Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (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)

Conscious states—state that there is something it is like to be in—seem both rich or full of detail and ineffable or hard to fully describe or recall. The problem of ineffability, in particular, is a longstanding issue in philosophy that partly motivates the explanatory gap: the belief that consciousness cannot be reduced to underlying physical processes. Here, we provide an information theoretic dynamical systems perspective on the richness and ineffability of consciousness. In our framework, the richness of conscious experience corresponds (...) to the amount of information in a conscious state and ineffability corresponds to the amount of information lost at different stages of processing. We describe how attractor dynamics in working memory would induce impoverished recollections of our original experiences, how the discrete symbolic nature of language is insufficient for describing the rich and high-dimensional structure of experiences, and how similarity in the cognitive function of two individuals relates to improved communicability of their experiences to each other. While our model may not settle all questions relating to the explanatory gap, it makes progress toward a fully physicalist explanation of the richness and ineffability of conscious experience—two important aspects that seem to be part of what makes qualitative character so puzzling. (shrink)

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

I argue that Smith proposed a new kind of imperialism, which we would describe as a species of ‘federalism,’ and that his plan influenced Bentham and Kant in their federal projects, although they seem to have been unaware of each other’s proposals. In what follows, I outline Smith’s position. I then describe Kant’s and Bentham’s debts to Smith in turn. This will also allow for greater clarity about the nature of early liberalism.

In this article, I argue that intentional psychology (i.e. the interpretation of human behaviour in terms of intentional states and propositional attitudes) plays an essential role in the sciences of the mind. However, this role is not one of identifying scientifically respectable states of the world. Rather, I argue that intentional psychology acts as a type of phenomenological model, as opposed to a mechanistic one. I demonstrate that, like other phenomenological models in science, intentional psychology is a methodological tool with (...) its own benefits and insights that complements our mechanistic understanding of systems. As a result, intentional psychology's distinctive scientific benefit is its ability to model systems in unique, non-mechanistic, ways. This allows us to generate predictions that we cannot otherwise generate using the mechanistic models of neuroscience and cognitive psychology necessary for various scientific tasks. (shrink)

This paper articulates and defends a novel hybrid account of well-being. We will call our view a Robust Hybrid. We call it robust because it grants a broad and not subservient role to both objective and subjective values. In this paper we assume, we think plausibly but without argument, that there is a significant objective component to well-being. Here we clarify what it takes for an account of well-being to have a subjective component. Roughly, we argue, it must allow that (...) favoring attitudes that are not warranted by the lights of objective values can ground benefits. Given this understanding, we show that there is an important and unrecognized expansion in the resources available to fully objectivist views: namely that such views can help themselves to the value of warranted love of objective goods. Such a move by the objectivist can help them respond to concerns that, on their view, a person’s well-being can be too alien to them. We next argue that, nonetheless, such objectivist views are still unconvincing due to their lack of a subjective component. This motivates a move from fully objective accounts to hybrid accounts. We show that many prominent hybrid theories in the literature are inadequate because they implausibly minimize the subjective component. This motivates a move to a robust hybrid view that has an expanded subjectivist component. We conclude with some remarks about the interrelation between the subjective and objective components in the hybrid account that we favor and a role for resonance in a theory of well-being other than serving as a hard constraint on any benefit. (shrink)

Replicating or exceeding human intelligence, not just in particular domains but in general, has always been a major goal of Artificial Intelligence (AI). We argue here that “human intelligence” is not only ill-defined, but often conflated with broader aspects of human psychology. Standard arguments for replicating it are morally unacceptable. We then suggest a reframing: that the proper goal of AI is not to replicate humans, but to complement them by creating diverse intelligences capable of collaborating with humans. This goal (...) renders issues of theory of mind, empathy, and caring, or community engagement, central to AI. It also challenges AI to better understand the circumstances in which human intelligence, including human moral intelligence, fails. (shrink)

