In this paper I articulate a view of doxastic control that helps defend the legitimacy of our practice of blaming people for their beliefs. I distinguish between three types of doxastic control: intention-based, reason-based, and influence-based. First I argue that, although we lack direct intention-based control over our beliefs, such control is not necessary for legitimate doxastic blame. Second, I suggest that we distinguish two types of reason-responsiveness: sensitivity to reasons and appreciation of reasons. I argue that while both capacities (...) are necessary for satisfying the control condition, neither is sufficient. Finally, I defend an influence-based view of doxastic control according to which we have the capacity to execute intentions to engage in reflection that causally influences our beliefs in positive epistemic ways. This capacity is both necessary and sufficient for satisfying the control condition for legitimate doxastic blame. I end by defending the view from two objections: that reflection is not necessary for meeting the control condition, and that it is not sufficient. (shrink)

This paper seeks to answer the question: Can contemporary forms of artificial intelligence be creative? To answer this question, I consider three conditions that are commonly taken to be necessary for creativity. These are novelty, value, and agency. I argue that while contemporary AI models may have a claim to novelty and value, they cannot satisfy the kind of agency condition required for creativity. From this discussion, a new condition for creativity emerges. Creativity requires curiosity, a motivation to pursue epistemic (...) goods. I argue that contemporary AI models do not satisfy this new condition. Because they lack both agency and curiosity, it is a mistake to attribute the same sort of creativity to AI that we prize in humans. Finally, I consider the question of whether these AI models stand to make human creativity in the arts and sciences obsolete, despite not being creative themselves. I argue, optimistically, that this is unlikely. (shrink)

A background assumption in much contemporary political philosophy is that justice is the first virtue of social institutions, taking priority over other values such as beneficence. This assumption is typically treated as a methodological starting point, rather than as following from any particular moral or political theory. In this paper, I challenge this assumption. To frame my discussion, I argue, first, that justice doesn’t in principle override beneficence, and second, that justice doesn’t typically outweigh beneficence, since, in institutional contexts, the (...) stakes of beneficence are often extremely high. While there are various ways one might resist this argument, none challenge the core methodological point that political philosophy should abandon its preoccupation with justice and begin to pay considerably more attention to social beneficence—that is, to beneficence understood as a virtue of social institutions. Along the way, I also highlight areas where focusing on social beneficence would lead political philosophers in new and fruitful directions, and where normative ethicists focused on personal beneficence might scale up their thinking to the institutional case. GPI Working Paper No. 11-2022. (shrink)

In this chapter, we explore whether agents have an epistemic duty to eradicate implicit bias. Recent research shows that implicit biases are widespread and they have a wide variety of epistemic effects on our doxastic attitudes. First, we offer some examples and features of implicit biases. Second, we clarify what it means to have an epistemic duty, and discuss the kind of epistemic duties we might have regarding implicit bias. Third, we argue that we have an epistemic duty to eradicate (...) implicit biases that have negative epistemic impact. Finally, we defend this view against the objection that we lack the relevant control over implicit bias that’s required for such a duty. We argue that we have a kind of reflective control over the implicit biases that we are duty-bound to eradicate. And since, as we show, we have this control over a wide variety of implicit biases, there are a lot of implicit biases that we have epistemic duties to eradicate. (shrink)

This paper presents a simple pair of first-order theories that are not definitionally (nor Morita) equivalent, yet are mutually conservatively translatable and mutually 'surjectively' translatable. We use these results to clarify the overall geography of standards of equivalence and to show that the structural commitments that theories make behave in a more subtle manner than has been recognized.

Forgiveness and reconciliation are central to moral life; after all, everyone will be wronged by others and will then face the dual decisions of whether to forgive and whether to reconcile. It is therefore important that we have a clear analysis of each, as well as a thoroughly articulated understanding of how they relate to and differ from each other. -/- Forgiveness has received considerably more attention in the Western philosophical literature than has reconciliation. In this paper I aim to (...) give it the attention it deserves and develop an account of interpersonal reconciliation. On my view reconciliation is fundamentally bilateral (whereas forgiveness is fundamentally unilateral). It entails transparency and agreement between the wrongdoer and the victim as to the nature of a past wrong or set of wrongs. And, it requires that moral repair be made between the two parties (which entails that both parties bear proper attitudes towards each other). In making my case I contrast reconciliation with toleration and collaboration, in order to demonstrate that reconciliation also entails forgiveness (though forgiveness does not entail reconciliation). (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

