Patient-centered care (PCC) is an approach to healthcare that values patients’ preference, need, and autonomy. The estimation of healthcare partly depends on how well PCC is implemented. In addition, the result of clinical research can inform the assessment of the implementation of PCC. In clinical research, health-related quality of life (HRQL) theoretical models offer a conceptual toolbox that informs clinical research and guides the hypotheses generation. Wilson and Cleary (1995) developed the most widely used HRQL theoretical model (Bakas et al., (...) 2012). Ontological assumptions about causation in Wilson and Cleary’s model will influence which kind of hypotheses will be generated. I will argue that Wilson and Cleary’s model instilled a kind of causal bias into hypothesis generation in clinical research on HRQL. Causation from biomedical factors to non-biomedical factors is frequently hypothesized while causation from non-biomedical factors to biomedical factors is rarely hypothesized. It leads to that the interdependence and interaction between constituent parts of patients are ignored, which is an obstacle to the implementation of PCC. In addition, I will propose a revised HRQL theoretical model which avoids the causal bias brought by Wilson and Cleary’s model. By doing so, I leave room for the improvement of the practice of healthcare by analyzing the ontological assumptions about causation. (shrink)

Psychological measurement has received strong criticism throughout the history of psychological science. Nevertheless, measurements of attributes such as emotions or intelligence continue to be widely used in research and society. I address this puzzle by presenting a new causal perspective to psychological measurement. I start with assumptions that both critics and proponents of psychological measurement are likely to accept: a minimal causal condition and the observation that most psychological concepts are ill-defined or ambiguous. Based on this, I argue (...) that psychological measurement is fundamentally different from measurement in the physical sciences but can nevertheless be useful. (shrink)

We review the recently proposed universal concept of dynamic complexity and its new mathematics based on the unreduced interaction problem solution. We then consider its progress-bringing applications at various levels of complex world dynamics, including complex-dynamical nanometal physics and living condensed matter, unreduced nanobiosystem dynamics and the integral medicine concept, causally complete management of complex economical and social dynamics, and the ensuing concept of truly sustainable world governance.

I discuss two categories of causal relationships: primitive causal interactions of the sort characterized by Phil Dowe and the more general manipulable causal relationships as defined by James Woodward. All primitive causal interactions are manipulable causal relationships, but there are manipulable causal relationships that are not primitive causal interactions. I’ll call the latter constructed causal relationships, and I’ll argue that constructed causal relationships serve as a foundation for both computing and complex (...) systems. -/- Perhaps even more interesting are autonomous causal relationships. These are constructed causal relationships in which the causal mechanism resides primarily in the effect. A typical example is a software execution engine. Software execution engines are on the effect side of a cause-effect relationship in which software is the cause and the behavior of the execution engine is the effect. The mechanism responsible for that causal relationship resides in the execution engine. (shrink)

This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of (...) these models is due to their failure to include relevant spatial and structural information in a way that does not render the model non-explanatory, unmanageable, or inconsistent with basic assumptions of causal graph theory. (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)

The deep crisis in modern fundamental science development is ever more evident and openly recognised now even by mainstream, official science professionals and leaders. By no coincidence, it occurs in parallel to the world civilisation crisis and related global change processes, where the true power of unreduced scientific knowledge is just badly missing as the indispensable and unique tool for the emerging greater problem solution and further progress at a superior level of complex world dynamics. Here we reveal the mathematically (...) exact reason for the crisis in conventional science, containing also the natural and unified problem solution in the form of well-specified extension of usual, artificially restricted paradigm. We show how that extended, now causally complete science content provides various "unsolvable" problem solutions and opens new development possibilities for both science and society, where the former plays the role of the main, direct driver for the latter. We outline the related qualitative changes in science organisation, practice and purposes, giving rise to the sustainability transition in the entire civilisation dynamics towards the well-specified superior level of its unreduced, now well understood and universally defined complexity. (shrink)

