Mechanistic philosophy of science views a large part of scientific activity as engaged in modelling mechanisms. While science textbooks tend to offer qualitative models of mechanisms, there is increasing demand for models from which one can draw quantitative predictions and explanations. Casini et al. (Theoria 26(1):5–33, 2011) put forward the Recursive Bayesian Networks (RBN) formalism as well suited to this end. The RBN formalism is an extension of the standard Bayesian net formalism, an extension that allows for modelling the hierarchical (...) nature of mechanisms. Like the standard Bayesian net formalism, it models causal relationships using directed acyclic graphs. Given this appeal to acyclicity, causal cycles pose a prima facie problem for the RBN approach. This paper argues that the problem is a significant one given the ubiquity of causal cycles in mechanisms, but that the problem can be solved by combining two sorts of solution strategy in a judicious way. (shrink)

This article assesses how people reason with categories whose features are related in causal cycles. Whereas models based on causal graphical models have enjoyed success modeling category-based judgments as well as a number of other cognitive phenomena, CGMs are only able to represent causal structures that are acyclic. A number of new formalisms that allow cycles are introduced and evaluated. Dynamic Bayesian networks represent cycles by unfolding them over time. Chain graphs augment CGMs by (...) allowing the presence of undirected links that model feedback relations between variables. Unfolded chain graphs are chain graphs that unfold over time. An existing model of causal cycles is also evaluated. Four experiments in which subjects reason about categories with cyclically related features provided evidence against DBNs and alpha centrality and for the two types of chain graphs. Chain graphs—a mechanism for representing the equilibrium distribution of a dynamic system—may thus be good candidates for modeling how people reason causally with complex systems. Applications of chain graphs to areas of cognition other than category-based judgments are discussed. (shrink)

Mechanisms play an important role in many sciences when it comes to questions concerning explanation, prediction, and control. Answering such questions in a quantitative way requires a formal represention of mechanisms. Gebharter (2014) suggests to represent mechanisms by means of one or more causal arrows of an acyclic causal net. In this paper we show how this approach can be extended in such a way that it can also be fruitfully applied to mechanisms featuring causal feedback.

We investigate the context of discovery of two significant achievements of twentieth century biochemistry: the chemiosmotic mechanism of oxidative phosphorylation and the dark reaction of photosynthesis. The pursuit of these problems involved discovery strategies such as the transfer, recombination and reversal of previous causal and mechanistic knowledge in biochemistry. We study the operation and scope of these strategies by careful historical analysis, reaching a number of systematic conclusions: even basic strategies can illuminate “hard cases” of scientific discovery that go (...) far beyond simple extrapolation or analogy; the causal–mechanistic approach to discovery permits a middle course between the extremes of a completely substrate-neutral and a completely domain-specific view of scientific discovery; the existing literature on mechanism discovery underemphasizes the role of combinatorial approaches in defining and exploring search spaces of possible problem solutions; there is a subtle interplay between a fine-grained mechanistic and a more coarse-grained causal level of analysis, and both are needed to make discovery processes intelligible. (shrink)

We investigate the context of discovery of two significant achievements of twentieth century biochemistry: the chemiosmotic mechanism of oxidative phosphorylation and the dark reaction of photosynthesis. The pursuit of these problems involved discovery strategies such as the transfer, recombination and reversal of previous causal and mechanistic knowledge in biochemistry. We study the operation and scope of these strategies by careful historical analysis, reaching a number of systematic conclusions: even basic strategies can illuminate “hard cases” of scientific discovery that go (...) far beyond simple extrapolation or analogy; the causal–mechanistic approach to discovery permits a middle course between the extremes of a completely substrate-neutral and a completely domain-specific view of scientific discovery; the existing literature on mechanism discovery underemphasizes the role of combinatorial approaches in defining and exploring search spaces of possible problem solutions; there is a subtle interplay between a fine-grained mechanistic and a more coarse-grained causal level of analysis, and both are needed to make discovery processes intelligible. (shrink)

v. I. Cycles, causality, ecology -- v. II. Evolution & appendices.

Studies exploring how students learn and understand science processes such as diffusion and natural selection typically find that students provide misconceived explanations of how the patterns of such processes arise (such as why giraffes’ necks get longer over generations, or how ink dropped into water appears to “flow”). Instead of explaining the patterns of these processes as emerging from the collective interactions of all the agents (e.g., both the water and the ink molecules), students often explain the pattern as being (...) caused by controlling agents with intentional goals, as well as express a variety of many other misconceived notions. In this article, we provide a hypothesis for what constitutes a misconceived explanation; why misconceived explanations are so prevalent, robust, and resistant to instruction; and offer one approach of how they may be overcome. In particular, we hypothesize that students misunderstand many science processes because they rely on a generalized version of narrative schemas and scripts (referred to here as a Direct-causal Schema) to interpret them. For science processes that are sequential and stage-like, such as cycles of moon, circulation of blood, stages of mitosis, and photosynthesis, a Direct-causal Schema is adequate for correct understanding. However, for science processes that are non-sequential (or emergent), such as diffusion, natural selection, osmosis, and heat flow, using a Direct Schema to understand these processes will lead to robust misconceptions. Instead, a different type of general schema may be required to interpret non-sequential processes, which we refer to as an Emergent-causal Schema. We propose that students lack this Emergent Schema and teaching it to them may help them learn and understand emergent kinds of science processes such as diffusion. Our study found that directly teaching students this Emergent Schema led to increased learning of the process of diffusion. This article presents a fine-grained characterization of each type of Schema, our instructional intervention, the successes we have achieved, and the lessons we have learned. (shrink)

