate. An example of such emergent results is mental characteristics that emerge from neural processes, but are not considered among the characteristics of neural processes of components - which are their origin. Philosophical debates about emergentism and reductionism focus on the mind-brain relationship, but as many philosophers have noted, they can be generalized to apply to any hierarchical set of features. The cognitive revolution reactivated a 19th century controversy between theorists of Identity and dualism. The theorists of Identity believe in reductionist materialism and elimination of metaphysics, according to which the mind is nothing more than the biological, while the dualists believe that the mind and the brain are distinct from each other. Emergence has been considered as a third way between the theories of Identity and dualism. -/- METHODOLOGY Interdisciplinarity Is fundamentally indicated by the dominance of open systems as well as social and emerging systems at different levels. Therefore, as long as we are facing a new emergentism, there will necessarily be different fields and an interdisciplinary method. The commonality of social sciences and cognitive sciences on the issue of emergence provides the possibility of interaction and exchange of concepts between these two for deeper research. Therefore, in this research, apart from the concepts of Subvenience and downward causation, we have used multiple realization and wildly disjunctive, which are used to explain the emerging concept in cognitive sciences, including neurobiology, psychology, and philosophy. For analytical and interdisciplinary approaches, after examining the concepts of subvenience, and wildly disjunctive, Individualistic and collectivist emergentism have been reviewed. And then their adequacy is criticized and evaluated in meeting strong emergence conditions. -/- FINDINGS Philosophers of the mind have been able to define the conditions of irreducibility and downward causation, which are essential for strong emergence, by using the principle of subvenience with the help of multiple realization and wildly disjunctive principles. Therefore, by definition, emergentist individualism suffers from the problem of how to explain downward causality and irreducibility, and emergentist collectivism faces the challenge of reification. The analysis of the challenges facing the two methodological approaches of individualism and collectivism leads us to three unresolved issues about the emerging phenomenon, which are realism, downward causality, and mechanism. Despite the differences in the stances of these two approaches regarding the aforementioned triple problems, individualists and collectivists both agree that some social characteristics are reducible; and some others are irreducible due to their complexity, the determination of which, depends on the case study of the mechanism of emergence of each social characteristic. -/- CONCLUSION An emergence that is consistent with reductionism is called a weak emergence. And strong emergence includes the principle of irreducibility and downward causality. According to strong emergence, the characteristics of social phenomena have downward causal power, which cannot be reduced to the causal forces. The principle of subvenience, together with multiple realization and wildly disjunctive, can provide the conditions of irreducibility and downward causality, which are essential conditions of strong emergence. Based on the philosophical analysis of two methodological approaches, individualist and collectivist, it can be concluded that emergentist individualism suffers from the problem of how to explain downward causality and irreducibility, and reification collectivism faces the challenge of reification. The analysis of the problems faced by these two approaches leads us to three unresolved issues, which are realism, downward causality, and mechanism. individualist emergentists acknowledge the existence of emergent social characteristics, but despite this, they believe that these characteristics are not real but merely analytical constructs that require explanation based on individuals and their mutual actions. But collectivists argue that emergentism yields a categorical ontology and supports social realism. They accept the dependence of social