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)

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)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. 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 COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (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)

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)

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.

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)

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)

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)

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.

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)

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)

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)

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)

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)

Information can be public among a group. Whether or not information is public matters, for example, for accounts of interdependent rational choice, of communication, and of joint intention. A standard analysis of public information identifies it with (some variant of) common belief. The latter notion is stipulatively defined as an infinite conjunction: for p to be commonly believed is for it to believed by all members of a group, for all members to believe that all members believe it, and so (...) forth. This analysis is often presupposed without much argument in philosophy. Theoretical entrenchment or intuitions about cases might give some traction on the question, but give little insight about why the identification holds, if it does. The strategy of this paper is to characterize a practical-normative role for information being public, and show that the only things that play that role are (variants of) common belief as stipulatively characterized. In more detail: a functional role for “taking a proposition for granted” in non-isolated decision making is characterized. I then present some minimal conditions under which such an attitude is correctly held. The key assumption links this attitude to beliefs about what is public. From minimal a priori principles, we can argue that a proposition being public among a group entails common commitment to believe among that group. Later sections explore partial converses to this result, the factivity of publicity and publicity from the perspective of outsiders to the group, and objections to the aprioricity of the result deriving from a posteriori existential presuppositions. (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)

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)

The AGI alignment problem has a bimodal distribution of outcomes with most outcomes clustering around the poles of total success and existential, catastrophic failure. Consequently, attempts to solve AGI alignment should, all else equal, prefer false negatives (ignoring research programs that would have been successful) to false positives (pursuing research programs that will unexpectedly fail). Thus, we propose adopting a policy of responding to points of philosophical and practical uncertainty associated with the alignment problem by limiting and choosing necessary assumptions (...) to reduce the risk of false positives. Herein we explore in detail two relevant points of uncertainty that AGI alignment research hinges on---meta-ethical uncertainty and uncertainty about mental phenomena---and show how to reduce false positives in response to them. (shrink)

In a recent article Duncan Purves, Ryan Jenkins, and B. J. Strawser argue that in order for a decision in war to be just, or indeed the decision to resort to war to be just, it must be the case that the decision is made for the right reasons. Furthermore, they argue that this requirement holds regardless of how much good is produced by said action. In this essay I argue that their argument is flawed, in that it mistakes what (...) makes an agent morally good for what makes an act morally good. I argue that the main thrust of Purves et al.’s argument in fact undermines the conclusion they wish to draw, and that the reasons for one’s action do not make an in principle difference to the morality of actions in war. I further argue that this position undermines the traditional ad bellum just war constraint of right intention, and that the morality of actions in war is, at core, only concerned with outcomes. I conclude by clarifying that one’s reasons for action do in fact matter when deciding to enter war or kill in war, but only because one’s reasons significantly impact the way in which one acts. The purpose of this paper is to clear the theoretical space by showing why intentions/reasons do not in principle matter when assessing the morality of war (or killing), but this should not be taken as an argument that we should ignore intentions/reasons altogether. (shrink)

If the world itself is metaphysically indeterminate in a specified respect, what follows? In this paper, we develop a theory of metaphysical indeterminacy answering this question.

In this chapter, the embodied consciousness of clubbing and raving is considered through the theory of extended mind, according to which the mind is a distributed system where brain, body, and environment play equal parts. Building on the idea of music as affective atmosphere, a case is made for considering the vibe of a dance party as cognitively, socially, and affectively distributed. The chapter suggests that participating in the vibe affords primary musical consciousness—a kind of pre-reflexive state characterized by affective (...) and bodily knowledge—and speculates about the neural correlates of clubbing and raving by means of an analogy with brain research on psychedelic states. (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)

Some have objected to human enhancement on the grounds that it violates the autonomy of the enhanced. These objections, however, overlook the interesting possibility that autonomy itself could be enhanced. How, exactly, to enhance autonomy is a difficult problem due to the numerous and diverse accounts of autonomy in the literature. Existing accounts of autonomy enhancement rely on narrow and controversial conceptions of autonomy. However, we identify one feature of autonomy common to many mainstream accounts: reasoning ability. Autonomy can then (...) be enhanced by improving people’s reasoning ability, in particular through cognitive enhancement; given how valuable autonomy is usually taken to be, this gives us extra reason to pursue such cognitive enhancements. Moreover, autonomy-based objections will be especially weak against such enhancements. As we will argue, those who are worried that enhancements will inhibit people’s autonomy should actually embrace those enhancements that will improve autonomy. (shrink)