In this paper, I solve a puzzle generated by three conflicting claims about the relationship between faith, belief, and control: according to the Identity Thesis, faith is a type of belief, and according to Fideistic Voluntarism, we sometimes have control over whether or not we have faith, but according to Doxastic Involuntarism, we never have control over what we believe. To solve the puzzle, I argue that the Identity Thesis is true, but that either Fideistic Voluntarism or Doxastic Voluntarism is (...) false, depending on how we understand "control." I distinguish two notions of control: direct intention-based control and indirect reflective control. I argue that though we have direct intention-based control over neither belief nor faith, we have indirect reflective control over each of them. Moreover, indirect reflective control helps explain how we can be held accountable for each. (shrink)

It is often held that people have a moral right to believe and say whatever they want. For instance, one might claim that they have a right to believe racist things as long as they keep those thoughts to themselves. Or, one might claim that they have a right to pursue any philosophical question they want as long as they do so with a civil tone. In this paper I object to those claims and argue that no one has such (...) unlimited moral rights. In Part 1 I explore the value of the freedoms of thought and expression. In Part 2 I argue against the unlimited moral right to free expression, focusing in particular on the special obligations and moral constraints that obtain for academics. In Part 3 I argue against the unlimited moral right to free thought. (shrink)

This paper explores some of the ways that fear can be both a manifestation of and major contributor to oppression. It argues for a pluralistic account of the reasons that justify feeling fear or working to let go of fear and provides a framework to grapple fruitfully with the question of when someone should work to let go of fear and work to avoid contributing to the fear of others. Part 1 argues that emotions are an appropriate target of moral (...) evaluation; we are often not only responsible for our outwardly observable actions, but also for our emotional lives. It then details six different criteria by which we can engage in such evaluation. Part 2 evaluates fear in particular, in light of its relationship to oppressive ideologies and social structures. Part 3 explores some of the ways that people ought to respond to oppressive fear, in light of the relation they bear to it. (shrink)

Over the course of her career, Jean Harvey contributed many invaluable insights that help to make sense of both injustice and resistance. Specifically, she developed an account of what she called “civilized oppression,” which is pernicious in part because it can be difficult to perceive. One way that we ought to pursue what she calls a “life of moral endeavor” is by increasing our perceptual awareness of civilized oppression and ourselves as its agents. In this article I argue that one (...) noxious form of civilized oppression is what Miranda Fricker calls “testimonial injustice.” I then follow Harvey in arguing that one of the methods by which we should work to avoid perpetrating testimonial injustice is by empathizing with others. This is true for two reasons. The first is that in order to manifest what Fricker calls the virtue of testimonial justice, we must have a method by which we “correct” our prejudices or implicit biases, and empathy serves as such a corrective. The second is that there are cases where the virtue of testimonial justice wouldn't in fact correct for testimonial injustice in the way that Fricker suggests, but that actively working to empathize would. (shrink)

We make the case that scientifically accurate and politically feasible responses to the climate crisis require a complex understanding of human cultural practices of niche construction that moves beyond the adaptive significance of culture. We develop this thesis in two related ways. First, we argue that cumulative cultural practices of niche construction can generate stable equilibria and runaway selection processes that result in long-term existential risks within and across cultural groups. We dub this the back of the invisible hand. Second, (...) we argue that the ability of cultural groups to innovate technological solutions to environmental problems is highly constrained in ways that are exacerbated by sustained intergroup conflict, inequality and by inherently unpredictable cascades in climate change and human migration patterns. After developing these theoretical points about human cultural practices of niche construction in detail, we conclude our discussion with some tentative practical suggestions about the way that cultural evolutionary history can more fruitfully be used in efforts to remit the climate crisis and contribute to sustainable practices of human climate change adaptation. (shrink)

This chapter argues that for human, technological, and human-technological reasons, disagreement, critique, and counterspeech on social media fall squarely into the province of non-ideal theory. It concludes by suggesting a modest but challenging disposition that can help us when we are torn between opposing oppression and contributing to a flame war.