Across the world, the lives of men and women who are otherwise similarly situated tend to differ from each other systematically. Although gender disparities varywidely within and among regions, women everywhere are disproportionately vulnerable to poverty, abuse and political marginalization. This article proposes thatglobal gender disparities are caused by a network of norms, practices, policies, and institutions that include transnational as well as national elements. These interlaced and interacting factors frequently modify and sometimes even reduce gendered vulnerabilities but their overall (...) effect is to maintain and often intensify them. Women’s vulnerabilities in different areas of life mutually reinforce each other and I follow other authors in referring to such causal feedback loops as cycles of gendered vulnerability. I argue that these cycles now operate on a transnational as well as national scale and I illustrate this by discussing the examples of domestic work and sex work. If global institutional arrangements do indeed contribute to maintaining or intensifying distinctively gendered vulnerabilities, these arrangements deserve criti cal scrutiny from philosophers concerned with global justice. (shrink)

I present a decision problem in which causal decision theory appears to violate the independence of irrelevant alternatives (IIA) and normal-form extensive-form equivalence (NEE). I show that these violations lead to exploitable behavior and long-run poverty. These consequences appear damning, but I urge caution. This decision should lead causalists to a better understanding of what it takes for a decision between some collection of options to count as a subdecision of a decision between a larger collection of options. And (...) with this better understanding of subdecisions in hand, causalists will not violate the IIA or the NEE. This decision will also teach causalists that, in sequential decisions, a rational agent may be led to make a series of choices which are causally dominated by some other sequence of choices they could have made instead. I will encourage causalists to recognise this as an intrapersonal tragedy of the commons. (shrink)

ABSTRACTThe concepts of radicalisation and de-radicalisation are primarily defined by the assumption they make that there is a causal relationship between ideas and action. However, the causal role of ideas in informing behaviour has been strongly contested and has thus far eluded and undermined radicalisation and de-radicalisation conceptually and practically. The following article provides a theoretical basis for identifying the causal relationship between ideas and action through Margaret Archer’s critical realist ontology. Drawing on fieldwork conducted in Northern (...) Ireland, the article identifies processes of ideational causal reproduction and morphogenesis in the Provisional Irish Republican Army’s thinking on armed struggle during its transition away from armed violence. It argues that the adoption of the Armalite and Ballot Box strategy in the 1980s introduced a contradiction in the movement’s ideology and that the movement was pressured to address this contradiction through three corrective cycles throughout the peace-process, subsequently softening its position on armed struggle. (shrink)

According to behavioural theories deriving from pragmatism, gestalt psychology, existentialism, and ecopsychology, knowledge about the world is gained by intentional action followed by learning. In terms of the neurodynamics described here, if the intending of an act comes to awareness through reafference, it is perceived as a cause. If the consequences of an act come to awareness through proprioception and exteroception, they are perceived as an effect. A sequence of such states of awareness comprises consciousness, which can grow in complexity (...) to include self-awareness. Intentional acts do not require awareness, whereas voluntary acts require self-awareness. Awareness of the action/perception cycle provides the cognitive metaphor of linear causality as an agency. Humans apply this metaphor to objects and events in the world to predict and control them, and to assign social responsibility. Thus, linear causality is the bedrock of technology and social contracts. Complex material systems with distributed non-linear feedback, such as brains and their neural and behavioural activities, cannot be explained by linear causality. They can be said to operate by circular causality without agency. The nature of self-control is described by breaking the circle into a forward limb, the intentional self, and a feedback limb, awareness of the self and its actions. The two limbs are realized through hierarchically stratified kinds of neural activity. Intentional acts are produced by the self-organized microscopic neural activity of cortical and subcortical components in the brain. Awareness supervenes as a macroscopic ordering state, that defers action until the self-organizing microscopic process has reached closure in reflective prediction. Agency, which is removed from the causal hierarchy by the appeal to circularity, re-appears as a metaphor by which events in the world are anthropomorphized, making them appear subject to human control. (shrink)

