REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks — from the way monkeys in a troop communicate, to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this paper, we argue there is a tension between how Skyrms talks of signalling networks and his (...) formal measure of information. Although Skyrms refers to both how information flows through networks and that signals carry information, we show that his formal measure only captures the latter. We then suggest that to capture the notion of flow in signalling networks, we need to treat them as causal networks. This provides the formal tools to define a measure that does capture flow, and we do so by drawing on recent work defining causal specificity. Finally, we suggest that this new measure is crucial if we wish to explain how evolution creates information. For signals to play a role in explaining their own origins and stability, they can’t just carry information about acts: they must be difference-makers for acts. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Truth by convention, once thought to be the foundation of a uniquely promising approach to explaining our access to the truth in nonempirical domains, is nowadays widely considered an absurdity. Its fall from grace has been due largely to the influence of an argument that can be sketched as follows: our linguistic conventions have the power to make it the case that a sentence expresses a particular proposition, but they can’t by themselves generate truth; whether a given proposition is true—and (...) so whether the sentence that expresses it is true—is a matter of what the world is like, which means it isn’t a matter of convention alone. The consensus is that this argument is decisive against truth by convention. Strikingly, though, it has rarely been formulated with much precision. Here I provide a new rendering of the argument, one that reveals its structure and makes transparent just what assumptions it requires, and then I assess conventionalists’ prospects for resisting each of those assumptions. I conclude that the consensus is mistaken: contrary to what is almost universally thought, there remains a promising way forward for the conventionalist project. Along the way, I clarify conventionalists’ commitments by thinking about what truth by convention would need to be like in order for conventionalism to do the epistemological work it’s intended to do. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

A Benacerraf–Field challenge is an argument intended to show that common realist theories of a given domain are untenable: such theories make it impossible to explain how we’ve arrived at the truth in that domain, and insofar as a theory makes our reliability in a domain inexplicable, we must either reject that theory or give up the relevant beliefs. But there’s no consensus about what would count here as a satisfactory explanation of our reliability. It’s sometimes suggested that giving such (...) an explanation would involve showing that our beliefs meet some modal condition, but realists have claimed that this sort of modal interpretation of the challenge deprives it of any force: since the facts in question are metaphysically necessary and so obtain in all possible worlds, it’s trivially easy, even given realism, to show that our beliefs have the relevant modal features. Here I show that this claim is mistaken—what motivates a modal interpretation of the challenge in the first place also motivates an understanding of the relevant features in terms of epistemic possibilities rather than metaphysical possibilities, and there are indeed epistemically possible worlds where the facts in question don’t obtain. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Some sensory experiences are pleasant, some unpleasant. This is a truism. But understanding what makes these experiences pleasant and unpleasant is not an easy job. Various difficulties and puzzles arise as soon as we start theorizing. There are various philosophical theories on offer that seem to give different accounts for the positive or negative affective valences of sensory experiences. In this paper, we will look at the current state of art in the philosophy of mind, present the main contenders, critically (...) compare and contrast them. In particular, we want to examine how they handle the reason-giving power of affective states. We will look into two representationalist proposals (Evaluativism and Imperativism) and a functionalist proposal, and argue that, contrary to their own advertisements, the representationalist proposals don’t have good accounts of why and how sensory affect can motivate, rationalize, and justify subsequent behavior and intentional mental activity. We will show that our own functionalist proposal does a much better job in this regard, and that when the representationalist proposals are modified to do a better job, they fare better not because of their representationalist credentials but due to their functionalist ones. (shrink)

In domains as disparate as playing Go and predicting the structure of proteins, artificial intelligence (AI) technologies have begun to perform at levels beyond which any humans can achieve. Does this fact represent something lamentable? Does superhuman AI performance somehow undermine the value of human achievements in these areas? Go grandmaster Lee Sedol suggested as much when he announced his retirement from professional Go, blaming the advances of Go-playing programs like AlphaGo for sapping his will to play the game at (...) a high level. In this paper, I attempt to make sense of Sedol’s lament. I consider a number of ways that the existence of superhuman-performing AI technologies could undermine the value of human achievements. I argue there is very little in the nature of the technology itself that warrants such despair. (Compare: does the existence of a fighter jet undermine the value of being the fastest human sprinter?) But I also argue there are several more localized domains where these technologies threaten to displace human beings from being able to achieve valuable things at all. This is a particular worry for those in unequal societies, I argue, given the difficulty of many achievements and the corresponding amount of resources needed to achieve great things. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

