Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

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

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Recent research has relied on trolley-type sacrificial moral dilemmas to study utilitarian versus nonutili- tarian modes of moral decision-making. This research has generated important insights into people’s attitudes toward instrumental harm—that is, the sacrifice of an individual to save a greater number. But this approach also has serious limitations. Most notably, it ignores the positive, altruistic core of utilitarianism, which is characterized by impartial concern for the well-being of everyone, whether near or far. Here, we develop, refine, and validate a (...) new scale—the Oxford Utilitarianism Scale—to dissociate individual differences in the ‘negative’ (permissive attitude toward instrumental harm) and ‘positive’ (impartial concern for the greater good) dimensions of utilitarian thinking as manifested in the general population. We show that these are two independent dimensions of proto-utilitarian tendencies in the lay population, each exhibiting a distinct psychological profile. Empathic concern, identification with the whole of humanity, and concern for future generations were positively associated with impartial beneficence but negatively associated with instrumental harm; and although instrumental harm was associated with subclinical psychopathy, impartial beneficence was associated with higher religiosity. Importantly, although these two dimensions were independent in the lay population, they were closely associated in a sample of moral philosophers. Acknowledging this dissociation between the instrumental harm and impartial beneficence components of utilitarian thinking in ordinary people can clarify existing debates about the nature of moral psychology and its relation to moral philosophy as well as generate fruitful avenues for further research. (shrink)

Theoretical ethics includes both metaethics (the meaning of moral terms) and normative ethics (ethical theories and principles). Practical ethics involves making decisions about every day real ethical problems, like decisions about euthanasia, what we should eat, climate change, treatment of animals, and how we should live. It utilizes ethical theories, like utilitarianism and Kantianism, and principles, but more broadly a process of reflective equilibrium and consistency to decide how to act and be.

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

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

Recent research has begun treating the perennial philosophical question, “what makes a person the same over time?” as an empirical question. A long tradition in philosophy holds that psychological continuity and connectedness of memories are at the heart of personal identity. More recent experimental work, following Strohminger & Nichols (2014), has suggested that persistence of moral character, more than memories, is perceived as essential for personal identity. While there is a growing body of evidence supporting these findings, a critique by (...) Starmans & Bloom (2018) suggests that this research program conflates personal identity with mere similarity. To address this criticism, we explore how loss of someone’s morality or memories influence perceptions of identity change, and perceptions of moral duties towards the target of the change. We present participants with a classic ‘body switch’ thought experiment and after assessing perceptions of identity persistence, we present a moral dilemma, asking participants to imagine that one of the patients must die (Study 1) or be left alone in a care home for the rest of their life (Study 2). Our results highlight the importance of the continuity of moral character, suggesting lay intuitions are tracking (something like) personal identity, not just mere similarity. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

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

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

This paper challenges the assumption that to consider the subjective interests of others is to take on a burden that constrains our personal freedom. The nature of compassion will be examined as a disposition to have a certain subjective insight into a given social atmosphere. The inquiry will develop by showing the role that this emotive quality plays in freeing the will from perceptive constraints. The discussion will take place within the context of both Analytic and Buddhist philosophies of moral (...) psychology in order to show that together they provide a coherent groundwork in support of the thesis at hand. (shrink)

Within the debate concerning reason and rationality, instrumental incoherence was for a long time conceived of as the paradigm of irrationality. However, with the emergence of the so-called ‘bootstrapping objection’ and the debate concerning the ‘scope’ of rational requirements, the innocuous status of the normative significance of (instrumental) coherence became subject to. This led to a paradigmatic shift in how to understand the relationship between rational requirements and normativity. While there now exists considerable doubt that rational requirements are normative, it (...) is commonly agreed that one’s normative point of view is a key feature of one’s rationality. Here the question is not only if one can hold a particular normative judgement and still be rational; what is significant too is whether your normative outlook coheres appropriately with your motivation. In fact, it is now commonly agreed that rationality requires us to intend to make the world fit with our first-personal ought beliefs. Enkrasia (i.e. coherence between your normative views and your motivation) is thus seen as a rational ideal and as a source of rational requirements. Nevertheless, many elementary questions regarding the application, content, and significance of an enkrasia-requirement remain unanswered, or subject to debate. This special issue on ‘The Nature of the Enkratic Requirement of Rationality’ aims to answer some of these fundamental questions. (shrink)