I argue that silencing (the act of preventing someone from communicating, broadly construed) can be an act of both interpersonal and institutional violence. My argument has two main steps. First, I follow others in analyzing violence as violation of integrity and show that undermining someone’s capacities as a knower can be such a violation. Second, I argue that silencing someone can violate their epistemic capacities in that way. I conclude by exploring when silencing someone might be morally justifiable, even if (...) doing so is an act of violence. (shrink)

We consider two ways one might use algorithmic randomness to characterize a probabilistic law. The first is a generative chance* law. Such laws involve a nonstandard notion of chance. The second is a probabilistic* constraining law. Such laws impose relative frequency and randomness constraints that every physically possible world must satisfy. While each notion has virtues, we argue that the latter has advantages over the former. It supports a unified governing account of non-Humean laws and provides independently motivated solutions to (...) issues in the Humean best-system account. On both notions, we have a much tighter connection between probabilistic laws and their corresponding sets of possible worlds. Certain histories permitted by traditional probabilistic laws are ruled out as physically impossible. As a result, such laws avoid one variety of empirical underdetermination, but the approach reveals other varieties of underdetermination that are typically overlooked. (shrink)

Most social policies cannot be defended without making inductive inferences. For example, consider certain arguments for racial profiling and affirmative action, respectively. They begin with statistics about crime or socioeconomic indicators. Next, there is an inductive step in which the statistic is projected from the past to the future. Finally, there is a normative step in which a policy is proposed as a response in the service of some goal—for example, to reduce crime or to correct socioeconomic imbalances. In comparison (...) to the normative step, the inductive step of a policy defense may seem trivial. We argue that this is not so. Satisfying the demands of the inductive step is difficult, and doing so has important but underappreciated implications for the normative step. In this paper, we provide an account of induction in social contexts and explore its implications for policy. Our account helps to explain which normative principles we ought to accept, and as a result it can explain why it is acceptable to make inferences involving race in some contexts (e.g., in defense of affirmative action) but not in others (e.g., in defense of racial profiling). (shrink)

I argue for an account of creativity that unifies creative achievements in the arts, sciences, and other domains and identifies its characteristic value. This account draws upon case studies of creative work in both the arts and sciences to identify creativity as a kind of successful exploration. I argue that if creativity is properly understood in this way, then it is fundamentally a property of processes, something only agents can achieve, something that comes in degrees, subjectively novel, and non-formulaic. As (...) I develop the account, I show how it avoids challenges faced by other accounts of creativity, especially concerning creativity’s value. Hills and Bird (2018, 2019) have together argued that creativity is not necessarily valuable. My account challenges this view. If I am right that creativity is a kind of successful exploration, then creativity does have a characteristic value, specifically epistemic value. (shrink)

Over the course of her career, Jean Harvey argued that as agents engaged in a “life of moral endeavor,” we should understand ourselves and others to be moral works in progress, always possessing the potential to grow beyond and become more than the sum of our past wrongs. In this paper I follow Harvey and argue that in order to live a life of moral endeavor, it is not enough merely to know about injustice. Instead, we must engage in the (...) difficult and often painful task of overcoming deep-seated cognitive biases that cause us to fail to perceive the ubiquitous injustice that pervades our world. I conclude by arguing that education, empathy, and love can each help us to increase our perceptual awareness of injustice and so should be recognized to be crucial parts of a life of moral endeavor. (shrink)