At some point in the future – perhaps within the next few decades – it will be possible for foetuses to develop completely outside the womb. Ectogenesis, as this technology is called, raises substantial issues for the abortion debate. One such issue is that it will become possible for a woman to have an abortion, in the sense of having the foetus removed from her body, but for the foetus to be kept alive. We argue that while there is a (...) right to an abortion, there are reasons to doubt that there is a right to the death of the foetus. Our strategy in this essay is to consider and reject three arguments in favour of this latter right. The first claims that women have a right not to be biological mothers, the second that women have a right to genetic privacy, and the third that a foetus is one's property. Furthermore, we argue that it follows from rejecting the third claim that genetic parents also lack a right to the destruction of cryopreserved embryos used for in vitro fertilization. The conclusion that a woman possesses no right to the death of the foetus builds upon the claims that other pro-choice advocates, such as Judith Jarvis Thomson, have made. (shrink)

This dissertation is a contribution to the debate about ‘climate justice’, i.e. a call for a just and feasible distribution of responsibility for addressing climate change. The main argument is a proposal for a cautious, practicable, and necessary step in the right direction: given the set of theoretical and practical obstacles to climate justice, we must begin by making contemporary development practices sustainable. In times of climate change, this is done by recognising and responding to the fact that emissions of (...) greenhouse gases, with climate change as their result, are an immanent threat to any reflectively embraced development project. In the universal pursuit of progress, basic needs of both present and future people are put at risk. Even so, a political stalemate and business-as-usual prevail. The situation is locked up by an uncertainty about the exact impacts of choices made and by the reasonable disagreement of modern societies. The result is passiveness, and the passing on of a slowly and indiscernibly growing problem to future generations. This dissertation brings out a crucial message about the need to make our development sustainable. Instead of delaying action through trying to resolve the intractable epistemic and normative uncertainty fully, the focus should be on vindicating already shared points of practical convergence. On the constructivist method here adopted, the task is to characterise the agent and the situation faced from a practical and first-person point of view. More specifically, to specify the practical problem climate change gives rise to; the moral importance of needs (chapter three); how a principled priority of basic needs can be defended (chapter four), intergenerationally (chapter five) and internationally (chapter six); and what natural and social limits there are to development (chapter seven). These conceptions narrows the practice of development in the present context: it can be concluded that development must not risk the basic needs of anyone implicated. This common ground brackets off disagreement irrelevant to the urgent need to act, and so brings together otherwise deeply divided agents. A sufficientarian basic needs-principle, as the focus of an overlapping consensus, is practicable and anticipatory in the disuniting moral conundrum of climate change. (shrink)

Metaphors have computable semantics. A program called NETMET both generates metaphors and produces partial literal interpretations of metaphors. NETMET is based on Kittay's semantic field theory of metaphor and Black's interaction theory of metaphor. Input to NETMET consists of a list of literal propositions. NETMET creates metaphors by finding topic and source semantic fields, producing an analogical map from source to topic, then generating utterances in which terms in the source are identified with or predicated of terms in the topic. (...) Given a metaphor, NETMET utilizes if-then rules to generate the implication complex of that metaphor. The literal leaves of the implication complex comprise a partial literal interpretation. (shrink)

In this paper, I develop a novel account of concept acquisition for an atomistic theory of concepts. Conceptual atomism is rarely explored in cognitive science because of the feeling that atomistic treatments of concepts are inherently nativistic. My model illustrates, on the contrary, that atomism does not preclude the learning of a concept.