Analyzing causation in terms of Woodward's interventionist theory and describing the structure of the world in terms of causal powers are usually regarded as quite different projects in contemporary philosophy. Interventionists aim to give an account of how causal relations can be empirically discovered and described, without committing themselves to views about what causation really is. Causal powers theorists engage in precisely the latter project, aiming to describe the metaphysical structure of the world. In this paper, I (...) argue that interventionism can benefit from incorporating considerations about causal powers. I describe a previously undiscussed problem for Woodward's definition of an intervention variable that arises when interventionist causal models include disjunctive variables. This problem is solved not by excluding disjunctive (or logically compound) variables per se, but by excluding variables whose values represent disjunctions of too different causal powers. This suggests that interventionism and causal powers theories may be less distant from each other than is often assumed. (shrink)

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)

Unified and causal complex-dynamic origin of standard (special and general) relativistic and quantum effects revealed previously at the lowest levels of world interaction dynamics is explicitly generalised to all higher levels of unreduced interaction processes, thus additionally confirming the causally complete character of complex-dynamical, naturally quantised relativity, which does not contain any artificially added, abstract postulates. We demonstrate some elementary applications of this generalised quantum relativity at higher levels of complex brain and social interaction dynamics.

It is an ongoing controversy whether natural selection is a cause of population change, or a mere statistical description of how individual births and deaths accumulate. In this paper I restate the problem in terms of the reference class problem, and propose how the structure of stable equilibrium can provide a solution in continuity with biological practice. Insofar natural selection can be understood as a tendency towards equilibrium, key statisticalist criticisms are avoided. Further, in a modification of the Newtonian-force analogy, (...) it can be suggested that a better metaphor for natural selection is that of an emergent force, similar in nature to entropic forces: with magnitude and direction, but lacking a spatiotemporal origin or point of application. (shrink)

Causal models show promise as a foundation for the semantics of counterfactual sentences. However, current approaches face limitations compared to the alternative similarity theory: they only apply to a limited subset of counterfactuals and the connection to counterfactual logic is not straightforward. This paper addresses these difficulties using exogenous interventions, where causal interventions change the values of exogenous variables rather than structural equations. This model accommodates judgments about backtracking counterfactuals, extends to logically complex counterfactuals, and validates familiar principles (...) of counterfactual logic. This combines the interventionist intuitions of the causal approach with the logical advantages of the similarity approach. (shrink)

Modern fundamental science tends to avoid the principle of physical causality and realism, replacing it with heuristically postulated and separated mathematical constructions that impose their own rules before being adjusted to measurement results. While it is officially accepted as the single possible kind of rigorous knowledge, we argue that another, explicitly extended kind of science can provide the causally complete picture of reality avoiding the glaring gaps, growing problems and persisting stagnation of the artificially reduced knowledge paradigm. The logic of (...) science development and especially its current state call for the urgently needed transition to the extended, causally complete kind of knowledge and related sustainable progress at superior creativity levels of self-aware, reason-based society. (shrink)

Martin and Deutscher’s causal theory of remembering holds that a memory trace serves as a necessary causal link between any genuine episode of remembering and the event it enables one to recall. In recent years, the causal theory has come under fire from researchers across philosophy and cognitive science, who argue that results from the scientific study of memory are incompatible with the kinds of memory traces that Martin and Deutscher hold essential to remembering. Of special note, (...) these critics observe, is that a single memory trace can be shaped by multiple past experiences. This appears to prevent traces from underwriting Martin and Deutscher’s distinction between remembering an event and merely forming an accurate representation of it. This paper accepts such criticisms of the standard causal theory and, through considering the phenomenon forgetting through repetition, raises several others. A substantially revised causal theory is then developed, compatible with the thesis that individual memory traces are shaped by multiple past experiences. The key strategy is to conceive of episodic remembering not as the simple retrieval and projection of a static memory trace, but as a complex quasi-inferential process that makes use of multiple forms of information and cues—“prop-like” memory traces included—in generating the experience known as episodic remembering. When remembering is understood as a multi-componential process, there are a variety of ways in which a representation of the past may be appropriately causally dependent upon a prior experience of the event remembered. (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)

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)