characteristics on individuals, but claim that social entities and structures are ontologically independent. Individualists and collectivists both agree that some social characteristics are reducible; and others are irreducible due to their complexity; and the only way to recognize this is to engage in empirical studies of the mechanisms and temporal processes of "emergence" that create social characteristics. -/- NOVELTY The newness of this compact article is as follows: a) Presenting an interdisciplinary approach using the analysis of philosophy of cognitive sciences, including the philosophy of mind, neurobiology and psychology to formulate the issue of social emergence; b) Criticizing individualist and collectivist methodological approaches to the issue of social emergence and explaining the sufficiency and shortcomings of both in providing weak and strong emerging conditions; c) Explaining and categorizing the challenges facing methodological approaches in explaining the phenomenon of social emergence, in three categories: realism, downward causality, and mechanism. BIBLIOGRAPHY Beckermann, A., Flohr, H., & Kim, J. (eds.) (1992). Emergence or reduction? Essays on the prospects of nonreductive physicalism. Berlin: Walter de Gruyter. Bhaskar, R. (1979). The possibility of Naturalism. New York: Routledge. Bhaskar, R., Danermark, B. & Price, L. (2018). Interdisciplinarity and wellbeing: A critical realist general theory of interdisciplinarity. London and New York: Routledge. Blau, P.M. (1981). Introduction: diverse views of social structure and their common denominator. In Blau, P.M. & Merton, R.K. (eds.), Continuity in Structural Inquiry (pp. 1–23). Beverly Hills: Sage. Blau, P.M. (1987). Microprocess and macrostructure. In K.S. Cook (ed.), Social Exchange Theory (pp. 83–100). Newbury Park, CA: Sage. Brooks, R.A., & Maes, P. (eds). (1994). Artificial life IV; proceedings of the Fourth International Workshop on the Synthesis and Simulation of Living Systems. Cambridge, Mass: MIT Press. Clark, A. (1997). Being there: Putting brain, body, and world together again. Cambridge, Mass.: MIT Press. Coleman, J. S. (1987). Microfoundations and macrosocial behavior. In: J. C. Alexander, B. Giesen, R. Munch, & Neil J. Smelser (Eds.). The Micro-Macro Link (pp. 153–73). Berkeley: University of California. Coleman, J. S. (1990). Foundations of social theory. Cambridge, MA: Harvard University Press. Elster, J. (1985). Making sense of Marx. New York: Cambridge University Press. Fodor, J.A. (1974). Special sciences (Or: The disunity of science as a working hypothesis). Synthese, 28(2), 97–115. Fodor, J.A. (1989). Making mind matter more. Philosophical Topics, 17, 59-79. Giddens, A. (1984). The constitution of society: Outline of the theory of structuration. Berkeley: University of California Press. Hempel, C.G. (1965). Aspects of scientific explanation and other essays in the philosophy of science. New York: The Free Press. Horgan, T. (1993). From supervenience to superdupervenience: meeting the demands of a material world. Mind, 102, 555-586. Humphreys, P. (1997). How properties emerge”. Philosophy of Science, 64, 1-17. Kim, J. (1999). Making sense of emergence. Philosophical Studies, 95, 3–36. Kincaid, H. (1997). Individualism and the unity of science. New York: Rowman & Littlefield. Lewis, D.K. (1986). The plurality of worlds. Oxford: Oxford University Press. Nigel, G., & Conte, R. (eds.) (1995). Artificial societies; The computer simulation of social life. London: UCL Press. O’Connor, T. (1994). Emergent properties. American Philosophical Quarterly, 31, 91-104. Popper, K.R. (1968). Conjectures and refutations: The Growth of Scientific Knowledge. New York: Harper & Row. Sawyer, R. K. (2001). Emergence in sociology: contemporary philosophy of mind and some implications for sociological theory. American Journal of Sociology, 107, 551-585. Sawyer, R. K. (2004). The mechanisms of emergence. Philosophy of the Social Sciences, 34, 260–282. Sawyer, R. K. (2005). Social emergence: societies as complex systems. Cambridge: Cambridge University Press. Sawyer, R.K. (2003). Nonreductive individualism: Part 2, Social causation. Philosophy of the Social Sciences, 33, 203–224. Winch, P. (1993). The idea of a social science and its relation to philosophy‭ (SAMT, Trans.). Tehran, Iran: SAMT. (shrink)