An important component in the interventionist account of causal explanation is an interpretation of counterfactual conditionals as statements about consequences of hypothetical interventions. The interpretation receives a formal treatment in the framework of functional causal models. In Judea Pearl’s influential formulation, functional causal models are assumed to satisfy a “unique-solution” property; this class of Pearlian causal models includes the ones called recursive. Joseph Halpern showed that every recursive causal model is Lewisian, in the sense that (...) from the causal model one can construct a possible worlds model in David Lewis’s well-known semantics that satisfies the exact same formulas in a certain language. Moreover, he demonstrated that some Pearlian (non-recursive) models are not Lewisian in this sense. This raises the question regarding the exact contour of Lewisian causal models. In this paper, we provide a characterization of the class of Lewisian causal models and a complete axiomatization with respect to this class. Our results have philosophically interesting consequences, two of which are especially worth noting. First, the class of Stalnakerian causal models, a subclass of Lewisian causal models, is precisely the class of Pearlian models that do not contain any cycle of counterfactual dependence (in a sense of counterfactual dependence akin to Lewis’s famous relation between distinct events). Second, a more natural class of causal models is actually a superclass of Lewisian causal models, the logic of which respects only weak centering rather than centering. (shrink)

Charles Peirce, Mikhail Bakhtin and Thomas Sebeok all develop original research itineraries around the sign and, despite terminological differences, canbe related with reference to the concept of dialogism and modelling. Jakob von Uexküll’s biosemiosic “functional cycle”, a model for semiosic processes, is alsoimplied in the relation between dialogue and communication.Biological models which describe communication as a self-referential, autopoietic and semiotically closed system (e.g., the models proposed by Maturana,Varela, and Thure von Uexküll) contrast with both the linear (Shannon and Weaver) and (...) the circular (Saussure) paradigms. The theory of autopoietic systems is only incompatible with dialogism if reference is to a linear causal model which describes communication as developing from source to destination, or to the conversation model governed by the turning around together rule. Dialogism understood in biosemiotic terms overlaps with the concepts of interconnectivity,interrelation, intercorporeity and presupposes the otherness relation.As Uexküll says, the relation with the umwelt in nonhuman living beings is stable and concerns the species; on the contrary, in human beings it is, changeableand concerns the single individual, which is at once an advantage and a disadvantage. Thanks to “syntactics”, human beings can construct, deconstruct and reconstruct an infinite number of worlds from a finite number of elements. This distinguishes human beings from other animals and determines their capacity for posing problems and asking questions. The human being not only produces his or her own world, but can also endanger it, and even destroy it to the point of causing the extinction of all other life forms on Earth. The unique capacity for reflection on signs makes human beings responsible for life across the planet, both human and nonhuman. Such reflections shift semiotic research in the direction of semioethics. (shrink)

I examine the adequacy of the causal graph-structural equations approach to causation for modeling biological mechanisms. I focus in particular on mechanisms with complex dynamics such as the PER biological clock mechanism in Drosophila. I show that a quantitative model of this mechanism that uses coupled differential equations – the well-known Goldbeter model – cannot be adequately represented in the standard causal graph framework, even though this framework does permit causal cycles. The reason is that the (...) model contains dynamical information about the mechanism that concerns causal properties but that does not correspond to variables that could be subject to independent interventions. Thus, a representation of the mechanisms as a causal structural model necessarily suppresses causally relevant information. (shrink)

Substantial evidence implicates fast axonal transport (FAT) defects in neurodegeneration. In Alzheimer's disease (AD), it is controversial whether transport defects cause or arise from amyloid‐β (Aβ)‐induced toxicity. Using a novel, unbiased genetic screen, Morihara et al. identified kinesin light chain‐1 splice variant E (KLC1vE) as a modifier of Aβ accumulation. Here, we propose three mechanisms to explain this causal role. First, KLC1vE reduces APP transport, leading to Aβ accumulation. Second, reduced transport of APP by KLC1vE triggers an ER stress (...) response that activates the amyloidogenic pathway. Third, KLC1vE impairs transport of other KLC1 cargos that regulate amyloidogenesis, promoting Aβ retention within the secretory pathway. Collectively, KLC1vE perpetuates a vicious cycle of Aβ generation, kinase dysregulation, and global FAT impairment that inevitably leads to cellular toxicity. These concepts implicate alternative splicing of KLC1 in AD and suggest that the reciprocal influence of transport mechanisms on disease states contributes to neurodegeneration. (shrink)

Ecological developmental biology (eco‐devo) explores the mechanistic relationships between the processes of individual development and environmental factors. Recent studies imply that some of these relationships have deep evolutionary origins, and may even pre‐date the divergences of the simplest extant animals, including cnidarians and sponges. Development of these early diverging metazoans is often sensitive to environmental factors, and these interactions occur in the context of conserved signaling pathways and mechanisms of tissue homeostasis whose detailed molecular logic remain elusive. Efficient methods for (...) transgenesis in cnidarians together with the ease of experimental manipulation in cnidarians and sponges make them ideal models for understanding causal relationships between environmental factors and developmental mechanisms. Here, we identify major questions at the interface between animal evolution and development and outline a road map for research aimed at identifying the mechanisms that link environmental factors to developmental mechanisms in early diverging metazoans.Also watch the Video Abstract. (shrink)