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

I offer an interpretation of the puzzle posed by Greenberg’s failure to come to terms with the explosion of postmodernist experimentation in the 1960’s. Greenberg, one of the most influential critics of the immediately preceding period and a strong supporter of New York abstract expressionism and color field painting, is indelibly associated with modernist schools of painting. His short essay, “Modernist Painting”, valorized precisely these movements and was a tour de force catapulting Greenberg into critic superstar status; it is still (...) one of the central documents in debates about modernism. Because Greenberg there makes references to Kant’s aesthetics in identifying the virtues of modernism his account is usually interpreted in terms of the formalism of the period and Kant’s analytic of the beautiful. This offers a reading of Greenberg as a formalist and as identifying modernism with a concern for the formal properties of art, the flatness of the picture frame and the formal relations between the aesthetic properties. Greenberg was also celebrated as having a legendary acuteness of aesthetic appreciation—a critical eye penetrating immediately to a work’s aesthetic depth. (shrink)

Traditionally, a scientific model is thought to provide a good scientific explanation to the extent that it satisfies certain scientific goals that are thought to be constitutive of explanation. Problems arise when we realize that individual scientific models cannot simultaneously satisfy all the scientific goals typically associated with explanation. A given model’s ability to satisfy some goals must always come at the expense of satisfying others. This has resulted in philosophical disputes regarding which of these goals are in fact necessary (...) for explanation, and as such which types of models can and cannot provide explanations. Explanatory monists argue that one goal will be explanatory in all contexts, while explanatory pluralists argue that the goal will vary based on pragmatic considerations. In this paper, I argue that such debates are misguided, and that both monists and pluralists are incorrect. Instead of any goal being given explanatory priority over others in a given context, the different goals are all deeply dependent on one another for their explanatory power. Any model that sacrifices some explanatory goals to attain others will always necessarily undermine its own explanatory power in the process. And so when forced to choose between individual scientific models, there can be no explanatory victors. Given that no model can satisfy all the goals typically associated with explanation, no one model in isolation can provide a good scientific explanation. Instead we must appeal to collections of models. Collections of models provide an explanation when they satisfy the web of interconnected goals that justify the explanatory power of one another. (shrink)

Anil Gupta’s Conscious Experience: A Logical Inquiry provides an impressive and novel account of rational justification based on conscious experience which is used as a foundation for a new theory of empiricism. In this critical notice, I argue that Gupta’s project is fascinating, but is often hampered by a lack of sufficient philosophical justification and clarity regarding some essential features of his project, as well as a lack of engagement with relevant scientific domains that would directly bear on it, such (...) as computational neuroscience, cognitive neuroscience, and cognitive psychology. This limits the sort of logical inquiry available to him in problematic ways. (shrink)

The Standard View of personal identity says that someone who exists now can exist at another time only if there is continuity of her mental contents or capacities. But no person is psychologically continuous with a fetus, for a fetus, at least early in its career, has no mental features at all. So the Standard View entails that no person was ever a fetus--contrary to the popular assumption that an unthinking fetus is a potential person. It is also mysterious what (...) does ordinarily happen to a human fetus, if it does not come to be a person. Although an extremely complex variant of the Standard View may allow one to persist without psychological continuity before one becomes a person but not afterwards, a far simpler solution is to accept a radically non-psychological account of our identity. (shrink)

Most philosophers are familiar with the metaphysical puzzle of the statue and the clay. A sculptor begins with some clay, eventually sculpting a statue from it. Are the clay and the statue one and the same thing? Apparently not, since they have different properties. For example, the clay could survive being squashed, but the statue could not. The statue is recently formed, though the clay is not, etc. Godehart Link 1983’s highly influential analysis of the count/mass distinction recommends that English (...) draws a distinction between uncountable “stuff” and countable “things”. There are two mereological relations, related in specific ways. Our primary question here is whether an empirically adequate account of the mass/count distinction really does require distinguishing “things” from “stuff”, and thus postulating two corresponding mereological relations, or if instead positing only one sort of entity and corresponding mereological relation is sufficient, as other semantic theories would have it. This question is meant to be one of what we call natural language mereology. We are asking about the mereological commitments of English, or perhaps competent speakers of English, and not about ultimate reality as such. There is no pretense that we will definitively solve the metaphysical puzzle of the statue and clay. (shrink)