One common attitude toward abstract objects is a kind of platonism: a view on which those objects are mind-independent and causally inert. But there's an epistemological problem here: given any naturalistically respectable understanding of how our minds work, we can't be in any sort of contact with mind-independent, causally inert objects. So platonists, in order to avoid skepticism, tend to endorse epistemological theories on which knowledge is easy, in the sense that it requires no such contact—appeals to Boghossian’s notion of (...) epistemic analyticity are particularly common here, as are appeals to some broadly pragmatic account of the good standing of basic beliefs. I argue, though, that these appeals are hopeless: an argument adapted from the Benacerraf–Field challenge shows that, even if some such theory can deliver the verdict that our beliefs about abstract objects have some prima facie good standing, this good standing will inevitably be defeated. (shrink)

The notion of a genetic program has been widely criticized by both biologists and philosophers. But the debate has revolved around a narrow conception of what programs are and how they work, and many criticisms are linked to this same conception. To remedy this, I outline a modern and more apt idea of a program that possesses many of the features critics thought missing from programs. Moving away from over-simplistic conceptions of programs opens the way to a more fruitful interplay (...) of ideas between the complexity of biology and our most complex engineering discipline. (shrink)

Sensitivity has sometimes been thought to be a highly epistemologically significant property, serving as a proxy for a kind of responsiveness to the facts that ensure that the truth of our beliefs isn’t just a lucky coincidence. But it's an imperfect proxy: there are various well-known cases in which sensitivity-based anti-luck conditions return the wrong verdicts. And as a result of these failures, contemporary theorists often dismiss such conditions out of hand. I show here, though, that a sensitivity-based understanding of (...) epistemic luck can be developed that respects what was attractive about sensitivity-based approaches in the first place but that's immune to these failures. (shrink)

We argue that the concept of practical wisdom is particularly useful for organizing, understanding, and improving human-machine interactions. We consider the relationship between philosophical analysis of wisdom and psychological research into the development of wisdom. We adopt a practical orientation that suggests a conceptual engineering approach is needed, where philosophical work involves refinement of the concept in response to contributions by engineers and behavioral scientists. The former are tasked with encoding as much wise design as possible into machines themselves, as (...) well as providing sandboxes or workspaces to help various stakeholders build practical wisdom in systems that are sufficiently realistic to aid transferring skills learned to real-world use. The latter are needed for the design of exercises and methods of evaluation within these workspaces, as well as ways of empirically assessing the transfer of wisdom from workspace to world. Systematic interaction between these three disciplines (and others) is the best approach to engineering wisdom for the machine age. (shrink)

Which rules should guide our reasoning? Human reasoners often use reasoning shortcuts, called heuristics, which function well in some contexts but lack the universality of reasoning rules like deductive implication or inference to the best explanation. Does it follow that human reasoning is hopelessly irrational? I argue: no. Heuristic reasoning often represents human reasoners reaching a local rational maximum, reasoning more accurately than if they try to implement more “ideal” rules of reasoning. I argue this is a genuine rational achievement. (...) Our ideal rational advisors would advise us to reason with heuristic rules, not more complicated ideal rules. I argue we do not need a radical new account of epistemic norms to make sense of the success of heuristic reasoning. (shrink)

Representationalism is the view that the phenomenal character of experiences is identical to their representational content of a certain sort. This view requires a strong transparency condition on phenomenally conscious experiences. We argue that affective qualities such as experienced pleasantness or unpleasantness are counter-examples to the transparency thesis and thus to the sort of representationalism that implies it.

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

I argue that Quinean naturalists’ holism-based arguments against analyticity and apriority are more difficult to resist than is generally supposed, for two reasons. First, although opponents of naturalism sometimes dismiss these arguments on the grounds that the holistic premises on which they depend are unacceptably radical, it turns out that the sort of holism required by these arguments is actually quite minimal. And second, although it’s true, as Grice and Strawson pointed out long ago, that these arguments can succeed only (...) if there isn’t any principled criterion for meaning change, such a criterion turns out to be hard to come by. David Chalmers has recently argued that such a criterion must exist, since the norms governing belief revision are subject to obvious exceptions that can be explained only by appeal to meaning change. But this, I argue, is incorrect: if choices about how to use language are themselves rationally assessable, then there are no such exceptions to be explained. To show that this is so, I formulate a new kind of coherence norm that may be useful for reasoning formally about the relationship between meaning and evidence. (shrink)

I identify an undertheorized problem with decisions we make with the aid of algorithms: the problem of inauthenticity. When we make decisions with the aid of algorithms, we can make ones that go against our commitments and values in a normatively important way. In this paper, I present a framework for algorithm-aided decision-making that can lead to inauthenticity. I then construct a taxonomy of the features of the decision environment that make such outcomes likely, and I discuss three possible solutions (...) to the problem. (shrink)