Recently, it has been argued that the use of Big Data transforms the sciences, making data-driven research possible and studying causality redundant. In this paper, I focus on the claim on causal knowledge by examining the Big Data project EXPOsOMICS, whose research is funded by the European Commission and considered capable of improving our understanding of the relation between exposure and disease. While EXPOsOMICS may seem the perfect exemplification of the data-driven view, I show how causal knowledge is (...) necessary for the project, both as a source for handling complexity and as an output for meeting the project’s goals. Consequently, I argue that data-driven claims about causality are fundamentally flawed and causal knowledge should be considered a necessary aspect of Big Data science. In addition, I present the consequences of this result on other data-driven claims, concerning the role of theoretical considerations. I argue that the importance of causal knowledge and other kinds of theoretical engagement in EXPOsOMICS undermine theory-free accounts and suggest alternative ways of framing science based on Big Data. (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)

Applied Evolutionary Epistemology is a scientific-philosophical theory that defines evolution as the set of phenomena whereby units evolve at levels of ontological hierarchies by mechanisms and processes. This theory also provides a methodology to study evolution, namely, studying evolution involves identifying the units that evolve, the levels at which they evolve, and the mechanisms and processes whereby they evolve. Identifying units and levels of evolution in turn requires the development of ontological hierarchy theories, and examining mechanisms and processes necessitates theorizing (...) about causality. Together, hierarchy and causality theories explain how biorealities form and diversify with time. This paper analyzes how Applied EE redefines both hierarchy and causality theories in the light of the recent explosion of network approaches to causal reasoning associated with studies on reticulate and macroevolution. Causality theories have often been framed from within a rigid, ladder-like hierarchy theory where the rungs of the ladder represent the different levels, and the elements on the rungs represent the evolving units. Causality then is either defined reductionistically as an upward movement along the strands of a singular hierarchy, or holistically as a downward movement along that same hierarchy. Upward causation theories thereby analyze causal processes in time, i.e. over the course of natural history or phylogenetically, as Darwin and the founders of the Modern Synthesis intended. Downward causation theories analyze causal processes in space, ontogenetically or ecologically, as the current eco-evo-devo schools are evidencing. This work demonstrates how macroevolution and reticulate evolution theories add to the complexity by examining reticulate causal processes in space–time, and the interactional hierarchies that such studies bring forth introduce a new form of causation that is here called reticulate causation. Reticulate causation occurs between units and levels belonging to different as well as to the same ontological hierarchies. This article concludes that beyond recognizing the existence of multiple units, levels, and mechanisms or processes of evolution, also the existence of multiple kinds of evolutionary causation as well as the existence of multiple evolutionary hierarchies needs to be acknowledged. This furthermore implies that evolution is a pluralistic process divisible into different kinds. (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)

Especially in the appendix to the opening part of his Ethics, Spinoza discusses teleology in a manner that has earned him the status of a staunch critic of final causes. Much of the recent lively discussion concerning this complex and difficult issue has revolved around the writings of Jonathan Bennett who maintains that Spinoza does, in fact, reject all teleology. Especially important has been the argument claiming that because of his basic ontology, Spinoza cannot but reject thoughtful teleology, that is, (...) teleology involved in the actions of conscious cognitive beings who have thoughts of future states of affairs. For Spinoza, a particular idea is a modification of the thinking substance the object of which is a certain modification of the extended substance, and Bennett’s central argumentative move is to claim that there is no room in Spinoza’s system for a key ingredient in thoughtful teleology, the tenet that representative content of ideas is causally efficacious. In what follows, I begin by presenting Bennett’s argument. As his position has received much criticism, I then take up the ways in which it has been discussed and found wanting. I think that Bennett’s position really is something that should not be endorsed; however, and despite the lively discussion, it also seems to me that there is more to be said about what is at stake here. Thus, I aim at offering an analysis of the nature of Bennett’s argument and the ensuing discussion with the aim of discerning the philosophical source from which Bennett’s interpretation draws its force. (shrink)

