In this article, I explore how researchers’ metaphysical commitments can be conducive—or unconducive—to progress in animal cognition research. The methodological dictum known as Morgan’s Canon exhorts comparative psychologists to countenance the least mentalistic fair interpretation of animal actions. This exhortation has frequently been misread as a blanket condemnation of mentalistic interpretations of animal behaviors that could be interpreted behavioristically. But Morgan meant to demand only that researchers refrain from accepting default interpretations of (apparent) actions until other fair interpretations have been (...) duly considered. The Canon backfired largely because of Morgan’s background metaphysical commitment to a univocal, hierarchical, and anthropocentric account of cognitive architecture. I make the case that, going forward, comparative psychologists would do well to pair judicious use of Morgan’s Canon with an openness to the existence of non-humanlike animal minds comprising phenomena belonging to distinct cognitive and folk psychological ontologies. And I argue that this case gives us pragmatic reason to reconcile deep—e.g., psychofunctionalist—and superficial—e.g., dispositionalist—approaches to the metaphysics of belief. (shrink)

I have proposed wedding the theories of belief known as dispositionalism and interpretivism. Krzysztof Poslajko objects that dispositionalism does just fine on its own and, moreover, is better off without interpretivism’s metaphysical baggage. I argue that Poslajko is wrong: in order to secure a principled criterion for individuating beliefs, dispositionalism must either collapse into psychofunctionalism (or some other non-superficial theory) or accept interpretivism’s hand in marriage.

What’s so good about John Ames? The narrator of Marilynne Robinson’s Gilead has been much admired, but it’s far from obvious why. His life is quiet and unassuming, and has for the most part been uneventful in the extreme. In this chapter I draw on Iris Murdoch’s moral philosophy to explain the moral arc of the novel, and suggest that the novel in turn can shed light on Murdoch’s key ethical ideas. What is so notable about John Ames, I suggest, (...) is his commitment to seeing the world justly and lovingly—a commitment which for Murdoch is at the heart of virtuous agency. (shrink)

Philosophers of mind (from eliminative materialists to psychofunctionalists to interpretivists) generally assume that a normative ideal delimits which mental phenomena exist (though they disagree about how to characterize the ideal in question). This assumption is dubious. A comprehensive ontology of mind includes some mental phenomena that are neither (a) explanatorily fecund posits in any branch of cognitive science that aims to unveil the mechanistic structure of cognitive systems nor (b) ideal (nor even progressively closer to ideal) posits in any given (...) folk psychological practice. Indeed, one major function of scientific psychology has been (and will be) to introduce just such (normatively suboptimal but real) mental phenomena into folk psychological taxonomies. The development and public dissemination of IQ research over the course of the 20th century is a case in point. (shrink)

The mind and brain sciences influence how human beings understand one another. Histories of the concepts of repression, implicit bias, ADHD, IQ, and personhood reveal that scientific psychology has played a role, not just in shaping people's thinking about minds, but also (and thereby) in shaping minds themselves. These case studies may thus be seen as supporting the contentious thesis that science aids in the social construction of minds. Three considerations are relevant to determining how seriously we should take that (...) contention: (1) to what extent was it inevitable that socially sophisticated animals would come to describe minds in the ways that 21st century humans do?; (2) to what extent do human sociocognitive practices accurately describe the inherent structure of the mind?; (3) to what extent can historical stability in descriptions of minds be chalked up to the fact that people are accurately describing the structure of the mind? (shrink)

This article reconsiders the relationship between interpretivism about belief and normative standards. Interpretivists have traditionally taken beliefs to be fixed in relation to norms of interpretation. However, recent work by philosophers and psychologists reveals that human belief attribution practices are governed by a rich diversity of normative standards. Interpretivists thus face a dilemma: either give up on the idea that belief is constitutively normative or countenance a context-sensitive disjunction of norms that constitute belief. Either way, interpretivists should embrace the intersubjective (...) indeterminacy of belief. (shrink)

Introductory but opinionated essay on what (and why) minds are.

Anselm’s ontological argument is an argument for the existence of God. This paper presents Iris Murdoch’s ontological argument for the existence of the Good. It discusses her interpretation of Anselm’s argument, her distinctive appropriation of it, as well as some of the merits of her version of the argument. In doing so, it also shows how the argument integrates some key Murdochian ideas: morality’s wide scope, the basicness of vision to morality, moral realism, and Platonism.