Post-traumatic stress disorder is a “young” disorder formally recognized in the early 1980s, although the symptoms have been noted for centuries particularly in relation to military conflicts. PTSD may develop after a serious traumatic experience that induces feelings of intense fear, helplessness or horror. It is currently characterized by three key classes of symptoms which must cause clinically significant distress or impairment of functioning: persistent and distressing re-experiencing of the trauma; persistent avoidance of stimuli associated with the trauma and numbing (...) of general responsiveness; and persistent symptoms of hyper-arousal. One of the possible symptoms within the second class is difficulty in remembering an important aspect of the traumatic event.PTSD is not an uncommon condition, with an estimated lifetime prevalence of about 7-9% based on studies conducted in the United States and Canada, with women at higher risk than men. While not everyone who experiences a significant trauma will go on to develop PTSD, about a third will do so. Sexual assault, along with other forms of assaultive violence, pose a comparatively high risk of PTSD. (shrink)

Although advance directives are widely believed to be a key way to safeguard the autonomy of incompetent medical patients, significant questions exist about their moral authority. The main philosophical concern involves cases in which an incompetent patient no longer possesses the desires on which her advance directive was based. The question is, does that entail that prior expressions of medical choices are no longer morally binding? I believe that the answer is “yes.” I argue that a patient’s autonomy is not (...) respected by honoring the desires she used to have but no longer does. I also consider and reject the view that honoring an advance directive that reflects the patient’s previous values must be in that patient’s best interests. If that is correct, then advance directives in the kind of case at issue are not morally binding. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

According to one interpretation of Aristotle’s famous thesis, to say that action is the conclusion of practical reasoning is to say that action is itself a judgment about what to do. A central motivation for the thesis is that it suggests a path for understanding the non-observational character of practical knowledge. If actions are judgments, then whatever explains an agent’s knowledge of the relevant judgment can explain her knowledge of the action. I call the approach to action that accepts Aristotle’s (...) thesis so understood Normativism. There are many reasons to doubt Normativism. My aim in this paper is to defend Normativism from a pair of arguments that purport to show that a normative judgment could not constitute an event in material reality and also the knowledge of such a happening. Both highlight a putative mismatch between the natures of, on the one hand, an agent’s knowledge of her normative judgment and, on the other, her knowledge of her own action. According to these objections, knowledge of action includes (a) perceptual knowledge and (b) knowledge of what one has already done. But knowledge of a normative judgment includes neither. Hence knowledge of action cannot simply be knowledge of a normative judgment. (shrink)

Mathematics is obviously important in the sciences. And so it is likely to be equally important in any effort that aims to understand God in a scientifically significant way or that aims to clarify the relations between science and theology. The degree to which God has any perfection is absolutely infinite. We use contemporary mathematics to precisely define that absolute infinity. For any perfection, we use transfinite recursion to define an endlessly ascending series of degrees of that perfection. That series (...) rises to an absolutely infinite degree of that perfection. God has that absolutely infinite degree. We focus on the perfections of knowledge, power, and benevolence. Our model of divine infinity thus builds a bridge between mathematics and theology. (shrink)

In this paper, we argue that promoting patient values is a legitimate goal of medicine. Our view offers a justification for certain current practices, including birth control and living organ donation, that are widely accepted but do not fit neatly within the most common extant accounts of the goals of medicine. Moreover, we argue that recognising value promotion as a goal of medicine will expand the scope of medical practice by including some procedures that are sometimes rejected as being outside (...) the scope of acceptable medical practice, such as certain forms of physician-assisted death. We then rebut some common and possible objections to this view. Our aim is not to argue that other accounts are mistaken—except when they argue for a single goal that does not include patient values—but rather to show that value promotion should play a more central role in discussions about the goals of medicine. (shrink)

This paper, which is a homage to the life and work of Stephen Gaukroger, explores competing receptions of Spencer’s programmatic synthetic philosophy. In so doing, I show how T.H Huxley and C.S. Peirce reconfigured a familiar, long-standing debate about cosmogeny and cosmology in the early modern period.