The purpose of this paper is to address a well-known dilemma for physicalism. If mental properties are type identical to physical properties, then their causal efficacy is secure, but at the cost of ruling out mentality in creatures very different to ourselves. On the other hand, if mental properties are multiply realizable, then all kinds of creatures can instantiate them, but then they seem to be causally redundant. The causal exclusion problem depends on the widely held principle that (...) realized properties inherit their causal powers from their realizers. While this principle holds for functional realization, it fails on a broader notion of realization that permits the realization of complex qualitative properties such as spatial and temporal patterns. Such properties are best seen as dependent powerful qualities, which have their causal roles in virtue of being the qualities they are, and do not inherit powers from their realizers. Recent studies have identified one such property—neural synchrony—as a correlate of consciousness. If synchrony is also partially constitutive of consciousness, then phenomenal properties are both multiply realizable and causally novel. I outline a version of representationalism about consciousness on which this constitution claim holds. (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)

This summary of the original paradigm of the universal science of complexity starts with the discovered exact origin of the stagnating "end" of conventional, unitary science paradigm and development traditionally presented by its own estimates as the only and the best possible kind of scientific knowledge. Using a transparent generalisation of the exact mathematical formalism of arbitrary interaction process, we show that unitary science approach and description, including its imitations of complexity and chaoticity, correspond to artificial and ultimately (...) strong reduction of the natural plurality of unreduced interaction results called realisations to a single, "average" or "exact", realisation. This severe reduction of the natural world dynamics in unitary science underlies all its unsolvable "mysteries" and "paradoxes", persisting "difficult problems", and finally the modern "end" of the progress of just that, actually very special kind of knowledge, whose irreducible limits lead to the modern deep crisis of the global civilisation development. We show then how the rigorously substantiated restoration of the full richness of real-world dynamics within the intrinsically unified knowledge of the universal science of complexity provides not only the causally complete solution to the old and new problems of unitary science but opens practically unlimited possibilities for the new progress of science and civilisation as a result of this crucial extension, which we call complexity revolution. The unreduced analysis of the universal complexity science shows that at the current critical bifurcation point of development, we have only two incompatible possibilities and emerging tendencies, either the dangerously growing degradation within the dominating unitary science and thinking limits (irrespective of purely empirical technology power becoming even dangerous here) or the new golden age of scientific discoveries and civilisation progress with the qualitatively extended approach and results of unreduced complexity science and the new thinking it implies. (shrink)

Causal selection is the cognitive process through which one or more elements in a complex causal structure are singled out as actual causes of a certain effect. In this paper, we report on an experiment in which we investigated the role of moral and temporal factors in causal selection. Our results are as follows. First, when presented with a temporal chain in which two human agents perform the same action one after the other, subjects tend to judge (...) the later agent to be the actual cause. Second, the impact of temporal location on causal selection is almost canceled out if the later agent did not violate a norm while the former did. We argue that this is due to the impact that judgments of norm violation have on causal selection—even if the violated norm has nothing to do with the obtaining effect. Third, moral judgments about the effect influence causal selection even in the case in which agents could not have foreseen the effect and did not intend to bring it about. We discuss our findings in connection to recent theories of the role of moral judgment in causal reasoning, on the one hand, and to probabilistic models of temporal location, on the other. (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)

The review first discusses componential explanations of automaticity, which specify non/automaticity features (e.g., un/controlled, un/conscious, non/efficient, fast/slow) and their interrelations. Reframing these features as factors that influence processes (e.g., goals, attention, and time) broadens the range of factors that can be considered (e.g., adding stimulus intensity and representational quality). The evidence reviewed challenges the view of a perfect coherence among goals, attention, and consciousness, and supports the alternative view that (a) these and other factors influence the quality of representations in (...) an additive way (e.g., little time can be compensated by extra attention or extra stimulus intensity) and that (b) a first threshold of this quality is required for unconscious processing and a second threshold for conscious processing. The review closes with a discussion of causal explanations of automaticity, which specify factors involved in automatization such as repetition and complexity, and a discussion of mechanistic explanations, which specify the low-level processes underlying automatization. (shrink)