In Go Set a Watchman, Harper Lee reveals that American man of integrity Atticus Finch harbors deep-seated racist beliefs. Bob Ewell, Finch's nemesis in To Kill a Mockingbird, harbors the same beliefs. But the two men live out their shared racist beliefs in dramatically different fashions. This article argues that extant dispositionalist accounts of belief lack the tools to accommodate Finch and Ewell's divergent styles of believing. It then draws on literary and philosophical character studies to construct the required tools.

In a recent article in this journal, Krzysztof Poslajko reconstructs—and endorses as probative—a dilemma for interpretivism first posed by Alex Byrne. On the first horn of the dilemma, the interpretivist takes attitudes to emerge in relation to an ideal interpreter (and thus loses any connection with actual folk psychological practices). On the second horn, the interpretivist takes attitudes to emerge in relation to individuals’ judgements (and thus denies the possibility of error). I show that this is a false dilemma. By (...) taking a model-theoretic approach to folk psychology, and marrying interpretivism with dispositionalism, interpretivists can viably reject the notion of an ideal (or canonical) interpreter—and relativize attitudes to actual lay interpreters—without taking on board the unacceptable epistemological consequences of allowing that attitudes are judgement-dependent. (shrink)

Many recent philosophers have been tempted by epistemic partialism. They hold that epistemic norms and those of friendship constitutively conflict. In this paper, I suggest that underpinning this claim is the assumption that friendship is not an epistemically rich state, an assumption that even opponents of epistemic partiality have not questioned. I argue that there is good reason to question this assumption, and instead regard friendship as essentially involving knowledge of the other. If we accept this account of friendship, the (...) possibility of epistemic partialism does not arise. (shrink)

Double dissociations between perceivable colors and physical properties of colored objects have led many philosophers to endorse relationalist accounts of color. I argue that there are analogous double dissociations between attitudes of belief—the beliefs that people attribute to each other in everyday life—and intrinsic cognitive states of belief—the beliefs that some cognitive scientists posit as cogs in cognitive systems—pitched at every level of psychological explanation. These dissociations provide good reason to refrain from conflating attitudes of belief with intrinsic cognitive states (...) of belief. I suggest that interpretivism provides an attractive account of the former. Like colors, attitudes of belief evolved to be ecological signifiers, not cogs in cognitive systems. (shrink)

Many psychologists studying lay belief attribution and behavior explanation cite Donald Davidson in support of their assumption that people construe beliefs as inner causes. But Davidson’s influential argument is unsound; there are no objective grounds for the intuition that the folk construe beliefs as inner causes that produce behavior. Indeed, recent experimental work by Ian Apperly, Bertram Malle, Henry Wellman, and Tania Lombrozo provides an empirical framework that accords well with Gilbert Ryle’s alternative thesis that the folk construe beliefs as (...) patterns of living that contextualize behavior. (shrink)

In a recent paper, Strabbing (2020) argues that forgiveness is openness to reconciliation relative to a relationship level. In this paper, we argue that the openness-to-reconciliation account of forgiveness does not constitute an improvement on the forswearing-resentment account. We argue that it does not fit well with our ordinary practices of forgiving and cannot allow for plausible cases of forgiveness without reconciliation. We also argue that the features Strabbing identifies as distinct advantages of her account are features of the forswearing-resentment (...) account as well. (shrink)

Two doxastically significant demands of friendship have been discussed in recent literature, a demand to be epistemically partial and a demand to take our friends seriously. Though less discussed than epistemic partialism, I suggest that the demand to take our friends seriously is motivated by similar cases and considerations, and can avoid key objections to epistemic partialism that have been raised. I further suggest that it does justice to what we care about in friendship, and thus is to be preferred.

Is calculation possible without language? Or is the human ability for arithmetic dependent on the language faculty? To clarify the relation between language and arithmetic, we studied numerical cognition in speakers of Mundurukú, an Amazonian language with a very small lexicon of number words. Although the Mundurukú lack words for numbers beyond 5, they are able to compare and add large approximate numbers that are far beyond their naming range. However, they fail in exact arithmetic with numbers larger than 4 (...) or 5. Our results imply a distinction between a nonverbal system of number approximation and a language-based counting system for exact number and arithmetic. (shrink)

A pluralistic approach to folk psychology must countenance the evaluative, regulatory, predictive, and explanatory roles played by attributions of intelligence in social practices across cultures. Building off of the work of the psychologist Robert Sternberg and the philosophers Gilbert Ryle and Daniel Dennett, I argue that a relativistic interpretivism best accounts for the many varieties of intelligence that emerge from folk discourse. To be intelligent is to be comparatively good at solving intellectual problems that an interpreter deems worth solving.

