The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

What are the philosophical views of professional philosophers, and how do these views change over time? The 2020 PhilPapers Survey surveyed around 2000 philosophers on 100 philosophical questions. The results provide a snapshot of the state of some central debates in philosophy, reveal correlations and demographic effects involving philosophers' views, and reveal some changes in philosophers' views over the last decade.

We investigated, experimentally, the contention that the folk view, or naïve theory, of time, amongst the population we investigated is dynamical. We found that amongst that population, ~ 70% have an extant theory of time that is more similar to a dynamical than a non-dynamical theory, and ~ 70% of those who deploy a naïve theory of time deploy a naïve theory that is more similar to a dynamical than a non-dynamical theory. Interestingly, while we found stable results across our (...) two experiments regarding the percentage of participants that have a dynamical or non-dynamical extant theory of time, we did not find such stability regarding which particular dynamical or non-dynamical theory of time they take to be most similar to our world. This suggests that there might be two extant theories in the population—a broadly dynamical one and a broadly non-dynamical one—but that those theories are sufficiently incomplete that participants do not stably choose the same dynamical theory as being most similar to our world. This suggests that while appeals to the ordinary view of time may do some work in the context of adjudicating disputes between dynamists and non-dynamists, they likely cannot do any such work adjudicating disputes between particular brands of dynamism. (shrink)

This paper offers both a theoretical and an experimental perspective on the relationship between connectionist and Classical (symbol-processing) models. Firstly, a serious flaw in Fodor and Pylyshyn’s argument against connectionism is pointed out: if, in fact, a part of their argument is valid, then it establishes a conclusion quite different from that which they intend, a conclusion which is demonstrably false. The source of this flaw is traced to an underestimation of the differences between localist and distributed representation. It has (...) been claimed that distributed representations cannot support systematic operations, or that if they can, then they will be mere implementations of traditional ideas. This paper presents experimental evidence against this conclusion: distributed representations can be used to support direct structure-sensitive operations, in a man- ner quite unlike the Classical approach. Finally, it is argued that even if Fodor and Pylyshyn’s argument that connectionist models of compositionality must be mere implementations were correct, then this would still not be a serious argument against connectionism as a theory of mind. (shrink)

Empirical work has lately confirmed what many philosophers have taken to be true: people are ‘biased toward the future’. All else being equal, we usually prefer to have positive experiences in the future, and negative experiences in the past. According to one hypothesis, the temporal metaphysics hypothesis, future-bias is explained either by our beliefs about temporal metaphysics—the temporal belief hypothesis—or alternatively by our temporal phenomenology—the temporal phenomenology hypothesis. We empirically investigate a particular version of the temporal belief hypothesis according to (...) which future-bias is explained by the belief that time robustly passes. Our results do not match the apparent predictions of this hypothesis, and so provide evidence against it. But we also find that people give more future-biased responses when asked to simulate a belief in robust passage. We take this to suggest that the phenomenology that attends simulation of that belief may be partially responsible for future-bias, and we examine the implications of these results for debates about the rationality of future-bias. (shrink)

This paper empirically investigates one aspect of the folk concept of time by testing how the presence or absence of directedness impacts judgements about whether there is time in a world. Experiment 1 found that dynamists, showed significantly higher levels of agreement that there is time in dynamically directed worlds than in non-dynamical non-directed worlds. Comparing our results to those we describe in Latham et al., we report that while ~ 70% of dynamists say there is time in B-theory worlds, (...) only ~ 45% say there is time in C-theory worlds. Thus, while the presence of directedness makes dynamists more inclined to say there is time in a world, a substantial subpopulation of dynamists judge that there is time in non-directed worlds. By contrast, a majority of non-dynamists judged that there was time in both growing block worlds and C-theory worlds, with no significant differences between the means. Experiment 2 found that when participants are only presented with non-dynamical worlds—namely, a directed world and a non-directed world—they report significantly higher levels of agreement that there is time in B-theory worlds. However, the majority of participants still judge that there is time in C-theory worlds. We conclude that while the presence of directedness bolsters judgements that there is time, most people do not judge it to be necessary for time. (shrink)