Recently, a strong hylomorphic reading of Aristotelian emotions has been put forward, one that allegedly eliminates the problem of causal interaction between soul and body. Taking the presentation of emotions in de An. I 1 as a starting point and basic thread, but relying also on the discussion of Rh. II, I will argue that this reading only takes into account two of the four causes of emotions, and that, if all four of them are included into the picture, (...) then a causal interaction of mind and body remains within Aristotelian emotions, independent of how strongly their hylomorphism is understood. Beyond the discussion with this recent reading, the analysis proposed of the fourfold causal structure of emotions is also intended as a hermeneutical starting point for a comprehensive analysis of particular emotions in Aristotle. Through the different causes Aristotle seems to account for many aspects of the complex phenomenon of emotion, including its physiological causes, its mental causes, and its intentional object. (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)

In clinical medicine, a diagnosis can offer an explanation of a patient's symptoms by specifying the pathology that is causing them. Diagnoses in psychiatry are also sometimes presented in clinical texts as if they pick out pathological processes that cause sets of symptoms. However, current evidence suggests the possibility that many diagnostic categories in psychiatry are highly causally heterogeneous. For example, major depressive disorder may not be associated with a single type of underlying pathological process, but with a range of (...) different causal pathways, each involving complex interactions of various biological, psychological, and social factors. This paper explores the implications of causal heterogeneity for whether psychiatric diagnoses can be said to serve causal explanatory roles in clinical practice. I argue that while they may fall short of picking out a specific cause of the patient's symptoms, they can nonetheless supply different sorts of clinically relevant causal information. In particular, I suggest that some psychiatric diagnoses provide negative information that rules out certain causes, some provide approximate or disjunctive information about the range of possible causal processes, and some provide causal information about the relations between the symptoms themselves. (shrink)

I welcome with great enthusiasm Meling and Scheidegger’s (2023; henceforth “M&S”) timely contribution to advance an enactive approach to psychedelic therapy, especially to the complex causality involved. Their two main research questions concerned:(i) the causal interaction between the psychedelic molecule and brain activity; and (ii) the causal interaction between brain activity and the psychedelic experience. While I largely agree with and celebrate much of what is proposed by M&S, especially their employment of key enactive concepts to advance our (...) understanding of the first research question, in the following, I will present some worries regarding their answers to the second. Although I agree that there is probably a two-way reciprocal relationship between neural activity and experience, I have several points of contention regarding M&S’s proposal. My hope is to stimulate discussion on M&S’s important contribution, and to help advance a much-needed enactive science of psychedelics. (shrink)

It is widely held that whether a person is morally responsible for an outcome partly depends on whether certain causal relations obtain between that person and the outcome. This paper argues that, regardless of whether the preceding claim about moral responsibility is true, moral blameworthiness is independent of such causal considerations. This conclusion is motivated by considering cases from Carolina Sartorio and Sara Bernstein. The causal structures of these cases are complex. Sartorio and Bernstein believe that reaching (...) conclusions about moral responsibility and blameworthiness requires wading through this complexity. But it is argued here that getting clear on these causal structures does not help us assess blameworthiness (regardless of the relevance of such considerations for drawing conclusions about moral responsibility). Moral blameworthiness simply does not turn on the considerations relevant to figuring out whether an agent causally contributed to an outcome. (shrink)

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)

In biomedical measurement, biomarkers are used to achieve reliable prediction of, and useful causal information about patient outcomes while minimizing complexity of measurement, resources, and invasiveness. A biomarker is an assayable metric that discloses the status of a biological process of interest, be it normative, pathophysiological, or in response to intervention. The greatest utility from biomarkers comes from their ability to help clinicians (and researchers) make and evaluate clinical decisions. In this paper we discuss a specific methodological use (...) of clinical biomarkers in pharmacological measurement: Some biomarkers, called ‘surrogate markers’, are used to substitute for a clinically meaningful endpoint corresponding to events and their penultimate risk factors. We confront the reliability of clinical biomarkers that are used to gather information about clinically meaningful endpoints. Our aim is to present a systematic methodology for assessing the reliability of multiple surrogate markers (and biomarkers in general). To do this we draw upon the robustness analysis literature in the philosophy of science and the empirical use of clinical biomarkers. -/- After introducing robustness analysis we present two problems with biomarkers in relation to reliability. Next, we propose an intervention-based robustness methodology for organizing the reliability of biomarkers in general. We propose three relevant conditions for a robust methodology for biomarkers: (R1) Intervention-based demonstration of partial independence of modes: In biomarkers partial independence can be demonstrated through exogenous interventions that modify a process some number of “steps” removed from each of the markers. (R2) Comparison of diverging and converging results across biomarkers: By systematically comparing partially-independent biomarkers we can track under what conditions markers fail to converge in results, and under which conditions they successfully converge. (R3) Information within the context of theory: Through a systematic cross-comparison of the markers we can make causal conclusions as well as eliminate competing theories. We apply our robust methodology to currently developing Alzheimer’s research to show its usefulness for making causal conclusions. (shrink)