A large class of the dynamical laws for causal sets described by a classical process of sequential growth yields a cyclic universe, whose cycles of expansion and contraction are punctuated by single ‘‘origin elements’’ of the causal set. We present evidence that the effective dynamics of the immediate future of one of these origin elements, within the context of the sequential growth dynamics, yields an initial period of de Sitter-like exponential expansion, and argue that the resulting picture (...) has many attractive features as a model of the early universe, with the potential to solve some of the standard model puzzles without any fine-tuning. (shrink)

We show that if any number of variables are allowed to be simultaneously and independently randomized in any one experiment, log2(N ) + 1 experiments are sufficient and in the worst case necessary to determine the causal relations among N ≥ 2 variables when no latent variables, no sample selection bias and no feedback cycles are present. For all K, 0 < K <.

In this article we address the so-called argument of «individual causal inefficacy» (ICI), according to which CO2-emission-generating actions are morally neutral with regards to climate change, in so far as, taken in their singularity, they are neither sufficient nor necessary to cause climate change. In the first part, we address the main substantive objection to ICI: if a single emission, analysed in isolation, does not cause any disutility, it is impossible to explain why climate change (which is the result (...) of a sum of emissions) is the source of an enormous disutility; thus, ICI should be rejected in so far as it leads to a conclusion that is logically inconsistent. We argue, contrary to this, that it is possible to hold together ICI and individual moral responsibility for climate change, given the characteristics of the natural carbon cycle and of net-zero emissions. In the second part, accordingly, we propose a theory of individual responsibility for climate change which is based on the distinction between individual and collective freedom to emit, compatibly with a given mitigation target. This theory allows us to maintain that there exists a moral duty to reduce individual emissions, without having to demonstrate the fallacy of ICI. This duty is based on distributive reasons, which can prescind from the direct causal relationship between individual polluting actions and climate damage. (shrink)

David Bohm's interpretation of quantum mechanics yields a quantum potential, Q. In his early work, the effects of Q are understood in causal terms as acting through a real (quantum) field which pushes particles around. In his later work (with Basil Hiley), the causal understanding of Q appears to have been abandoned. The purpose of this paper is to understand how the use of certain metaphors leads Bohm away from a causal treatment of Q, and to evaluate (...) the use of those metaphors. (shrink)

This article offers a reading of Eriugena’s thought that is inspired by Heidegger’s claim according to which being is constituted in a dialectical interplay of revelation and concealment. Beginning with an analysis of how “causality as concealing revelation” works on the level of God’s inner-Trinitarian life, the piece moves on to a consideration of the way in which the human soul reveals itself in successive stages of exteriorization that culminate in the creation of the body, its “image.” The body, however, (...) conceals as much as it reveals true human nature. Moreover, it is shown that for Eriugena all of reality, as theophany, possesses this character of concealing its fundamental truth. These insights lead Eriugena to a recognition of radical human finitude, as genuine wisdom requires an acknowledgement of our fundamental ignorance. (shrink)

This paper defends the notion of downward causation. I will seek to elucidate this notion, explain why it is a useful way of thinking, and respond to criticisms attacking its intelligibility. My account of downward causation will be in many respects similar to the account recently advanced by Ellis. The overall framework I will adopt is the interventionist treatment of causation I have defended elsewhere: X causes Y when Y changes under a suitable manipulation of X. When X is at (...) a higher “level” than Y this allows for the possibility of downward causation from X to Y. True claims of downward causation must meet certain additional conditions, some of which have already been discussed by Ellis. These include the condition that X must have a homogenous effect on Y in the sense that the effect of X on Y must be the same regardless of how X is “realized” at lower levels. In addition, the most plausible examples of downward causation will involve causes X, that in a sense that I will try to specify, are capable of being manipulated by macro-level interventions that have a coordinated or organized impact on them, as when one manipulates the temperature of a gas by placing it in a heat bath.Three common criticisms of the notion of downward causation that I will consider are: the claim that this involves a whole acting downward on its parts which is an objectionable idea because wholes and parts are not sufficiently distinct to stand in causal relationships, that downward causation commits us to the existence of causal cycles in which X causes Y which in turn causes X and that the asymmetric nature of the causal relation rules out such cycles, and causal exclusion type worries, according to which all of the causal action occurs among “low level” variables, so that upper level variables are deprived of causal efficacy. In response I will argue that plausible examples of downward causation in the scientific literature do not involve whole to part causation, there is nothing wrong with causal cycles, which are common in, for example, biological contexts, exclusion type worries do not arise within the interventionist framework that I favor. (shrink)