Moorean arguments are a popular and powerful way to engage highly revisionary philosophical views, such as nihilism about motion, time, truth, consciousness, causation, and various kinds of skepticism (e.g., external world, other minds, inductive, global). They take, as a premise, a highly plausible first-order claim (e.g., cars move, I ate breakfast before lunch, it’s true that some fish have gills) and conclude from it the falsity of the highly revisionary philosophical thesis. Moorean arguments can be used against nihilists in ethics (...) (error theorists), too. Recently, error theorists have recognized Moorean arguments as a powerful challenge and have tried to meet it. They’ve argued that moral Moorean premises seem highly credible to us, but aren’t, by offering various debunking explanations. These explanations all appeal to higher-order evidence—evidence of error in our reasoning. I argue that drawing attention to higher-order evidence is a welcome contribution from error theorists, but that the higher-order evidence actually counts further against error theoretic arguments—including their debunking explanations—and further in favor of Moorean arguments and the commonsense views they support. Along the way I answer a few prominent objections to Moorean arguments: that they are objectionably question-begging, rely on categorizing some facts as “Moorean Facts”, and that reports of one’s credence in a proposition bears no interesting relation to that proposition’s credibility. (shrink)

The guiding thread of the paper is the diagnosis that the advanced division of cognitive labor (that is, intellectual specialization) engenders a set of perennial, political and epistemic challenges (Millgram 2015) that, simultaneously, also generate opportunities for philosophy. In this paper, I re-characterize the nature of synthetic philosophy as a means to advance and institutionalize philosophy. For my definition of synthetic philosophy see section 2. In section 1, I treat Plato’s Republic as offering two models to represent philosophy's relationship to (...) the other sciences within the advanced division of labor. I highlight that for Plato intellectual specialization is central not just to economic, but also to political life. And, yet, that the very dispersion of scientific expertise, and its esoteric nature, also generates non-trivial challenges to the recognition and political utilization of knowledge. From Plato we can infer that in imperfect circumstances, philosophy’s self-constitution is, in part, a response to these challenges in political epistemology. However, how philosophy is institutionalized differs through time. In section 2, I re-introduce my conceptualization of synthetic philosophy and restate it. This makes visible that synthetic philosophy is already widely practiced in the profession as philosophy of the special sciences, PPE, formal modelling, public philosophy, etc. I use recent work by Dorst (2023) to illustrate synthetic philosophy and to identify some of the processes that give rise to the need for it. In sections 2-3, I contrast my account with the evolving ways that Philip Kitcher has conceptualized synthetic philosophy in order to make more precise the version promoted here. I do so not just because Kitcher and I use the same term, ‘synthetic philosophy,’ but because the temptations inherent in Kitcher’s approach should be resisted. -/- . (shrink)

After presenting evidence about categorization behavior, this paper argues for the following theses: 1) that there is a border between perception and cognition; 2) that the border is to be characterized by perception being modular (and cognition not being so); 3) that perception outputs conceptualized representations, so views that posit that the output of perception is solely non-conceptual are false; and 4) that perceptual content consists of basic-level categories and not richer contents.

The overwhelming majority of those who theorize about implicit biases posit that these biases are caused by some sort of association. However, what exactly this claim amounts to is rarely specified. In this paper, I distinguish between different understandings of association, and I argue that the crucial senses of association for elucidating implicit bias are the cognitive structure and mental process senses. A hypothesis is subsequently derived: if associations really underpin implicit biases, then implicit biases should be modulated by counterconditioning (...) or extinction but should not be modulated by rational argumentation or logical interventions. This hypothesis is false; implicit biases are not predicated on any associative structures or associative processes but instead arise because of unconscious propositionally structured beliefs. I conclude by discussing how the case study of implicit bias illuminates problems with popular dual-process models of cognitive architecture. (shrink)

A Bayesian mind is, at its core, a rational mind. Bayesianism is thus well-suited to predict and explain mental processes that best exemplify our ability to be rational. However, evidence from belief acquisition and change appears to show that we do not acquire and update information in a Bayesian way. Instead, the principles of belief acquisition and updating seem grounded in maintaining a psychological immune system rather than in approximating a Bayesian processor.