The article advances a new way of thinking about classifications in general and the classification of mental disorders in particular. By applying insights from measurement practice to the context of classification, I defend a notion of epistemic accuracy that allows one to evaluate and improve classifications by comparing different classifying methods to each other. Progress in classification arises from the mutual development of classification systems and classifying methods. Based on this notion of accuracy, the article illustrates with an example how (...) psychiatric classifications can be improved via circumscribed comparisons of different perspectives on mental disorders, without relying on complete models of their complex aetiology. When applying this strategy, the traditional opposition between symptom-based and causal approaches is of little consequence for making progress in the epistemic accuracy of psychiatric classification. (shrink)

The notion of representation in neuroscience has largely been predicated on localizing the components of computational processes that explain cognitive function. On this view, which I call “algorithmic homuncularism,” individual, spatially and temporally distinct parts of the brain serve as vehicles for distinct contents, and the causal relationships between them implement the transformations specified by an algorithm. This view has a widespread influence in philosophy and cognitive neuroscience, and has recently been ably articulated and defended by Shea. Still, I (...) am skeptical about algorithmic homuncularism, and I argue against it by focusing on recent methods for complex data analysis in systems neuroscience. I claim that analyses such as principle components analysis and linear discriminant analysis prevent individuating vehicles as algorithmic homuncularism recommends. Rather, each individual part contributes to a global state space, trajectories of which vary with important task parameters. I argue that, while homuncularism is false, this view still supports a kind of “vehicle realism,” and I apply this view to debates about the explanatory role of representation. (shrink)

Instead of postulated fixed structures and abstract principles of usual positivistic science, the unreduced diversity of living world reality is consistently derived as dynamically emerging results of unreduced interaction process development, starting from its simplest configuration of two coupled homogeneous protofields. The dynamically multivalued, or complex and intrinsically chaotic, nature of these real interaction results extends dramatically the artificially reduced, dynamically single-valued projection of standard theory and solves its stagnating old and accumulating new problems, “mysteries” and “paradoxes” within the unified (...) and causally complete picture of intrinsically evolving, dynamically complex reality. The permanently unfolding complexity progress thus revealed is fundamentally unlimited and does not need to stop at the directly observed diversity of usual matter complexity. The exciting, but rigorously substantiated and objectively inevitable prospects of further civilisation complexity development towards its superior levels of genuine sustainability and global Noosphere are outlined, with practically important conclusions for today’s critical problem solution. (shrink)

This paper explores some of the factors that make complex systems complex. We first examine the history of complex systems. It was Aristotle’s insight that how elements are joined together helps determine the properties of the resulting whole. We find (a) that scientific reductionism does not provide a sufficient explanation; (b) that to understand complex systems, one must identify and trace energy flows; and (c) that disproportionate causality, including global tipping points, are all around us. Disproportionate causality results from the (...) wide availability of energy stores. We discuss three categories of emergent phenomena—static, dynamic, and adaptive—and recommend retiring the term emergent, except perhaps as a synonym for creative. Finally, we find that virtually all communication is stigmergic. (shrink)

To justify inductive inference and vanquish classical skepticisms about human memory, external world realism, etc., Richard Fumerton proposes his “inferential internalism,” an epistemology whereby humans ‘see’ by Russellian acquaintance Keynesian probable relations (PRs) between propositions. PRs are a priori necessary relations of logical probability, akin to but not reducible to logical entailments, such that perceiving a PR between one’s evidence E and proposition P of unknown truth value justifies rational belief in P to an objective degree. A recent critic of (...) inferential internalism is Alan Rhoda, who questions its psychological plausibility. Rhoda argues that in order to see necessary relations between propositions E and P, one would need acquaintance with too many propositions at once, since our evidence E is often complex. In this paper, I criticize Rhoda’s implausibility objection as too quick. Referencing the causal status effect (CSE) from psychology, I argue that some of the complex features of evidence E contribute to our type-categorizing it as E-type, and thus we do not need to ‘see’ all of the complex features when we see the PR between E and P. My argument leaves unchanged Fumerton’s justificatory role for the PR, but enhances its psychological plausibility. (shrink)