Deflationists hold that it does not seem to us, in experience, as though time robustly passes. There is some recent empirical evidence that appears to support this contention. Equally, empirical evidence suggests that we naïvely represent time as dynamical. Thus deflationists are faced with an explanatory burden. If, as they maintain, the world seems to us in experience as though it is non-dynamical, then why do we represent time as dynamical? This paper takes up the challenge of investigating, on the (...) part of the deflationist, one candidate explanation. We hypothesise that people’s belief that the future is what we call deliberatively open partly explains why they represent time as dynamical. In a series of two experiments we test this hypothesis. We find no evidence that beliefs about deliberative openness explain why people represent time as dynamical. Hence there remains an explanatory burden for the deflationist to discharge. (shrink)

Mental capacities for perceiving, remembering, thinking, and planning involve the processing of structured mental representations. A compositional semantics of such representations would explain how the content of any given representation is determined by the contents of its constituents and their mode of combination. While many have argued that semantic theories of mental representations would have broad value for understanding the mind, there have been few attempts to develop such theories in a systematic and empirically constrained way. This paper contributes to (...) that end by developing a semantics for a ‘fragment’ of our mental representational system: the visual system’s representations of the bounding contours of objects. At least three distinct kinds of composition are involved in such representations: ‘concatenation’, ‘feature composition’, and ‘contour composition’. I sketch the constraints on and semantics of each of these. This account has three principal payoffs. First, it models a working framework for compositionally ascribing structure and content to perceptual representations, while highlighting core kinds of evidence that bear on such ascriptions. Second, it shows how a compositional semantics of perception can be compatible with holistic, or Gestalt, phenomena, which are often taken to show that the whole percept is ‘other than the sum of its parts’. Finally, the account illuminates the format of a key type of perceptual representation, bringing out the ways in which contour representations exhibit domain-specific form of the sort that is typical of structured icons such as diagrams and maps, in contrast to typical discursive representations of logic and language. (shrink)

We explain and explore class-theoretic potentialism—the view that one can always individuate more classes over a set-theoretic universe. We examine some motivations for class-theoretic potentialism, before proving some results concerning the relevant potentialist systems (in particular exhibiting failures of the $\mathsf {.2}$ and $\mathsf {.3}$ axioms). We then discuss the significance of these results for the different kinds of class-theoretic potentialists.

Quilty-Dunn et al.'s wide-ranging defense of the Language of Thought Hypothesis (LoTH) argues that vision traffics in abstract, structured representational formats. We agree: Vision, like language, is compositional – just as words compose into phrases, many visual representations contain discrete constituents that combine in systematic ways. Here, we amass evidence extending this proposal, and explore its implications for how vision interfaces with the rest of the mind.

In the debate on how we ought to define political freedom, some definitions are criticized for implying that no one can ever be free to perform any action. In this paper, I show how the possibility of freedom depends on a definition that finds an appropriate balance between absence of interference and protection against interference. To assess the possibility of different conceptions of freedom, I consider the trade-offs they make between these two dimensions. I find that pure negative freedom is (...) clearly possible. Republican freedom might also be possible, though its protection requirement is too vague for a definitive verdict. Finally, the recently proposed ‘freedom as independence’ is impossible since it is an attempt to avoid the unavoidable trade-off. (shrink)

It has widely been assumed, by philosophers, that most people unambiguously have a phenomenology as of time passing, and that this is a datum that philosophical theories must accommodate. Moreover, it has been assumed that the greater the extent to which people have said phenomenology, the more likely they are to endorse a dynamical theory of time. This paper is the first to empirically test these assumptions. Surprisingly, our results do not support either assumption. One experiment instead found the reverse (...) correlation: people were more likely to report having passage phenomenology if they endorsed a non-dynamical theory of time. Given that people do not have an unambiguous phenomenology as of time passing, we conclude that this is suggestive evidence in favor of veridical non-dynamism—the view that our phenomenology is veridical, and that it does not unambiguously represent that time passes. Instead, our phenomenology veridically has some quite different content. (shrink)