Recent discussions of moral testimony have focused on the acceptability of forming beliefs on the basis of moral testimony, but there has been little acknowledgement of the limits to testimony's capacity to convey moral knowledge. In this paper I outline one such limit, drawing on Iris Murdoch's conception of private moral concepts. Such concepts, I suggest, plausibly play an important role in moral thought, and yet moral knowledge expressed in them cannot be testimonially acquired.

Psychometric g—a statistical factor capturing intercorrelations between scores on different IQ tests—is of theoretical interest despite being a low-fidelity model of both folk psychological intelligence and its cognitive/neural underpinnings. Psychometric g idealizes away from those aspects of cognitive/neural mechanisms that are not explanatory of the relevant variety of folk psychological intelligence, and it idealizes away from those varieties of folk psychological intelligence that are not generated by the relevant cognitive/neural substrate. In this manner, g constitutes a high-fidelity bridge model of (...) the relationship between its two targets and, thereby, helps demystify the relationship between folk and scientific psychology. (shrink)

The aim of this paper is to evaluate the level of gender bias in Aristotle’s Generation of Animals while exercising due care in the analysis of its arguments. I argue that while the GA theory is clearly sexist, the traditional interpretation fails to diagnose the problem correctly. The traditional interpretation focuses on three main sources of evidence: (1) Aristotle’s claim that the female is, as it were, a “disabled” (πεπηρωμένον) male; (2) the claim at GA IV.3, 767b6-8 that females are (...) a departure from the kind; and (3) Aristotle’s supposed claim at GA IV.3, 768a21-8 that the most ideal outcome of reproduction is a male offspring that perfectly resembles its father. I argue that each of these passages has either been misunderstood or misrepresented by commentators. In none of these places is Aristotle suggesting that females are imperfect members of the species or that they result from the failure to achieve some teleological goal. I defend the view that the GA does not see reproduction as occurring for the sake of producing males; rather, what sex an embryo happens to become is determined entirely by non-teleological forces operating through material necessity. This interpretation is consistent with Aristotle’s view in GA II.5 that females have the same soul as the male (741a7) as well as the argument in Metaphysics X.9 that sexual difference is not part of the species form but is an affection (πάθος) arising from the matter (1058b21-4). While the traditional interpretation has tended to exaggerate the level of sexism in Aristotle’s
developmental biology, the GA is by no means free of gender bias as some recent scholarship has claimed. In the final section of the paper I point to one passage where Aristotle clearly falls back on sexist assumptions in order to answer the difficult question, “Why are animals divided into sexes?”. I argue that this passage in particular poses a serious challenge
to anyone attempting to absolve Aristotle’s developmental biology of the charge of sexism. (shrink)

In this paper I explore Aristotle’s views on natural kinds and the compatibility of pluralism and realism, a topic that has generated considerable interest among contemporary philosophers. I argue that, when it came to zoology, Aristotle denied that there is only one way of organizing the diversity of the living world into natural kinds that will yield a single, unified system of classification. Instead, living things can be grouped and regrouped into various cross-cutting kinds on the basis of objective similarities (...) and differences in ways that subserve the explanatory context. Since the explanatory aims of zoology are diverse and variegated, the kinds it recognizes must be equally diverse and variegated. At the same time, there are certain constraints on which kinds can be selected. And those constraints derive more from the causal structure of the world than from the proclivities of the classifier (hence the realism). This distinguishes Aristotle’s version of pluralistic realism from those contemporary versions (like Dupré’s “promiscuous realism”) that treat all or most classifications of a given domain as equally legitimate and not just a sub-set of kinds recognized by the science that studies it. By contrast, Aristotle privileges scientifically important kinds on the basis of their role in causal investigations. On this picture natural kinds are those kinds with the sort of causal structure that allows them to enter into scientific explanations. In the final section I argue that Aristotle’s zoology should remain of interest to philosophers and biologists alike insofar as it combines a pluralistic form of realism with a rank-free approach to classification. (shrink)