Quantum mechanics admits a “linguistic interpretation” if one equates preliminary any quantum state of some whether quantum entity or word, i.e. a wave function interpret-able as an element of the separable complex Hilbert space. All possible Feynman pathways can link to each other any two semantic units such as words or term in any theory. Then, the causal reasoning would correspond to the case of classical mechanics (a single trajectory, in which any next point is causally conditioned), and the (...) probabilistic reasoning, to the case of quantum mechanics (many Feynman trajectories). Frame semantics turns out to be the natural counterpart of that linguistic interpretation of quantum mechanics. (shrink)

We explain why exactly the simplified abstract scheme of reality within the standard science paradigm cannot provide the consistent picture of “truly fundamental” reality and how the unreduced, causally complete description of the latter is regained within the extended, provably complete solution to arbitrary interaction problem and the ensuing concept of universal dynamic complexity. We emphasize the practical importance of this extension for both particular problem solution and further, now basically unlimited fundamental science development (otherwise dangerously stagnating within its (...) traditional paradigm). (shrink)

We review some of the main implications of the free-energy principle (FEP) for the study of the self-organization of living systems – and how the FEP can help us to understand (and model) biotic self-organization across the many temporal and spatial scales over which life exists. In order to maintain its integrity as a bounded system, any biological system - from single cells to complex organisms and societies - has to limit the disorder or dispersion (i.e., the long-run entropy) of (...) its constituent states. We review how this can be achieved by living systems that minimize their variational free energy. Variational free energy is an information theoretic construct, originally introduced into theoretical neuroscience and biology to explain perception, action, and learning. It has since been extended to explain the evolution, development, form, and function of entire organisms, providing a principled model of biotic self-organization and autopoiesis. It has provided insights into biological systems across spatiotemporal scales, ranging from microscales (e.g., sub- and multicellular dynamics), to intermediate scales (e.g., groups of interacting animals and culture), through to macroscale phenomena (the evolution of entire species). A crucial corollary of the FEP is that an organism just is (i.e., embodies or entails) an implicit model of its environment. As such, organisms come to embody causal relationships of their ecological niche, which, in turn, is influenced by their resulting behaviors. Crucially, free-energy minimization can be shown to be equivalent to the maximization of Bayesian model evidence. This allows us to cast natural selection in terms of Bayesian model selection, providing a robust theoretical account of how organisms come to match or accommodate the spatiotemporal complexity of their surrounding niche. In line with the theme of this volume; namely, biological complexity and self-organization, this chapter will examine a variational approach to self-organization across multiple dynamical scales. (shrink)

This paper outlines the methodological and empirical limitations of analysing the potential relationship between complex social phenomena such as democracy and inequality. It shows that the means to assess how they may be related is much more limited than recognised in the existing literature that is laden with contradictory hypotheses and findings. Better understanding our scientific limitations in studying this potential relationship is important for research and policy because many leading economists and other social scientists such as Acemoglu and Robinson (...) mistakenly claim to identify causal linkages between inequality and democracy but at times still inform policy. In contrast to the existing literature, the paper argues that ‘structural’ or ‘causal’ mechanisms that may potentially link the distribution of economic wealth and different political regimes will remain unknown given reasons such as their highly complex and idiosyncratic characteristics, fundamental econometric constraints and analysis at the macro-level. Neither new data sources, different analysed time periods nor new data analysis techniques can resolve this question and provide robust, general conclusions about this potential relationship across countries. Researchers are thus restricted to exploring rough correlations over specific time periods and geographic contexts with imperfect data that are very limited for cross-country comparisons. (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)