People are ‘biased toward the future’: all else being equal, we typically prefer to have positive experiences in the future, and negative experiences in the past. Several explanations have been suggested for this pattern of preferences. Adjudicating among these explanations can, among other things, shed light on the rationality of future-bias: For instance, if our preferences are explained by unjustified beliefs or an illusory phenomenology, we might conclude that they are irrational. This paper investigates one hypothesis, according to which future-bias (...) is explained by our having a phenomenology that we describe, or conceive of, as being as of time robustly passing. We empirically tested this hypothesis and found no evidence in its favour. Our results present a puzzle, however, when compared with the results of an earlier study. We conclude that although robust passage phenomenology on its own probably does not explain future-bias, having this phenomenology and taking it to be veridical may contribute to future-bias. (shrink)

There are two kinds of time-bias: near-bias and future-bias. While philosophers typically hold that near-bias is rationally impermissible, many hold that future-bias is rationally permissible. Call this normative hybridism. According to arbitrariness objections, certain patterns of preference are rationally impermissible because they are arbitrary. While arbitrariness objections have been levelled against both near-bias and future-bias, the kind of arbitrariness in question has been different. In this paper we investigate whether there are forms of arbitrariness that are common to both kinds (...) of preferences, and hence whether there are versions of the arbitrariness objection that are objections both to near-bias and future-bias. If there are, then this might go some way towards undermining normative hybridism and to defending a thorough-going time-neutralism. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

A standard line in the contemporary philosophical literature has it that physical theories are equivalent only when they agree on their empirical content, where this empirical content is often understood as being encoded in the equations of motion of those theories. In this article, we question whether it is indeed the case that the empirical content of a theory is exhausted by its equations of motion, showing that (for example) considerations of boundary conditions play a key role in the empirical (...) equivalence (or otherwise) of theories. Having argued for this, we show that philosophical claims made by Weatherall (2016) that electromagnetism in the Faraday tensor formalism is equivalent to electromagnetism in the vector potential formalism, and by Knox (2011) that general relativity is equivalent to teleparallel gravity, can both be called into question. We then show that properly considering the role of boundary conditions in theory structure can potentially restore these claims of equivalence and close with some remarks on the pragmatics of adjudications on theory identity. (shrink)

Philosophers have long noted, and empirical psychology has lately confirmed, that most people are “biased toward the future”: we prefer to have positive experiences in the future, and negative experiences in the past. At least two explanations have been offered for this bias: belief in temporal passage and the practical irrelevance of the past resulting from our inability to influence past events. We set out to test the latter explanation. In a large survey, we find that participants exhibit significantly less (...) future bias when asked to consider scenarios where they can affect their own past experiences. This supports the “practical irrelevance” explanation of future bias. It also suggests that future bias is not an inflexible preference hardwired by evolution, but results from a more general disposition to “accept the things we cannot change”. However, participants still exhibited substantial future bias in scenarios in which they could affect the past, leaving room for complementary explanations. Beyond the main finding, our results also indicate that future bias is stake-sensitive and that participants endorse the normative correctness of their future-biased preferences and choices. In combination, these results shed light on philosophical debates over the rationality of future bias, suggesting that it may be a rational response to empirical realities rather than a brute, arational disposition. (shrink)

As there is currently a neo-Aristotelian revival currently taking place within contemporary metaphysics and dispositions, or causal powers are now being routinely utilised in theories of causality and modality, more attention is beginning to be paid to a central Aristotelian concern: the metaphysics of substantial unity, and the doctrine of hylomorphism. In this paper, I distinguish two strands of hylomorphism present in the contemporary literature and argue that not only does each engender unique conceptual difficulties, but neither adequately captures the (...) metaphysics of Aristotelian hylomorphism. Thus both strands of contemporary hylomorphism, I argue, fundamentally misunderstand what substantial unity amounts to in the hylomorphic framework – namely, the metaphysical inseparability of matter and form. (shrink)