Achieving Coherence introduces a transformative framework for understanding and managing the complexities of dynamic systems. In a world where uncertainty and interconnected challenges define the landscape, the SPARC framework (Spectrum of Possibility and Recursive Choice) offers a unified model to address these issues, bridging the gap between theory and application across disciplines. This work explores the principles of coherence, constraint satisfaction, and recursive feedback, shedding light on how systems maintain stability and adapt in the face of evolving constraints (...) and environmental noise. By integrating dimensional transitions, multi-constraint optimization, and resilience to stochastic influences, SPARC provides a novel approach to modeling systems that are inherently complex and interdependent. Applications range from stabilizing critical infrastructure and managing ecosystems under stress to advancing artificial intelligence and optimizing multi-agent systems. By demonstrating how local behaviors interact with global dynamics and how systems can thrive under variability, Achieving Coherence presents a compelling vision for navigating complexity and driving innovation in an interconnected world. (shrink)

Climatology is a paradigmatic complex systems science. Understanding the global climate involves tackling problems in physics, chemistry, economics, and many other disciplines. I argue that complex systems like the global climate are characterized by certain dynamical features that explain how those systems change over time. A complex system's dynamics are shaped by the interaction of many different components operating at many different temporal and spatial scales. Examining the multidisciplinary and holistic methods of climatology can (...) help us better understand the nature of complex systems in general. -/- Questions surrounding climate science can be divided into three rough categories: foundational, methodological, and evaluative questions. "How do we know that we can trust science?" is a paradigmatic foundational question (and a surprisingly difficult one to answer). Because the global climate is so complex, questions like "what makes a system complex?" also fall into this category. There are a number of existing definitions of `complexity,' and while all of them capture some aspects of what makes intuitively complex systems distinctive, none is entirely satisfactory. Most existing accounts of complexity have been developed to work with information-theoretic objects (signals, for instance) rather than the physical and social systems studied by scientists. -/- Dynamical complexity, a concept articulated in detail in the first third of the dissertation, is designed to bridge the gap between the mathematics of contemporary complexity theory (in particular the formalism of "effective complexity" developed by Gell-Mann and Lloyd [2003]) and a more general account of the structure of science generally. Dynamical complexity provides a physical interpretation of the formal tools of mathematical complexity theory, and thus can be used as a framework for thinking about general problems in the philosophy of science, including theories, explanation, and lawhood. -/- Methodological questions include questions about how climate science constructs its models, on what basis we trust those models, and how we might improve those models. In order to answer questions about climate modeling, it's important to understand what climate models look like and how they are constructed. Climate model families are significantly more diverse than are the model families of most other sciences (even sciences that study other complex systems). Existing climate models range from basic models that can be solved on paper to staggeringly complicated models that can only be analyzed using the most advanced supercomputers in the world. I introduce some of the central concepts in climatology by demonstrating how one of the most basic climate models might be constructed. I begin with the assumption that the Earth is a simple featureless blackbody which receives energy from the sun and releases it into space, and show how to model that assumption formally. I then gradually add other factors (e.g. albedo and the greenhouse effect) to the model, and show how each addition brings the model's prediction closer to agreement with observation. After constructing this basic model, I describe the so-called "complexity hierarchy" of the rest of climate models, and argue that the sense of "complexity" used in the climate modeling community is related to dynamical complexity. -/- With a clear understanding of the basics of climate modeling in hand, I then argue that foundational issues discussed early in the dissertation suggest that computation plays an irrevocably central role in climate modeling. "Science by simulation" is essential given the complexity of the global climate, but features of the climate system--the presence of non-linearities, feedback loops, and chaotic dynamics--put principled limits on the effectiveness of computational models. This tension is at the root of the staggering pluralism of the climate model hierarchy, and suggests that such pluralism is here to stay, rather than an artifact of our ignorance. Rather than attempting to converge on a single "best fit" climate model, we ought to embrace the diversity of climate models, and view each as a specialized tool designed to predict and explain a rather narrow range of phenomena. Understanding the climate system as a whole requires examining a number of different models, and correlating their outputs. This is the most significant methodological challenge of climatology. -/- Climatology's role contemporary political discourse raises an unusually high number of evaluative questions for a physical science. The two leading approaches to crafting policy surrounding climate change center on mitigation (i.e. stopping the changes from occurring) and adaptation (making post hoc changes to ameliorate the harm caused by those changes). Crafting an effective socio-political response to the threat of anthropogenic climate change, however, requires us to integrate multiple perspectives and values: the proper response will be just as diverse and pluralistic as the climate models themselves, and will incorporate aspects of both approaches. I conclude by offering some concrete recommendations about how to integrate this value pluralism into our socio-political decision making framework. (shrink)

This paper discusses von Wright's theory of causation from Explanation and Understanding and Causality and Determinism in contemporary context. I argue that there are two important common points that von Wright's view shares with the version of manipulability currently supported by Woodward: the analysis of causal relations in a system modelled on controlled experiments, and the explanation of manipulability through counterfactuals - with focus on the counterfactual account of unmanipulable causes. These points also mark von Wright's departure from previous (...) action-based theories of causation. Owing to these two features, I argue that, upon classifying different versions of manipulability theories, von Wright's view should be placed closer to the interventionist approach than to the agency theory, where it currently stands. Furthermore, given its relevance in contemporary context, which this paper aims to establish, I claim that von Wright's theory can be employed to solve present problems connected to manipulability approaches to causation. (shrink)

As far as treatments of causation are concerned, the pre-Kantian 18th century German context has long been dismissed as a period of uniform and unrepentant Leibnizian dogmatism. While there is no question that discussions of issues relating to causation in this period inevitably took Leibniz as their point of departure, it is certainly not the case that the resulting positions were in most cases dogmatically, or in some cases even recognizably, Leibnizian. Instead, German theorists explored a range of (...) positions regarding the nature of causal powers, the appropriate systems to explain the observed agreement between the states of substances, and the ground of free actions, or so I will argue in this chapter. Focusing on these three issues, I will here sketch the development of the debates relating to causation and trace the evolution of positions among the philosophers within the so-called Leibnizian-Wolffian philosophy as well as among its many opponents. (shrink)