“Love hurts”—as the saying goes—and a certain amount of pain and difficulty in intimate relationships is unavoidable. Sometimes it may even be beneficial, since adversity can lead to personal growth, self-discovery, and a range of other components of a life well-lived. But other times, love can be downright dangerous. It may bind a spouse to her domestic abuser, draw an unscrupulous adult toward sexual involvement with a child, put someone under the insidious spell of a cult leader, and even inspire (...) jealousy-fueled homicide. How might these perilous devotions be diminished? The ancients thought that treatments such as phlebotomy, exercise, or bloodletting could “cure” an individual of love. But modern neuroscience and emerging developments in psychopharmacology open up a range of possible interventions that might actually work. These developments raise profound moral questions about the potential uses—and misuses—of such anti-love biotechnology. In this article, we describe a number of prospective love-diminishing interventions, and offer a preliminary ethical framework for dealing with them responsibly should they arise. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The requirements of rationality are fundamental in practical and theoretical philosophy. Nonetheless, there exists no correct account of what constitutes rational requirements. This paper attempts to provide a correct constitutive account of ‘rationality requires’. I argue that rational requirements are grounded in ‘necessary explanations of subjective incoherence’, as I shall put it. Rationality requires of you to X if and only if your rational capacities, in conjunction with the fact that you not-X, explain necessarily why you have a non-maximal degree (...) of subjective coherence. (shrink)

Background: Recent literature on addiction and judgments about the characteristics of agents has focused on the implications of adopting a ‘brain disease’ versus ‘moral weakness’ model of addiction. Typically, such judgments have to do with what capacities an agent has (e.g., the ability to abstain from substance use). Much less work, however, has been conducted on the relationship between addiction and judgments about an agent’s identity, including whether or to what extent an individual is seen as the same person after (...) becoming addicted. Methods: We conducted a series of vignette-based experiments (total N = 3,620) to assess lay attitudes concerning addiction and identity persistence, systematically manipulating key characteristics of agents and their drug of addiction. Conclusions: In Study 1, we found that US participants judged an agent who became addicted to drugs as being closer to ‘a completely different person’ than ‘completely the same person’ as the agent who existed prior to the addiction. In Studies 2-6, we investigated the intuitive basis for this result, finding that lay judgments of altered identity as a consequence of drug use and addiction are driven primarily by perceived negative changes in the moral character of drug users, who are seen as having deviated from their good true selves. (shrink)

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

Today, dramatically increasing economic inequality, imminent climatological calamity, and a global pandemic now place the timeless debate over capitalism into stark relief. Though many seek to pin the blame on capitalism’s excesses, they would do well to recall the historical record of socialism’s deficiencies, namely, stifling innovation, lumbering inefficiency, and stagnation. Fortunately, our moral psychology affords a middle way between these two extremes. For while economic incentives have a tendency to let our civic and prosocial impulses atrophy from disuse, these (...) can also be rekindled when we are faced with highly compelling reasons to think and act for the greater good of all concerned. The coronavirus pandemic now unfolding might well offer us an opportunity to instill a culture of heightened moral self-awareness spurring a more virtuous form of capitalism. (shrink)

Much disease and disability is the result of lifestyle behaviours. For example, the contribution of imprudence in the form of smoking, poor diet, sedentary lifestyle, and drug and alcohol abuse to ill-health is now well established. More importantly, some of the greatest challenges facing humanity as a whole – climate change, terrorism, global poverty, depletion of resources, abuse of children, overpopulation – are the result of human behaviour. In this chapter, we will explore the possibility of using advances in the (...) cognitive sciences to develop strategies to intentionally manipulate human motivation and behaviour. While our arguments apply also to improving prudential motivation and behaviour in relation to health, we will focus on the more controversial instance: the deliberate targeted use of biomedicine to improve moral motivation and behaviour. We do this because the challenge of improving human morality is arguably the most important issue facing humankind (Persson and Savulescu, forthcoming). We will ask whether using the knowledge from the biological and cognitive sciences to influence motivation and behaviour erodes autonomy and, if so, whether this makes it wrong. (shrink)

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

A core challenge for contemporary bioethics is how to address the tension between respecting an individual’s autonomy and promoting their wellbeing when these ideals seem to come into conflict (Not...