The leading models of disability struggle to fully encompass all aspects of “disability.” This difficulty arises, the author argues, because the models fundamentally misunderstand the nature of disability. Current theoretical approaches to disability can be understood as “nounal,” in that they understand disability as a thing that is caused or embodied. In contrast, this paper presents an adverbial perspective on disability, which shows that disability is experienced as a personally irremediable impediment to daily-living tasks or goals-like-ours. The picture theory of (...) disability technically constitutes a species of relational approach because its analysis references the interplay between an individual and their environment; it differs from other relational accounts, however, by interpreting disability as a certain kind of negative experience—rather than a function of that relationship. This purely descriptive theory makes no normative claims about disability and operates as both a mechanism for the evaluation of the experience of disability and a heuristic device for the proper interpretation of disability. When disability is reframed in this way, the theory offers a particularist perspective which shows if, when, where, and how disability is experienced. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

This paper concerns a distinction between circumstantial truths that hold because of the circumstances and acircumstantial truths that hold regardless of, or transcend, the circumstances. Previous discussions of the distinction tended to focus on its applications, such as to modality, logical truth, and essence. This paper focuses on developing the distinction largely, but not entirely, in abstraction from its potential applications. As such, the paper’s main contribution is to further clarify the distinction itself. An indirect contribution is to help guide (...) its future applications. (shrink)

The advent of contemporary evolutionary theory ushered in the eventual decline of Aristotelian Essentialism (Æ) – for it is widely assumed that essence does not, and cannot have any proper place in the age of evolution. This paper argues that this assumption is a mistake: if Æ can be suitably evolved, it need not face extinction. In it, I claim that if that theory’s fundamental ontology consists of dispositional properties, and if its characteristic metaphysical machinery is interpreted within the framework (...) of contemporary evolutionary developmental biology, an evolved essentialism is available. The reformulated theory of Æ offered in this paper not only fails to fall prey to the typical collection of criticisms, but is also independently both theoretically and empirically plausible. The paper contends that, properly understood, essence belongs in the age of evolution. (shrink)

This chapter defends the account of metaphysical indeterminacy of Barnes and Williams against Eklund's objections.

Many manipulation arguments against compatibilism rely on the claim that manipulation is relevantly similar to determinism. But we argue that manipulation is nothing like determinism in one relevant respect. Determinism is a "universal" phenomenon: its scope includes every feature of the universe. But manipulation arguments feature cases where an agent is the only manipulated individual in her universe. Call manipulation whose scope includes at least one but not all agents "existential manipulation." Our responsibility practices are impacted in different ways by (...) universal and existential phenomena. And this is a relevant difference, especially on Strawsonian approaches to moral responsibility, which take facts about our responsibility practices to be deeply connected to the nature of responsibility itself. We argue that Strawsonian accounts of moral responsibility are immune to manipulation arguments, and no attempt to modify the scope of manipulation or determinism featured in these arguments will help incompatibilists secure their desired conclusion. (shrink)

This article argues that if panpsychism is true, then there are grounds for thinking that digitally-based artificial intelligence may be incapable of having coherent macrophenomenal conscious experiences. Section 1 briefly surveys research indicating that neural function and phenomenal consciousness may be both analog in nature. We show that physical and phenomenal magnitudes—such as rates of neural firing and the phenomenally experienced loudness of sounds—appear to covary monotonically with the physical stimuli they represent, forming the basis for an analog relationship between (...) the three. Section 2 then argues that if this is true and micropsychism—the panpsychist view that phenomenal consciousness or its precursors exist at a microphysical level of reality—is also true, then human brains must somehow manipulate fundamental microphysical-phenomenal magnitudes in an analog manner that renders them phenomenally coherent at a macro level. However, Sect. 3 argues that because digital computation abstracts away from microphysical-phenomenal magnitudes—representing cognitive functions non-monotonically in terms of digits—digital computation may be inherently incapable of realizing coherent macroconscious experience. Thus, if panpsychism is true, digital AI may be incapable of achieving phenomenal coherence. Finally, Sect. 4 briefly examines our argument’s implications for Tononi’s Integrated Information Theory theory of consciousness, which we contend may need to be supplanted by a theory of macroconsciousness as analog microphysical-phenomenal information integration. (shrink)