The conceptual history of the term “organization” begins in Medieval times with the reception and transformation of Aristotle’s philosophy of life. It designates the corporeal structure and conditions of identity of natural “organic bodies,” a term that had been used to refer to living beings since antiquity. The term played an important role in specifying the ontological status of living beings. At the same time, it offered a basis for their mechanistic understanding. Starting with mechanistic models of life in the (...) second half of the seventeenth century, “organization” and “life” were increasingly used interchangeably. This conjunction of meaning transformed “living beings” into “organisms.” Within physiological accounts of the eighteenth century, the living organization was compared to a causal cycle of interdependency. Philosophically, this conjunction was adapted at the end of the century in Kant’s philosophy of “organized beings of nature” in which he located the idea of causal cyclicity within a teleological framework and specified an “organized being” in causal terms as a system of interacting and interdependent parts characterized by functional closure. Thus, “organization” refers to the constitution of living beings as a particular kind of causal system. In the nineteenth century, the term achieves the status of a signal word for the life sciences and starts being applied in a wide variety of contexts, from comparative anatomy to physiology and ecology. It was supplemented by two other fundamental notions, namely, “regulation” and “evolution,” the first referring to the stabilization and the second to the long-term transformation of natural organizations. The twentieth century saw a further intensification of the complementarity of the perspectives associated with these three terms. Finally, in recent years, a substantial improvement in understanding the causal structure of “organization” was achieved by analyzing it in terms of the “closure of constraints.”. (shrink)

What I shall do in this paper is to propose an analysis of ‘Agent P tries to A’ in terms of a subjunctive conditional, that avoids some of the problems that beset most alternative accounts of trying, which I call ‘referential views’. They are so-named because on these alternative accounts, ‘P tries to A’ entails that there is a trying to A by P, and therefore the expression ‘P’s trying to A’ can occur in the subject of a sentence and (...) be used to refer to a particular, namely an act or event of trying. A conditional account such as mine avoids having to answer questions about those alleged particulars, for example their location and their causal relation to physical actions, or alternatively their identity to physical actions. In brief, the analysis I propose eschews any need to quantify over any sort of trying particulars. I both clarify the proposal and deal with five possible objections to it: metaphysically impossible actions: cases of finking and reverse-cycle finking; the empirical emptiness of preventers and blockers; proximate intentions and trying; and alleged explanatory loss. (shrink)

This article considers categorical perception (CP) as a crucial process involved in all sort of communication throughout the biological hierarchy, i.e. in all of biosemiosis. Until now, there has been consideration of CP exclusively within the functional cycle of perception–cognition–action and it has not been considered the possibility to extend this kind of phenomena to the mere physiological level. To generalise the notion of CP in this sense, I have proposed to distinguish between categorical perception (CP) and categorical sensing (CS) (...) in order to extend the CP framework to all communication processes in living systems, including intracellular, intercellular, metabolic, physiological, cognitive and ecological levels. The main idea is to provide an account that considers the heterarchical embeddedness of many instances of CP and CS. This will take me to relate the hierarchical nature of categorical sensing and perception with the equally hierarchical issues of the “binding problem”, “triadic causality”, the “emergent interpretant” and the increasing semiotic freedom observed in biological and cognitive systems. (shrink)

Science and philosophy study well-being with different but complementary methods. Marry these methods and a new picture emerges: To have well-being is to be "stuck" in a positive cycle of emotions, attitudes, traits and success. This book unites the scientific and philosophical worldviews into a powerful new theory of well-being.

I argue that Sellars’s naturalization of Kant should be understood in terms of how he used behavioristic psychology and cybernetics. I first explore how Sellars used Edward Tolman’s cognitive-behavioristic psychology to naturalize Kant in the early essay “Language, Rules, and Behavior”. I then turn to Norbert Wiener’s understanding of feedback loops and circular causality. On this basis I argue that Sellars’s distinction between signifying and picturing, which he introduces in “Being and Being Known,” can be understood in terms of what (...) I call cybernetic behaviorism. I interpret picturing in terms of cycles of cybernetic behavior and signifying in terms of coordination between cybernetic behavior systems, or what I call triangulated cybernetic behavior. This leads to a formal, naturalistic understanding of personhood as the capacity to engage in triangulated cybernetic behavior. I conclude by showing that Sellars’s thought has the resources, which he did not exploit, for introducing the concept of second-order cybernetics. This suggests that Sellars’s philosophy of mind could be developed in the direction of autopoiesis and enactivism. (shrink)

Abstract If asked about the Darwinian influence on William James, some might mention his pragmatic position that ideas are “mental modes of adaptation,” and that our stock of ideas evolves to meet our changing needs. However, while this is not obviously wrong, it fails to capture what James deems most important about Darwinian theory: the notion that there are independent cycles of causation in nature. Versions of this idea undergird everything from his campaign against empiricist psychologies to his theories (...) of mind and knowledge to his pluralistic worldview; and all of this together undergirds his attempts to challenge determinism and defend freewill. I begin this paper by arguing that James uses Darwinian thinking to bridge empiricism and rationalism, and that this merger undermines environmental determinism. I then discuss how Darwinism informs his concept of pluralism; how his concept challenges visions of a causally welded “block universe”; and how it also casts doubt on the project of reducing all reality to physical reality, and therewith the wisdom of dismissing consciousness as an inert by-product of physiology. I conclude by considering how Darwinism helps him justify the pragmatic grounds upon which he defends freewill. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