This book consolidates emerging research on Aristotle's science and ethics in order to explore the extent to which the concepts, methods, and practices he developed for scientific inquiry and explanation are used to investigate moral phenomena. Each chapter shows, in a different way, that Aristotle's ethics is much more like a science than it is typically represented. The upshot of this is twofold. First, uncovering the links between Aristotle's science and ethics promises to open up new and innovative directions for (...) research into his moral philosophy. Second, showing why Aristotle thinks ethics can never be fully assimilated to the model of science will help shed new light on his views about the limits of science. The volume thus promises to make a significant contribution to our understanding of the epistemological, metaphysical, and psychological foundations of Aristotle's ethics. (shrink)

In this paper I address an important question in Aristotle’s biology, What are the causal mechanisms behind the transmission of biological form? Aristotle’s answer to this question, I argue, is found in Generation of Animals Book 4 in connection with his investigation into the phenomenon of inheritance. There we are told that an organism’s reproductive material contains a set of "movements" which are derived from the various "potentials" of its nature (the internal principle of change that initiates and controls development). (...) These movements, I suggest, function as specialized vehicles for communicating the parts of the parent’s heritable form during the act of reproduction. After exploring the details of this mechanism, I then take up Aristotle’s theory of inheritance proper. At the heart of the theory are three general principles (or 'laws') that govern the interactions between the maternal and paternal movements, the outcome of which determines the pattern of inheritance for the offspring. Although this paper is primarily aimed at providing a detailed analysis of Aristotle’s account of inheritance, the results of that analysis have implications for other areas of Aristotle’s biology. One of the most interesting of these is the question of whether Aristotle’s biology is anti-evolutionary (as traditionally assumed) or whether (as I argue) it leaves room for a theory of evolution by natural selection, even if Aristotle himself never took that step. (shrink)

Historically embryogenesis has been among the most philosophically intriguing phenomena. In this paper I focus on one aspect of biological development that was particularly perplexing to the ancients: self-organisation. For many ancients, the fact that an organism determines the important features of its own development required a special model for understanding how this was possible. This was especially true for Aristotle, Alexander, and Simplicius, who all looked to contemporary technology to supply that model. However, they did not all agree on (...) what kind of device should be used. In this paper I explore the way these ancients made use of technology as a model for the developing embryo. I argue that their different choices of device reveal fundamental differences in the way each thinker understood the nature of biological development itself. In the final section of the paper I challenge the traditional view (dating back to Alexander's interpretation of Aristotle) that the use of automata in GA can simply be read off from their use in the de motu. (shrink)

This article intervenes in recent formalist and ecocritical debates, drawing on the philosophy of Charles Darwin and Édouard Glissant to develop an ecopoetic theory of relational form. Gathering perspectives from ecocriticism and new materialism, literary criticism and comparative literature, the history and philosophy of science, postcolonial theory, critical race theory, and Black studies, it reads form as an interdisciplinary object that is part of the world, rather than an imposed feature of human language or perception. In this way, it produces (...) a relational theory of form that is not hylomorphic or defined through the relation between form and content but, rather, is defined by the relation between a content and extant and, so, an interaction of relation and repetition. Drawing on the history of ecological science, it further explores how forms combine, how they amplify and interfere with each other, and how they support relations of harm and care. Finally, it uses this ecopoetic theory of form to read the histories of racial violence and migration in Matthew Arnold’s “Dover Beach” (1867) and Helen Oyeyemi’s White Is for Witching (2009). (shrink)

What is common to all instances of friendship? Given their seemingly heterogeneous character, Phelan (2019. “Rethinking Friendship.” Inquiry) suggests that friendships are relationships that result from collaborative norm-manipulation. In this paper, I suggest that this proposal fails to account for all friendships without relying on the notion of some kind of care.

A concise review of skeptician in the Carterian model with a discussion of the reframing of the Cartesian paradigm by John McDowell in the 20th century.