Everyone thinks they know who Prince Zuko is and can be. His father, Fire Lord Ozai, and sister, Azula, think him weak, disobedient, and undeserving of the crown. His Uncle Iroh thinks him good, if troubled, but ultimately worthy of his faith. The kids initially think him a villain, but eventually come to see him as a person – neither monster nor saint – someone who can choose to go in a new way. Zuko himself shows great ambivalence between these (...) conflicting stories about who he is, though each one helps to craft his own self-understanding. In this paper, we apply Hilde Lindemann’s narrative account of the self to explore the ways that others “hold” Zuko in one identity or “let him go” from others. According to Lindemann, our personal identities consist of the first- and third-person stories that cluster around significant acts, relationships, and commitments in our lives. Our identities are fundamentally relational, formed by the interaction between our own self-conception and the ways in which others see us. As such, others’ stories can enable or prevent us from imaginatively projecting ourselves into a particular future. This can lead us to becoming trapped in our identities; without the possibility of being perceived differently by others, we might find ourselves unable to try different ways of being or acting. The converse is also true, in that others can open up new possible identities by seeing things in us that we have trouble seeing in ourselves. If others in our moral community see us as wicked, beyond redemption and unable to repair our wrongs, we are held in the role of the villain and might come to live into that role without question. Zuko’s story is a perfect illustration of Jean Harvey’s reminder that, “it is just not true that once a thief, always a thief” and that agents can choose to go in a new way, can choose to change. How does Zuko change? We argue that Zuko’s redemption is enabled by those in his moral community holding him in identities in which he is a good person, capable and deserving of care, friendship, and love. While the identity he has in relation to his father and sister closes down many possible futures, his uncle Iroh in particular persists in holding him in an identity in which he is loved and worthy of love. And in doing so - in holding this space for him - Iroh opens up a way for Zuko to exercise agency and choose to become a different kind of person than the one he thought he was destined to be. (shrink)

There is an underappreciated respect in which the widespread availability of generative artificial intelligence (AI) models poses a threat to human connection. My central contention is that human creativity is especially capable of helping us connect to others in a valuable way, but the widespread availability of generative AI models reduces our incentives to engage in various sorts of creative work in the arts and sciences. I argue that creative endeavors must be motivated by curiosity, and so they must disclose (...) the creative agent’s inquisitive self. It is through self-disclosure, including the disclosure of the inquisitive self, that we put ourselves in a position to be seen by and connect with others through our creative pursuits. Because relying on AI for certain generative tasks is less self-disclosive than the creative work such technologies supplant, this reliance threatens to weaken our connections to one another. (shrink)

This paper analyzes the relationship between love and social justice activism, focusing in particular on ways in which activists rely on either the union account of love (to argue that when one person is oppressed everyone is oppressed), the sentimentalist account of love (to argue that overcoming injustice is fundamentally about how we feel about one another), or love as fate (to argue that it is in love’s nature to triumph over hatred and injustice). All three accounts, while understandable and (...) attractive, are seriously problematic, as they tend either to obscure important differences in the ways that various groups are socially situated or to enable inaction by trusting that justice is inevitable. Alternative, deeper interpretations of each account (and their relationships to activism) are explored. (shrink)

Eleonore Stump insightfully develops Aquinas’s theodicy to account for a significant source of human suffering, namely the undermining of desires of the heart. Stump argues that what justifies God in allowing such suffering are benefits made available to the sufferer through her suffering that can defeat the suffering by contributing to the fulfillment of her heart’s desires. We summarize Stump’s arguments for why such suffering requires defeat and how it is defeated. We identify three problems with Stump’s account of how (...) such suffering is defeated and offer solutions to each. We defend and strengthen Stump’s response to the hardest cases for her view, and explain what her view demands of God. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

The purpose of this paper is to examine in detail a particularly interesting pair of first-order theories. In addition to clarifying the overall geography of notions of equivalence between theories, this simple example yields two surprising conclusions about the relationships that theories might bear to one another. In brief, we see that theories lack both the Cantor-Bernstein and co-Cantor-Bernstein properties.

We critique two popular philosophical definitions of intellectual humility: the “low concern for status” and the “limitations-owning.” accounts. Based upon our analysis, we offer an alternative working definition of intellectual humility: the virtue of accurately tracking what one could non-culpably take to be the positive epistemic status of one’s own beliefs. We regard this view of intellectual humility both as a virtuous mean between intellectual arrogance and diffidence and as having advantages over other recent conceptions of intellectual humility. After defending (...) this view, we sketch remaining questions and issues that may bear upon the psychological treatment of intellectual humility such as whether evidence will help determine how this construct relates to general social humility on the one hand, and intellectual traits such as open-mindedness, curiosity, and honesty on the other. (shrink)