This paper proposes a new and testable view about the nature of species and other evolving lineages, according to which they are feedback systems. On this view, it is a mistake to think gene flow, niche sharing, and trait frequency similarities between populations are among variables that interact to cause some further downstream variable that distinguishes evolving lineages from each other, some sort of “species cohesion” for example. Instead, gene flow, niche sharing, similarities between populations, and other causal variables (...) feed into each other—instances of these at earlier times help cause instances of these same variables at later times. And any lineage-identifying cohesion just is the recurrence or cycling of these feedback relations within metapopulations over generations. Such cohesion can then be represented as variable M within multi-dimensional variable spaces, where values of M vary dynamically with the frequency and magnitude of feedback relations. Related conditions for being a species or other evolving lineage are then clarified. To argue for the development and testing of this view, the paper shows how it improves upon others. (shrink)

Ockham’s razor is the characteristic scientific penchant for simpler, more testable, and more unified theories. Glymour’s early work on confirmation theory eloquently stressed the rhetorical plausibility of Ockham’s razor in scientific arguments. His subsequent, seminal research on causal discovery still concerns methods with a strong bias toward simpler causal models, and it also comes with a story about reliability—the methods are guaranteed to converge to true causal structure in the limit. However, there is a familiar gap between (...) convergent reliability and scientific rhetoric: convergence in the long run is compatible with any conclusion in the short run. For that reason, Carnap suggested that the proper sense of reliability for scientific inference should lie somewhere between short-run reliability and mere convergence in the limit. One natural such concept is straightest possible convergence to the truth, where straightness is explicated in terms of minimizing reversals of opinion and cycles of opinion prior to convergence. We close the gap between scientific rhetoric and scientific reliability by showing that Ockham’s razor is necessary for cycle-optimal convergence to the truth, and that patiently waiting for information to resolve conflicts among simplest hypotheses is necessary for reversal-optimal convergence to the truth. (shrink)

Heterogeneity in mitochondrial content has been previously suggested as a major contributor to cellular noise, with multiple studies indicating its direct involvement in biomedically important cellular phenomena. A recently published dataset explored the connection between mitochondrial functionality and cell physiology, where a non‐linearity between mitochondrial functionality and cell size was found. Using mathematical models, we suggest that a combination of metabolic scaling and a simple model of cell death may account for these observations. However, our findings also suggest the existence (...) of alternative competing hypotheses, such as a non‐linearity between cell death and cell size. While we find that the proposed non‐linear coupling between mitochondrial functionality and cell size provides a compelling alternative to previous attempts to link mitochondrial heterogeneity and cell physiology, we emphasise the need to account for alternative causal variables, including cell cycle, size, mitochondrial density and death, in future studies of mitochondrial physiology. (shrink)

: Gandhi can serve as a valuable catalyst allowing us to rethink our philosophical positions on violence, nonviolence, and education. Especially insightful are Gandhi's formulations of the multidimensionality of violence, including educational violence, and the violence of the status quo. His peace education offers many possibilities for dealing with short-term violence, but its greatest strength is its long-term preventative education and socialization. Key to Gandhi's peace education are his ethical and ontological formulations of means-ends relations; the need to uncover root (...) causes and causal determinants and to free oneself from entrapment in escalating cycles of violence; and the dynamic complex relation between relative and absolute truth that includes analysis of situated embodied consciousness, tolerant diversity and inclusiveness, and an approach to unavoidable violence. (shrink)

It has long been recognized that productivity growth and the business cycle are closely interrelated. Yet, until recently, the two phenomena have been investigated separately in the economics literature. This book provides the first consistent attempt to analyze the effects of macroeconomic volatility on productivity growth, and also the reverse causality from growth to business cycles. The authors show that by looking at the economy through the lens of private entrepreneurs, who invest under credit constraints, one can go some (...) way towards explaining persistent macroeconomic volatility and the effects of volatility on growth. Beginning with an analysis of the effects of volatility on growth, the authors argue that the lower the level of financial development in a country the more detrimental the effect of volatility on growth. This prediction is confirmed by cross-country panel regressions. The data also suggests that a fixed exchange rate regime or more countercyclical budgetary policies are growth-enhancing in countries with a lower level of financial development. The former reduce aggregate volatility whereas the latter reduce the negative effects of volatility on long-term productivity-enhancing investment by firms. The book concludes with an investigation into how the interplay between credit constraints and pecuniary externalities is sufficient to generate persistent business cycles and to explain the occurrence of currency crises. (shrink)

Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the cosmos, (...) freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection—and perhaps self-organization—could occur on many worlds via different causal mechanisms. Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the organization of process in the expected biological work cycles to create the diversity in our observable biosphere. Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which, in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe. (shrink)