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)

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

Numerous high-profile ethics scandals, rising inequality, and the detrimental effects of climate change dramatically underscore the need for business schools to instill a commitment to social purpose in their students. At the same time, the rising financial burden of education, increasing competition in the education space, and overreliance on graduates’ financial success as the accepted metric of quality have reinforced an instrumentalist climate. These conflicting aims between social and financial purpose have created an existential crisis for business education. To resolve (...) this impasse, we draw on the concept of moral self-awareness to offer a system-theoretical strategy for crowding-in a culture of ethics within business schools. We argue that to do so, business schools will need to (1) reframe the purpose of business, (2) reframe the meaning of professional success, and (3) reframe the ethos of business education itself. (shrink)

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

There is growing concern that a global economic system fueled predominately by financial incentives may not maximize human flourishing and social welfare externalities. If so, this presents a challenge of how to get economic actors to adopt a more virtuous motivational mindset. Relying on historical, psychological, and philosophical research, we show how such a mindset can be instilled. First, we demonstrate that historically, financial self-interest has never in fact been the only guiding motive behind free markets, but that markets themselves (...) are representations of our individual and collective moral identities. Building on this understanding, we review the research on how economic incentives crowd out virtue-oriented concerns. We then introduce the concept of moral self-awareness (MSA), an evolving mindset informed by reflection on moral identity, namely what one’s actions say about oneself given the impacts on others or society that one’s action may effect. MSA comprises three fundamental aspects of virtue-oriented reasoning: pride, shame, and guilt. Finally, we offer a four-stage model anchored in systems theory, yielding ever more refined motivating strategies for maximizing human flourishing and social welfare externalities. (shrink)

In this article I present the concept of human evolution by Hoene- Wroński. I believe that his ideas are still an unexplored resource which can lead us to the better understanding of the evolution of humanity and of our destiny. I follow closely his discussion of human evolution and describe its seven stages. Further, I argue that the case of human evolution is strongly supported by new scientific theories, especially by quantum theory and the novel perspectives that it opens for (...) humankind. I end my article with the conclusion that the insights on human evolution derived from the Hoene-Wroński’s writings and from new scientific theories can guide us to the new politics based on the awareness of human identity that can overcome old divisions among humankind and conflicts derived from them. Ultimately, they can initiate evolutionity – the new evolutionary epoch, which will replace modernity and postmodernity. On. (shrink)

This paper aims to provide a theoretical framework for explaining the subjective character of pain experience in terms of what we will call ‘embodied predictive processing’. The predictive processing (PP) theory is a family of views that take perception, action, emotion and cognition to all work together in the service of prediction error minimisation. In this paper we propose an embodied perspective on the PP theory we call the ‘embodied predictive processing (EPP) theory. The EPP theory proposes to explain pain (...) in terms of processes distributed across the whole body. The prediction error minimising system that generates pain experience comprises the immune system, the endocrine system, and the autonomic system in continuous causal interaction with pathways spread across the whole neural axis. We will argue that these systems function in a coordinated and coherent manner as a single complex adaptive system to maintain homeostasis. This system, which we refer to as the neural-endocrine-immune (NEI) system, maintains homeostasis through the process of prediction error minimisation. We go on to propose a view of the NEI ensemble as a multiscale nesting of Markov blankets that integrates the smallest scale of the cell to the largest scale of the embodied person in pain. We set out to show how the EPP theory can make sense of how pain experience could be neurobiologically constituted. We take it to be a constraint on the adequacy of a scientific explanation of subjectivity of pain experience that it makes it intelligible how pain can simultaneously be a local sensing of the body, and, at the same time, a more global, all-encompassing attitude towards the environment. Our aim in what follows is to show how the EPP theory can meet this constraint. (shrink)

What is the appropriate legal response to terrorist threats? This question is discussed by politician Tony McWalter, The Philosophers' Magazine editor Julian Baggini, and philosophers Catherine Audard, Saladin Meckled-Garcia, and Alex Voorhoeve.

The authors respond to a wide range of objections defending our argument that some forms of behaviour modification utilising advances in the cognitive sciences are desirable and need not necessarily undermine autonomy or freedom.