Numerous studies of the beliefs of people with anorexia nervosa (AN) suggest that a subset of such individuals may experience delusions. We first describe what makes a belief delusional and conclude that such characteristics can be appropriately applied to some beliefs of people with AN. Next, we outline how delusional beliefs may relate to the broader psychopathological process in AN, including: (1) they may be epiphenomenal; (2) they may be an initial partial cause of AN; (3) they may be caused (...) by aspects of AN; or (4) they may be sustaining causes, possibly involved in reciprocal causal relations with aspects of AN. We argue that there is good reason to believe that delusional beliefs of people with AN are not merely epiphenomenal, but rather that they’re causally connected to AN. Because of this, empirical studies can be designed to test for the presence of causal relations. We describe how these studies should be designed. The results of such studies have important implications for understanding the experience of individuals with AN and for the treatment of AN. We outline these implications. (shrink)

We argue against some of Reichenbach's claims about causal forks are incorrect. We do not see why the Second Law of Thermodynamics rules out the existence of conjunctive forks open to the past. In addition, we argue that a common effect rarely forms a conjunctive fork with its joint causes, but it sometimes does. Nevertheless, we think there is something to be said for Reichenbach's idea that forks of various kinds are relevant to explaining why we know more about the (...) past than about the future. And entropy turns out to play a role in the explanation, though not the determining role that Reichenbach envisions. (shrink)

Recent work in cognitive science of religion (CSR) is beginning to converge on a very interesting thesis—that, given the ordinary features of human minds operating in typical human environments, we are naturally disposed to believe in the existence of gods, among other religious ideas (e.g., seeAtran [2002], Barrett [2004; 2012], Bering [2011], Boyer [2001], Guthrie [1993], McCauley [2011], Pyysiäinen [2004; 2009]). In this paper, we explore whether such a discovery ultimately helps or hurts the atheist position—whether, for example, it (...) lends credence to atheism by explaining away religious belief or whether it actually strengthens some already powerful arguments against atheism in the relevant philosophical literature.We argue that the recent discoveries of CSR hurt, not help, the atheist position—that CSR, if anything, should not give atheists epistemic assurance. (shrink)

We set out longtermist political philosophy as a research field by exploring the case for, and the implications of, ‘institutional longtermism’: the view that, when evaluating institutions, we should give significant weight to their very long-term effects. We begin by arguing that the standard case for longtermism may be more robust when applied to institutions than to individual actions or policies, both because institutions have large, broad, and long-term effects, and because institutional longtermism can plausibly sidestep various objections to individual (...) longtermism. We then address points of contact between longtermism and some central values of mainstream political philosophy, focusing on justice, equality, freedom, legitimacy, and democracy. While each value initially seems to conflict with institutional longtermism, we find that these conflicts are less clear-cut upon closer inspection, and that some political values might even provide independent support for institutional longtermism. We end with a grab bag of related questions that we lack space to explore here. (shrink)

Mathematicians, physicists, and philosophers of physics often look to the symmetries of an object for insight into the structure and constitution of the object. My aim in this paper is to explain why this practice is successful. In order to do so, I present a collection of results that are closely related to (and in a sense, generalizations of) Beth’s and Svenonius’ theorems.

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

We consider how an epistemic network might self-assemble from the ritualization of the individual decisions of simple heterogeneous agents. In such evolved social networks, inquirers may be significantly more successful than they could be investigating nature on their own. The evolved network may also dramatically lower the epistemic risk faced by even the most talented inquirers. We consider networks that self-assemble in the context of both perfect and imperfect communication and compare the behaviour of inquirers in each. This provides a (...) step in bringing together two new and developing research programs, the theory of self-assembling games and the theory of network epistemology. (shrink)

The animal agriculture industry causes animals a tremendous amount of pain and suffering. Many ethical vegans argue that we therefore have an obligation to abstain from animal products in order to reduce this suffering. But this argument faces a challenge: thanks to the size and structure of the animal agriculture industry, any individual’s dietary choices are overwhelmingly unlikely to make a difference. In this paper, we criticize common replies to this challenge and develop an alternative argument for ethical veganism. Specifically, (...) we argue that individuals should abstain from animal products because vegans, as a group, successfully reduce animal suffering, and individuals are obligated to participate in, rather than free ride on, this collective endeavor. Or, at the very least, individuals have strong reasons to purchase fewer inhumanely raised animal products—even if they are not obligated to go vegan per se. (shrink)