Moral enhancement is an ostensibly laudable project. Who wouldn’t want people to become more moral? Still, the project’s approach is crucial. We can distinguish between two approaches for moral enhancement: direct and indirect. Direct moral enhancements aim at bringing about particular ideas, motives or behaviors. Indirect moral enhancements, by contrast, aim at making people more reliably produce the morally correct ideas, motives or behaviors without committing to the content of those ideas, motives and/or actions. I will argue, on Millian grounds, (...) that the value of disagreement puts serious pressure on proposals for relatively widespread direct moral enhancement. A more acceptable path would be to focus instead on indirect moral enhancements while staying neutral, for the most part, on a wide range of substantive moral claims. I will outline what such indirect moral enhancement might look like, and why we should expect it to lead to general moral improvement. (shrink)

Contemporary Western societies are obsessed with the “obesity epidemic,” dieting, and fitness. Fat people violate the Western conscience by violating a thinness norm. In virtue of violating the thinness norm, fat people suffer many varied consequences. Is their suffering morally permissible, or even obligatory? In this paper, I argue that the answer is no. I examine contemporary philosophical accounts of oppression and draw largely on the work of Sally Haslanger to generate a set of conditions sufficient for some phenomena to (...) count as oppression, and I illustrate the account’s value using the example of gender oppression. I then apply the account to fat people, examine empirical evidence, and argue that the suffering of fat people counts as oppression. (shrink)

Two attitudes are possible: one, that the world is an absolute jungle and that the exercise of coercive power by rulers is only a manifestation of this; and the other, that it is both necessary and right that there should be this exercise of power, that through it the world is much less of a jungle than it could possibly be without it, so that one should in principle be glad of the existence of such power, and only take exception (...) to its unjust exercise. (shrink)

The current prevailing view is that participation in biomedical research is above and beyond the call of duty. While some commentators have offered reasons against this, we propose a novel public goods argument for an obligation to participate in biomedical research. Biomedical knowledge is a public good, available to any individual even if that individual does not contribute to it. Participation in research is a critical way to support an important public good. Consequently, all have a duty to participate. The (...) current social norm is that individuals participate only if they have a good reason to do so. The public goods argument implies that individuals should participate unless they have a good reason not to. Such a shift would be of great aid to the progress of biomedical research, eventually making society significantly healthier and longer lived. (shrink)

It has recently been argued that reproductive genetic manipulation technologies like mitochondrial replacement and germline CRISPR modifications cannot be said to save anyone’s life because, counterfactually, no one would suffer more or die sooner absent the intervention. The present article argues that, on the contrary, reproductive genetic manipulations may be life-saving (and, from this, have therapeutic value) under an appropriate population health perspective. As such, popular reports of reproductive genetic manipulations potentially saving lives or preventing disease are not necessarily mistaken, (...) though such terminology still requires further empirical validation. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

While philosophers are often concerned with the conditions for moral knowledge or justification, in practice something arguably less demanding is just as, if not more, important – reliably making correct moral judgments. Judges and juries should hand down fair sentences, government officials should decide on just laws, members of ethics committees should make sound recommendations, and so on. We want such agents, more often than not and as often as possible, to make the right decisions. The purpose of this paper (...) is to propose a method of enhancing the moral reliability of such agents. In particular, we advocate for a procedural approach; certain internal processes generally contribute to people’s moral reliability. Building on the early work of Rawls, we identify several particular factors related to moral reasoning that are specific enough to be the target of practical intervention: logical competence, conceptual understanding, empirical competence, openness, empathy and bias. Improving on these processes can in turn make people more morally reliable in a variety of contexts and has implications for recent debates over moral enhancement. (shrink)

Fichte assigns ‘intellectual intuition’ a new meaning after Kant. But in 1799, his doctrine of intellectual intuition is publicly deemed indefensible by Kant and nihilistic by Jacobi. I propose to defend Fichte’s doctrine against these charges, leaving aside whether it captures what he calls the ‘spirit’ of transcendental idealism. I do so by articulating three problems that motivate Fichte’s redirection of intellectual intuition from being to acting: (1) the regress problem, which states that reflecting on empirical facts of consciousness leads (...) only to further facts and so cannot yield a first principle; (2) the rhapsody problem, which states that the categories form a haphazard set and so lack necessity unless they derive from a first principle; and (3) the nihilism problem, which states that a first principle cannot lie outside our cognition of it, lest it be the cause of our cognition and, being first, the cause of all our actions, reducing us to machines. Crucially, Fichte’s three motivating problems are in fact aspects of a single problem. Leaving any aspect unsolved spoils putative solutions to the other two. Consequently, Fichte requires a single unified solution to all three, which his doctrine of intellectual intuition provides. (shrink)