Can we employ the property of rationality in establishing what rationality requires? According to a central and formal thesis of John Broome’s work on rational requirements, the answer is ‘no’ – at least if we expect a precise answer. In particular, Broome argues that (i) the property of full rationality (i.e. whether or not you are fully rational) is independent of whether we formulate conditional requirements of rationality as having a wide or a narrow logical scope. That is, (ii) by (...) replacing a wide-scope requirement with a corresponding narrow-scope requirement (or vice versa), we do not alter the situations in which a person is fully rational. As a consequence, (iii) the property of full rationality is unable to guide us in determining whether a rational requirement has a wide or a narrow logical scope. We cannot resolve the wide/narrow scope debate by appealing to a theory of fully rational attitudes. This paper argues that (i), (ii) and (iii) are incorrect. Replacing a wide- with a corresponding narrow-scope requirement (or vice versa) can alter the set of circumstances in which a person is fully rational. The property of full rationality is therefore not independent of whether we formulate conditional requirements of rationality as having a wide or a narrow logical scope. As a consequence, the property of full rationality can guide us in determining what rationality requires – even in cases where we expect a precise answer. (shrink)

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

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

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

The SIMS model claims that it is by means of an embodied simulation that we determine the meaning of an observed smile. This suggests that crucial interpretative work is done in the mapping that takes us from a perceived smile to the activation of one's own facial musculature. How is this mapping achieved? Might it depend upon a prior interpretation arrived at on the basis of perceptual and contextual information?

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

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

Delusions have traditionally been considered the hallmark of mental illness, and their conception, diagnosis and treatment raise many of the fundamental conceptual and practical questions of psychopathology. One of these fundamental questions is whether delusions are understandable. In this paper, we propose to consider the question of understandability of delusions from a philosophy of language perspective. For this purpose, we frame the question of how delusions can be understood as a question about the meaning of delusional utterances. Accordingly, we ask: (...) “what meaning(s) can delusional utterances possibly have?”. We argue that in the current literature, there is a standard approach to the meaning of delusional utterances, namely the descriptive account which assumes that a delusional utterance “p” means that p is the case. Drawing on Speech Act Theory, we argue that solely relying on the descriptive account disregards essential ways of how linguistic meaning is constituted. Further, we show that Speech Act Theory can prove a helpful addition to the theoretical and clinical “toolbox” used for attempting to understand delusional utterances. This, we believe, may address some of the theoretical and clinical shortcomings of using only the currently predominant descriptive account. (shrink)

A popular positivistic line of thinking seems to be cropping up again, declaring that the sciences are on the verge of a paradigmatic shift. One that will merge science and philosophy to finally answer all the great big questions once and for all. Questions such as What is life? What is consciousness? What makes individuals who they are? Why does our universe seem fine-tuned for our existence? How did it all begin? While such questions are undoubtedly important, the truth is, (...) they are essentially philosophical. That is to say, they escape the kind of exactness required of the hard sciences. The upshot is that they are at best only answerable to a limited extent, if they are even answerable at all. (shrink)

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)

One intuition we have about critical discourse is that we can distinguish between aesthetic and non-aesthetic assertions. When we say that a composition has a quick tempo and makes much use of staccato, we are remarking upon non-aesthetic features of the work. When we say of the same composition that it is vibrant, we are, in some sense, referring to an aesthetic feature. How should we draw the line between the aesthetic and non-aesthetic features of a work, and what import (...) does the distinction have? Frank Sibley has famously claimed that there is a way to draw a line between our aesthetic and non-aesthetic terms, and moreover that the existence of this distinction supports the existence of realistic aesthetic properties. The ensuing discussions of Sibley’s claim indicate that whatever is at stake here is of great significance to aesthetics. (shrink)

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

Extant research suggests that individuals employ traditional moral heuristics to support their observed altruistic behavior; yet findings have largely been limited to inductive extrapolation and rely on relatively few traditional frames in so doing, namely, deontology in organizational behavior and virtue theory in law and economics. Given that these and competing moral frames such as utilitarianism can manifest as identical behavior, we develop a moral framing instrument—the Philosophical Moral-Framing Measure (PMFM)—to expand and distinguish traditional frames associated and disassociated with observed (...) altruistic behavior. The validation of our instrument based on 1015 subjects in 3 separate real stakes scenarios indicates that heuristic forms of deontology, virtue-theory, and utilitarianism are strongly related to such behavior, and that egoism is an inhibitor. It also suggests that deontic and virtue-theoretical frames may be commonly perceived as intertwined and opens the door for new research on self-abnegation, namely, a perceived moral obligation toward suffering and self-denial. These findings hold the potential to inform ongoing conversations regarding organizational citizenship and moral crowding out, namely, how financial incentives can undermine altruistic behavior. (shrink)