The phenomenon of ‘plant sleep’ – whereby vegetables rhythmically open and close their leaves or petals in daily cycles – has been a continual source of fascination for those with botanical interests, from the Portuguese physician Cristóbal Acosta and the Italian naturalist Prospero Alpini in the sixteenth century to Percy Bysshe Shelley and Charles Darwin in the nineteenth. But it was in 1757 that the topic received its earliest systemic treatment on English shores with the prodigious author, botanist, actor, (...) and Royal Society critic John Hill’s The Sleep of Plants, and Cause of Motion in the Sensitive Plant. As the present article aims to illustrate, Hill and his respondents used this remarkable behaviour, exhibited by certain plants, as a lens through which to reassess the nature of vegetables, and to address pressing questions of wider natural philosophical import, particularly the degree of continuity between the structures and functions of plants and animals and whether similar mechanisms necessarily account for related movements in different life forms. These disputes, this paper contends, also had profound methodological implications regarding the proper way to conduct experiments, the extent to which it was acceptable to extrapolate from observations, and the status of causal explanations. (shrink)

This article compares the work of Jakob von Uexkull and Charles S. Peirce to elucidate two contrasting yet connected images of ecosemiotics. The intent is not simply to oppose their work, but to explore a tension which has implications for the ethical dimension of this emerging discipline. Uexkull’s functional cycle is associated with the image of a circle, which, while emphasizing the integration of organism and environment, is shown to invoke solipsism, and an overly deterministic depiction of ecological relations. Peirce’s (...) drawing of a labyrinth is taken to represent a maze, which, while exemplifying the evolutionary play of ecosystems, may entail a level of unpredictability that is catastrophically chaotic. The root of these diverging depictions is identified with the role of subjectivity in engendering semiotic relations in the work of both Uexkull and Peirce. Where the more regressive aspects of Uexkull’s theoretical biology are mitigated by a teleological interpretation of life’s underlying causality, orientating agency within Peirce’s work depends upon attention to the idea of the self in his philosophy of signs. In conclusion, Eduardo Kohn’s conception of an ‘ecology of selves’ is cited, and the status of the organism as a living symbol of its environment is reaffirmed. (shrink)

ABSTRACTThe paper examines the relevance of the nomological view of nature to three discussions of tide in the thirteenth century. A nomological conception of nature assumes that the basic explanatory units of natural phenomena are universally binding rules stated in quantitative terms. Robert Grosseteste introduced an account of the tide based on the mechanism of rarefaction and condensation, stimulated by the Moon's rays and their angle of incidence. He considered the Moon's action over the sea an example of the general (...) efficient causality exerted through the universal activity of light or species. Albert the Great posited a plurality of causes which cannot be reduced to a single cause. The connaturality of the Moon and the water is the only principle of explanation which he considered universal. Connaturality, however, renders neither formulation nor quantification possible. While Albert stressed the variety of causes of the tide, Roger Bacon emphasized regularity and reduced the various causes producing tides into forces. He replaced the terminology of ‘natures’ by one of ‘forces’. Force, which in principle can be accurately described and measured, thus becomes a commensurable aspect of a diverse cosmos. When they reasoned why waters return to their place after the tide, Grosseteste argued that waters return in order to prevent a vacuum, Albert claimed that waters ‘follow their own nature’, while Bacon held that the ‘proper force’ of the water prevails over the distant force of the first heaven. I exhibit, for the thirteenth century, moments of the move away from the Aristotelian concerns. The basic elements of these concerns were essences and natures which reflect specific phenomena and did not allow for an image of nature as a unified system. In the new perspective of the thirteenth century the key was a causal link between the position of the Moon and the tide cycle, a link which is universal and still qualitative, yet expressed as susceptible to quantification. (shrink)

ABSTRACT The phenomenon of ‘plant sleep’ – whereby vegetables rhythmically open and close their leaves or petals in daily cycles – has been a continual source of fascination for those with botanical interests, from the Portuguese physician Cristóbal Acosta and the Italian naturalist Prospero Alpini in the sixteenth century to Percy Bysshe Shelley and Charles Darwin in the nineteenth. But it was in 1757 that the topic received its earliest systemic treatment on English shores with the prodigious author, botanist, (...) actor, and Royal Society critic John Hill’s The Sleep of Plants, and Cause of Motion in the Sensitive Plant. As the present article aims to illustrate, Hill and his respondents used this remarkable behaviour, exhibited by certain plants, as a lens through which to reassess the nature of vegetables, and to address pressing questions of wider natural philosophical import, particularly the degree of continuity between the structures and functions of plants and animals and whether similar mechanisms necessarily account for related movements in different life forms. These disputes, this paper contends, also had profound methodological implications regarding the proper way to conduct experiments, the extent to which it was acceptable to extrapolate from observations, and the status of causal explanations. (shrink)