In this article, I explore the consequences of two commonsensical premises in semantics and epistemology: (1) natural language is a complex system rooted in the communal life of human beings within a given environment; and (2) linguistic knowledge is essentially dependent on natural language. These premises lead me to emphasize the process-socio-environmental character of linguistic meaning and knowledge, from which I proceed to analyse a number of long-standing philosophical problems, attempting to throw new light upon them on these grounds. (...) In particular, I criticize the use of expressions such as ‘absolute truth’, ‘absolute existence’ and ‘the thing in itself’, arguing that they lead to what I call ‘the ultralinguistic paradox’ (a fatal antinomy). In the same way, I review a number of mainstream topics in philosophical semantics, epistemology and metaphysics, reformulating them in terms much more naturalistic – and less mysterious – than usual. (shrink)

Despite the huge and constant progress in the molecular and cellular neuroscience fields, our capability to understand brain alterations and treat mental illness is still limited. Therefore, a paradigm shift able to overcome such limitation is warranted. Behavior and the associated mental states are the interface between the central nervous system and the living environment. Since, in any system, the interface is a key regulator of system organization, behavior is proposed here as a unique and privileged level of control and (...) orchestration of brain structure and activity. This view has relevant scientific and clinical implications. First, the study of behavior represents a singular starting point for the investigation of neural activity in an integrated and comprehensive fashion. Second, behavioral changes, accomplished through psychotherapy or environmental interventions, are expected to have the highest impact to specifically reorganize the complexity of the human mind and thus achieve a solid and long-lasting improvement in mental health. (shrink)

In this paper the central ideas and history of the theory of complex systems are described. It is shown how this theory lends itself to different interpretations and, correspondingly, to different political conclusions.

At the dawn of the computational era, immunology is at a crossroads: Its efforts to frame microbial-host interactions in combative, war-related terms no longer fit the larger picture of immune protection, and its focus on antimicrobial responses barely captures the diverse functions of the immune system, from tissue maintenance to cancer surveillance to development. As the classical view of immune processes becomes increasingly complex, the problem of self, individuality, mind-body interactions, and disease causation have stimulated extensive philosophical comment. (...) Relating these disparate research topics to changing avenues of theoretical studies, philosophy of immunology helps to reframe basic conceptions of the organism from an atomistic, insular entity to one characterized by fluidity, hybridity, and porosity. In addition, highlighting the role of the observer in experimental research, this interdisciplinary field has redefined classical demarcations between science and culture while advancing our understanding of biology as a fundamentally human endeavor. (shrink)

This paper presents a unified theory of reality, which integrates two interdependent frameworks: Cellular Primary Consciousness Theory (CPCT) and Open and Closed Systems Theory (OCST). Although CPCT and OCST can each stand as individual theories, they are, in this work, combined to form a cohesive explanation of both the mechanics and purpose of the universe. CPCT posits that consciousness is a fundamental aspect of all life, extending to even the simplest cells, rather than being an emergent property exclusive to (...) complex neural systems. Drawing upon evidence from quantum mechanics, cell biology, and systems theory, CPCT challenges traditional views on the origins of consciousness by suggesting that awareness is a universal property present from the cellular level. OCST, which forms the second component of this unified theory, examines the nature of the universe as a closed system subject to the laws of entropy. This theory explores how the universe is moving toward maximum entropy, where meaning and contrasts dissolve. However, beyond this closed system lies the realm of an open system—a domain of infinite potential that transcends the dualities and limitations of the physical universe. This open system offers a philosophical explanation for existence and the possibility of eternal meaning. Together, these two theories provide a novel and cohesive framework that addresses both the mechanics of consciousness and the ultimate purpose of the universe. The integration of CPCT and OCST bridges scientific evidence from quantum biology and systems theory with philosophical explorations of existence, presenting a comprehensive vision of reality as both a closed physical system and an open metaphysical one. This unified theory encourages a reexamination of our place in the cosmos, suggesting that beyond the observable universe lies an infinite realm of potential where consciousness and meaning endure. (shrink)