In a recent study, we found a negative association between psychopathy and violence against genetic relatives. We interpreted this result as a form of nepotism and argued that it failed to support the hypothesis that psychopathy is a mental disorder, suggesting instead that it supports the hypothesis that psychopathy is an evolved life history strategy. This interpretation and subsequent arguments have been challenged in a number of ways. Here, we identify several misunderstandings regarding the harmful dysfunction definition of mental disorder (...) as it applies to psychopathy and regarding the meaning of nepotism. Furthermore, we examine the evidence provided by our critics that psychopathy is associated with other disorders, and we offer a comment on their alternative model of psychopathy. We conclude that there remains little evidence that psychopathy is the product of dysfunctional mechanisms. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

In their 2010 book, Biology’s First Law, D. McShea and R. Brandon present a principle that they call ‘‘ZFEL,’’ the zero force evolutionary law. ZFEL says (roughly) that when there are no evolutionary forces acting on a population, the population’s complexity (i.e., how diverse its member organisms are) will increase. Here we develop criticisms of ZFEL and describe a different law of evolution; it says that diversity and complexity do not change when there are no evolutionary causes.

How do people decide what category an artifact belongs to? Previous studies have suggested that adults and, to some degree, children, categorize artifacts in accordance with the design stance, a categorization system which privileges the designer’s original intent in making categorization judgments. However, these studies have all been conducted in Western, technologically advanced societies, where artifacts are mass produced. In this study, we examined intuitions about artifact categorization among the Shuar, a hunter-horticulturalist society in the Amazon region of Ecuador. We (...) used a forced-choice method similar to previous studies, but unlike these studies, our scenarios involved artifacts that would be familiar to the Shuar. We also incorporated a community condition to examine the possible effect of community consensus on how artifacts are categorized. The same scenarios were presented to university student participants in the UK. Across populations and conditions, participants tended to categorize artifacts in terms of a creator’s intent as opposed to a differing current use. This lends support to the view that the design stance may be a universal feature of human cognition. However, we conclude with some thoughts on the limitations of the present method for studying artifact concepts. (shrink)

In the literature on multiple realizability and the identity theory, cases of neural plasticity have enjoyed a very limited role. The present article attempts to remedy this small influence by arguing that clinical and experimental evidence of quite extensive neural reorganization offers compelling support for the claim that psychological kinds are multiply realized in neurological kinds, thus undermining the identity theory. In particular, cases are presented where subjects with no measurable psychological deficits also have vast, though gradually received, neurological damage. (...) Common objections and concerns are also discussed and rejected. 1 Introduction2 The GRP, Serial Lesion Effect, and Multiple Realizability2.1 A case study of the serial lesion effect2.2 Evaluating the case study’s evidence for multiple realizability3 The GRP More Generally4 Objections to the GRP as Evidence for Multiple Realizability4.1 Small plastic effects and neurological taxonomies4.2 But do neural regions and locations even matter at all?4.3 But are there not other options besides location?5 Conclusion. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

This article is about a very important metaphysical concept, macrocosm/microcosm and its appearance in Doric thought which in turn influenced Socrates and Plato. But since this concept has been gainsaid and negated in recent articles and distorted by some ancient thinkers it will be necessary to conduct reconstructive surgery to restore it to its pristine condition. Hopefully, this paper will illustrate how metaphysics is done with the use of the Mind's eye, in the reading of reality that was part and (...) parcel of the Greek mind but also in understanding the ancient Greeks themselves and their culture especially in the creation of the classical republican form of government. This account will discuss what macrocosm/microcosm is, its part in the Cosmos and hence its centrality in the Natural Law and in philosophy (wisdom). Second, it will prove the concept thru another natural law principle, righteousness. Third, point out it's provenance in Doric thought. In a corollary, it points to what the impact macrocosm/microcosm has on the true meaning "to be a lover of wisdom" and its importance in the concept of theosis. More than a research/academic article, this paper is also an exposition in which it will attempt to demonstrate the use and the mechanics of this principle by using a saying of Homer and the tripartite paradigm of the family. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

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

While several tests and strategies are recommended for colorectal cancer (CRC) screening, studies suggest that primary care providers often recommend colonoscopy without providing information about its risks or alternatives. These observations raise concerns about the quality of informed consent for screening colonoscopy.

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.