Among advocates and critics of the “extended evolutionary synthesis” (EES), “reciprocal causation” refers to the view that adaptive evolution is a bidirectional phenomenon, whereby organisms and environments impinge on each other through processes of niche construction and natural selection. I argue that reciprocal causation is incompatible with the view that natural selection is a metaphysically emergent causal process. The emergent character of selection places reciprocal causation on the horns of dilemma, and neither horn can rescue it. I conclude that (...) proponents of the EES must abandon the claim that the process of natural selection features in cycles of reciprocal causation. (shrink)

The so-called Buddhist momentarists, such as Dharmakīrti and his followers, defend the momentariness of all things. However, with equal force they also defend the persistence of all things, not just within a single lifetime but over an indefinite cycle of rebirth. Naturally, they have an interesting theory of persistence, according to which things persist without being self-identical over time. The theory is best presented in the Lokāyatāparīkṣā chapter of Śāntarakṣita’s Tattvasaṃgraha and Kamalaśīla’s Paṅjikā, as they clearly articulate the criteria of (...) persistence without identity. The purpose of this paper is to formulate a Buddhist theory of persistence through the analysis of these texts. Here is the basic formula: Things persist as series, which is constituted by momentary entities that are causally related as upādāna and upādeya. Upādāna causal relation is demarcated from other causal relations by the principle of changeability with temporal restriction, and the principle adopts further qualifications to accommodate complex cases and personal persistence. I have addressed a problem that contemporary physicalism might pose a threat to the Buddhist account of personal persistence, and argued that the problem can be evaded by regarding persons as psycho-physical entities rather than strictly non-physical. In its general outlook, the Buddhist theory of persistence is close to Theodore Sider’s stage theory in that persistence is a matter of distinct individuals standing in a special causal relationship. As regards personal persistence, the Buddhist has a stricter condition than Parfit’s IDM thesis, which states that psychological connectedness with any cause is what matters for survival. The Buddhist would say it is moral connectedness with a special cause called upādāna. (shrink)

In this paper we will show that Hempel's covering law model can't deal very well with explanations that are based on incomplete knowledge. In particular the symmetry thesis, which is an important aspect of the covering law model, turns out to be problematic for these explanations. We will discuss an example of an electric circuit, which clearly indicates that the symmetry of explanation and prediction does not always hold. It will be argued that an alternative logic for causal explanation (...) is needed. And we will investigate to what extent non-monotonic epistemic logic can provide such an alternative logical framework. Finally we will show that our non-monotonic logical analysis of explanation is not only suitable for simple cases such as the electric circuit, but that it also sheds new light on more controversial causal explanations such as Milton Friedman's explanation of the business cycle. (shrink)

Metaphysics relies on the presupposition of the non-being of the world: since the world has once not existed it is necessary to postulate a cause for its existence, i.e. an extrinsic principle to explain the absolute beginning of the causal series of all things that constitute the world. After the critique of theologizing metaphysics by authors like Kant, Hegel and Nietzsche, the notion of an absolute beginning still persists though in a field in which it often goes as such (...) unnoticed, while it factually enjoys wide acceptance, namely in epistemology. It sounds as a truism that knowledge begins: personal inexistence (birth-death cycle) and the phenomenon of unconsciousness (sleep-wake cycle) seem to endorse the obviousness of that statement. Now, to link the beginning of the phenomenal series of subjective acts of knowledge with the existence of an external world that causes the specific content of our temporary cognitive acts relies, however, on two presuppositions, namely on the thesis of a complete non-being or nothingness of knowledge and, intrinsically related to this first presupposition, on the thesis of an absolute beginning of cognitive activity. If knowledge begins from its own nothingness, there must be a cause that is external to the totality of acts of knowledge, a cause that it doesn´t belong to the series of cognitive acts and, therefore, that it is not caused by any of them: this uncaused cause of contentful knowledge is supposed to be the real world external to the knowing subject. In my paper I make explicit the relation between realist-empiricist approachs to epistemology and the double presupposition of the nothingness and absolute beginning of knowledge, I explain the difficulties implied by these two presuppositions and, finally, I propose as a plausible solution to those difficulties some key theoretical claims of absolute idealism. (shrink)

Anton de Bary is best known for his elucidation of the life cycle of Phytopthora infestans, the causal organism of late blight of potato and the crop losses that caused famine in nineteenth-century Europe. But while practitioner histories often claim this accomplishment as a founding moment of modern plant pathology, closer examination of de Bary’s experiments and his published work suggest that his primary motiviation for pursing this research was based in developmental biology, not agriculture. De Bary shied away (...) from making any recommendations for agricultural practice, and instead focused nearly exclusively on spontaneous generation and fungal development – both concepts promoted through prize questions posted by the Académie des Sciences in the 1850s and 1860s. De Bary’s submission to the Académie’s 1859 Alhumbert prize question illustrates his own contributions to debates about spontaneous generation and demonstrates the practical applications of seemingly philosophical questions – such as the origin of life. (shrink)