We have recently started to understand that fundamental aspects of complex systems such as emergence, the measurement problem, inherent uncertainty, complex causality in connection with unpredictable determinism, time­irreversibility and non­locality all highlight the observer's participatory role in determining their workings. In addition, the principle of 'limited universality' in complex systems, which prompts us to search for the appropriate 'level of description in which unification and universality can be expected', looks like a version of Bohr's 'complementarity (...) principle'. It is more or less certain that the different levels of description possible of a complex whole ­­ actually partial objectifications ­­ are projected on to and even redefine its constituent parts. Thus it is interesting that these fundamental complexity issues don't just bear a formal resemblance to, but reveal a profound connection with, quantum mechanics. Indeed, they point to a common origin on a deeper level of description. (shrink)

Reconstructability analysis (RA) decomposes wholes, namely data in the form either of set theoretic relations or multivariate probability distributions, into parts, namely relations or distributions involving subsets of variables. Data is modeled and compressed by variable-based decomposition, by more general state-based decomposition, or by the use of latent variables. Models, which specify the interdependencies among the variables, are selected to minimize error and complexity.

Probably the most challenging issue in science and advanced technology is the ever increasing complexity. The term complexity refers to the experience that the complex whole is more than the sum of the parts. Emergence of new properties is observed at all levels, from relatively simple physical systems up to high-end evolution in biology or state-of-the-art microprocessors in technology. In this study an effort is made to arrive at an understanding of the underlying ontological basis in terms of (...) the classical philosophy of Aristotle and Aquinas. In addition, the value of philosophy is emphasized as a means to develop the capacity for intuition. Only with this capacity it is possible to acquire an understanding of the great variety of concepts needed in the multidisciplinary approach to complex systems. (shrink)

I defend a theory of mental representation that satisfies naturalistic constraints. Briefly, we begin by distinguishing (i) what makes something a representation from (ii) given that a thing is a representation, what determines what it represents. Representations are states of biological organisms, so we should expect a unified theoretical framework for explaining both what it is to be a representation as well as what it is to be a heart or a kidney. I follow Millikan in explaining (i) in terms (...) of teleofunction, explicated in terms of natural selection. -/- To explain (ii), we begin by recognizing that representational states do not have content, that is, they are neither true nor false except insofar as they both “point to” or “refer” to something, as well as “say” something regarding whatever it is they are about. To distinguish veridical from false representations, there must be a way for these separate aspects to come apart; hence, we explain (ii) by providing independent theories of what I call f-reference and f-predication (the ‘f’ simply connotes ‘fundamental’, to distinguish these things from their natural language counterparts). -/- Causal theories of representation typically founder on error, or on what Fodor has called the disjunction problem. Resemblance or isomorphism theories typically founder on what I’ve called the non-uniqueness problem, which is that isomorphisms and resemblance are practically unconstrained and so representational content cannot be uniquely determined. These traditional problems provide the motivation for my theory, the structural preservation theory, as follows. F-reference, like reference, is a specific, asymmetric relation, as is causation. F-predication, like predication, is a non-specific relation, as predicates typically apply to many things, just as many relational systems can be isomorphic to any given relational system. Putting these observations together, a promising strategy is to explain f-reference via causal history and f-predication via something like isomorphism between relational systems. -/- This dissertation should be conceptualized as having three parts. After motivating and characterizing the problem in chapter 1, the first part is the negative project, where I review and critique Dretske’s, Fodor’s, and Millikan’s theories in chapters 2-4. Second, I construct my theory about the nature of representation in chapter 5 and defend it from objections in chapter 6. In chapters 7-8, which constitute the third and final part, I address the question of how representation is implemented in biological systems. In chapter 7 I argue that single-cell intracortical recordings taken from awake Macaque monkeys performing a cognitive task provide empirical evidence for structural preservation theory, and in chapter 8 I use the empirical results to illustrate, clarify, and refine the theory. (shrink)

A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most comprehensive (...) explanations. A more standard investigation in biology occurs within a single subarea, and uses well-defined experiments with very specific conditions. This paper is about causation and related explanation in plant phenome research and its relevance to Aristotle’s Theory of Four Causes. I argue that there are causes which resemble Aristotle’s formal, material, and efficient causes in phenotype explanation and occurrence; but causes which resemble Aristotle’s final causes occur in phenotype explanation only, not in the occurrence. (shrink)