This article considers two important traditions concerning the chemical elements. The first is the meaning of the term “element” including the distinctions between element as basic substance, as simple substance and as combined simple substance. In addition to briefly tracing the historical development of these distinctions, I make comments on the recent attempts to clarify the fundamental notion of element as basic substance for which I believe the term “element” is best reserved. This discussion has focused on the writings of (...) Fritz Paneth which are here analyzed from a new perspective. The other tradition concerns the reduction of chemistry to quantum mechanics and an understanding of chemical elements through their microscopic components such as protons, neutrons and electrons. I claim that the use of electronic configurations has still not yet settled the question of the placement of several elements and discuss an alternative criterion based on maximizing triads of elements. I also point out another possible limitation to the reductive approach, namely the failure, up to now, to obtain a derivation of the Madelung rule. Mention is made of some recent similarity studies which could be used to clarify the nature of ‘elements’. Although it has been suggested that the notion of element as basic substance should be considered in terms of fundamental particles like protons and electrons, I resist this move and conclude that the quantum mechanical tradition has not had much impact on the question of what is an element which remains an essentially philosophical issue. (shrink)

In some recent works, Crupi and Iacona have outlined an analysis of ‘if’ based on Chrysippus’ idea that a conditional holds whenever the negation of its consequent is incompatible with its antecedent. This paper presents a sound and complete system of conditional logic that accommodates their analysis. The soundness and completeness proofs that will be provided rely on a general method elaborated by Raidl, which applies to a wide range of systems of conditional logic.

This paper takes up Bethesda Game Studios' Starfield (2023) as an aesthetic artefact, carefully attending to the thematics of the game's narrative in their operation as structuring "thought patterns" for the player's experience of the game, thought patterns that give form to the "sensible fabric" of the game and so constitute an imaginary or "distribution of the sensible" that requires critique (Rancière, 2013). Utilizing the aesthetic and material-economic theories of Nicolas Bourriaud, Jacques Rancière, Jussi Parikka, and David Graeber, this paper (...) examines the aesthetics of the techno-ecological imaginary that Starfield institutes, close reading the play of perspectives into which the game invites the player-character, and analysing this play in its problematic orientation to the key dramatic revelation of planetary catastrophe that occurs late in the game's main campaign. If, as climate and games scholar Benjamin Abraham writes (2022), "[b]ringing the climate crisis 'home' to all of our lives, all of our workplaces, all of our hobbies, is the necessary first step in acting to reverse climate action," then illuminating and critiquing Starfield's deployment of such a crisis will help players, scholars, and developers alike take the first step in learning to pay attention to the very "modes of perception" that prevent us from effecting real change in the global technological systems that have brought us to the brink of planetary collapse. (shrink)

This chapter argues that the standard conception of Spinoza as a fellow-travelling mechanical philosopher and proto-scientific naturalist is misleading. It argues, first, that Spinoza’s account of the proper method for the study of nature presented in the Theological-Political Treatise (TTP) points away from the one commonly associated with the mechanical philosophy. Moreover, throughout his works Spinoza’s views on the very possibility of knowledge of nature are decidedly sceptical (as specified below). Third, in the seventeenth-century debates over proper methods in the (...) sciences, Spinoza sided with those that criticized the aspirations of those (the physico-mathematicians, Galileo, Huygens, Wallis, Wren, etc) who thought the application of mathematics to nature was the way to make progress. In particular, he offers grounds for doubting their confidence in the significance of measurement as well as their piece-meal methodology (see section 2). Along the way, this chapter offers a new interpretation of common notions in the context of treating Spinoza’s account of motion (see section 3). (shrink)