It has become somewhat of a platitude to call Aristotle the first epigenesist insofar as he thought form and structure emerged gradually from an unorganized, amorphous embryo. But modern biology now recognizes two senses of “epigenesis”. The first is this more familiar idea about the gradual emergence of form and structure, which is traditionally opposed to the idea of preformationism. But modern biologists also use “epigenesis” to emphasize the context-dependency of the process itself. Used in this sense development is not (...) simply the unfolding of a pre-determined sequence of changes specified in advance by the organism’s genotype. It is also sensitive to inputs from the internal and external environment, which help determine in real-time which of the many potential developmental pathways are actualized during the process. Within this paradigm developing embryos are viewed as dynamic and responsive systems that react to inputs from the internal and external environment ‘on the fly’. In this paper I argue that, while Aristotle was an epigenesist in the first sense, he would have rejected epigenesis in the more modern sense. First, Aristotle’s model of choice for a developing embryo is the automaton that executes a set of preset movements (GA 734b9-13, 741b7-15). The automatons he has in mind are not dynamic AI systems capable of modifying their behaviour on the fly in response to environmental cues but completely deterministic mechanisms whose movements are fixed by their original design. Second, given Aristotle’s views about the different kinds of causal powers there are, it looks like only intentional agents endowed with actual decision-making powers could be capable of the sort of plasticity at the core of a more dynamic epigenesis. For that kind of epigenesis requires powers for alternative outcomes, and Aristotle is explicit that such powers require rational desires (προαίρεσις) that control which of those alternatives to bring about. If I am right, then he could not have made sense of the idea of a developing embryo (as a non-intentional system) making adjustments to its phenotype on the fly in response to emerging problems and opportunities, given the conceptual resources available to him. (shrink)

This article offers an interpretation of Descartes’s method of doubt. It wields an examination of Descartes’s pedagogy—as exemplified by The Search for Truth as well as the Meditations—to make the case for the sincerity (as opposed to artificiality) of the doubts engendered by the First Meditation. Descartes was vigilant about balancing the need to use his method of doubt to achieve absolute certainty with the need to compensate for the various foibles of his scholastic and unschooled readers. Nevertheless, Descartes endeavored (...) to instill willful, context-independent, universal doubt across his readership. If all goes well, readers of the Meditations are like method actors; the Meditator is the character they are meant to bring to life, via the method of meditating on reasons for doubt. The article concludes with the suggestion that Descartes was the same kind of skeptic as the early Academic skeptics Arcesilaus and Carneades. (shrink)

In this paper I examine the role of optimality reasoning in Aristotle’s natural science. By “optimality reasoning” I mean reasoning that appeals to some conception of “what is best” in order to explain why things are the way they are. We are first introduced to this pattern of reasoning in the famous passage at Phaedo 97b8-98a2, where (Plato’s) Socrates invokes “what is best” as a cause (aitia) of things in nature. This passage can be seen as the intellectual ancestor of (...) Aristotle’s own principle, expressed by the famous dictum “nature does nothing in vain but always what is best for the substance from among the possibilities concerning each kind of animal” (Progression of Animals II, 704b12-18). The paper is focused around exploring three questions that arise in connection with Aristotle’s use of this optimality principle: (1) How do we understand the concept of “the best” at work in the principle? (2) How does Aristotle conceive of “the range of possibilities”? And, finally, (3) what role does optimality reasoning play in Aristotle’s natural science? Is it a special form of demonstration in which the optimality principle functions as one of its premises, or is it a heuristic device that helps uncover those causally relevant features of a natural substances that ultimately serve as middle terms in demonstrations? In the final section I return to the comparison between Plato and Aristotle and argue that, while both see the natural world as the product of an optimizing agent and while both see this assumption as licensing a pattern of reasoning that appeals to a certain conception of “the best”, they disagree fundamentally over what the optimization agent is and how it operates. Thus, despite their general agreement, it would be a mistake to think that Aristotle simply took over Plato’s use of optimality reasoning without significant modifications. (shrink)

Descartes held the following view of declarative memory: to remember is to reconstruct an idea that you intellectually recognize as a reconstruction. Descartes countenanced two overarching varieties of declarative memory. To have an intellectual memory is to intellectually reconstruct a universal idea that you recognize as a reconstruction, and to have a sensory memory is to neurophysiologically reconstruct a particular idea that you recognize as a reconstruction. Sensory remembering is thus a capacity of neither ghosts nor machines, but only of (...) human beings qua mind-body unions. This interpretation unifies Descartes’s various remarks (and conspicuous silences) about remembering, from the 1628 Rules for the Direction of the Mind through the suppressed-in-1633 Treatise of Man to the 1649 Passions of the Soul. It also rebuts a prevailing thesis in the current secondary literature—that Cartesian critters can remember—while incorporating the textual evidence for that thesis—Descartes’s detailed descriptions of the corporeal mechanisms that construct sensory memories. (shrink)