It is proposed that conscious qualia arise when and only when the 'running' of physical processes takes a special, complex form. Running in general is the unified unfolding of processes through time, and is claimed to be an additional quality of physical processes beyond their state trajectories. The type of running needed for conscious qualia is reflexive in physically affecting and responding to itself. Intuitively, running is essentially the flow of causation, and the self-affecting/responding is a matter of (...) causation bearing a causal relationship to itself: that is, causation can itself be reflexive. The proposal potentially makes temporal qualia the most fundamental qualia, with others derivatively arising. The proposal is neutral about whether a conscious process occurs in a natural organism, in a physically implemented computational system, or in some other physical substrate, as long as the substrate involves the special reflexive runningness. (shrink)

In this paper I suggest a new interpretation of the relations of inherence, causation and conception in Spinoza. I discuss the views of Don Garrett on this issue and argue against Della Rocca's recent suggestion that a strict endorsement of the PSR leads necessarily to the identification of the relations of inherence, causation and conception. I argue that Spinoza never endorsed this identity, and that Della Rocca's suggestion could not be considered as a legitimate reconstruction or friendly amendment (...) to Spinoza 's system because it creates several severe and irresolvable problems in the system. -/- In the first part of the paper, I present the considerations and arguments that motivated Don Garrett's and Della Rocca's interpretations. In the second part, I present and examine several problems that result from Della Rocca's reading. In the third and final part, I present my own view on the relation among inherence, causation, and conception; offer a new interpretation of the conceived through relation in Spinoza ; and finally, defend and justify the presence of bifurcations at the very center of Spinoza 's system. (shrink)

This paper aims at introducing a French audience to the Intelligent Design debate. It starts by reviewing recent attacks on any possibility of a rational account of theism in light of the contemporary theory of evolution. A section is devoted to outlining the genesis of the "wedge" strategy, to distinguish it from young earth creationism, and to highlight the questioning of evolution as our meta-narrative bearing on overall conceptions of the scientific endeavor. The arguments propounded by Behe are reviewed in (...) detail, as the example of blood coagulation as a purported irreducibly complex mechanism is contrasted to the question of system boundaries. Counter-arguments by Miller are reviewed, and a few bottom-line questions are directed to invite a further consideration of the type of engineering this could testify to. The concept of complex specified information is then presented, and contrasted to traditional and lingering axiomatic problems in the theory of probabilities. The problem of the recognition of an intrinsic pattern is also brought together with some work in recent philosophy of causation and explanation. The two opposing strategies, naturalistic evolutionism and intelligent design, are seen as caught in each other's rhetoric, and some probing is offered in the direction of a theory that could surpass those stalling factors. (shrink)

Delineating the framework for a fundamental model of long-range coherence in biological systems is said to rely on principles beyond parameters addressed by current physical science. Just as phenomena of quantum mechanics lay beyond tools of classical Newtonian mechanics we must now enter a 3rd regime of unified field, UF mechanics. In this paper we present a battery of nine empirical protocols for manipulating long-range coherence in complex self-organized living systems (SOLS) in a manner surmounting the Copenhagen (...) Interpretation of quantum uncertainty (space-quantization) thereby allowing empirical access to underlying coherent biophysical principles driving self-organization. Interestingly, while the UF is not indicative of a 5th fundamental force in the usual phenomenal sense of quantal transfer during field interactions; it does however provide an inherent ‘force of coherence’ in an energyless ontological sense by a process called ‘topological switching’ of higher dimensional (HD) brane dynamics. It is this putative inherent property that produces long-range coherence and leads to the possibility of its direct experimental mediation. (shrink)

Many tasks in statistical and causal inference can be construed as problems of entailment in a suitable formal language. We ask whether those problems are more difficult, from a computational perspective, for causal probabilistic languages than for pure probabilistic (or “associational”) languages. Despite several senses in which causal reasoning is indeed more complex—both expressively and inferentially—we show that causal entailment (or satisfiability) problems can be systematically and robustly reduced to purely probabilistic problems. Thus there is no jump in computational (...) complexity. Along the way we answer several open problems concerning the complexity of well-known probability logics, in particular demonstrating the ${\exists \mathbb {R}}$ -completeness of a polynomial probability calculus, as well as a seemingly much simpler system, the logic of comparative conditional probability. (shrink)

Many biological processes and objects can be described by fractals. The paper uses a new type of objects – blinking fractals – that are not covered by traditional theories considering dynamics of self-similarity processes. It is shown that both traditional and blinking fractals can be successfully studied by a recent approach allowing one to work numerically with infinite and infinitesimal numbers. It is shown that blinking fractals can be applied for modeling complex processes of growth of biological systems (...) including their season changes. The new approach allows one to give various quantitative characteristics of the obtained blinking fractals models of biological systems. (shrink)