“What is the structure of thought?” is as central a question as any in cognitive science. A classic answer to this question has appealed to a Language of Thought (LoT). We point to emerging research from disparate branches of the field that supports the LoT hypothesis, but also uncovers diversity in LoTs across cognitive systems, stages of development, and species. Our letter formulates open research questions for cognitive science concerning the varieties of rules and representations that underwrite various LoT-based systems (...) and how these variations can help researchers taxonomize cognitive systems. (shrink)

It has commonly been argued that certain types of mental descriptions, specifically those characterized in terms of propositional attitudes, are part of a folk psychological understanding of the mind. Recently, however, it has also been argued that this is the case even when such descriptions are employed as part of scientific theories in domains like social psychology and comparative psychology. In this paper, I argue that there is no plausible way to understand the distinction between folk and scientific psychology that (...) can support such claims. Moreover, these sorts of claims can have adverse consequences for the neuroscientific study of the brain by downplaying the value of many psychological theories that provide information neuroscientists need in order to build and test neurological models. (shrink)

This article investigates multi-species relations in a group of science fiction narratives featuring extraterrestrial beings, paying particular attention to the Alien movie series. The concept of “cosmopolitical ecology” is elaborated as a tool to map relations between the different kinds of beings that populate the modern imagination in SF, especially those between humans, machines, animals and alien entities. Two apparently opposing modes of relation are highlighted in the narratives: domestication and predation. But those modes, intrinsically connected to a broader colonial (...) imaginary, seem to be themselves entangled in complex ways. If modernity is marked by what Ghassan Hage calls “generalized domestication,” then what is the place of predation in modern metaphysics? An ambiguous position often attached to a dangerous other, the role of the predator also emerges as a feature of modern humans, a trace that they sometimes recognize in themselves when they look at an alien mirror. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

One of the deepest and longest-lasting debates in ethics concerns a version of the Euthyphro question: are choiceworthy things choiceworthy because agents have certain attitudes toward them or are they choiceworthy independent of any agents’ attitudes? Reasons internalists, such as Bernard Williams, Michael Smith, Mark Schroeder, Sharon Street, Kate Manne, Julia Markovits, and David Sobel answer in the first way. They think that all of an agent’s normative reasons for action are grounded in facts about that agent’s pro-attitudes (e.g., her (...) desires, valuing states, normative judgments). According to the most popular brand of internalism, idealizing internalism, an agent’s reasons are grounded, not in her actual pro-attitudes, but rather in what her pro-attitudes would be in suitably idealized conditions. Idealizing internalists presuppose that, for any agent with an irrational set of attitudes, there is one uniquely rational set that that agent would have if she were to undergo the relevant idealizing process. I argue that this assumption is false and that it raises two puzzles for idealizing internalism: one about the existence of practical reasons and another about their normative weight. I argue that idealizing internalists have an adequate solution to the first puzzle but not the second. Indeed, when they try to solve the second puzzle, they confront a dilemma. This second puzzle and the associated dilemma thus constitutes a powerful, but so far unnoticed, difficulty for idealizing internalism. (shrink)

I describe a phenomenon that has not yet been described in the epistemology literature. I label this phenomenon expression-style exclusion. Expression-style exclusion is an example of how s...

A god is a cosmic designer-creator. Atheism says the number of gods is 0. But it is hard to defeat the minimal thesis that some possible universe is actualized by some possible god. Monotheists say the number of gods is 1. Yet no degree of perfection can be coherently assigned to any unique god. Lewis says the number of gods is at least the second beth number. Yet polytheists cannot defend an arbitrary plural number of gods. An alternative is that, (...) for every ordinal, there is a god whose perfection is proportional to it. The n -th god actualizes the best universe(s) in the n -th level of an axiological hierarchy of possible universes. Despite its unorthodoxy, ordinal polytheism has many metaphysically attractive features and merits more serious study. (shrink)