In this paper, I argue that Kant has a far more communitarian theory of aesthetic life than is usually acknowledged. I focus on two aspects of Kant’s theory that might otherwise be taken to support an individualist reading, namely, Kant’s emphasis on aesthetic autonomy and his characterization of judgments of taste as involving demands for agreement. I argue that the full expression of autonomy in fact requires being a member of an aesthetic community and that within such a community, judgments (...) of taste are issued as invitations to others to engage their faculties towards the goal of shared aesthetic appreciation. (shrink)

Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...) in a more primitive one – namely, the homeodynamic capacity for the “specified variation of form”. In introducing a novel type of causal power – a „structural power‟ – we claim that it is the persistence of their dynamic potential to produce a specified series of structurally adaptive morphologies which grounds organisms‟ privileged status as metaphysically “one over many” over time. (shrink)

Many philosophers hold that ‘one-instant worlds’—worlds that contain a single instant—fail to contain time. We experimentally investigate whether these worlds satisfy the folk concept of time. We found that ~50% of participants hold that there is time in such worlds. We argue that this suggests one of two possibilities. First, the population disagree about whether at least one of the A-, B-, or C-series is necessary for time, with there being a substantial sub-population for whom the presence of neither an (...) A-, B-, nor C-series, is necessary for time, and hence those folk have a radically more minimal concept of time than has been attributed to them by philosophers. Or, second, the population do not disagree about whether at least one of the A-, B-, or C-series is necessary for time, but disagree about what it takes for a world to fail to contain even a C-series. (shrink)

In this paper, I discuss whether different interpretations of the ‘aim’ of belief—both the teleological and normative interpretations—have the resources to explain certain descriptive and normative features of suspended belief (suspension). I argue that, despite the recent efforts of theorists to extend these theories to account for suspension, they ultimately fail. The implication is that we must either develop alternative theories of belief that can account for suspension, or we must abandon the assumption that these theories ought to be able (...) to account for suspension. To close, I briefly consider some of the reasons we have in favour of pursing each of these options, and I suggest that it is worth exploring the possibility that suspension is best understood as its own attitude, independently of theories of belief’s ‘aim’. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

I critically analyze Kevin Elliott’s A Tapestry of Values in order to tease out his views on the nature and status of values or value judgments in the text. I show there is a tension in Elliott’s view that is closely connected to a major lacuna in the philosophical literature on values in science: the need for a better theory of values.

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Under what conditions are material objects, such as particles, parts of a whole object? This is the composition question and is a longstanding open question in philosophy. Existing attempts to specify a non-trivial restriction on composition tend to be vague and face serious counterexamples. Consequently, two extreme answers have become mainstream: composition (the forming of a whole by its parts) happens under no or all conditions. In this paper, we provide a self-contained introduction to the integrated information theory of consciousness (...) (IIT). We show that IIT specifies a non-trivial restriction on composition: composition happens when integrated information is maximized. We compare the IIT-restriction to existing proposals and argue that the IIT-restriction has significant advantages, especially in response to the problems of vagueness and counterexamples. An appendix provides an introduction to calculating parts and wholes with a simple system. (shrink)