As opposed to a ‘one size fits all’ approach, precision medicine uses relevant biological, medical, behavioural and environmental information about a person to further personalize their healthcare. This could mean better prediction of someone’s disease risk and more effective diagnosis and treatment if they have a condition. Big data allows for far more precision and tailoring than was ever before possible by linking together diverse datasets to reveal hitherto-unknown correlations and causal pathways. But it also raises ethical issues relating to (...) the balancing of interests, viability of anonymization, familial and group implications, as well as genetic discrimination. This article analyses these issues in light of the values of public benefit, justice, harm minimization, transparency, engagement and reflexivity and applies the deliberative balancing approach found in theEthical Framework for Big Data in Health and Research to a case study on clinical genomic data sharing. Please refer to that article for an explanation of how this framework is to be used, including a full explanation of the key values involved and the balancing approach used in the case study at the end. Our discussion is meant to be of use to those involved in the practice as well as governance and oversight of precision medicine to address ethical concerns that arise in a coherent and systematic manner. (shrink)

The right to withdraw from participation in research is recognized in virtually all national and international guidelines for research on human subjects. It is therefore surprising that there has been little justification for that right in the literature. We argue that the right to withdraw should protect research participants from information imbalance, inability to hedge, inherent uncertainty, and untoward bodily invasion, and it serves to bolster public trust in the research enterprise. Although this argument is not radical, it provides a (...) useful way to determine how the right should be applied in various cases. (shrink)

This paper aims to show that Godel's ontological argument can be parodied in much the same kind of way in which Gaunilo parodied Anselm's Proslogion argument. The parody in this paper fails; there is a patch provided in "Reply to Gettings" (Analysis 60, 4, 2000, 363-7).

Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phe- notypes, niches, ecosystems. We wish to argue that the evo- lution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon dis- cussing the variability of the very ”contexts of life”: the in- teractions between organisms, biological niches and ecosys- tems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of (...) time the ”niches” which constitute the boundary conditions on selec- tion. More generally, by the mathematical unprestatability of the ”phase space”, no laws of mo- tion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound concep- tual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of symmetries as invariant preserving transformations will allow us to under- stand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of ”enablement”. Life lives in a web of enablement and radical emergence. This will restrict causal analyses to differential cases. Mutations or other causal differ- ences will allow us to stress that ”non conservation princi- ples” are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as sym- metries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to ”extended criticality” as a conceptual frame for a better understanding of the living state of matter. (shrink)

The prospect of consumable meat produced in a laboratory setting without the need to raise and slaughter animals is both realistic and exciting. Not only could such in vitro meat become popular due to potential cost savings, but it also avoids many of the ethical and environmental problems with traditional meat productions. However, as with any new technology, in vitro meat is likely to face some detractors. We examine in detail three potential objections: 1) in vitro meat is disrespectful, either (...) to nature or to animals; 2) it will reduce the number of happy animals in the world; and 3) it will open the door to cannibalism. While each objection has some attraction, we ultimately find that all can be overcome. The upshot is that in vitro meat production is generally permissible and, especially for ethical vegetarians, worth promoting. (shrink)

This paper is a critical examination of Stephen Neale's *The Philosophical Significance of Godel's slingshot*. I am sceptical of the philosophical significance of Godel’s Slingshot (and of Slingshot arguments in general). In particular, I do not believe that Godel’s Slingshot has any interesting and important philosophical consequences for theories of facts or for referential treatments of definite descriptions. More generally, I do not believe that any Slingshot arguments have interesting and important philosophical consequences for theories of facts or for referential (...) treatments of definite descriptions. Friends of facts and referential treatments of definite descriptions can, and should, proceed with the construction of their theories, blithely ignoring the many Slingshots which now litter the landscape. (Of course, there may be other considerations which should give such theorists pause -- but those are other considerations.). (shrink)

Background Several jurisdictions, including Singapore, Australia, New Zealand and most recently Ireland, have a public interest or public good criterion for granting waivers of consent in biomedical research using secondary health data or tissue. However, the concept of the public interest is not well defined in this context, which creates difficulties for institutions, institutional review boards and regulators trying to implement the criterion. Main text This paper clarifies how the public interest criterion can be defensibly deployed. We first explain the (...) ethical basis for requiring waivers to only be granted to studies meeting the public interest criterion, then explore how further criteria may be set to determine the extent to which a given study can legitimately claim to be in the public interest. We propose an approach that does not attempt to measure magnitude of benefit directly, but rather takes into account metrics that are more straightforward to apply. To ensure consistent and justifiable interpretation, research institutions and IRBs should also incorporate procedural features such as transparency and public engagement in determining which studies satisfy the public interest requirement. Conclusion The requirement of public interest for consent waivers in secondary biomedical research should be guided by well-defined criteria for systematic evaluation. Such a criteria and its application need to be periodically subject to intra-committee and intra-institution review, reflection, deliberation and amendment. (shrink)