The intellectual history of evolutionary theory really does not begin in earnest until the late seventeenth/early eighteenth century. Prior to that, the idea that species might have evolved over time was not a serious possibility for most naturalists and philosophers. There is certainly no substantive debate in antiquity about evolution in the modern sense. There were really only two competing explanations for how living things came to have the parts they do: design or blind chance. Ancient Greek Atomism, for example, (...) taught that all composite bodies, including living things, are generated through the random collision of atoms as they rebel and move in the void. Plato and Aristotle both dismissed this possibility on the grounds that living things are too complex and too well-adapted to be products of chance. This eventually became the central premise in Galen’s own Argument from Design. That species forms might have gradually evolved over time by a process of natural selection was not seen as a plausible alternative. Of course, such a theory had been proposed by Empedocles in the fifth century BCE. But because his theory still relied heavily on chance, it was not taken seriously by any of the later ancient Greek or Roman thinkers. My aim in this paper is to investigate the reasons why evolutionary thinking failed to gain momentum in antiquity after its introduction by Empedocles. (shrink)

A general article discussing philosophical issues arising in connection with Aristotle's "Generation of Animals" (Chapter from Blackwell's Companion to Aristotle).

If mourning is a proof of value, how could it be appropriate to move on when one has truly loved and valued someone? Assuming that it is appropriate to value others extremely highly – perhaps even infinitely – how could it ever make sense for one’s grief to abate? Do loss and proper mourning thus present us with a choice between living well and loving well? This paper aims to vindicate the pressing nature of these questions while arguing that we (...) do not need to choose between living well and loving well. It discusses how these questions become pressing, some empirical research seeming to imply that humans do not tend to love well at all, and finally, offers an explanation of why ceasing to mourn need not be a failure of love. In particular, we offer an account of how ceasing to mourn can be a fitting response to the object of love, as well as compatible with living well. (shrink)

Taking pride in being better than others in some regard is not uncommon. In a recent paper, Christopher Morgan-Knapp argues that such pride is misguided: it ‘presents things as being some way they are not’. I argue that Morgan-Knapp's arguments do not succeed in showing that comparative pride is theoretically mistaken.

The word “hacker” has an interesting double meaning: one vastly more widespread connotation of technological mischief, even criminality, and an original meaning amongst the tech savvy as a term of highest approbation. Both meanings, however, share the idea that hackers possess a superior ability to manipulate technology according to their will (and, as with God, this superior ability to exercise will is a source of both mystifying admiration and fear). This book mainly concerns itself with the former meaning. To Thomas (...) this simultaneously mystified and vilified, elusive set of individuals exemplifies “the performance of technology” xx), showing the way in which “the cultural, social and political history of the computer...is fraught with complexity and contradictions” ix). In fact, he claims that hacking is more a cultural than technological phenomenon, citing Heidegger’s, “[t]he essence of technology is not anything technological” (56). (shrink)

This poised and articulate volume addresses an area of pragmatist philosophy as yet relatively unexplored in pragmatism's welcome revival. Neopragmatism's preoccupation with changing philosophers' view of the relation between language (or as Rorty puts it: "vocabularies") and reality, has largely focussed their discussions on the 'metaphysics & epistemology', rather than the 'value' side of philosophy, apart from Rorty's brief flirtations with edifying Western political discourse. Yet the nature of truth in ethics has been a topic of keen discussion in recent (...) mainstream philosophy, and it's widely acknowledged that pragmatism has original and interesting things to say about truth. This book seeks to contribute in particular to discussions of objectivity in ethics which are arguably somewhat bogged down in a wealth of finely divergent terminologies and positions: prescriptivism, fictionalism, intuitionism, quasi-realism and expressivism, to name just a few. Heney organises her own discussion around a distinction between cognitivism and non-cognitivism about moral claims. (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)

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 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)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (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)

Coronavirus disease 2019 can lead to respiratory failure. Some patients require extracorporeal membrane oxygenation support. During the current pandemic, health care resources in some cities have been overwhelmed, and doctors have faced complex decisions about resource allocation. We present a case in which a pediatric hospital caring for both children and adults seeks to establish guidelines for the use of extracorporeal membrane oxygenation if there are not enough resources to treat every patient. Experts in critical care, end-of-life care, bioethics, and (...) health policy discuss if age should guide rationing decisions. (shrink)