Recently, there has been an increased interest in employing model-based definitions of actual causation in legal inquiry. The formal precision of such approaches promises to be an improvement over more traditional approaches. Yet model-based approaches are viable only if suitable models of legal cases can be provided, and providing such models is sometimes difficult. I argue that causal-model-based definitions benefit legal inquiry in an indirect way. They make explicit the causal assumptions that need to be made plausible to (...) defend a particular claim of actual causation. My argument concerns the analysis of legal cases involving a combination of double prevention and causal redundancy. I show that discussions among legal theorists about such cases sometimes suffer from ambiguous assumptions about the causal structure. My account illustrates that causal models can act as a heuristic tool for clarifying such assumptions, and that causal models provide a framework for more accurate analyses of legal cases involving complex causal structure. (shrink)

The method of contrast is used within philosophy of perception in order to demonstrate that a specific property could be part of our perception. The method is based on two passages. I argue that the method succeeds in its task only if the intuition of the difference, which constitutes the core of the first passage, has two specific traits. The second passage of the method consists in the evaluation of the available explanations of this difference. Among the three outlined options, (...) I will demonstrate that only in the third option – as we shall see, the case of the scenario that remains the same but is perceived in two different ways by the same perceiver – the intuition purports a difference that posses the necessary characteristics, namely being immediately evident and extremely complex and multifaceted, which determine its tensive nature. The application within auditory perception of this third option will generate two cases, a diachronic one and a synchronic one, which clearly show that we can auditorily perceive causality as a link between two sonorous episodes. The causal explanation is the only possible explanation among the many evaluated within the second passage of the method of contrast. (shrink)

Despite recent efforts to improve on counterfactual theories of causation, failures to explain how effects depend on their causes are still manifest in a variety of cases. In particular, theories that do a decent job explaining cases of causal preemption have problems accounting for cases of causal intransitivity. Moreover, the increasing complexity of the counterfactual accounts makes it difficult to see why the concept of causation would be such a central part of our cognition. In this paper, (...) I propose an account of our causal thinking that not only explains the hitherto puzzling variety of causal judgments, but also makes it intelligible why we would employ such an elusive concept. (shrink)

Bradford Hill (1965) highlighted nine aspects of the complex evidential situation a medical researcher faces when determining whether a causal relation exists between a disease and various conditions associated with it. These aspects are widely cited in the literature on epidemiological inference as justifying an inference to a causal claim, but the epistemological basis of the Hill aspects is not understood. We offer an explanatory coherentist interpretation, explicated by Thagard's ECHO model of explanatory coherence. The ECHO model captures (...) the complexity of epidemiological inference and provides a tractable model for inferring disease causation. We apply this model to three cases: the inference of a causal connection between the Zika virus and birth defects, the classic inference that smoking causes cancer, and John Snow’s inference about the cause of cholera. (shrink)

Transdisciplinary research challenges the divide between Indigenous and academic knowledge by bringing together epistemic resources of heterogeneous stakeholders. The aim of this article is to explore causal explanations in a traditional fishing community in Brazil that provide resources for transdisciplinary collaboration, without neglecting differences between Indigenous and academic experts. Semi-structured interviews were carried out in a fishing village in the North shore of Bahia and our findings show that community members often rely on causal explanations for local ecological (...) phenomena with different degrees of complexity. While these results demonstrate the ecological expertise of local community members, we also argue that recognition of local expertise needs to reflect on differences between epistemic communities by developing a culturally sensitive model of transdisciplinary knowledge negotiation. (shrink)

This chapter argues that Simon anticipated what has emerged as the consensus view about human cognition: embodied functionalism. According to embodied functionalism, cognitive processes appear at a distinctively cognitive level; types of cognitive processes (such as proving a theorem) are not identical to kinds of neural processes, because the former can take various physical forms in various individual thinkers. Nevertheless, the distinctive characteristics of such processes — their causal structures — are determined by fine-grained properties shared by various, often (...) especially bodily related, physical processes that realize them. Simon’s apparently anti-embodiment views are surveyed and are shown to be consistent with his many claims that lend themselves to an embodied interpretation and that, to a significant extent, helped to lay the groundwork for an embodied cognitive science. (shrink)