It is generally unquestioned that human subjects research review boards should assess the ethical acceptability of protocols. It says so right on the tin, after all: they are explicitly called research ethics committees in the UK. But it is precisely those sorts of unchallenged assumptions that should, from time to time, be assessed and critiqued, in case they are in fact unfounded. John Stuart Mill's objection to suppressers of dissent is instructive here: “If the opinion is right, they are deprived (...) of the opportunity of exchanging error for truth: if wrong, they lose, what is almost as great a benefit, the clearer perception and livelier impression of truth, produced by its collision with error”.1 Andrew Moore and Andrew Donnelly's compelling article, “The job of ‘ethics committees’”, is just this sort of challenge to conventional wisdom, a rejection of the notion that review boards should be considering ethical matters at all.2 If true, we should be substantially reforming our research ethics policies. And if false, rebuttals would help strengthen and ground the otherwise unquestioned assumption of the role of ethics committees. As it happens, I will argue that their critiques fall into the second category. While mistaken, they present a valuable opportunity to clarify the role of ethics committees and their relationship to relevant codes. In particular, I will defend a hybrid account where codes have strict primacy, but leave significant room for review boards …. (shrink)

In the Vocation of Man, Fichte makes the striking claim that life is eternal, rational, our true being, and the final cause of nature in general and of death in particular. How can we make sense of this claim? I argue that the public lectures that compose the Vocation are a popular expression of Fichte’s pre-existing commitment to what I call immortalism, the view that life is the unconditioned condition of intelligibility. Casting the I as an absolutely self-active or living (...) power enables his philosophical account of both the intelligibility of objects and of what it means to die. This explains his characterization of the Wissenschaftslehre as a system in which ‘all is act, movement, and life’. In Sect. 1, I explain the context of Jacobi’s use of ‘caput mortuum’ as a term for the thing in itself. In Sects. 2 and 3, I reconstruct two immortalist arguments from Fichte’s Jena period. The first is that the I’s self-activity rules out the existence of the thing in itself and thereby vanquishes ‘death’s head’. The second is that, insofar as the I charges us with the moral perfection of nature, it is the final cause of our entire life, including its end. This is to say that the I puts our every moment into question, even our last. In Sect. 4, I use these immortalist arguments to interpret the striking claim from the Vocation. (shrink)

With the recent report of a live birth after use of Mitochondrial replacement therapy, sometimes called ‘Three-parent IVF’, the clinical application of the technique is fast becoming a reality. While the United Kingdom allows the procedure under regulatory scrutiny, it remains effectively outlawed in many other countries. We argue that such prohibitions may violate individuals’ procreative rights, grounded in individuals’ interest in genetic affinity. The interest in genetic affinity was recently endorsed by Singapore’s highest court, reflecting an emphasis on the (...) importance of biological ties found across the globe. We apply that reasoning to make the case for a right to ‘Three-parent IVF’. (shrink)

Throughout his career, Schelling assigns knowledge of the absolute first principle of philosophy to intellectual intuition. Schelling's doctrine of intellectual intuition raises two important questions for interpreters. First, given that his doctrine undergoes several changes before and after his identity philosophy, to what extent can he be said to “hold onto” the same “sense” of it by the 1830s, as he claims? Second, given that his doctrine of intellectual intuition restricts absolute idealism to what he calls a “science of reason”, (...) which he says cannot prove the absolute’s existence, what other doctrine does he require in order to prove this? I will answer these questions by tracing the shifts in Schelling’s doctrine of intellectual intuition from the 1790s to the 1830s and drawing out its evolving methodological role within his science of intelligibility. (shrink)

Mitochondrial replacement therapy requires oocytes of women whose mitochondrial DNA will be transmitted to resultant children. These techniques are scientifically, ethically and socially controversial; it is likely that some women who donate their oocytes for general in vitro fertilisation usage would nevertheless oppose their genetic material being used in MRT. The possibility of oocytes being used in MRT is therefore relevant to oocyte donation and should be included in the consent process when applicable. In present circumstances, specific consent should be (...) obtained. However, once MRT becomes more routine, such consent could be incorporated into the general consent process for oocyte donation. The reported lack of proper consent for MRT from the oocyte donor in the first baby born via the technique is an ethical failing and should be corrected in any future practice of MRT. (shrink)

This paper offers a short extension of the dialogue between Anselm and the Fool that is contained in "The Ontological Argument Simplified" by Gary Matthews and Lynne Rudder Baker. My extension of the dialogue ends with the Fool proclaiming that "what looks like an argument of elegant simplicity turns out to be no argument at all".

This article is a reply to Michael Gettings' criticisms of a previous paper of mine on Godel's ontological argument. (All relevant bibliographical details may be found in the article.) I provide a patch to my previous -- faulty -- attempt to provide a parody of Godel's ontological argument on the model of Gaunilo's parody of Anselm's Proslogion 2 argument.