This paper empirically investigates the contention that the folk concept of time is a functional concept: a concept according to which time is whatever plays a certain functional role or roles. This hypothesis could explain why, in previous research, surprisingly large percentages of participants judge that there is time at worlds that contain no one-dimensional substructure of ordered instants. If it seems to participants that even in those worlds the relevant functional role is played, then this could explain why they (...) judge that there is time in those worlds. While our experiment supported the finding that participants are reticent to judge that there is no time, actually, we found no evidence that this is because they deploy a functionalist concept, at least of the kind proposed in recent research. Our findings are, however, consistent with the folk deploying a much more minimal functionalist concept according to which time is just whatever it is—regardless of its nature—that plays the role of grounding our temporal phenomenology. (shrink)

This paper argues for a view of free will that I will call the conceptual impossibility of the truth of free will error theory - the conceptual impossibility thesis. I will argue that given the concept of free will we in fact deploy, it is impossible for our free will judgements - judgements regarding whether some action is free or not - to be systematically false. Since we do judge many of our actions to be free, it follows from the (...) conceptual impossibility thesis that many of our actions are in fact free. Hence it follows that free will error theory - the view that no judgement of the form ‘action A was performed freely’ - is false. I will show taking seriously the conceptual impossibility thesis helps makes good sense of some seemingly inconsistent results in recent experimental philosophy work on determinism and our concept of free will. Further, I will present some reasons why we should expect to find similar results for every other factor we might have thought was important for free will. (shrink)

Dispositional properties are often referred to as ‘causal powers’, but what does dispositional causation amount to? Any viable theory must account for two fundamental aspects of the metaphysics of causation – the causal complexity and context sensitivity of causal interactions. The theory of mutual manifestations attempts to do so by locating the complexity and context sensitivity within the nature of dispositions themselves. But is this theory an acceptable first step towards a viable theory of dispositional causation? This paper argues that (...) the reconceptualization that the theory entails comes at too high a price, and is an unnecessary step in the wrong direction: these two central aspects concerning the metaphysics of causation can and should be accounted for in a dispositional account of causation without it. (shrink)

One debate surrounding Derk Pereboom’s (2001, 2014) four-case argument against compatibilism focuses on whether, and why, we judge manipulated agents to be neither free nor morally responsible. In this paper, we propose a novel explanation. The four-case argument features cases where an agent is the only individual in her universe who has been manipulated. Let us call manipulation whose scope includes at least one but not all agents existential manipulation. Contrast this with universal manipulation, which affects all agents within a (...) universe. We propose that we find agents in Pereboom’s manipulation cases less free and morally responsible in part because they are the target of existential manipulation. We empirically tested this hypothesis and found that people’s free will and moral responsibility judgments were sensitive to the scope of manipulation: people judged existentially manipulated agents significantly less free and responsible than universally manipulated agents. (shrink)

The paper attempts to outline the actual academic debates around the concept of PR ethics. The first part aims to show the intimate link between professionalism and ethics as well as their bearing on the reputation of the PR field. Whether and how ethical public relations are possible is the main issue analyzed in the second part of the article. The two paradigms of public relations, “the attorney-adversary system” and “the two-way symmetrical model”, are put face to face in order (...) to better understand the arguments of their proponents as to the way of approaching to the ethical matters. A main concern of the third part is to answer the question if something is wrong with situational ethics. The problem is approached in the light of virtue ethics, which is itself situational in Aristotel’s sense of the term. In the final part, the paper suggests the possibility to use W. D. Ross’s pluralist deontology as a conceptual structure from which to build a practical model for the analysis of moral dilemmas in the PR practice. (shrink)

The purpose of this essay is to offer support for the substance view of persons, the philosophical anthropology defended by Patrick Lee in his essay. In order to accomplish this the author presents a brief definition of the substance view; argues that the substance view has more explanatory power in accounting for why we believe that human persons are intrinsically valuable even when they are not functioning as such, why human persons remain identical to themselves over time, and why it (...) follows from these points that the unborn are human persons; and responds to two arguments that attempt to establish the claim that the early human being is not a unified substance until at least fourteen days after conception. (shrink)