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

The purpose of this project is to argue that we possess a minimal self. It will demonstrate that minimal selfhood arrives early in our development and continues to remain and influence us throughout our entire life. There are two areas of research which shape my understanding of the minimal self: phenomenology and enactivism. Phenomenology emphasizes the sense of givenness, ownership, or mineness that accompanies all of our experiences. Enactivism says there is a sensorimotor coupling that occurs between us and the (...) environment in a way which modulates the dynamic patterns of our self development; the laying down of these basic patterns helps make us who we are and gives rise to the phenomenological, experiential mineness. Drawing on these two core ideas, I will be arguing for a Phenomenological-Enactive Minimal Self. I will be emphasizing the role of the body and the role of affects as the most important components relevant to understanding minimal selfhood. Put more concretely, the set of conditions which constitute the PEMS view are: The minimal self is the experiential subject; the minimal sense of self is present whenever there is awareness. It is the subjectivity of experience, the sense of mineness, or givenness which our experiences contain. The phenomenological part of the PEMS view turns on the idea of a bodily and dynamic integration of sensorimotor coupling and affective experience. It is, ontologically speaking, the lived body in enactive engagement with the environment. It is this embodied subject which anchors and forms the foundation for the later ‘narrative’ self, which emerges from it and which is continually influenced by it. It is the subject enactively engaged with others, dependent on sensorimotor processes and affects. We have an identity, but it emerges from relational and dynamic processes. (shrink)

While there has been significant discussion in the health sciences and ethics literatures about problems associated with publication practices (e.g., ghost- and gift-authorship, conflicts of interest), there has been relatively little practical guidance developed to help researchers determine how they should fairly allocate credit for multi-authored publications. Fair allocation of credit requires that participating authors be acknowledged for their contribution and responsibilities, but it is not obvious what contributions should warrant authorship, nor who should be responsible for the quality and (...) content of the scientific research findings presented in a publication. In this paper, we review arguments presented in the ethics and health science literatures, and the policies or guidelines proposed by learned societies and journals, in order to explore the link between author contribution and responsibility in multi-author multidisciplinary health science publications. We then critically examine the various procedures used in the field to help researchers fairly allocate authorship. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

Robin McKenna’s excellent Non-Ideal Epistemology is, among other things, a testament to restraint. McKenna does not want to unnecessarily inflame tensions between ideal and non-ideal theorists in epistemology. Often ideal and non-ideal projects are aimed at different target domains and not in tension with one another (though not always; e.g. McKenna 2023, ch. 6, especially pp. 112-21). In this commentary, I will have much less tact. I sketch a route by which the non-ideal epistemologist might become more belligerent towards their (...) ideal counterparts. I do this by focusing on an area that McKenna mostly sets aside: non-ideal individual epistemology. (shrink)

Implicit attitudes are mental states posited by psychologists to explain behaviors including implicit racial and gender bias. In this paper I investigate the belief view of the implicit attitudes, on which implicit attitudes are a kind of implicit belief. In particular, I focus on why implicit attitudes, if they are beliefs, are often resistant to updating in light of new evidence. I argue that extant versions of the belief view do not give a satisfactory account of this phenomenon. This is (...) because proponents of the belief view have focused on overly narrow explanations of recalcitrance in terms of belief storage. Expanding the focus of the belief view to the kinds of irrational and arational transitions between beliefs and other mental states provides compelling (if preliminary) explanations of recalcitrance. (shrink)

The thesis that agents should calibrate their beliefs in the face of higher-order evidence—i.e., should adjust their first-order beliefs in response to evidence suggesting that the reasoning underlying those beliefs is faulty—is sometimes thought to be in tension with Bayesian approaches to belief update: in order to obey Bayesian norms, it’s claimed, agents must remain steadfast in the face of higher-order evidence. But I argue that this claim is incorrect. In particular, I motivate a minimal constraint on a reasonable treatment (...) of the evolution of self-locating beliefs over time and show that calibrationism is compatible with any generalized Bayesian approach that respects this constraint. I then use this result to argue that remaining steadfast isn’t the response to higher-order evidence that maximizes expected accuracy. (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)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Hilary Greaves and David Wallace argue that conditionalization maximizes expected accuracy and so is a rational requirement, but their argument presupposes a particular picture of the bridge between rationality and accuracy: the Best-Plan-to-Follow picture. And theorists such as Miriam Schoenfield and Robert Steel argue that it's possible to motivate an alternative picture—the Best-Plan-to-Make picture—that does not vindicate conditionalization. I show that these theorists are mistaken: it turns out that, if an update procedure maximizes expected accuracy on the Best-Plan-to-Follow picture, it's (...) guaranteed to maximize expected accuracy on the Best-Plan-to-Make picture as well, in which case moving from the former to the latter can't help us avoid the conclusion that conditionalization is a rational requirement. If there's a problem with Greaves and Wallace’s argument, it must lie elsewhere. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