Whole Brain Emulation has been championed as the most promising, well-defined route to achieving both human-level artificial intelligence and superintelligence. It has even been touted as a viable route to achieving immortality through brain uploading. WBE is not a fringe theory: the doctrine of Computationalism in philosophy of mind lends credence to the in-principle feasibility of the idea, and the standing of the Human Connectome Project makes it appear to be feasible in practice. Computationalism is a popular, independently plausible theory, (...) and Connectomics a well-funded empirical research program, so optimism about WBE is understandable. However, this optimism may be misplaced. This article argues that WBE is, at best, no more compelling than any of the other far-flung routes to achieving superintelligence. Similarly skeptical conclusions are found regarding immortality. The essay concludes with some positive considerations in favor of the Biological Theory of consciousness, as well as morals about the limits of Computationalism in both artificial intelligence and the philosophy of mind more generally. (shrink)

I consider the intertextuality between Chinese and Western thought by exploring how images, metaphors, and ideas from the texts associated with Zhuangzi and Laozi were appropriated in early twentieth-century German philosophy. This interest in “Lao-Zhuang Daoism” encompasses a diverse range of thinkers including Buber and Heidegger. I examine how the problematization of utility, usefulness, and “purposiveness” in Zhuangzi and Laozi becomes a key point for their German philosophical reception; how it is the poetic character of the Zhuangzi that hints at (...) an appropriate response to the crisis and loss of meaning that characterizes technological modernity and its instrumental technological rationality; that is, how the “poetic” and “spiritual” world perceived in Lao-Zhuang thought became part of Buber's and Heidegger's critical encounter and confrontation with technological modernity; and how their concern with Zhuangzi does not signify a return to a dogmatic religiosity or otherworldly mysticism; it anticipates a this-worldly spiritual or poetic way of dwelling immanently within the world. (shrink)

This essay attempts to clarify the nature and structure of aliefs. First I distinguish between a robust notion of aliefs and a deflated one. A robust notion of aliefs would introduce aliefs into our psychological ontology as a hitherto undiscovered kind, whereas a deflated notion of aliefs would identify aliefs as a set of pre-existing psychological states. I then propose the following dilemma: one the one hand, if aliefs have propositional content, then it is unclear exactly how aliefs differ from (...) psychological states we already countenance, in which case there is no robust notion of aliefs; on the other, if aliefs just contain associative content, then they cannot do the explanatory work set out for them, in which case there is no reason to posit aliefs at all. Thus, it appears that we have little reason to posit the novel category of robust aliefs. (shrink)

You can survive after death in various kinds of artifacts. You can survive in diaries, photographs, sound recordings, and movies. But these artifacts record only superficial features of yourself. We are already close to the construction of programs that partially and approximately replicate entire human lives (by storing their memories and duplicating their personalities). A digital ghost is an artificially intelligent program that knows all about your life. It is an animated auto-biography. It replicates your patterns of belief and desire. (...) You can survive after death in a digital ghost. We discuss a series of digital ghosts over the next 50 years. As time goes by and technology advances, they are progressively more perfect replicas of the lives of their original authors. (shrink)

The empirical study of belief is emerging at a rapid clip, uniting work from all corners of cognitive science. Reliance on belief in understanding and predicting behavior is widespread. Examples can be found, inter alia, in the placebo, attribution theory, theory of mind, and comparative psychological literatures. Research on belief also provides evidence for robust generalizations, including about how we fix, store, and change our beliefs. Evidence supports the existence of a Spinozan system of belief fixation: one that is automatic (...) and independent of belief rejection. Independent research supports the existence of a system of fragmented belief storage: one that relies on large numbers of causally isolated, context-sensitive stores of belief in memory. Finally, empirical and observational data support at least two systems of belief change. One system adheres, mostly, to epistemological norms of updating; the other, the psychological immune system, functions to guard our most centrally held beliefs from potential inconsistency with newly formed beliefs. Refining our under- standing of these systems can shed light on pressing real-world issues, such as how fake news, propaganda, and brainwashing exploit our psychology of belief, and how best to construct our modern informational world. (shrink)