In this paper, I defend teleological theories of belief against the exclusivity objection. I argue that despite the exclusive influence of truth in doxastic deliberation, multiple epistemic aims interact when we consider what to believe. This is apparent when we focus on the processes involved in specific instances (or concrete cases) of doxastic deliberation, such that the propositions under consideration are specified. First, I out- line a general schema for weighing aims. Second, I discuss recent attempts to defend the teleological (...) position in relation to this schema. And third, I develop and defend my proposal that multiple epistemic aims interact in doxastic deliberation—a possibility which, as of yet, has received no serious attention in the literature. (shrink)

There is an ethics of blaming the person who deserves blame. The Christian scriptures imply the following no-vengeance condition: a person should not vengefully overtly blame a wrongdoer even if she gives the wrongdoer the exact negative treatment that he deserves. I explicate and defend this novel condition and argue that it demands a revolution in our blaming practices. First, I explain the no-vengeance condition. Second, I argue that the no-vengeance condition is often violated. The most common species of blame (...) involves anger; anger conceptually includes a desire for vengeance; and there are many pleasures in payback. Third, I clarify that it is possible to blame non-vengefully in anger and highlight three good uses for anger in non-vengeful blame. Fourth, I offer two reasons that justify the divine command prohibiting vengeance, and I note that the Christian God is merely sufficient to make non-vengeance morally obligatory. Fifth, I defend the no-vengeance condition against four biblical objections. (shrink)

We take kelp as material entities immersed in a multitude of relations with other creatures (for whom kelp serves as both nourishment and shelter) and inorganic elements of the milieu it resides in, on the one hand, and as a figuration: a material-semiotic “map of contestable worlds” that encompasses entangled threads of “knowledge, practice and power” (Haraway 1997, 11) in its local and global sense, on the other. While drawing on our field notes from the congress and feminist posthumanities and (...) environmental humanities literatures (e.g. Alaimo 2016; Åsberg & Braidotti 2018; Sandilands & Erickson 2010; Iovino & Opperman 2014) – with a special focus on the so-called blue humanities/oceanic humanities (e.g. DeLoughrey 2019) – that unpack human/nonhuman relations in the context of the current environmental crisis and the accompanying “slow violence” (Nixon 2011), we mobilise a reflection on and make a proposal for “thinking with kelp” as a multi-faceted methodology of transversal and transdisciplinary knowledge production and practices: situated (Haraway 1988), enfleshed, transcorporeal (Alaimo 2010), collaborative, and committed to an ethics of multispecies response-ability (Haraway 2008). (shrink)

Forty years have passed since video-games were first made widely available to the public and subsequently playing games has become a favorite past-time for many. Players continuously engage with dynamic visual displays with success contingent on the time-pressured deployment, and flexible allocation, of attention as well as precise bimanual movements. Evidence to date suggests that both brief and extensive exposure to video-game play can result in a broad range of enhancements to various cognitive faculties that generalize beyond the original context. (...) Despite promise, video-game research is host to a number of methodological issues that require addressing before progress can be made in this area. Here an effort is made to consolidate the past 30 years of literature examining the effects of video-game play on cognitive faculties and, more recently, neural systems. Future work is required to identify the mechanism that allows the act of video-game play to generate such a broad range of generalized enhancements. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Spinoza, le spinozisme et les fondements de la sécularisation est un ouvrage dédié à la mémoire d’Emmanuel Levinas, dont l’auteur a été l’élève durant plusieurs années. Il vise, à travers une analyse d’ordre philosophique, historique, épistémologique et théologique, à mettre au jour les conditions d’émergence interrelatées du spinozisme et de la sécularisation. Pour ce faire, il souligne, entre autres, l’importance des polémiques anti-maimonidiennes, des débats sur les attributs divins, la substance, l’infini, du marranisme et de la Kabbale sur la formation (...) du spinozisme, ainsi que son rapport à la pensée contemporaine. Il mène une recherche interdisciplinaire devant permettre d’éclairer l’origine des difficultés théoriques que ce système philosophique présente. (shrink)