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)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

We offer a sceptical examination of a thesis recently advanced in a monograph published by Princeton University Press, entitled Greek Buddha: Pyrrho’s Encounter with Early Buddhism in Central Asia. In this dense and probing work, Christopher I. Beckwith, a professor of Central Eurasian studies at Indiana University, Bloomington, argues that Pyrrho of Elis adopted a form of early Buddhism during his years in Bactria and Gandhāra, and that early Pyrrhonism must be understood as a sect of early Buddhism. In making (...) his case Beckwith claims that virtually all scholars of Greek, Indian, and Chinese philosophy have been operating under flawed assumptions and with flawed methodologies, and so have failed to notice obvious and undeniable correspondences between the philosophical views of the Buddha and of Pyrrho. In this study we take Beckwith’s proposal and challenge seriously, and we examine his textual basis and techniques of translation, his methods of examining passages, his construal of problems and his reconstruction of arguments. We find that his presuppositions are contentious and doubtful, his own methods are extremely flawed, and that he draws unreasonable conclusions. Although the result of our study is almost entirely negative, we think it illustrates some important general points about the methodology of comparative philosophy. (shrink)

This is the first book-length philosophical study of Husserl’s transcendental phenomenology and Freud’s theory of the unconscious. The book investigates the possibility for Husserl’s transcendental phenomenology to clarify Freud’s concept of the unconscious with a focus on the theory of repression as its centre. Repression is the unconscious activity of pushing something away from consciousness, while making sure that it remains active as something foreign within us. How this is possible is the main problem addressed in the work. Unlike previous (...) literature (including Ricœur, Merleau-Ponty and Derrida) this book makes full use of the resources of genetic phenomenology and passivity in the attempt to clarify the Freudian unconscious. The central argument developed is that the structure of the lebendige Gegenwart as the core of Husserl’s theory of passivity consists of preliminary forms of bodily kinaesthesia, feelings and drives in a constantly ongoing process where repression occurs as a necessary part of all constitution. The clarification of Freudian repression thus takes place by showing how it presupposes a broad conception of consciousness such as that presented by Husserl’s genetic phenomenology. By arguing that “repression” is central to any philosophical account of subjectivity, this book takes on the most distinct challenge to philosophy posed by Freud. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (shrink)

If media studies are to become established as a genuine science, then it needs to be determined what the subject matter of this science is to be. I propose a specification of this subject matter as consisting in: 1. the new sorts of digital entities that have been added to social reality through the invention of the digital computer, and 2. the new sorts of interactions involving human beings which such entities make possible. I support this proposal by examining examples (...) of some of the ways in which the digital products of emerging media differ from entities of other sorts. I then draw consequences from this examination to demonstrate how these products mark out a new realm within the larger domain of social ontology. (shrink)

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which (...) could afford to be ignored. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

In his book The Sensory Order, Hayek anticipates many of the central ideas behind what we now call the connectionist paradigm, and develops on this basis a theory of the workings of the human mind that extends the thinking of Hume and Mach. He shows that the idea of neural networks is can be applied not only in psychology and neurology but also in the sphere of economics. For the mind, from the perspective of The Sensory Order, is a dynamic, (...) relational affair that is in many respects analogous to a market process. The mind, as Hayek puts it, is a 'continuous stream of impulses, the significance of each and every contribution of which is determined by the place in the pattern of channels through which they flow' , so that the flow of representative neural impulses can be compared 'to a stock of capital being nourished by inputs and giving a continuous stream of outputs'. (shrink)

There is something puzzling about statistical evidence. One place this manifests is in the law, where courts are reluctant to base affirmative verdicts on evidence that is purely statistical, in spite of the fact that it is perfectly capable of meeting the standards of proof enshrined in legal doctrine. After surveying some proposed explanations for this, I shall outline a new approach – one that makes use of a notion of normalcy that is distinct from the idea of statistical frequency. (...) The puzzle is not, however, merely a legal one. Our unwillingness to base beliefs on statistical evidence is by no means limited to the courtroom, and is at odds with almost every general principle that epistemologists have proposed as to how we ought to manage our beliefs. (shrink)

Many epistemologists have responded to the lottery paradox by proposing formal rules according to which high probability defeasibly warrants acceptance. Douven and Williamson present an ingenious argument purporting to show that such rules invariably trivialise, in that they reduce to the claim that a probability of 1 warrants acceptance. Douven and Williamson’s argument does, however, rest upon significant assumptions – amongst them a relatively strong structural assumption to the effect that the underlying probability space is both finite and uniform. In (...) this paper, I will show that something very like Douven and Williamson’s argument can in fact survive with much weaker structural assumptions – and, in particular, can apply to infinite probability spaces. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)